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+title: "Acclimatization"
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+source: "https://en.wikipedia.org/wiki/Acclimatization"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:01.114425+00:00"
+instance: "kb-cron"
+---
+
+Acclimatization or acclimatisation (also called acclimation or acclimatation) is the process in which an individual organism adjusts to a change in its environment (such as a change in altitude, temperature, humidity, photoperiod, or pH), allowing it to maintain fitness across a range of environmental conditions. Acclimatization occurs in a short period of time (hours to weeks), and within the organism's lifetime (compared to adaptation, which is evolution, taking place over many generations). This may be a discrete occurrence (for example, when mountaineers acclimate to high altitude over hours or days) or may instead represent part of a periodic cycle, such as a mammal shedding heavy winter fur in favor of a lighter summer coat. Organisms can adjust their morphological, behavioral, physical, and/or biochemical traits in response to changes in their environment. While the capacity to acclimate to novel environments has been well documented in thousands of species, researchers still know very little about how and why organisms acclimate the way that they do.
+
+
+== Names ==
+The nouns acclimatization and acclimation (and the corresponding verbs acclimatize and acclimate) are widely regarded as synonymous, both in general vocabulary and in medical vocabulary. The synonym acclimation is less commonly encountered, and fewer dictionaries enter it.
+
+
+== Methods ==
+
+
+=== Biochemical ===
+In order to maintain performance across a range of environmental conditions, there are several strategies organisms use to acclimate. In response to changes in temperature, organisms can change the biochemistry of cell membranes making them more fluid in cold temperatures and less fluid in warm temperatures by increasing the number of membrane proteins. In response to certain stressors, some organisms express so-called heat shock proteins that act as molecular chaperones and reduce denaturation by guiding the folding and refolding of proteins. It has been shown that organisms which are acclimated to high or low temperatures display relatively high resting levels of heat shock proteins so that when they are exposed to even more extreme temperatures the proteins are readily available. Expression of heat shock proteins and regulation of membrane fluidity are just two of many biochemical methods organisms use to acclimate to novel environments.
+
+
+=== Morphological ===
+Organisms are able to change several characteristics relating to their morphology in order to maintain performance in novel environments. For example, birds often increase their organ size to increase their metabolism. This can take the form of an increase in the mass of nutritional organs or heat-producing organs, like the pectorals (with the latter being more consistent across species).
+
+
+== The theory ==
+While the capacity for acclimatization has been documented in thousands of species, researchers still know very little about how and why organisms acclimate in the way that they do. Since researchers first began to study acclimation, the overwhelming hypothesis has been that all acclimation serves to enhance the performance of the organism. This idea has come to be known as the beneficial acclimation hypothesis. Despite such widespread support for the beneficial acclimation hypothesis, not all studies show that acclimation always serves to enhance performance (See beneficial acclimation hypothesis). One of the major objections to the beneficial acclimation hypothesis is that it assumes that there are no costs associated with acclimation. However, there are likely to be costs associated with acclimation. These include the cost of sensing the environmental conditions and regulating responses, producing structures required for plasticity (such as the energetic costs in expressing heat shock proteins), and genetic costs (such as linkage of plasticity-related genes with harmful genes).
+Given the shortcomings of the beneficial acclimation hypothesis, researchers are continuing to search for a theory that will be supported by empirical data.
+The degree to which organisms are able to acclimate is dictated by their phenotypic plasticity or the ability of an organism to change certain traits. Recent research in the study of acclimation capacity has focused more heavily on the evolution of phenotypic plasticity rather than acclimation responses. Scientists believe that when they understand more about how organisms evolved the capacity to acclimate, they will better understand acclimation.
+
+
+== Examples ==
+
+
+=== Plants ===
+Many plants, such as maple trees, irises, and tomatoes, can survive freezing temperatures if the temperature gradually drops lower and lower each night over a period of days or weeks. The same drop might kill them if it occurred suddenly. Studies have shown that tomato plants that were acclimated to higher temperature over several days were more efficient at photosynthesis at relatively high temperatures than were plants that were not allowed to acclimate.
+In the orchid Phalaenopsis, phenylpropanoid enzymes are enhanced in the process of plant acclimatisation at different levels of photosynthetic photon flux.
+
+
+=== Animals ===
+
+Animals acclimatize in many ways. Sheep grow very thick wool in cold, damp climates. Fish are able to adjust only gradually to changes in water temperature and quality. Tropical fish sold at pet stores are often kept in acclimatization bags until this process is complete. Lowe & Vance (1995) were able to show that lizards acclimated to warm temperatures could maintain a higher running speed at warmer temperatures than lizards that were not acclimated to warm conditions. Fruit flies that develop at relatively cooler or warmer temperatures have increased cold or heat tolerance as adults, respectively (See Developmental plasticity).
+
+
+==== Humans ====
+
+The salt content of sweat and urine decreases as people acclimatize to hot conditions. Plasma volume, heart rate, and capillary activation are also affected.
+Acclimatization to high altitude continues for months or even years after initial ascent, and ultimately enables humans to survive in an environment that, without acclimatization, would kill them. Humans who migrate permanently to a higher altitude naturally acclimatize to their new environment by developing an increase in the number of red blood cells to increase the oxygen carrying capacity of the blood, in order to compensate for lower levels of oxygen intake.
+
+
+== See also ==
+
+
+== References ==
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+title: "Adaptation"
+chunk: 1/6
+source: "https://en.wikipedia.org/wiki/Adaptation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:02.299236+00:00"
+instance: "kb-cron"
+---
+
+In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the population during that process. Thirdly, it is a phenotypic trait or adaptive trait, with a functional role in each individual organism, that is maintained and has evolved through natural selection. 
+Historically, adaptation has been described from the time of the ancient Greek philosophers such as Empedocles and Aristotle. In 18th and 19th-century natural theology, adaptation was taken as evidence for the existence of a deity. Charles Darwin and Alfred Russel Wallace proposed instead that it was explained by natural selection.
+Adaptation is related to biological fitness, which governs the rate of evolution as measured by changes in allele frequencies. Often, two or more species co-adapt and co-evolve as they develop adaptations that interlock with those of the other species, such as with flowering plants and pollinating insects. In mimicry, species evolve to resemble other species; in mimicry this is a mutually beneficial co-evolution as each of a group of strongly defended species (such as wasps able to sting) come to advertise their defences in the same way. Features evolved for one purpose may be co-opted for a different one, as when the insulating feathers of dinosaurs were co-opted for bird flight.
+Adaptation is a major topic in the philosophy of biology, as it concerns function and purpose (teleology). Some biologists try to avoid terms which imply purpose in adaptation, not least because they suggest a deity's intentions, but others note that adaptation is necessarily purposeful.
+
+== History ==
+
+Adaptation is an observable fact of life accepted by philosophers and natural historians from ancient times, independently of their views on evolution, but their explanations differed. Empedocles did not believe that adaptation required a final cause (a purpose), but thought that it "came about naturally, since such things survived." Aristotle did believe in final causes, but assumed that species were fixed.
+
+In natural theology, adaptation was interpreted as the work of a deity and as evidence for the existence of God. William Paley believed that organisms were perfectly adapted to the lives they led, an argument that shadowed Gottfried Wilhelm Leibniz, who had argued that God had brought about "the best of all possible worlds." Voltaire's satire Dr. Pangloss is a parody of this optimistic idea, and David Hume also argued against design. Charles Darwin broke with the tradition by emphasising the flaws and limitations which occurred in the animal and plant worlds.
+Jean-Baptiste Lamarck proposed a tendency for organisms to become more complex, moving up a ladder of progress, plus "the influence of circumstances", usually expressed as use and disuse. This second, subsidiary element of his theory is what is now called Lamarckism, a proto-evolutionary hypothesis of the inheritance of acquired characteristics, intended to explain adaptations by natural means.
+Other natural historians, such as Buffon, accepted adaptation, and some also accepted evolution, without voicing their opinions as to the mechanism. This illustrates the real merit of Darwin and Alfred Russel Wallace, and secondary figures such as Henry Walter Bates, for putting forward a mechanism whose significance had only been glimpsed previously. A century later, experimental field studies and breeding experiments by people such as E. B. Ford and Theodosius Dobzhansky produced evidence that natural selection was not only the 'engine' behind adaptation, but was a much stronger force than had previously been thought.
+
+== General principles ==
+The significance of an adaptation can only be understood in relation to the total biology of the species.
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+title: "Adaptation"
+chunk: 2/6
+source: "https://en.wikipedia.org/wiki/Adaptation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:02.299236+00:00"
+instance: "kb-cron"
+---
+
+=== What adaptation is ===
+Adaptation is primarily a process rather than a physical form or part of a body. An internal parasite (such as a liver fluke) can illustrate the distinction: such a parasite may have a very simple bodily structure, but nevertheless the organism is highly adapted to its specific environment. From this we see that adaptation is not just a matter of visible traits: in such parasites critical adaptations take place in the life cycle, which is often quite complex. However, as a practical term, "adaptation" often refers to a product: those features of a species which result from the process. Many aspects of an animal or plant can be correctly called adaptations, though there are always some features whose function remains in doubt. By using the term adaptation for the evolutionary process, and adaptive trait for the bodily part or function (the product), one may distinguish the two different senses of the word.
+Adaptation is one of the two main processes that explain the observed diversity of species, such as the different species of Darwin's finches. The other process is speciation, in which new species arise, typically through reproductive isolation. An example widely used today to study the interplay of adaptation and speciation is the evolution of cichlid fish in African lakes, where the question of reproductive isolation is complex.
+Adaptation is not always a simple matter where the ideal phenotype evolves for a given environment. An organism must be viable at all stages of its development and at all stages of its evolution. This places constraints on the evolution of development, behaviour, and structure of organisms. The main constraint, over which there has been much debate, is the requirement that each genetic and phenotypic change during evolution should be relatively small, because developmental systems are so complex and interlinked. However, it is not clear what "relatively small" should mean, for example polyploidy in plants is a reasonably common large genetic change. The origin of eukaryotic endosymbiosis is a more dramatic example.
+All adaptations help organisms survive in their ecological niches. The adaptive traits may be structural, behavioural or physiological. Structural adaptations are physical features of an organism, such as shape, body covering, armament, and internal organization. Behavioural adaptations are inherited systems of behaviour, whether inherited in detail as instincts, or as a neuropsychological capacity for learning. Examples include searching for food, mating, and vocalizations. Physiological adaptations permit the organism to perform special functions such as making venom, secreting slime, and phototropism, but also involve more general functions such as growth and development, temperature regulation, ionic balance and other aspects of homeostasis. Adaptation affects all aspects of the life of an organism.
+The following definitions are given by the evolutionary biologist Theodosius Dobzhansky:
+
+1. Adaptation is the evolutionary process whereby populations of organisms become better able to live in a habitat or habitats.
+2. Adaptedness is the state of being adapted: the degree to which an organism is able to live and reproduce in a given set of habitats.
+3. An adaptive trait is an aspect of the developmental pattern of the organism which enables or enhances the probability of that organism surviving and reproducing.
+
+=== What adaptation is not ===
+
+Adaptation differs from flexibility, acclimatization, and learning, all of which are changes during life which are not inherited. Flexibility deals with the relative capacity of an organism to maintain itself in different habitats: its degree of specialization. Acclimatization describes automatic physiological adjustments during life; learning means alteration in behavioural performance during life.
+Flexibility stems from phenotypic plasticity, the ability of an organism with a given genotype (genetic type) to change its phenotype (observable characteristics) in response to changes in its habitat, or to move to a different habitat. The degree of flexibility is inherited, and varies between individuals. A highly specialized animal or plant lives only in a well-defined habitat, eats a specific type of food, and cannot survive if its needs are not met. Many herbivores are like this; extreme examples are koalas which depend on Eucalyptus, and giant pandas which require bamboo. A generalist, on the other hand, eats a range of food, and can survive in many different conditions. Examples are humans, rats, crabs and many carnivores. The tendency to behave in a specialized or exploratory manner is inherited—it is an adaptation. Rather different is developmental flexibility: "An animal or plant is developmentally flexible if when it is raised in or transferred to new conditions, it changes in structure so that it is better fitted to survive in the new environment," writes the evolutionary biologist John Maynard Smith.
+If humans move to a higher altitude, respiration and physical exertion become a problem, but after spending time in high altitude conditions they acclimatize to the reduced partial pressure of oxygen, such as by producing more red blood cells. The ability to acclimatize is an adaptation, but the acclimatization itself is not. The reproductive rate declines, but deaths from some tropical diseases also go down. Over a longer period of time, some people are better able to reproduce at high altitudes than others. They contribute more heavily to later generations, and gradually by natural selection the whole population becomes adapted to the new conditions. This has demonstrably occurred, as the observed performance of long-term communities at higher altitude is significantly better than the performance of new arrivals, even when the new arrivals have had time to acclimatize.
+
+=== Adaptedness and fitness ===
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+title: "Adaptation"
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+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:02.299236+00:00"
+instance: "kb-cron"
+---
+
+There is a relationship between adaptedness and the concept of fitness used in population genetics. Differences in fitness between genotypes predict the rate of evolution by natural selection. Natural selection changes the relative frequencies of alternative phenotypes, insofar as they are heritable. However, a phenotype with high adaptedness may not have high fitness. Dobzhansky mentioned the example of the Californian redwood, which is highly adapted, but a relict species in danger of extinction. Elliott Sober commented that adaptation was a retrospective concept since it implied something about the history of a trait, whereas fitness predicts a trait's future.
+
+1. Relative fitness. The average contribution to the next generation by a genotype or a class of genotypes, relative to the contributions of other genotypes in the population. This is also known as Darwinian fitness, selection coefficient, and other terms.
+2. Absolute fitness. The absolute contribution to the next generation by a genotype or a class of genotypes. Also known as the Malthusian parameter when applied to the population as a whole.
+3. Adaptedness. The extent to which a phenotype fits its local ecological niche. Researchers can sometimes test this through a reciprocal transplant.
+
+Sewall Wright proposed that populations occupy adaptive peaks on a fitness landscape. To evolve to another, higher peak, a population would first have to pass through a valley of maladaptive intermediate stages, and might be "trapped" on a peak that is not optimally adapted.
+
+== Types ==
+Adaptation is the heart and soul of evolution.
+
+=== Changes in habitat ===
+Before Darwin, adaptation was seen as a fixed relationship between an organism and its habitat. It was not appreciated that as the climate changed, so did the habitat; and as the habitat changed, so did the biota. Also, habitats are subject to changes in their biota: for example, invasions of species from other areas. The relative numbers of species in a given habitat are always changing. Change is the rule, though much depends on the speed and degree of the change.
+When the habitat changes, three main things may happen to a resident population: habitat tracking, genetic change or extinction. In fact, all three things may occur in sequence. Of these three effects only genetic change brings about adaptation.
+When a habitat changes, the resident population typically moves to more suitable places; this is the typical response of flying insects or oceanic organisms, which have wide (though not unlimited) opportunity for movement. This common response is called habitat tracking. It is one explanation put forward for the periods of apparent stasis in the fossil record (the punctuated equilibrium theory).
+
+=== Genetic change ===
+Without mutation, the ultimate source of all genetic variation, there would be no genetic changes and no subsequent adaptation through evolution by natural selection. Genetic change occurs in a population when mutation increases or decreases in its initial frequency followed by random genetic drift, migration, recombination or natural selection act on this genetic variation. One example is that the first pathways of enzyme-based metabolism at the very origin of life on Earth may have been co-opted components of the already-existing purine nucleotide metabolism, a metabolic pathway that evolved in an ancient RNA world. The co-option requires new mutations and through natural selection, the population then adapts genetically to its present circumstances. Genetic changes may result in entirely new or gradual change to visible structures, or they may adjust physiological activity in a way that suits the habitat. The varying shapes of the beaks of Darwin's finches, for example, are driven by adaptive mutations in the ALX1 gene. The coat color of different wild mouse species matches their environments, whether black lava or light sand, owing to adaptive mutations in the melanocortin 1 receptor and other melanin pathway genes. Physiological resistance to the heart poisons (cardiac glycosides) that monarch butterflies store in their bodies to protect themselves from predators are driven by adaptive mutations in the target of the poison, the sodium pump, resulting in target site insensitivity. These same adaptive mutations and similar changes at the same amino acid sites were found to evolve in a parallel manner in distantly related insects that feed on the same plants, and even in a bird that feeds on monarchs through convergent evolution, a hallmark of adaptation. Convergence at the gene-level across distantly related species can arise because of evolutionary constraint.
+Habitats and biota do frequently change over time and space. Therefore, it follows that the process of adaptation is never fully complete. Over time, it may happen that the environment changes little, and the species comes to fit its surroundings better and better, resulting in stabilizing selection. On the other hand, it may happen that changes in the environment occur suddenly, and then the species becomes less and less well adapted. The only way for it to climb back up that fitness peak is via the introduction of new genetic variation for natural selection to act upon. Seen like this, adaptation is a genetic tracking process, which goes on all the time to some extent, but especially when the population cannot or does not move to another, less hostile area. Given enough genetic change, as well as specific demographic conditions, an adaptation may be enough to bring a population back from the brink of extinction in a process called evolutionary rescue. Adaptation does affect, to some extent, every species in a particular ecosystem.
+Leigh Van Valen thought that even in a stable environment, because of antagonistic species interactions and limited resources, a species must constantly had to adapt to maintain its relative standing. This became known as the Red Queen hypothesis, as seen in host-parasite interactions.
+Existing genetic variation and mutation were the traditional sources of material on which natural selection could act. In addition, horizontal gene transfer is possible between organisms in different species, using mechanisms as varied as gene cassettes, plasmids, transposons and viruses such as bacteriophages.
+
+=== Co-adaptation ===
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+title: "Adaptation"
+chunk: 4/6
+source: "https://en.wikipedia.org/wiki/Adaptation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:02.299236+00:00"
+instance: "kb-cron"
+---
+
+In coevolution, where the existence of one species is tightly bound up with the life of another species, new or 'improved' adaptations which occur in one species are often followed by the appearance and spread of corresponding features in the other species. In other words, each species triggers reciprocal natural selection in the other. These co-adaptational relationships are intrinsically dynamic, and may continue on a trajectory for millions of years, as has occurred in the relationship between flowering plants and pollinating insects.
+
+=== Mimicry ===
+
+Bates' work on Amazonian butterflies led him to develop the first scientific account of mimicry, especially the kind of mimicry which bears his name: Batesian mimicry. This is the mimicry by a palatable species of an unpalatable or noxious species (the model), gaining a selective advantage as predators avoid the model and therefore also the mimic. Mimicry is thus an anti-predator adaptation. A common example seen in temperate gardens is the hoverfly (Syrphidae), many of which—though bearing no sting—mimic the warning coloration of aculeate Hymenoptera (wasps and bees). Such mimicry does not need to be perfect to improve the survival of the palatable species.
+Bates, Wallace and Fritz Müller believed that Batesian and Müllerian mimicry provided evidence for the action of natural selection, a view which is now standard amongst biologists.
+
+=== Trade-offs ===
+All adaptations have a downside: horse legs are great for running on grass, but they cannot scratch their backs; mammals' hair helps temperature, but offers a niche for ectoparasites; the only flying penguins do is under water. Adaptations serving different functions may be mutually destructive. Compromise and makeshift occur widely, not perfection. Selection pressures pull in different directions, and the adaptation that results is some kind of compromise.It is a profound truth that Nature does not know best; that genetical evolution... is a story of waste, makeshift, compromise and blunder.
+Since the phenotype as a whole is the target of selection, it is impossible to improve simultaneously all aspects of the phenotype to the same degree.
+
+==== Examples ====
+Consider the antlers of the Irish elk, (often supposed to be far too large; in deer antler size has an allometric relationship to body size). Antlers serve positively for defence against predators, and to score victories in the annual rut. But they are costly in terms of resources. Their size during the last glacial period presumably depended on the relative gain and loss of reproductive capacity in the population of elks during that time. As another example, camouflage to avoid detection is destroyed when vivid coloration is displayed at mating time. Here the risk to life is counterbalanced by the necessity for reproduction.
+Stream-dwelling salamanders, such as Caucasian salamander or Gold-striped salamander have very slender, long bodies, perfectly adapted to life at the banks of fast small rivers and mountain brooks. Elongated body protects their larvae from being washed out by current. However, elongated body increases risk of desiccation and decreases dispersal ability of the salamanders; it also negatively affects their fecundity. As a result, fire salamander, less perfectly adapted to the mountain brook habitats, is in general more successful, have a higher fecundity and broader geographic range.
+
+The peacock's ornamental train (grown anew in time for each mating season) is a famous adaptation. It must reduce his maneuverability and flight, and is hugely conspicuous; also, its growth costs food resources. Darwin's explanation of its advantage was in terms of sexual selection: "This depends on the advantage which certain individuals have over other individuals of the same sex and species, in exclusive relation to reproduction." The kind of sexual selection represented by the peacock is called 'mate choice,' with an implication that the process selects the more fit over the less fit, and so has survival value. The recognition of sexual selection was for a long time in abeyance, but has been rehabilitated.
+The conflict between the size of the human foetal brain at birth, (which cannot be larger than about 400 cm3, else it will not get through the mother's pelvis) and the size needed for an adult brain (about 1400 cm3), means the brain of a newborn child is quite immature. The most vital things in human life (locomotion, speech) just have to wait while the brain grows and matures. That is the result of the birth compromise. Much of the problem comes from our upright bipedal stance, without which our pelvis could be shaped more suitably for birth. Neanderthals had a similar problem.
+As another example, the long neck of a giraffe brings benefits but at a cost. The neck of a giraffe can be up to 2 m (6 ft 7 in) in length. The benefits are that it can be used for inter-species competition or for foraging on tall trees where shorter herbivores cannot reach. The cost is that a long neck is heavy and adds to the animal's body mass, requiring additional energy to build the neck and to carry its weight around.
+
+== Shifts in function ==
+Adaptation and function are two aspects of one problem.
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+title: "Adaptation"
+chunk: 5/6
+source: "https://en.wikipedia.org/wiki/Adaptation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:02.299236+00:00"
+instance: "kb-cron"
+---
+
+=== Pre-adaptation ===
+Pre-adaptation occurs when a population has characteristics which by chance are suited for a set of conditions not previously experienced. For example, the polyploid cordgrass Spartina townsendii is better adapted than either of its parent species to their own habitat of saline marsh and mud-flats. Among domestic animals, the White Leghorn chicken is markedly more resistant to vitamin B1 deficiency than other breeds; on a plentiful diet this makes no difference, but on a restricted diet this preadaptation could be decisive.
+Pre-adaptation may arise because a natural population carries a huge quantity of genetic variability. In diploid eukaryotes, this is a consequence of the system of sexual reproduction, where mutant alleles get partially shielded, for example, by genetic dominance. Microorganisms, with their huge populations, also carry a great deal of genetic variability. The first experimental evidence of the pre-adaptive nature of genetic variants in microorganisms was provided by Salvador Luria and Max Delbrück who developed the Fluctuation Test, a method to show the random fluctuation of pre-existing genetic changes that conferred resistance to bacteriophages in Escherichia coli. The word is controversial because it is teleological and the entire concept of natural selection depends on the presence of genetic variation, regardless of the population size of a species in question.
+
+=== Co-option of existing traits: exaptation ===
+
+Features that now appear as adaptations sometimes arose by co-option of existing traits, evolved for some other purpose. The classic example is the ear ossicles of mammals, which we know from paleontological and embryological evidence originated in the upper and lower jaws and the hyoid bone of their synapsid ancestors, and further back still were part of the gill arches of early fish. The word exaptation was coined to cover these common evolutionary shifts in function. The flight feathers of birds evolved from the much earlier feathers of dinosaurs, which might have been used for insulation or for display.
+
+== Niche construction ==
+Animals including earthworms, beavers and humans use some of their adaptations to modify their surroundings, so as to maximize their chances of surviving and reproducing. Beavers create dams and lodges, changing the ecosystems of the valleys around them. Earthworms, as Darwin noted, improve the topsoil in which they live by incorporating organic matter. Humans have constructed extensive civilizations with cities in environments as varied as the Arctic and hot deserts.
+In all three cases, the construction and maintenance of ecological niches helps drive the continued selection of the genes of these animals, in an environment that the animals have modified.
+
+== Non-adaptive traits ==
+
+Some traits do not appear to be adaptive as they have a neutral or deleterious effect on fitness in the current environment. Because genes often have pleiotropic effects, not all traits may be functional: they may be what Stephen Jay Gould and Richard Lewontin called spandrels, features brought about by neighbouring adaptations, on the analogy with the often highly decorated triangular areas between pairs of arches in architecture, which began as functionless features.
+Another possibility is that a trait may have been adaptive at some point in an organism's evolutionary history, but a change in habitats caused what used to be an adaptation to become unnecessary or even maladapted. Such adaptations are termed vestigial. Many organisms have vestigial organs, which are the remnants of fully functional structures in their ancestors. As a result of changes in lifestyle the organs became redundant, and are either not functional or reduced in functionality. Since any structure represents some kind of cost to the general economy of the body, an advantage may accrue from their elimination once they are not functional. Examples: wisdom teeth in humans; the loss of pigment and functional eyes in cave fauna; the loss of structure in endoparasites.
+
+== Extinction and coextinction ==
+
+If a population cannot move or change sufficiently to preserve its long-term viability, then it will become extinct, at least in that locale. The species may or may not survive in other locales. Species extinction occurs when the death rate over the entire species exceeds the birth rate for a long enough period for the species to disappear. It was an observation of Van Valen that groups of species tend to have a characteristic and fairly regular rate of extinction.
+Just as there is co-adaptation, there is also coextinction, the loss of a species due to the extinction of another with which it is coadapted, as with the extinction of a parasitic insect following the loss of its host, or when a flowering plant loses its pollinator, or when a food chain is disrupted.
+
+== Origin of adaptive capacities ==
+The first stage in the evolution of life on earth is often hypothesized to be the RNA world in which short self-replicating RNA molecules proliferated before the evolution of DNA and proteins. By this hypothesis, life started when RNA chains began to self-replicate, initiating the three mechanisms of Darwinian selection: heritability, variation of type, and competition for resources. The fitness of an RNA replicator (its per capita rate of increase) would likely have been a function of its intrinsic adaptive capacities, determined by its nucleotide sequence, and the availability of resources. The three primary adaptive capacities may have been: (1) replication with moderate fidelity, giving rise to heritability while allowing variation of type, (2) resistance to decay, and (3) acquisition of resources. These adaptive capacities would have been determined by the folded configurations of the RNA replicators resulting from their nucleotide sequences.
+
+== Philosophical issues ==
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+---
+title: "Adaptation"
+chunk: 6/6
+source: "https://en.wikipedia.org/wiki/Adaptation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:02.299236+00:00"
+instance: "kb-cron"
+---
+
+Adaptation raises philosophical issues concerning how biologists speak of function and purpose, as this carries implications of evolutionary history – that a feature evolved by natural selection for a specific reason – and potentially of supernatural intervention – that features and organisms exist because of a deity's conscious intentions. In his biology, Aristotle introduced teleology to describe the adaptedness of organisms, but without accepting the supernatural intention built into Plato's thinking, which Aristotle rejected. Modern biologists continue to face the same difficulty. On the one hand, adaptation is purposeful: natural selection chooses what works and eliminates what does not. On the other hand, biologists by and large reject conscious purpose in evolution. The dilemma gave rise to a famous joke by the evolutionary biologist Haldane: "Teleology is like a mistress to a biologist: he cannot live without her but he's unwilling to be seen with her in public.'" David Hull commented that Haldane's mistress "has become a lawfully wedded wife. Biologists no longer feel obligated to apologize for their use of teleological language; they flaunt it." Ernst Mayr stated that "adaptedness... is an a posteriori result rather than an a priori goal-seeking", meaning that the question of whether something is an adaptation can only be determined after the event.
+
+== See also ==
+
+== References ==
+
+== Sources ==
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+---
+title: "Aerobic organism"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Aerobic_organism"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:03.488289+00:00"
+instance: "kb-cron"
+---
+
+An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. The ability to exhibit aerobic respiration may yield benefits to the aerobic organism, as aerobic respiration yields more energy than anaerobic respiration. Energy production of the cell involves the synthesis of ATP by an enzyme called ATP synthase. In aerobic respiration, ATP synthase is coupled with an electron transport chain in which oxygen acts as a terminal electron acceptor. In July 2020, marine biologists reported that aerobic microorganisms (mainly), in "quasi-suspended animation", were found in organically poor sediments, up to 101.5 million years old, 250 feet below the seafloor in the South Pacific Gyre (SPG) ("the deadest spot in the ocean"), and could be the longest-living life forms ever found.
+
+
+== Types ==
+Obligate aerobes need oxygen to grow. In a process known as cellular respiration, these organisms use oxygen to oxidize substrates (for example sugars and fats) and generate energy.
+Facultative anaerobes use oxygen if it is available, but also have anaerobic methods of energy production.
+Microaerophiles require oxygen for energy production, but are harmed by atmospheric concentrations of oxygen (21% O2).
+Aerotolerant anaerobes do not use oxygen but are not harmed by it.
+When an organism is able to survive in both oxygen and anaerobic environments, the use of the Pasteur effect can distinguish between facultative anaerobes and aerotolerant organisms. If the organism is using fermentation in an anaerobic environment, the addition of oxygen will cause facultative anaerobes to suspend fermentation and begin using oxygen for respiration. Aerotolerant organisms must continue fermentation in the presence of oxygen.
+Facultative organisms grow in both oxygen rich media and oxygen free media.
+
+
+== Aerobic respiration ==
+Aerobic organisms use a process called aerobic respiration to create ATP from ADP and a phosphate. Glucose (a monosaccharide) is oxidized to power the electron transport chain:
+This equation is a summary of what happens in three series of biochemical reactions: glycolysis, the Krebs cycle (also known as the Citric acid cycle), and oxidative phosphorylation.
+
+C6H12O6 + 6 O2 + 38 ADP + 38 phosphate → 6 CO2 + 44 H2O + 38 ATP
+In Oxidative phosphorylation, ATP is synthesized from ADP and a phosphate using ATP synthase. ATP synthase is powered by a proton-motive force created by using the energy generated from the electron transport chain. A hydrogen ion (H+) has a positive charge and if separated by a cellular membrane, it creates a difference in charge between the inside and outside of the membrane. Oxidative phosphorylation occurs in the mitochondria of eukaryotes. 
+Aerobic respiration needs O2 because it acts as the terminal electron acceptor in prokaryotes' electron transport chain. Molecular Oxygen is reduced to water in this process.
+
+
+== See also ==
+Aerobic digestion
+Aerobic vaginitis
+Anaerobic digestion
+Anaerobic organism
+Fermentation (biochemistry)
+Oxygenation (environmental)
+
+
+== References ==
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+---
+title: "Animal"
+chunk: 1/5
+source: "https://en.wikipedia.org/wiki/Animal"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:04.727619+00:00"
+instance: "kb-cron"
+---
+
+Animals are multicellular, eukaryotic organisms belonging to the biological kingdom Animalia (). With few exceptions, animals consume organic material, breathe oxygen, have myocytes and are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Animals form a clade, meaning that they arose from a single common ancestor. Over 1.5 million living animal species have been described, of which around 1.05 million are insects, over 85,000 are molluscs, and around 65,000 are vertebrates. It has been estimated there are as many as 7.77 million animal species on Earth. Animal body lengths range from 8.5 μm (0.00033 in) to 33.6 m (110 ft). They have complex ecologies and interactions with each other and their environments, forming intricate food webs. The scientific study of animals is known as zoology, and the study of animal behaviour is known as ethology.
+The animal kingdom is divided into five major clades, namely Porifera, Ctenophora, Placozoa, Cnidaria and Bilateria. Most living animal species belong to the clade Bilateria, a highly proliferative clade whose members have a bilaterally symmetric and significantly cephalised body plan, and the vast majority of bilaterians belong to two large clades: the protostomes, which includes organisms such as arthropods, molluscs, flatworms, annelids and nematodes; and the deuterostomes, which include echinoderms, hemichordates and chordates, the latter of which contains the vertebrates. The much smaller basal phylum Xenacoelomorpha have an uncertain position within Bilateria.
+Animals first appeared in the fossil record in the late Cryogenian period and diversified in the subsequent Ediacaran period in what is known as the Avalon explosion. Nearly all modern animal phyla first appeared in the fossil record as marine species during the Cambrian explosion, which began around 539 million years ago (Mya), and most classes during the Ordovician radiation 485.4 Mya. Common to all living animals, 6,331 groups of genes have been identified that may have arisen from a single common ancestor that lived about 650 Mya during the Cryogenian period.
+Historically, Aristotle divided animals into those with blood and those without. Carl Linnaeus created the first hierarchical biological classification for animals in 1758 with his Systema Naturae, which Jean-Baptiste Lamarck expanded into 14 phyla by 1809. In 1874, Ernst Haeckel divided the animal kingdom into the multicellular Metazoa (now synonymous with Animalia) and the Protozoa, single-celled organisms no longer considered animals. In modern times, the biological classification of animals relies on advanced techniques, such as molecular phylogenetics, which are effective at demonstrating the evolutionary relationships between taxa.
+Humans make use of many other animal species for food (including meat, eggs, and dairy products), for materials (such as leather, fur, and wool), as pets and as working animals for transportation, and services. Dogs, the first domesticated animal, have been used in hunting, in security and in warfare, as have horses, pigeons and birds of prey; while other terrestrial and aquatic animals are hunted for sports, trophies or profits. Non-human animals are also an important cultural element of human evolution, having appeared in cave arts and totems since the earliest times, and are frequently featured in mythology, religion, arts, literature, heraldry, politics, and sports.
+
+== Etymology ==
+The word animal comes from the Latin noun animal of the same meaning, which is itself derived from Latin animalis 'having breath or soul'. The biological definition includes all members of the kingdom Animalia. In colloquial usage, the term animal is often used to refer only to nonhuman animals. The term metazoa is derived from Ancient Greek μετα meta 'after' (in biology, the prefix meta- stands for 'later') and ζῷᾰ zōia 'animals', plural of ζῷον zōion 'animal'. A metazoan is any member of the group Metazoa.
+
+== Characteristics ==
+
+Animals have several characteristics that they share with other living things. Animals are eukaryotic, multicellular, and aerobic, as are plants and fungi. Unlike plants and algae, which produce their own food, animals cannot produce their own food, a feature they share with fungi. Animals ingest organic material and digest it internally.
+
+=== Structural features ===
+Animals have structural characteristics that set them apart from all other living things:
+
+cells surrounded by an extracellular matrix composed of
+collagen and
+elastic glycoproteins
+motility i.e. able to spontaneously move their bodies during at least part of their life cycle.
+a blastula stage during embryonic development
+Typically, there is an internal digestive chamber with either one opening (in Ctenophora, Cnidaria, and flatworms) or two openings (in most bilaterians).
+
+=== Development ===
+Animal development is controlled by Hox genes, which signal the times and places to develop structures such as body segments and limbs.
+During development, the animal extracellular matrix forms a relatively flexible framework upon which cells can move about and be reorganised into specialised tissues and organs, making the formation of complex structures possible, and allowing cells to be differentiated. The extracellular matrix may be calcified, forming structures such as shells, bones, and spicules. In contrast, the cells of other multicellular organisms (primarily algae, plants, and fungi) are held in place by cell walls, and so develop by progressive growth.
+
+=== Reproduction ===
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+---
+title: "Animal"
+chunk: 2/5
+source: "https://en.wikipedia.org/wiki/Animal"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:04.727619+00:00"
+instance: "kb-cron"
+---
+
+Nearly all animals make use of some form of sexual reproduction. They produce haploid gametes by meiosis; the smaller, motile gametes are spermatozoa and the larger, non-motile gametes are ova. These fuse to form zygotes, which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, and develop into a new sponge. In most other groups, the blastula undergoes more complicated rearrangement. It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm. In most cases, a third germ layer, the mesoderm, also develops between them. These germ layers then differentiate to form tissues and organs.
+Repeated instances of mating with a close relative during sexual reproduction generally leads to inbreeding depression within a population due to the increased prevalence of harmful recessive traits. Animals have evolved numerous mechanisms for avoiding close inbreeding.
+Some animals are capable of asexual reproduction, which often results in a genetic clone of the parent. This may take place through fragmentation; budding, such as in Hydra and other cnidarians; or parthenogenesis, where fertile eggs are produced without mating, such as in aphids.
+
+== Ecology ==
+
+Animals are categorised into ecological groups depending on their trophic levels and how they consume organic material. Such groupings include carnivores (further divided into subcategories such as piscivores, insectivores, ovivores, etc.), herbivores (subcategorised into folivores, graminivores, frugivores, granivores, nectarivores, algivores, etc.), omnivores, fungivores, scavengers/detritivores, and parasites. Interactions between animals of each biome form complex food webs within that ecosystem. In carnivorous or omnivorous species, predation is a consumer–resource interaction where the predator feeds on another organism, its prey, who often evolves anti-predator adaptations to avoid being fed upon. Selective pressures imposed on one another lead to an evolutionary arms race between predator and prey, resulting in various antagonistic/competitive coevolutions. Almost all multicellular predators are animals. Some consumers use multiple methods; for example, in parasitoid wasps, the larvae feed on the hosts' living tissues, killing them in the process, but the adults primarily consume nectar from flowers. Other animals may have very specific feeding behaviours, such as hawksbill sea turtles which mainly eat sponges.
+
+Most animals rely on biomass and bioenergy produced by plants and phytoplanktons (collectively called producers) through photosynthesis. Herbivores, as primary consumers, eat the plant material directly to digest and absorb the nutrients, while carnivores and other animals on higher trophic levels indirectly acquire the nutrients by eating the herbivores or other animals that have eaten the herbivores. Animals oxidise carbohydrates, lipids, proteins and other biomolecules in cellular respiration, which allows the animal to grow and to sustain basal metabolism and fuel other biological processes such as locomotion. Some benthic animals living close to hydrothermal vents and cold seeps on the dark sea floor consume organic matter produced through chemosynthesis (via oxidising inorganic compounds such as hydrogen sulfide) by archaea and bacteria.
+Animals originated in the ocean; all extant animal phyla, except for Micrognathozoa and Onychophora, feature at least some marine species. However, several lineages of arthropods begun to colonise land around the same time as land plants, probably between 510 and 471 million years ago, during the Late Cambrian or Early Ordovician. Vertebrates such as the lobe-finned fish Tiktaalik started to move on to land in the late Devonian, about 375 million years ago. Other notable animal groups that colonized land environments are Mollusca, Platyhelmintha, Annelida, Tardigrada, Onychophora, Rotifera, Nematoda.
+Animals occupy virtually all of earth's habitats and microhabitats, with faunas adapted to salt water, hydrothermal vents, fresh water, hot springs, swamps, forests, pastures, deserts, air, and the interiors of other organisms. Animals are however not particularly heat tolerant; very few of them can survive at constant temperatures above 50 °C (122 °F) or in the most extreme cold deserts of continental Antarctica.
+The collective global geomorphic influence of animals on the processes shaping the Earth's surface remains largely understudied, with most studies limited to individual species and well-known exemplars.
+
+== Diversity ==
+
+=== Size ===
+
+The blue whale (Balaenoptera musculus) is the largest animal that has ever lived, weighing up to 190 tonnes and measuring up to 33.6 metres (110 ft) long. The largest extant terrestrial animal is the African bush elephant (Loxodonta africana), weighing up to 12.25 tonnes and measuring up to 10.67 metres (35.0 ft) long. The largest terrestrial animals that ever lived were titanosaur sauropod dinosaurs such as Argentinosaurus, which may have weighed as much as 73 tonnes, and Supersaurus which may have reached 39 metres. Several animals are microscopic; some Myxozoa (obligate parasites within the Cnidaria) never grow larger than 20 μm, and one of the smallest species (Myxobolus shekel) is no more than 8.5 μm when fully grown.
+
+=== Numbers and habitats of major phyla ===
+The following table lists estimated numbers of described extant species for the major animal phyla, along with their principal habitats (terrestrial, fresh water, and marine), and free-living or parasitic ways of life. Species estimates shown here are based on numbers described scientifically; much larger estimates have been calculated based on various means of prediction, and these can vary wildly. For instance, around 25,000–27,000 species of nematodes have been described, while published estimates of the total number of nematode species include 10,000–20,000; 500,000; 10 million; and 100 million. Using patterns within the taxonomic hierarchy, the total number of animal species—including those not yet described—was calculated to be about 7.77 million in 2011.
+
+== Evolutionary origin ==
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+---
+title: "Animal"
+chunk: 3/5
+source: "https://en.wikipedia.org/wiki/Animal"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:04.727619+00:00"
+instance: "kb-cron"
+---
+
+Evidence of animals is found as long ago as the Cryogenian period. 24-Isopropylcholestane (24-ipc) has been found in rocks from roughly 650 million years ago; it is only produced by sponges and pelagophyte algae. Its likely origin is from sponges based on molecular clock estimates for the origin of 24-ipc production in both groups. Analyses of pelagophyte algae consistently recover a Phanerozoic origin, while analyses of sponges recover a Neoproterozoic origin, consistent with the appearance of 24-ipc in the fossil record.
+The first body fossils of animals appear in the Ediacaran, represented by forms such as Charnia and Spriggina. It had long been doubted whether these fossils truly represented animals, but the discovery of the animal lipid cholesterol in fossils of Dickinsonia establishes their nature. Animals are thought to have originated under low-oxygen conditions, suggesting that they were capable of living entirely by anaerobic respiration, but as they became specialised for aerobic metabolism they became fully dependent on oxygen in their environments.
+Many animal phyla first appear in the fossil record during the Cambrian explosion, starting about 539 million years ago, in beds such as the Burgess Shale. Extant phyla in these rocks include molluscs, brachiopods, onychophorans, tardigrades, arthropods, echinoderms and hemichordates, along with numerous now-extinct forms such as the predatory Anomalocaris. The apparent suddenness of the event may however be an artefact of the fossil record, rather than showing that all these animals appeared simultaneously. That view is supported by the discovery of Auroralumina attenboroughii, the earliest known Ediacaran crown-group cnidarian (557–562 mya, some 20 million years before the Cambrian explosion) from Charnwood Forest, England. It is thought to be one of the earliest predators, catching small prey with its nematocysts as modern cnidarians do.
+Some palaeontologists have suggested that animals appeared much earlier than the Cambrian explosion, possibly as early as 1 billion years ago. Early fossils that might represent animals appear for example in the 665-million-year-old rocks of the Trezona Formation of South Australia. These fossils are interpreted as most probably being early sponges. 
+Trace fossils such as tracks and burrows found in the Tonian period (from 1 gya) may indicate the presence of triploblastic worm-like animals, roughly as large (about 5 mm wide) and complex as earthworms. However, similar tracks are produced by the giant single-celled protist Gromia sphaerica, so the Tonian trace fossils may not indicate early animal evolution. Around the same time, the layered mats of microorganisms called stromatolites decreased in diversity, perhaps due to grazing by newly evolved animals. Objects such as sediment-filled tubes that resemble trace fossils of the burrows of wormlike animals have been found in 1.2 gya rocks in North America, in 1.5 gya rocks in Australia and North America, and in 1.7 gya rocks in Australia. Their interpretation as having an animal origin is disputed, as they might be water-escape or other structures.
+
+== Phylogeny ==
+
+=== External phylogeny ===
+Animals are monophyletic, meaning they are derived from a common ancestor. Animals are the sister group to the choanoflagellates, with which they form the Choanozoa. 
+Ros-Rocher and colleagues (2021) trace the origins of animals to unicellular ancestors, providing the external phylogeny shown in the cladogram. Uncertainty of relationships is indicated with dashed lines. The animal clade had certainly originated by 650 mya, and may have come into being as much as 800 mya, based on molecular clock evidence for different phyla.
+
+=== Internal phylogeny ===
+
+The relationships at the base of the animal tree have been debated. Other than Ctenophora, the Bilateria and Cnidaria are the only groups with symmetry, and other evidence shows they are closely related. In addition to sponges, Placozoa has no symmetry and was often considered a "missing link" between protists and multicellular animals. The presence of hox genes in Placozoa shows that they were once more complex.
+The Porifera (sponges) have long been assumed to be sister to the rest of the animals, but there is evidence that the Ctenophora may be in that position. Molecular phylogenetics has supported both the sponge-sister and ctenophore-sister hypotheses. In 2017, Roberto Feuda and colleagues, using amino acid differences, presented both, with the following cladogram for the sponge-sister view that they supported (their ctenophore-sister tree simply interchanging the places of ctenophores and sponges):
+
+Conversely, a 2023 study by Darrin Schultz and colleagues uses ancient gene linkages to construct the following ctenophore-sister phylogeny:
+
+=== Non-bilaterians ===
+
+Sponges are physically very distinct from other animals, and were long thought to have diverged first, representing the oldest animal phylum and forming a sister clade to all other animals. Despite their morphological dissimilarity with all other animals, genetic evidence suggests sponges may be more closely related to other animals than the comb jellies are. Sponges lack the complex organisation found in most other animal phyla; their cells are differentiated, but in most cases not organised into distinct tissues, unlike all other animals. They typically feed by drawing in water through pores, filtering out small particles of food.
+The Ctenophora and Cnidaria are radially symmetric and have digestive chambers with a single opening, which serves as both mouth and anus. Animals in both phyla have distinct tissues, but these are not organised into discrete organs. They are diploblastic, having only two main germ layers, ectoderm and endoderm.
+The tiny placozoans have no permanent digestive chamber and no symmetry; they superficially resemble amoebae. Their phylogeny is poorly defined, and under active research.
+
+=== Bilateria ===
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+---
+title: "Animal"
+chunk: 4/5
+source: "https://en.wikipedia.org/wiki/Animal"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:04.727619+00:00"
+instance: "kb-cron"
+---
+
+The remaining animals, the great majority—comprising some 29 phyla and over a million species—form the Bilateria clade, which have a bilaterally symmetric body plan. The Bilateria are triploblastic, with three well-developed germ layers, and their tissues form distinct organs. The digestive chamber has two openings, a mouth and an anus, and in the Nephrozoa there is an internal body cavity, a coelom or pseudocoelom. These animals have a head end (anterior) and a tail end (posterior), a back (dorsal) surface and a belly (ventral) surface, and a left and a right side. A modern consensus phylogenetic tree for the Bilateria is shown below.
+
+Having a front end means that this part of the body encounters stimuli, such as food, favouring cephalisation, the development of a head with sense organs and a mouth. Many bilaterians have a combination of circular muscles that constrict the body, making it longer, and an opposing set of longitudinal muscles, that shorten the body; these enable soft-bodied animals with a hydrostatic skeleton to move by peristalsis. They also have a gut that extends through the basically cylindrical body from mouth to anus. Many bilaterian phyla have primary larvae which swim with cilia and have an apical organ containing sensory cells. However, over evolutionary time, descendant spaces have evolved which have lost one or more of each of these characteristics. For example, adult echinoderms are radially symmetric (unlike their larvae), while some parasitic worms have extremely simplified body structures.
+Genetic studies have considerably changed zoologists' understanding of the relationships within the Bilateria. Most appear to belong to two major lineages, the protostomes and the deuterostomes. It is often suggested that the basalmost bilaterians are the Xenacoelomorpha, with all other bilaterians belonging to the subclade Nephrozoa. However, this suggestion has been contested, with other studies finding that xenacoelomorphs are more closely related to Ambulacraria than to other bilaterians.
+
+==== Protostomes and deuterostomes ====
+
+Protostomes and deuterostomes differ in several ways. Early in development, deuterostome embryos undergo radial cleavage during cell division, while many protostomes (the Spiralia) undergo spiral cleavage.
+Animals from both groups possess a complete digestive tract, but in protostomes the first opening of the embryonic gut develops into the mouth, and the anus forms secondarily. In deuterostomes, the anus forms first while the mouth develops secondarily. Most protostomes have schizocoelous development, where cells simply fill in the interior of the gastrula to form the mesoderm. In deuterostomes, the mesoderm forms by enterocoelic pouching, through invagination of the endoderm.
+The main deuterostome taxa are the Ambulacraria and the Chordata. Ambulacraria are exclusively marine and include acorn worms, starfish, sea urchins, and sea cucumbers. The chordates are dominated by the vertebrates (animals with backbones), which consist of fishes, amphibians, reptiles, birds, and mammals.
+
+The protostomes include the Ecdysozoa, named after their shared trait of ecdysis, growth by moulting, Among the largest ecdysozoan phyla are the arthropods and the nematodes. The rest of the protostomes are in the Spiralia, named for their pattern of developing by spiral cleavage in the early embryo. Major spiralian phyla include the annelids and molluscs.
+
+== History of classification ==
+
+In the classical era, Aristotle divided animals, based on his own observations, into those with blood (roughly, the vertebrates) and those without. The animals were then arranged on a scale from man (with blood, two legs, rational soul) down through the live-bearing tetrapods (with blood, four legs, sensitive soul) and other groups such as crustaceans (no blood, many legs, sensitive soul) down to spontaneously generating creatures like sponges (no blood, no legs, vegetable soul). Aristotle was uncertain whether sponges were animals, which in his system ought to have sensation, appetite, and locomotion, or plants, which did not: he knew that sponges could sense touch and would contract if about to be pulled off their rocks, but that they were rooted like plants and never moved about.
+In 1758, Carl Linnaeus created the first hierarchical classification in his Systema Naturae. In his original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then, the last four have all been subsumed into a single phylum, the Chordata, while his Insecta (which included the crustaceans and arachnids) and Vermes have been renamed or broken up. The process was begun in 1793 by Jean-Baptiste de Lamarck, who called the Vermes une espèce de chaos ('a chaotic mess') and split the group into three new phyla: worms, echinoderms, and polyps (which contained corals and jellyfish). By 1809, in his Philosophie Zoologique, Lamarck had created nine phyla apart from vertebrates (where he still had four phyla: mammals, birds, reptiles, and fish) and molluscs, namely cirripedes, annelids, crustaceans, arachnids, insects, worms, radiates, polyps, and infusorians.
+In his 1817 Le Règne Animal, Georges Cuvier used comparative anatomy to group the animals into four embranchements ('branches' with different body plans, roughly corresponding to phyla), namely vertebrates, molluscs, articulated animals (arthropods and annelids), and zoophytes (radiata) (echinoderms, cnidaria and other forms). This division into four was followed by the embryologist Karl Ernst von Baer in 1828, the zoologist Louis Agassiz in 1857, and the comparative anatomist Richard Owen in 1860.
+In 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms: Metazoa (multicellular animals, with five phyla: coelenterates, echinoderms, articulates, molluscs, and vertebrates) and Protozoa (single-celled animals), including a sixth animal phylum, sponges. The protozoa were later moved to the former kingdom Protista, leaving only the Metazoa as a synonym of Animalia.
+
+== In human culture ==
+
+=== Practical uses ===
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+---
+title: "Animal"
+chunk: 5/5
+source: "https://en.wikipedia.org/wiki/Animal"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:04.727619+00:00"
+instance: "kb-cron"
+---
+
+The human population exploits a large number of other animal species for food, both of domesticated livestock species in animal husbandry and, mainly at sea, by hunting wild species. Marine fish of many species are caught commercially for food. A smaller number of species are farmed commercially. Humans and their livestock make up more than 90% of the biomass of all terrestrial vertebrates, and almost as much as all insects combined.
+Invertebrates including cephalopods, crustaceans, insects—principally bees and silkworms—and bivalve or gastropod molluscs are hunted or farmed for food, fibres. Chickens, cattle, sheep, pigs, and other animals are raised as livestock for meat across the world. Animal fibres such as wool and silk are used to make textiles, while animal sinews have been used as lashings and bindings, and leather is widely used to make shoes and other items. Animals have been hunted and farmed for their fur to make items such as coats and hats. Dyestuffs including carmine (cochineal), shellac, and kermes have been made from the bodies of insects. Working animals including cattle and horses have been used for work and transport from the first days of agriculture.
+Animals such as the fruit fly Drosophila melanogaster serve a major role in science as experimental models. Animals have been used to create vaccines since their discovery in the 18th century. Some medicines such as the cancer drug trabectedin are based on toxins or other molecules of animal origin.
+
+People have used hunting dogs to help chase down and retrieve animals, and birds of prey to catch birds and mammals, while tethered cormorants have been used to catch fish. Poison dart frogs have been used to poison the tips of blowpipe darts.
+A wide variety of animals are kept as pets, from invertebrates such as tarantulas, octopuses, and praying mantises, reptiles such as snakes and chameleons, and birds including canaries, parakeets, and parrots all finding a place. However, the most kept pet species are mammals, namely dogs, cats, and rabbits. There is a tension between the role of animals as companions to humans, and their existence as individuals with rights of their own.
+A wide variety of terrestrial and aquatic animals are hunted for sport.
+
+=== Symbolic uses ===
+The signs of the Western and Chinese zodiacs are based on animals. In China and Japan, the butterfly has been seen as the personification of a person's soul, and in classical representation the butterfly is also the symbol of the soul.
+
+Animals have been the subjects of art from the earliest times, both historical, as in ancient Egypt, and prehistoric, as in the cave paintings at Lascaux. Major animal paintings include Albrecht Dürer's 1515 The Rhinoceros, and George Stubbs's c. 1762 horse portrait Whistlejacket. Insects, birds and mammals play roles in literature and film, such as in giant bug movies.
+Animals including insects and mammals feature in mythology and religion. The scarab beetle was sacred in ancient Egypt, and the cow is sacred in Hinduism. Among other mammals, deer, horses, lions, bats, bears, and wolves are the subjects of myths and worship.
+
+== See also ==
+Animal coloration – General appearance of an animal
+Ethology – Study of animal behaviour
+Lists of organisms by population
+World Animal Day – Observed on 4 October
+
+== Notes ==
+
+== References ==
+
+== External links ==
+
+Tree of Life Project. Archived 12 June 2011 at the Wayback Machine.
+Animal Diversity Web – University of Michigan's database of animals
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diff --git a/data/en.wikipedia.org/wiki/Archaea-0.md b/data/en.wikipedia.org/wiki/Archaea-0.md
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+---
+title: "Archaea"
+chunk: 1/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+Archaea (  ar-KEE-ə) is a domain of organisms. Traditionally, Archaea included only its prokaryotic members, but has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even though the domain Archaea cladistically includes eukaryotes, the term archaea (sing. archaeon  ar-KEE-on; from Ancient Greek  ἀρχαῖον arkhaîon 'ancient') in English still generally refers specifically to prokaryotic members of Archaea. 
+Archaea were initially classified as bacteria, receiving the name archaebacteria (, in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties distinguishing them from Bacteria and Eukaryota, including: cell membranes made of ether-linked lipids; metabolisms such as methanogenesis; and a unique motility structure known as an archaellum. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been identified only by their gene sequences in environmental samples. It is unknown whether they can produce endospores.
+Archaea are often similar to bacteria in size and shape, although a few have very different shapes, such as the flat, square cells of Haloquadratum walsbyi. Despite this, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. The salt-tolerant Halobacteria use sunlight as an energy source, and other species of archaea fix carbon (autotrophy), but unlike cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores. The first observed archaea were extremophiles, living in extreme environments such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.
+Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example. As of 2024, only one species of non-eukaryotic archaea has been found to be parasitic; many are mutualists or commensals, such as the methanogens (methane-producers) that inhabit the gastrointestinal tract in humans and ruminants, where their vast numbers facilitate digestion. Methanogens are used in biogas production and sewage treatment, while biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.
+
+== Discovery and classification ==
+
+=== Early concept ===
+
+For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. Microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, and the substances they consume. In 1965, Emile Zuckerkandl and Linus Pauling instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. This phylogenetic approach is the main method used today.
+Archaea were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox, based on their ribosomal RNA (rRNA) genes. (At that time only the methanogens were known). They called these groups the Urkingdoms of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms. Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of peptidoglycan in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three then thought to be natural domains known as the three-domain system: the Eukarya, the Bacteria and the Archaea, in what is now known as the Woesian Revolution.
+The word archaea comes from the Ancient Greek ἀρχαῖα, meaning "ancient things", as the first representatives of the domain Archaea were methanogens and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity, but as new habitats were studied, more organisms were discovered. Extreme halophilic and hyperthermophilic microbes were also included in Archaea. For a long time, archaea were seen as extremophiles that exist only in extreme habitats such as hot springs and salt lakes, but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature. This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory.
+
+=== Classification ===
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+---
+title: "Archaea"
+chunk: 2/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors. These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms (molecular phylogenetics). Most of the culturable and well-investigated species of archaea are members of two main kingdoms, the Methanobacteriati and the Thermoproteati (formerly TACK). Other groups have been tentatively created, such as the peculiar species Nanoarchaeum equitans – discovered in 2003 and assigned its own phylum, the Nanoarchaeota (reassigned to Nanobdellota in 2023). A new phylum "Korarchaeota" (now Thermoproteota) has also been proposed, containing a small group of unusual thermophilic species sharing features of both the main phyla. Other detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising Micrarchaeota and Parvarchaeota), which were discovered in 2006 and are some of the smallest organisms known.
+A superphylum – "TACK" (now kingdom Thermoproteati) – which includes the Thaumarchaeota (now Nitrososphaerota), "Augarchaeota", Crenarchaeota (now Thermoproteota), and "Korarchaeota" (now Thermoproteota) was proposed in 2011 to be related to the origin of eukaryotes. In 2017, the newly discovered and newly named "Asgard" (now kingdom Promethearchaeati) superphylum was proposed to be more closely related to the original eukaryote and a sister group to Thermoproteati / "TACK".
+In 2013, the superphylum "DPANN" (now kingdom Nanobdellati) was proposed to group "Nanoarchaeota", "Nanohaloarchaeota", Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising "Micrarchaeota" and "Parvarchaeota"), and other similar archaea. This archaeal superphylum encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, Nanobdellati/"DPANN" may include members obligately dependent on symbiotic interactions, and may even include novel parasites. However, other phylogenetic analyses found that Nanobdellati/"DPANN" does not form a monophyletic group, and that the apparent grouping is caused by long branch attraction (LBA), suggesting that all these lineages belong to Methanobacteriati.
+
+=== Phylogeny ===
+According to Tom A. Williams et al. 2017, Castelle & Banfield (2018) and GTDB release 10-RS226 (16th April 2025).
+
+=== Concept of species ===
+The classification of archaea into species is also controversial. Ernst Mayr's species definition – a reproductively isolated group of interbreeding organisms - does not apply, as archaea reproduce only asexually.
+Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma. On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning.
+Current knowledge on genetic diversity in archaeans is fragmentary, so the total number of species cannot be estimated with any accuracy. Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, so the level of diversity remains obscure. This situation is also seen in the Bacteria; many uncultured microbes present similar issues with characterization.
+
+== Prokaryotic phyla ==
+
+=== Valid phyla ===
+The following phyla have been validly published according to the Prokaryotic Code; belonging to the four kingdoms of archaea:
+
+Methanobacteriota
+Microcaldota
+Nanobdellota
+Promethearchaeota
+Thermoproteota
+
+=== Candidate phyla ===
+The following phyla have been proposed, but have not been validly published according to the Prokaryotic Code; phyla that do not belong to any kingdom are shown in bold:
+
+== Origin and evolution ==
+
+The age of the Earth is about 4.54 billion years. Scientific evidence suggests that life began on Earth at least 3.5 billion years ago. The earliest evidence for life on Earth is graphite found to be biogenic in 3.7-billion-year-old metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48-billion-year-old sandstone discovered in Western Australia. In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia.
+Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies, and fossil shapes cannot be used to identify them as archaea. Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago, though such data have since been questioned. These lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua district, which includes Earth's oldest known sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on Earth.
+Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. One possibility is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes. It is possible that the last common ancestor of bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" for archaea, and organisms that live in cooler environments appeared only later. Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term prokaryote may suggest a false similarity between them. However, structural and functional similarities between lineages often occur because of shared ancestral traits or evolutionary convergence. These similarities are known as a grade, and prokaryotes are best thought of as a grade of life, characterized by such features as an absence of membrane-bound organelles.
+
+=== Comparison with other domains ===
+The following table compares some major characteristics of the three domains, to illustrate their similarities and differences.
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+---
+title: "Archaea"
+chunk: 3/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule 16S rRNA is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this polynucleotide over generations. 16S rRNA is large enough to show organism-specific variations, but still small enough to be compared quickly. In 1977, Carl Woese, a microbiologist studying the genetic sequences of organisms, developed a new comparison method that involved splitting the RNA into fragments that could be sorted and compared with other fragments from other organisms. The more similar the patterns between species, the more closely they are related.
+Woese used his new rRNA comparison method to categorize and contrast different organisms. He compared a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes. These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea. His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria. The development of the nucleus occurred after the split between Bacteria and this common ancestor.
+One property unique to archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in bacteria and eukarya, which may be a contributing factor to the ability of many archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and salinity. Comparative analysis of archaeal genomes has also identified several molecular conserved signature indels and signature proteins uniquely present in either all archaea or different main groups within archaea. Another unique feature of archaea, found in no other organisms, is methanogenesis (the metabolic production of methane). Methanogenic archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas.
+This difference in the biochemical structure of Bacteria and Archaea has been explained by researchers through evolutionary processes. It is theorized that both domains originated at deep sea alkaline hydrothermal vents. At least twice, microbes evolved lipid biosynthesis and cell wall biochemistry. It has been suggested that the last universal common ancestor was a non-free-living organism. It may have had a permeable membrane composed of bacterial simple chain amphiphiles (fatty acids), including archaeal simple chain amphiphiles (isoprenoids). These stabilize fatty acid membranes in seawater; this property may have driven the divergence of bacterial and archaeal membranes, "with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the origin of life".
+
+=== Relationship to bacteria ===
+
+The relationships among the three domains are of central importance for understanding the origin of life. Most of the metabolic pathways, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in gene expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell structure is most similar to that of Gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus (exoskeleton) of varying chemical composition. In some phylogenetic trees based upon different gene / protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I; but the phylogeny of these genes was interpreted to reveal inter-domain gene transfer, and might not reflect the organismal relationship(s).
+It has been proposed that the archaea evolved from Gram-positive bacteria in response to antibiotic selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by Gram-positive bacteria, and that these antibiotics act primarily on the genes that distinguish archaea from bacteria. The proposal is that the selective pressure towards resistance generated by the gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics' target genes, and that these strains represented the common ancestors of present-day Archaea. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms; Cavalier-Smith has made a similar suggestion, the Neomura hypothesis. This proposal is also supported by other work investigating protein structural relationships and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.
+
+=== Relation to eukaryotes ===
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+---
+title: "Archaea"
+chunk: 4/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two.
+Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Thermoproteota is closer than the relationship between the Methanobacteriati and the phylum Thermoproteota and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima, from horizontal gene transfer. The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through symbiogenesis, the fusion of an archaean and a eubacterium, which formed the mitochondria; this hypothesis explains the genetic similarities between the groups. The eocyte hypothesis instead posits that Eukaryota emerged relatively late from the Archaea.
+A lineage of archaea discovered in 2015, Lokiarchaeum (of the proposed new phylum "Lokiarchaeota"), named for a hydrothermal vent called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes.
+Several sister phyla of "Lokiarchaeota" have since been found ("Thorarchaeota", "Odinarchaeota", "Heimdallarchaeota"), all together comprising a newly proposed supergroup "Asgard".
+Details of the relation of Promethearchaeati / "Asgard" members and eukaryotes are still under consideration, although, in January 2020, scientists reported that Promethearchaeum syntrophicum, a type of Promethearchaeati / "Asgard" archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago.
+
+== Morphology ==
+Individual archaea range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the Thermoproteota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum. Archaea in the genus Haloquadratum such as Haloquadratum walsbyi are flat, square specimens that live in hypersaline pools. These unusual shapes are probably maintained by both their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in archaea, and filaments form within their cells, but in contrast with other organisms, these cellular structures are poorly understood. In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae.
+Some species form aggregates or filaments of cells up to 200 μm long. These organisms can be prominent in biofilms. Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells. Archaea in the genus Pyrodictium produce an elaborate multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration. The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors. Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Methanobacteriati species are spaced along thin filaments that can range up to 15 centimetres (5.9 in) long; these filaments are made of a particular bacteria species.
+
+== Structure, composition development, and operation ==
+Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles. Like bacteria, the cell membranes of archaea are usually bounded by a cell wall and they swim using one or more flagella. Structurally, archaea are most similar to gram-positive bacteria. Most have a single plasma membrane and cell wall, and lack a periplasmic space; the exception to this general rule is Ignicoccus, which possess a particularly large periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.
+
+=== Cell wall and archaella ===
+
+Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall. In most archaea, the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail). This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane. Unlike bacteria, archaea lack peptidoglycan in their cell walls. Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid, substituting the latter with N-Acetyltalosaminuronic acid.
+Archaeal flagella are known as archaella, that operate like bacterial flagella – their long stalks are driven by rotatory motors at the base. These motors are powered by a proton gradient across the membrane, but archaella are notably different in composition and development. The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system, while archaeal flagella appear to have evolved from bacterial type IV pili. In contrast with the bacterial flagellum, which is hollow and assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.
+
+=== Membranes ===
+
+Archaeal membranes are made of molecules that are distinctly different from those in all other life forms, showing that archaea are related only distantly to bacteria and eukaryotes. In all organisms, cell membranes are made of molecules known as phospholipids. These molecules possess both a polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer.
+The phospholipids of archaea are unusual in four ways:
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+---
+title: "Archaea"
+chunk: 5/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+They have membranes composed of glycerol-ether lipids, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids. The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids, this is an ester bond, whereas in ether lipids this is an ether bond.
+The stereochemistry of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called enantiomers. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by enzymes adapted for the other. The archaeal phospholipids are built on a backbone of sn-glycerol-1-phosphate, which is an enantiomer of sn-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains.
+Archaeal lipid tails differ from those of other organisms in that they are based upon long isoprenoid chains with multiple side-branches, sometimes with cyclopentane or cyclohexane rings. By contrast, the fatty acids in the membranes of other organisms have straight chains without side branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures.
+In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile); this fusion may make their membranes more rigid and better able to resist harsh environments. For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in its highly acidic habitat.
+
+== Metabolism ==
+
+Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are chemotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. In these reactions, one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor. The energy released is used to generate adenosine triphosphate (ATP) through chemiosmosis, the same basic process that happens in the mitochondrion of eukaryotic cells.
+Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating photosynthesis does not occur in any of these organisms. Many basic metabolic pathways are shared among all forms of life; for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.
+
+Some Methanobacteriati are methanogens (archaea that produce methane as a result of metabolism) living in anaerobic environments, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. Other organic compounds such as alcohols, acetic acid or formic acid are used as alternative electron acceptors by methanogens. These reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas.
+
+Other archaea use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or another metabolic pathway called the 3-hydroxypropionate / 4-hydroxybutyrate cycle. The Thermoproteota also use the reverse Krebs cycle while the Methanobacteriati also use the reductive acetyl-CoA pathway. Carbon fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis. Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.
+Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of and into the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.
+
+== Genetics ==
+
+Archaea usually have a single circular chromosome, but many euryarchaea have been shown to bear multiple copies of this chromosome. The largest known archaeal genome as of 2002 was 5,751,492 base pairs in Methanosarcina acetivorans. The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.
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+---
+title: "Archaea"
+chunk: 6/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Methanobacteriati and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaeal features are the organization of genes of related function – such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.
+Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes, while archaeal translation shows signs of both bacterial and eukaryotic equivalents. Although archaea have only one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter, but other archaeal transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes.
+
+=== Horizontal gene transfer and genetic exchange ===
+Haloferax volcanii, an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.
+When the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius are exposed to DNA-damaging UV irradiation or to the agents bleomycin or mitomycin C, species-specific cellular aggregation is induced. Aggregation in S. solfataricus could not be induced by other physical stressors, such as pH or temperature shift, suggesting that aggregation is induced specifically by DNA damage. Ajon et al. showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in S. acidocaldarius. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al. and Ajon et al. hypothesized that cellular aggregation enhances species-specific DNA transfer between Sulfolobus cells in order to provide increased repair of damaged DNA by means of homologous recombination. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species-specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.
+
+=== Archaeal viruses ===
+Archaea are the target of a number of viruses in a diverse virosphere distinct from bacterial and eukaryotic viruses. They have been organized into 15–18 DNA-based families so far, but multiple species remain un-isolated and await classification. These families can be informally divided into two groups: archaea-specific and cosmopolitan. Archaeal-specific viruses target only archaean species and currently include 12 families. Numerous unique, previously unidentified viral structures have been observed in this group, including: bottle-shaped, spindle-shaped, coil-shaped, and droplet-shaped viruses. While the reproductive cycles and genomic mechanisms of archaea-specific species may be similar to other viruses, they bear unique characteristics that were specifically developed due to the morphology of host cells they infect. Their virus release mechanisms differ from that of other phages. Bacteriophages generally undergo either lytic pathways, lysogenic pathways, or (rarely) a mix of the two. Most archaea-specific viral strains maintain a stable, somewhat lysogenic, relationship with their hosts – appearing as a chronic infection. This involves the gradual, and continuous, production and release of virions without killing the host cell. Prangishyili (2013) noted that it has been hypothesized that tailed archaeal phages originated from bacteriophages capable of infecting haloarchaeal species. If the hypothesis is correct, it can be concluded that other double-stranded DNA viruses that make up the rest of the archaea-specific group are their own unique group in the global viral community. Krupovic et al. (2018) states that the high levels of horizontal gene transfer, rapid mutation rates in viral genomes, and lack of universal gene sequences have led researchers to perceive the evolutionary pathway of archaeal viruses as a network. The lack of similarities among phylogenetic markers in this network and the global virosphere, as well as external linkages to non-viral elements, may suggest that some species of archaea specific viruses evolved from non-viral mobile genetic elements (MGE).
+These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the Halorubrum pleomorphic virus 1 (Pleolipoviridae) infecting halophilic archaea, and the other one by the Aeropyrum coil-shaped virus (Spiraviridae) infecting a hyperthermophilic (optimal growth at 90–95 °C) host. Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.
+
+== Reproduction ==
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+---
+title: "Archaea"
+chunk: 7/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; mitosis and meiosis do not occur, so if a species of archaea exists in more than one form, all have the same genetic material. Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides. In the genus Sulfolobus, the cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting points (origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes.
+In Methanobacteriati the cell division protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents. In cren- and thaumarchaea, the cell division machinery Cdv fulfills a similar role. This machinery is related to the eukaryotic ESCRT-III machinery which, while best known for its role in cell sorting, also has been seen to fulfill a role in separation between divided cell, suggesting an ancestral role in cell division.
+Both bacteria and eukaryotes, but not archaea, make spores. Some species of Haloarchaea undergo phenotypic switching and grow as several different cell types, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.
+
+== Behavior ==
+
+=== Communication ===
+Quorum sensing was originally thought to not exist in Archaea, but recent studies have shown evidence of some species being able to perform cross-talk through quorum sensing. Other studies have shown syntrophic interactions between archaea and bacteria during biofilm growth. Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, displaying similarities with bacteria LuxR, and ultimately allowing for the detection of small molecules that are used in high density communication. Similarly to bacteria, Archaea LuxR solos have shown to bind to AHLs (lactones) and non-AHLs ligans, which is a large part in performing intraspecies, interspecies, and interkingdom communication through quorum sensing.
+
+=== Biofilms ===
+Archaea are known to form biofilms, a common strategy among microorganisms. Quorum sensing is thought to play a role in Archaeal biofilm formation, but less is known about Archaeal quorum sensing than Bacterial quorum sensing. Some Archaea have been observed to form biofilms when the pH is a specific value, without necessarily relying on quorum sensing for instance. These biofilms are sessile communities of micro-organisms (they can contain multiple different species) that produce extracellular polymeric substances, which are used to create a matrix, within which the micro-organisms can grow. Biofilms are beneficial as they: protect organisms from abiotic stresses; facilitate horizontal gene transfer; and enable syntropy to take place. 
+Biofilm formation has a number of stages: attachment; micro-colony formation; maturation; and dispersal. During the attachment phase the Archaea are reversibly attached to a surface by type-4 pili and archaella. Some Archaea possess other structures involved in attachment such as hami; fimbriae; or cannulae. During the micro colony phase, the extracellular polymeric substance matrix is produced, and numerous archaea have been observed to produce pills and nanowires between cells. During the maturation phase the matrix takes on a sophisticated architecture, such as including pathways for waste to exit the biofilms. Different archaea have been observed to produce biofilms with different architectures. Finally, dispersal can take place, where cells begin to leave the biofilm, this process has been observed in Archaea but the mechanisms behind it are not understood.
+
+== Ecology ==
+
+=== Habitats ===
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+---
+title: "Archaea"
+chunk: 8/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+Archaea exist in a broad range of habitats, are recognized as a major part of global ecosystems, and may represent about 20% of microbial cells in the oceans. However, the first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and soils. Similar to PGPR, Archaea are considered a source of plant growth promotion as well.
+Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles. These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a useful starting point for classification.
+Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and outnumber their bacterial counterparts at salinities greater than 20–25%. Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F). The archaeal Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism.
+Other archaea exist in very acidic or alkaline conditions. For example, one of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 molar sulfuric acid.
+This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. Some extremophile habitats are not dissimilar to those on Mars, leading to the suggestion that viable microbes could be transferred between planets in meteorites.
+Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. For example, archaea are common in cold oceanic environments such as polar seas. Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the plankton community (as part of the picoplankton). Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in pure culture. Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored. Some marine Thermoproteota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Thermoproteota may also use other sources of energy.
+Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom. It has been demonstrated that in all oceanic surface sediments (from 1,000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally.
+
+=== Role in chemical cycling ===
+
+Archaea recycle elements such as carbon, nitrogen, and sulfur through their various habitats. Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation).
+Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans. The archaea also appear crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter.
+In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as Sulfolobus, produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage.
+In the carbon cycle, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes, and sewage-treatment works.
+
+=== Interactions with other organisms ===
+
+The well-characterized interactions between archaea and other organisms are either mutual or commensal. There are no clear examples of known archaeal pathogens or parasites as of 2003, but some species of methanogens have been suggested to be involved in infections in the mouth, and Nanoarchaeum equitans may be a parasite of another species of archaea, since it only survives and reproduces within the cells of the Crenarchaeon Ignicoccus hospitalis, and appears to offer no benefit to its host.
+
+==== Mutualism ====
+Mutualism is an interaction between individuals of different species that results in positive (beneficial) effects on per capita reproduction and/or survival of the interacting populations. One well-understood example of mutualism is the interaction between protozoa and methanogenic archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites. In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy.
+In anaerobic protozoa, such as Plagiopyla frontata, Trimyema, Heterometopus and Metopus contortus, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes. Archaea associate with larger organisms, too. For example, the marine archaean Cenarchaeum symbiosum is an endosymbiont of the sponge Axinella mexicana.
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+---
+title: "Archaea"
+chunk: 9/9
+source: "https://en.wikipedia.org/wiki/Archaea"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:06.056512+00:00"
+instance: "kb-cron"
+---
+
+==== Commensalism ====
+Some archaea are commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen Methanobrevibacter smithii is by far the most common archaean in the human flora, making up about one in ten of the prokaryotes in the human gut. In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. Archaean communities associate with a range of other organisms, such as on the surface of corals, and in the region of soil that surrounds plant roots (the rhizosphere).
+
+==== Parasitism ====
+Although Archaea do not have a historical reputation of being pathogens, Archaea are often found with similar genomes to more common pathogens like E. coli, showing metabolic links and evolutionary history with today's pathogens. Archaea have been inconsistently detected in clinical studies because of the lack of categorization of Archaea into more specific species. The reduced genome of Candidatus Sukunaarchaeum mirabile suggests it is a specialized parasite highly dependant on its dinoflagellate host.
+
+== Significance in technology and industry ==
+
+Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions. These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular biology by allowing the polymerase chain reaction to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C (212 °F) allow food processing at high temperatures, such as the production of low lactose milk and whey. Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in green chemistry that synthesize organic compounds. This stability makes them easier to use in structural biology. Consequently, the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.
+In contrast with the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. Methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas. In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.
+Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Halobacteria and Sulfolobus. These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.
+
+== See also ==
+
+== References ==
+
+== Further reading ==
+
+== External links ==
+
+=== General ===
+Introduction to the Archaea, ecology, systematics and morphology
+Oceans of Archaea – E.F. DeLong, ASM News, 2003
+
+=== Classification ===
+NCBI taxonomy page on Archaea
+Genera of the domain Archaea – list of Prokaryotic names with Standing in Nomenclature
+Shotgun sequencing finds nanoorganisms – discovery of the ARMAN group of archaea
+
+=== Genomics ===
+Browse any completed archaeal genome at UCSC
+Comparative Analysis of Archaeal Genomes Archived 16 February 2013 at the Wayback Machine (at DOE's IMG system)
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+---
+title: "Autotroph"
+chunk: 1/2
+source: "https://en.wikipedia.org/wiki/Autotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:07.302269+00:00"
+instance: "kb-cron"
+---
+
+An autotroph is an organism that can convert abiotic sources of energy into energy stored in organic compounds, which can be used by other organisms. Autotrophs produce complex organic compounds (such as carbohydrates, fats, and proteins) using carbon from simple substances such as carbon dioxide, generally using energy from light or inorganic chemical reactions. Autotrophs do not need a living source of carbon or energy and are the producers in a food chain, such as plants on land or algae in water. Autotrophs can reduce carbon dioxide to make organic compounds for biosynthesis and as stored chemical fuel. Most autotrophs use water as the reducing agent, but some can use other hydrogen compounds such as hydrogen sulfide.
+The primary producers can convert the energy in the light (phototroph and photoautotroph) or the energy in inorganic chemical compounds (chemotrophs or chemolithotrophs) to build organic molecules, which are usually accumulated in the form of biomass and will be used as carbon and energy source by other organisms (e.g. heterotrophs and mixotrophs). The photoautotrophs are the main primary producers, converting the energy of the light into chemical energy through photosynthesis, ultimately building organic molecules from carbon dioxide, an inorganic carbon source. Examples of chemolithotrophs are some archaea and bacteria (unicellular organisms) that produce biomass from the oxidation of inorganic chemical compounds; these organisms are called chemoautotrophs, and are frequently found in hydrothermal vents in the deep ocean. Primary producers are at the lowest trophic level, and are the reasons why Earth sustains life to this day.
+Autotrophs use a portion of the ATP produced during photosynthesis or the oxidation of chemical compounds to reduce NADP+ to NADPH to form organic compounds. Most chemoautotrophs are lithotrophs, using inorganic electron donors such as hydrogen sulfide, hydrogen gas, elemental sulfur, ammonium, and ferrous oxide as reducing agents; and hydrogen sources for biosynthesis and chemical energy release. Chemolithoautotrophs are microorganisms that synthesize energy through the oxidation of inorganic compounds. They can sustain themselves entirely on atmospheric CO2 and inorganic chemicals without the need for light or organic compounds. They enzymatically catalyze redox reactions using mineral substrates to generate ATP energy. These substrates primarily include hydrogen, iron, nitrogen, and sulfur. Its ecological niche is often specialized to extreme environments, including deep marine hydrothermal vents, stratified sediment, and acidic hot springs.
+
+== History ==
+The term autotroph was coined by the German botanist Albert Bernhard Frank in 1892. It stems from the ancient Greek word τροφή (trophḗ), meaning "nourishment" or "food". The first autotrophic organisms likely evolved early in the Archean but proliferated across Earth's Great Oxidation Event with an increase to the rate of oxygenic photosynthesis by cyanobacteria. Photoautotrophs evolved from heterotrophic bacteria by developing photosynthesis. The earliest photosynthetic bacteria used hydrogen sulfide. Due to the scarcity of hydrogen sulfide, some photosynthetic bacteria evolved to use water in photosynthesis, leading to cyanobacteria.
+
+== Variants ==
+Some organisms rely on organic compounds as a source of carbon, but are able to use light or inorganic compounds as a source of energy. Such organisms are mixotrophs. An organism that obtains carbon from organic compounds but obtains energy from light is called a photoheterotroph, while an organism that obtains carbon from organic compounds and energy from the oxidation of inorganic compounds is termed a chemolithoheterotroph.
+Evidence suggests that some fungi may also obtain energy from ionizing radiation: Such radiotrophic fungi were found growing inside a reactor of the Chernobyl nuclear power plant.
+
+== Examples ==
+There are many different types of autotrophs in Earth's ecosystems. Lichens located in tundra climates are an exceptional example of a primary producer that, by mutualistic symbiosis, combines photosynthesis by algae (or additionally nitrogen fixation by cyanobacteria) with the protection of a decomposer fungus. As there are many examples of primary producers, two dominant types are coral and one of the many types of brown algae, kelp.
+
+== Photosynthesis ==
+Gross primary production occurs by photosynthesis. This is the main way that primary producers get energy and make it available to other forms of life. Plants, many corals (by means of intracellular algae), some bacteria (cyanobacteria), and algae do this. During photosynthesis, primary producers receive energy from the sun and use it to produce sugar and oxygen.
+
+== Ecology ==
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+---
+title: "Autotroph"
+chunk: 2/2
+source: "https://en.wikipedia.org/wiki/Autotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:07.302269+00:00"
+instance: "kb-cron"
+---
+
+Without primary producers, organisms that are capable of producing energy on their own, the biological systems of Earth would be unable to sustain themselves. Plants, along with other primary producers, produce the energy that other living beings consume, and the oxygen that they breathe. It is thought that the first organisms on Earth were primary producers located on the ocean floor.
+Autotrophs are fundamental to the food chains of all ecosystems in the world. They take energy from the environment in the form of sunlight or inorganic chemicals and use it to create fuel molecules such as carbohydrates. This mechanism is called primary production. Other organisms, called heterotrophs, take in autotrophs as food to carry out functions necessary for their life. Thus, heterotrophs – all animals, almost all fungi, and most bacteria and protozoa – depend on autotrophs, or primary producers, for the raw materials and fuel they need. Heterotrophs obtain energy by breaking down carbohydrates or oxidizing organic molecules (carbohydrates, fats, and proteins) obtained in food. Carnivorous organisms rely on autotrophs indirectly, as the nutrients obtained from their heterotrophic prey come from autotrophs they have consumed.
+Most ecosystems are supported by the autotrophic primary production of plants and cyanobacteria that capture photons initially released by the sun. Plants can only use a fraction (approximately 1%) of this energy for photosynthesis. The process of photosynthesis splits a water molecule (H2O), releasing oxygen (O2) into the atmosphere, and reducing carbon dioxide (CO2) to release hydrogen atoms that fuel the metabolic process of primary production. Plants convert and store the energy of the photons into the chemical bonds of simple sugars during photosynthesis. These plant sugars are polymerized for storage as long-chain carbohydrates, such as starch and cellulose; glucose is also used to make fats and proteins. When autotrophs are eaten by heterotrophs, i.e., consumers such as animals, the carbohydrates, fats, and proteins contained in them become energy sources for the heterotrophs. Proteins can be made using nitrates, sulfates, and phosphates in the soil.
+
+=== Primary production in tropical streams and rivers ===
+Aquatic algae are a significant contributor to food webs in tropical rivers and streams. This is displayed by net primary production, a fundamental ecological process that reflects the amount of carbon that is synthesized within an ecosystem. This carbon ultimately becomes available to consumers. Net primary production displays that the rates of in-stream primary production in tropical regions are at least an order of magnitude greater than in similar temperate systems.
+
+== Origin of autotrophs ==
+
+Researchers believe that the first cellular lifeforms were not heterotrophs as they would rely upon autotrophs since organic substrates delivered from space were either too heterogeneous to support microbial growth or too reduced to be fermented. Instead, they consider that the first cells were autotrophs. These autotrophs might have been thermophilic and anaerobic chemolithoautotrophs that lived at deep sea alkaline hydrothermal vents. This view is supported by phylogenetic evidence – the physiology and habitat of the last universal common ancestor (LUCA) is inferred to have also been a thermophilic anaerobe with a Wood-Ljungdahl pathway, its biochemistry was replete with FeS clusters and radical reaction mechanisms. It was dependent upon Fe, H2, and CO2. The high concentration of K+ present within the cytosol of most life forms suggests that early cellular life had Na+/H+ antiporters or possibly symporters. Autotrophs possibly evolved into heterotrophs when they were at low H2 partial pressures where the first form of heterotrophy were likely amino acid and clostridial type purine fermentations. It has been suggested that photosynthesis emerged in the presence of faint near-infrared light emitted by hydrothermal vents. The first photochemically active pigments are then thought to be Zn-tetrapyrroles.
+
+== See also ==
+Electrolithoautotroph
+Electrotroph
+Heterotrophic nutrition
+Organotroph
+Primary nutritional groups
+
+== References ==
+
+== External links ==
+
+"Lichen Biology and the Environment". lichen.com. Archived from the original on 8 June 2018. Retrieved 11 May 2014.
+"Fun facts about fungi: Lichens are Fungi!". herbarium.usu.edu. Archived from the original on 21 May 2017. Retrieved 11 February 2026.
+"Lichens". archive.bio.ed.ac.uk.
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+---
+title: "Bacteria"
+chunk: 1/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit the air, soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in mutualistic, commensal and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.
+Like all animals, humans carry vast numbers (approximately 1013 to 1014) of bacteria. Most are in the gut, though there are many on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, and many are beneficial, particularly the ones in the gut. However, several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, tuberculosis, tetanus and bubonic plague. The most common fatal bacterial diseases are respiratory infections. Antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. Bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector (biomining, bioleaching), as well as in biotechnology, and the manufacture of antibiotics and other chemicals.
+Once regarded as plants constituting the class Schizomycetes ("fission fungi"), bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells contain circular chromosomes, do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea. Unlike Archaea, bacteria contain ester-linked lipids in the cell membrane, possess elongation factors that are resistant to ADP-ribosylation by diphtheria toxin, use formylmethionine in protein synthesis initiation, and have numerous genetic differences, including a different 16S rRNA.
+
+== Etymology ==
+
+The word bacteria ( ; sg.: bacterium) is the plural of the Neo-Latin bacterium, which is the romanisation of the Ancient Greek βακτήριον (baktḗrion), the diminutive of βακτηρία (baktēría), meaning 'staff' or 'cane', because the first ones to be discovered were rod-shaped.
+
+== Knowledge of bacteria ==
+Although an estimated 43,000 species of bacteria have been named, most of them have never been studied. In fact, just 10 bacterial species account for half of all publications, whereas nearly 75% of all named bacteria have no academic research devoted to them. The best-studied species, Escherichia coli, has more than 300,000 studies published on it, but many of these papers likely use it only as a cloning vehicle to study other species, without providing any insight into its own biology. 90% of scientific studies on bacteria focus on less than 1% of species, mostly pathogenic bacteria relevant to human health.
+While E. coli is probably the best-studied bacterium, a quarter of its 4000 genes are poorly studied or remain uncharacterized. Some bacteria with minimal genomes (< 600 genes, e.g. Mycoplasma) usually have a large fraction of their genes functionally characterized, given that most of them are essential and conserved in many other species.
+
+== Origin and early evolution ==
+
+The ancestors of bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The most recent common ancestor (MRCA) of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. The earliest life on land may have been bacteria some 3.22 billion years ago.
+Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in species of amitochondrial protozoa). Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants. This is known as primary endosymbiosis.
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+title: "Bacteria"
+chunk: 2/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+== Habitat ==
+Bacteria are ubiquitous, living in every possible habitat on the planet including soil, underwater, deep in Earth's crust and even such extreme environments as acidic hot springs and radioactive waste. There are thought to be approximately 2×1030 bacteria on Earth, forming a biomass that is only exceeded by plants. They are abundant in lakes and oceans, in arctic ice, and geothermal springs where they provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. They live on and in plants and animals. Most do not cause diseases, are beneficial to their environments, and are essential for life. The soil is a rich source of bacteria and a few grams contain around a thousand million of them. They are all essential to soil ecology, breaking down toxic waste and recycling nutrients. They are even found in the atmosphere and one cubic metre of air holds around one hundred million bacterial cells. The oceans and seas harbour around 3 × 1026 bacteria which provide up to 50% of the oxygen humans breathe. Only around 2% of bacterial species have been fully studied.
+
+== Morphology ==
+
+Size. Bacteria display a wide diversity of shapes and sizes. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre long, Epulopiscium fishelsoni reaches 0.7 mm, and Thiomargarita magnifica can reach even 2 cm in length, which is 50 times larger than other known bacteria. Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses. Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied.
+Shape. Most bacterial species are either spherical, called cocci (singular coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped; others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of other unusual shapes have been described, such as star-shaped bacteria. This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.
+
+Multicellularity. Most bacterial species exist as single cells; others associate in characteristic patterns: Neisseria forms diploids (pairs), streptococci form chains, and staphylococci group together in "bunch of grapes" clusters. Bacteria can also group to form larger multicellular structures, such as the elongated filaments of Actinomycetota species, the aggregates of Myxobacteria species, and the complex hyphae of Streptomyces species. These multicellular structures are often only seen in certain conditions. For example, when starved of amino acids, myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells. In these fruiting bodies, the bacteria perform separate tasks; for example, about one in ten cells migrate to the top of a fruiting body and differentiate into a specialised dormant state called a myxospore, which is more resistant to drying and other adverse environmental conditions.
+Biofilms. Bacteria often attach to surfaces and form dense aggregations called biofilms and larger formations known as microbial mats. These biofilms and mats can range from a few micrometres in thickness to up to half a metre in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures, such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients. In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms. Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.
+
+== Cellular structure ==
+
+=== Intracellular structures ===
+The bacterial cell is surrounded by a cell membrane, which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components within the cell. Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells. However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalise aspects of bacterial metabolism, such as the carboxysome. Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division.
+Many important biochemical reactions, such as energy generation, occur due to differences in concentration of molecules across membranes, creating a electrochemical potential analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm. However, in many photosynthetic bacteria, the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane. These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.
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+---
+title: "Bacteria"
+chunk: 3/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid. The nucleoid contains the chromosome with its associated proteins and RNA. Like all other organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and archaea. Its translation process is also different.
+Some bacteria produce intracellular nutrient storage granules, such as glycogen, polyphosphate, sulfur or polyhydroxyalkanoates. Bacteria such as the photosynthetic cyanobacteria, produce internal gas vacuoles, which they use to regulate their buoyancy, allowing them to move up or down into water layers with different light intensities and nutrient levels.
+
+=== Extracellular structures ===
+
+Around the outside of the cell membrane is the cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids. Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively. The cell wall of bacteria is also distinct from that of archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin (produced by a fungus called Penicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.
+There are broadly speaking two different types of cell wall in bacteria, that classify bacteria into Gram-positive bacteria and Gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species.
+
+Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only members of the Bacillota group and actinomycetota (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement. These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa. Some bacteria have cell wall structures that are neither classically Gram-positive or Gram-negative. This includes clinically important bacteria such as mycobacteria which have a thick peptidoglycan cell wall like a Gram-positive bacterium, but also a second outer layer of lipids.
+In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell. This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse functions and are known to act as virulence factors in Campylobacter species and contain surface enzymes in Bacillus stearothermophilus.
+
+Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.
+Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometres in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells, and are essential for the virulence of some bacterial pathogens. Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or sex pili (see bacterial genetics, below). They can also generate movement where they are called type IV pili.
+Glycocalyx is produced by many bacteria to surround their cells, and varies in structural complexity: ranging from a disorganised slime layer of extracellular polymeric substances to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system). They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.
+The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.
+
+=== Endospores ===
+
+Some genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores. Endospores develop within the cytoplasm of the cell; generally, a single endospore develops in each cell. Each endospore contains a core of DNA and ribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins.
+Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation. In this dormant state, these organisms may remain viable for millions of years. Endospores even allow bacteria to survive exposure to the vacuum and radiation of outer space, leading to the possibility that bacteria could be distributed throughout the universe by space dust, meteoroids, asteroids, comets, planetoids, or directed panspermia.
+Endospore-forming bacteria can cause disease; for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus, which, like botulism, is caused by a toxin released by the bacteria that grow from the spores. Clostridioides difficile infection, a common problem in healthcare settings, is caused by spore-forming bacteria.
+
+== Metabolism ==
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+---
+title: "Bacteria"
+chunk: 4/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+Bacteria exhibit an extremely wide variety of metabolic types. The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications. Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the source of energy, the electron donors used, and the source of carbon used for growth.
+Phototrophic bacteria derive energy from light using photosynthesis, while chemotrophic bacteria breaking down chemical compounds through oxidation, driving metabolism by transferring electrons from a given electron donor to a terminal electron acceptor in a redox reaction. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that derive electrons from inorganic compounds such as hydrogen, carbon monoxide, or ammonia are called lithotrophs, while those that use organic compounds are called organotrophs. Still, more specifically, aerobic organisms use oxygen as the terminal electron acceptor, while anaerobic organisms use other compounds such as nitrate, sulfate, or carbon dioxide.
+Many bacteria, called heterotrophs, derive their carbon from other organic carbon. Others, such as cyanobacteria and some purple bacteria, are autotrophic, meaning they obtain cellular carbon by fixing carbon dioxide. In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.
+
+In many ways, bacterial metabolism provides traits that are useful for ecological stability and for human society. For example, diazotrophs have the ability to fix nitrogen gas using the enzyme nitrogenase. This trait, which can be found in bacteria of most metabolic types listed above, leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively. Bacterial metabolic processes are important drivers in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment. Nonrespiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves.
+
+== Reproduction and growth ==
+
+Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and some bacterial populations can double as quickly as every 17 minutes. In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by myxobacteria and aerial hyphae formation by Streptomyces species, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.
+In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when the measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.
+Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal and cyanobacterial blooms that often occur in lakes during the summer. Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms. In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).
+
+Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. The second phase of growth is the logarithmic phase, also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport. The final phase is the death phase where the bacteria run out of nutrients and die.
+
+== Genetics ==
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+---
+title: "Bacteria"
+chunk: 5/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii, to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum, to 16.0 Mbp in another soil-dwelling bacteria, Minicystis rosea. There are many exceptions to this; for example, some Streptomyces and Borrelia species contain a single linear chromosome, while some bacteria including species of Vibrio contain more than one chromosome. Some bacteria contain plasmids, small extra-chromosomal molecules of DNA that may contain genes for various useful functions such as antibiotic resistance, metabolic capabilities, or various virulence factors.
+Whether they have a single chromosome or more than one, almost all bacteria have a haploid genome. This means that they have only one copy of each gene encoding proteins. This is in contrast to eukaryotes, which are diploid or polyploid, meaning they have two or more copies of each gene. This means that unlike humans, who may still be able to create a protein if the gene becomes mutated (since the human genome has an extra copy in each cell), a bacterium will be completely unable to create the protein if its gene incurs an inactivating mutation.
+Bacterial genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA. Although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.
+Bacteria, as asexual organisms, inherit an identical copy of the parent's genome and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations arise from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Genetic changes in bacterial genomes emerge from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.
+Some bacteria transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment in a process called transformation. Many bacteria can naturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA. The development of competence in nature is usually associated with stressful environmental conditions and seems to be an adaptation for facilitating repair of DNA damage in recipient cells. Second, bacteriophages can integrate into the bacterial chromosome, introducing foreign DNA in a process known as transduction. Many types of bacteriophage exist; some infect and lyse their host bacteria, while others insert into the bacterial chromosome. Bacteria resist phage infection through restriction modification systems that degrade foreign DNA and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference. Third, bacteria can transfer genetic material through direct cell contact via conjugation.
+In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species, and this may have significant consequences, such as the transfer of antibiotic resistance. In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.
+
+== Behaviour ==
+
+=== Movement ===
+
+Many bacteria are motile (able to move themselves) and do so using a variety of mechanisms. The best studied of these are flagella, long filaments that are turned by a motor at the base to generate propeller-like movement. The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.
+
+Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk. Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The flagella of a group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.
+Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus, and gliding motility, that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward.
+Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis. In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media.
+Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.
+
+=== Communication ===
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+---
+title: "Bacteria"
+chunk: 6/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals.
+Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for intercell communication and engaging in coordinated multicellular behaviour.
+The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types. For example, bacteria in biofilms can have more than five hundred times the increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.
+One type of intercellular communication by a molecular signal is called quorum sensing. Quorum sensing determines whether the local population is dense enough to support investment in processes that are only successful if large numbers of similar organisms behave similarly, such as excreting digestive enzymes or emitting light. Quorum sensing enables bacteria to coordinate gene expression and to produce, release, and detect autoinducers or pheromones that accumulate with the growth in cell population.
+
+== Classification and identification ==
+
+Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, and Bergey's Manual of Systematic Bacteriology. The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria.
+Historically, bacteria were considered a part of the Plantae, the plant kingdom, and were called "Schizomycetes" (fission-fungi). For this reason, collective bacteria and other microorganisms in a host are often called "flora".
+The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology. However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. For example, Cavalier-Smith argued that the Archaea and Eukaryotes evolved from Gram-positive bacteria.
+The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns of hemolysis, and staining.
+
+=== Classification by staining ===
+The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid fastness on Ziehl–Neelsen or similar stains.
+
+=== Classification by culturing ===
+Culture techniques are designed to promote the growth and identify particular bacteria while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhea while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms. Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.
+
+=== Molecular classification ===
+As with bacterial classification, identification of bacteria is increasingly using molecular methods, and mass spectroscopy. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. The main way to characterize and classify these bacteria is to isolate their DNA from environmental samples and mass-sequence them. This approach has identified thousands, if not millions of candidate species. Based on some estimates, more than 43,000 species of bacteria have been described, but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species—and even these diverse estimates may be off by many orders of magnitude.
+
+== Phyla ==
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+---
+title: "Bacteria"
+chunk: 7/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+=== Valid phyla ===
+The following phyla have been validly published according to the Prokaryotic Code; phyla that do not belong to any kingdom are shown in bold:
+
+=== Candidate phyla ===
+The following phyla have been proposed, but have not been validly published according to the Prokaryotic Code; phyla that do not belong to any kingdom are shown in bold:
+
+== Interactions with other organisms ==
+
+Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism.
+
+=== Commensals ===
+The word "commensalism" is derived from the word "commensal", meaning "eating at the same table" and all plants and animals are colonised by commensal bacteria. In humans and other animals, trillions of them live on the skin, the airways, the gut and other orifices.
+Referred to as "normal flora", or "commensals", these bacteria usually cause no harm but may occasionally invade other sites of the body and cause infection. Escherichia coli is a commensal in the human gut but can cause urinary tract infections. Similarly, streptococci, which are part of the normal flora of the human mouth, can cause heart disease.
+
+=== Predators ===
+Some species of bacteria kill and then consume other microorganisms; these species are called predatory bacteria. These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter. Other bacterial predators either attach to their prey in order to digest them and absorb nutrients or invade another cell and multiply inside the cytosol. These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.
+
+=== Mutualists ===
+Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic archaea that consume hydrogen. The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.
+
+In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds. This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates. The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.
+Nearly all animal life is dependent on bacteria for survival as only bacteria and some archaea possess the genes and enzymes necessary to synthesise vitamin B12, also known as cobalamin, and provide it through the food chain. Vitamin B12 is a water-soluble vitamin that is involved in the metabolism of every cell of the human body. It is a cofactor in DNA synthesis and in both fatty acid and amino acid metabolism. It is particularly important in the normal functioning of the nervous system via its role in the synthesis of myelin.
+
+=== Pathogens ===
+
+The body is continually exposed to many species of bacteria, including beneficial commensals, which grow on the skin and mucous membranes, and saprophytes, which grow mainly in the soil and in decaying matter. The blood and tissue fluids contain nutrients sufficient to sustain the growth of many bacteria. The body has defence mechanisms that enable it to resist microbial invasion of its tissues and give it a natural immunity or innate resistance against many microorganisms. Unlike some viruses, bacteria evolve relatively slowly so many bacterial diseases also occur in other animals.
+If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus (caused by Clostridium tetani), typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy (caused by Mycobacterium leprae) and tuberculosis (caused by Mycobacterium tuberculosis). A pathogenic cause for a known medical disease may only be discovered many years later, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, and bacteria cause leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.
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+---
+title: "Bacteria"
+chunk: 8/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and sepsis, a systemic inflammatory response producing shock, massive vasodilation and death. Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia or urinary tract infection and may be involved in coronary heart disease. Some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people who are immunosuppressed or have cystic fibrosis. Some bacteria produce toxins, which cause diseases. These are endotoxins, which come from broken bacterial cells, and exotoxins, which are produced by bacteria and released into the environment. The bacterium Clostridium botulinum for example, produces a powerful exotoxin that cause respiratory paralysis, and Salmonellae produce an endotoxin that causes gastroenteritis. Some exotoxins can be converted to toxoids, which are used as vaccines to prevent the disease.
+Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics, and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome. Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations. Infections can be prevented by antiseptic measures such as sterilising the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilised to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.
+
+== Significance in technology and industry ==
+Bacteria, often lactic acid bacteria, such as Lactobacillus species and Lactococcus species, in combination with yeasts and moulds, have been used for thousands of years in the preparation of fermented foods, such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine, and yogurt.
+The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Fertiliser was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes. In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.
+Bacteria can also be used in place of pesticides in biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil-dwelling bacterium. Subspecies of this bacteria are used as Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide. Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators, and most other beneficial insects.
+Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics, and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes, and metabolic pathways in bacteria, then apply this knowledge to more complex organisms. This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested. This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.
+Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centres. This ensures the availability of the strain to scientists worldwide.
+
+== History of bacteriology ==
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+---
+title: "Bacteria"
+chunk: 9/9
+source: "https://en.wikipedia.org/wiki/Bacteria"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:08.686083+00:00"
+instance: "kb-cron"
+---
+
+Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. Leeuwenhoek did not recognize bacteria as a distinct category of microorganisms, referring to all microorganisms that he observed, including bacteria, protists, and microscopic animals, as animalcules. He published his observations in a series of letters to the Royal Society of London. Bacteria were Leeuwenhoek's most remarkable microscopic discovery. Their size was just at the limit of what his simple lenses could resolve, and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century. His observations also included protozoans, and his findings were looked at again in the light of the more recent findings of cell theory.
+Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828. In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria, as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.
+Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes the fermentation process and that this growth is not due to spontaneous generation (yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi). Along with his contemporary Robert Koch, Pasteur was an early advocate of the germ theory of disease. Before them, Ignaz Semmelweis and Joseph Lister had realised the importance of sanitised hands in medical work. Semmelweis, who in the 1840s formulated his rules for handwashing in the hospital, prior to the advent of germ theory, attributed disease to "decomposing animal organic matter". His ideas were rejected and his book on the topic condemned by the medical community. After Lister, however, doctors started sanitising their hands in the 1870s.
+Robert Koch, a pioneer in medical microbiology, worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he received a Nobel Prize in 1905. In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today.
+Ferdinand Cohn is said to be a founder of bacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology.
+Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochaete that causes syphilis—into compounds that selectively killed the pathogen. Ehrlich, who had been awarded a 1908 Nobel Prize for his work on immunology, pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl–Neelsen stain.
+A major step forward in the study of bacteria came in 1977 when Carl Woese recognised that archaea have a separate line of evolutionary descent from bacteria. This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA and divided prokaryotes into two evolutionary domains, as part of the three-domain system.
+
+== See also ==
+Bacteriohopanepolyol
+Genetically modified bacteria
+Marine prokaryotes
+
+== References ==
+
+== Bibliography ==
+Clark D (2010). Germs, Genes, & Civilization: how epidemics shaped who we are today. Upper Saddle River, N.J: FT Press. ISBN 978-0-13-701996-0. OCLC 473120711.
+Crawford D (2007). Deadly Companions: how microbes shaped our history. Oxford New York: Oxford University Press. ISBN 978-0-19-956144-5. OCLC 183198723.
+Hall B (2008). Strickberger's Evolution: the integration of genes, organisms and populations. Sudbury, Mass: Jones and Bartlett. ISBN 978-0-7637-0066-9. OCLC 85814089.
+Krasner R (2014). The Microbial Challenge: a public health perspective. Burlington, Mass: Jones & Bartlett Learning. ISBN 978-1-4496-7375-8. OCLC 794228026.
+Pommerville JC (2014). Fundamentals of Microbiology (10th ed.). Boston: Jones and Bartlett. ISBN 978-1-284-03968-9.
+Wheelis M (2008). Principles of modern microbiology. Sudbury, Mass: Jones and Bartlett Publishers. ISBN 978-0-7637-1075-0. OCLC 67392796.
+
+== External links ==
+On-line text book on bacteriology (2015) Archived 13 September 2008 at the Wayback Machine
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diff --git a/data/en.wikipedia.org/wiki/Biofact_(biology)-0.md b/data/en.wikipedia.org/wiki/Biofact_(biology)-0.md
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+---
+title: "Biofact (biology)"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Biofact_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:09.903564+00:00"
+instance: "kb-cron"
+---
+
+In biology, a biofact is dead material of a once-living organism.
+In 1943, the protozoologist Bruno M. Klein of Vienna (1891–1968) coined the term in his article Biofakt und Artefakt in the microscopy journal Mikrokosmos, though at that time it was not adopted by the scientific community. Klein's concept of biofact stressed the dead materials produced by living organisms as sheaths, such as shells.
+The word biofact is now widely used in the zoo/aquarium world, but was first used by Lisbeth Bornhofft in 1993 in the Education Department at the New England Aquarium, Boston, to refer to preserved items such as animal bones, skins, molts and eggs. The Accreditation Standards and Related Policies of the Association of Zoos and Aquariums states that biofacts can be useful education tools, and are preferable to live animals because of potential ethical considerations.
+
+
+== See also ==
+Biofact (archaeology)
+
+
+== References ==
\ No newline at end of file
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+---
+title: "Bioliteracy"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Bioliteracy"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:11.133438+00:00"
+instance: "kb-cron"
+---
+
+Bioliteracy is the ability to understand and engage with biological topics. The concept is used particularly in the contexts of biotechnology and biodiversity. 
+
+
+== Description ==
+In the biotechnology context, bioliteracy is considered important for promoting the biotechnology industry and the development of biological engineering products. It has also been defined as "the concept of imbuing people, personnel, or teams with an understanding of and comfort with biology and biotechnology." The use in the context of biodiversity is somewhat distinct, focusing on improving awareness of different organisms with the goal of conservation.
+Citizen science initiatives, such as iNaturalist, are considered effective ways to increase bioliteracy, engaging students with the direct observation of nature.
+
+
+== References ==
\ No newline at end of file
diff --git a/data/en.wikipedia.org/wiki/Biological_target-0.md b/data/en.wikipedia.org/wiki/Biological_target-0.md
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+---
+title: "Biological target"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Biological_target"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:12.337114+00:00"
+instance: "kb-cron"
+---
+
+A biological target is anything within a living organism to which some other entity (like an endogenous ligand or a drug) is directed and/or binds, resulting in a change in its behavior or function. Examples of common classes of biological targets are proteins and nucleic acids. The definition is context-dependent, and can refer to the biological target of a  pharmacologically active drug compound, the receptor target of a hormone (like insulin), or some other target of an external stimulus.  Biological targets are most commonly proteins such as enzymes, ion channels, and receptors, but in recent years DNA's and RNA's became more targeted than in the past.
+
+
+== Mechanism ==
+The external stimulus (i.e., the drug or ligand) physically binds to ("hits") the biological target. The interaction between the substance and the target may be:
+
+noncovalent – A relatively weak interaction between the stimulus and the target where no chemical bond is formed between the two interacting partners and hence the interaction is completely reversible.
+reversible covalent – A chemical reaction occurs between the stimulus and target in which the stimulus becomes chemically bonded to the target, but the reverse reaction also readily occurs in which the bond can be broken.
+irreversible covalent – The stimulus is permanently bound to the target through irreversible chemical bond formation.
+Depending on the nature of the stimulus, the following can occur:
+
+There is no direct change in the biological target, but the binding of the substance prevents other endogenous substances (such as activating hormones) from binding to the target.  Depending on the nature of the target, this effect is referred as receptor antagonism, enzyme inhibition, or ion channel blockade.
+A conformational change in the target is induced by the stimulus which results in a change in target function.  This change in function can mimic the effect of the endogenous substance in which case the effect is referred to as receptor agonism (or channel or enzyme activation) or be the opposite of the endogenous substance which in the case of receptors is referred to as inverse agonism.
+
+
+== Drug targets ==
+The term "biological target" is frequently used in pharmaceutical research to describe the native protein in the body whose activity is modified by a drug resulting in a specific effect, which may be a desirable therapeutic effect or an unwanted adverse effect.  In this context, the biological target is often referred to as a drug target. The most common drug targets of currently marketed drugs include:
+
+proteins
+G protein-coupled receptors  (target of 50% of drugs)
+enzymes (especially protein kinases, proteases, esterases, and phosphatases)
+ion channels
+ligand-gated ion channels
+voltage-gated ion channels
+nuclear hormone receptors
+structural proteins such as tubulin
+membrane transport proteins
+nucleic acids
+
+
+== Drug target identification ==
+Identifying the biological origin of a disease, and the potential targets for intervention, is the first step in the discovery of a medicine using the reverse pharmacology approach. Potential drug targets are not necessarily disease causing but must by definition be disease modifying.  An alternative means of identifying new drug targets is forward pharmacology based on phenotypic screening to identify "orphan" ligands whose targets are subsequently identified through target deconvolution.
+
+
+== Databases ==
+Databases containing biological targets information:
+
+Therapeutic Targets Database (TTD)
+DrugMap
+DrugBank
+Binding DB
+
+
+== Conservation ecology ==
+These biological targets are conserved across species, making pharmaceutical pollution of the environment a danger to species who possess the same targets. For example, the synthetic estrogen in human contraceptives, 17-R-ethinylestradiol, has been shown to increase the feminization of fish downstream from sewage treatment plants, thereby unbalancing reproduction and creating an additional selective pressure on fish survival. Pharmaceuticals are usually found at ng/L to low-μg/L concentrations in the aquatic environment. Adverse effects may occur in non-target species as a consequence of specific drug target interactions. Therefore, evolutionarily well-conserved drug targets are likely to be associated with an increased risk for non-targeted pharmacological effects.
+
+
+== See also ==
+Drug discovery
+Environmental impact of pharmaceuticals and personal care products
+
+
+== References ==
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diff --git a/data/en.wikipedia.org/wiki/Biomarker-0.md b/data/en.wikipedia.org/wiki/Biomarker-0.md
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+---
+title: "Biomarker"
+chunk: 1/3
+source: "https://en.wikipedia.org/wiki/Biomarker"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:13.536230+00:00"
+instance: "kb-cron"
+---
+
+In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. Biomarkers are used in many scientific fields.
+
+== Medicine ==
+Biomarkers used in the medical field, are a part of a relatively new clinical toolset categorized by their clinical applications. The four main classes are molecular, physiologic, histologic and radiographic biomarkers. All four types of biomarkers have a clinical role in narrowing or guiding treatment decisions and follow a sub-categorization of being either predictive, prognostic, or diagnostic.
+
+=== Predictive ===
+Predictive molecular, cellular, or imaging biomarkers that pass validation can serve as a method of predicting clinical outcomes. Predictive biomarkers are used to help optimize ideal treatments, and often indicate the likelihood of benefiting from a specific therapy. For example, in metastatic colorectal cancer, predictive biomarkers can serve as a way of evaluating and improving patient survival rates and in the individual case by case scenario, they can serve as a way of sparing patients from needless toxicity that arises from cancer treatment plans. Common examples of predictive biomarkers are genes such as estrogen receptor, progesterone receptor and HER2/neu in breast cancer, the Philadelphia chromosome in chronic myelogenous leukemia, c-KIT mutations in gastrointestinal stromal tumors and epidermal growth factor receptor mutations in non-small-cell lung cancer.
+
+=== Diagnostic ===
+
+Diagnostic biomarkers that meet a burden of proof can serve a role in narrowing down diagnosis. This can lead to diagnosis that are significantly more specific to individual patients. A biomarker can be a traceable substance that is introduced into an organism as a means to examine organ function or other aspects of health.
+It can also be a substance whose detection indicates a particular disease state, for example, the presence of an antibody may indicate an infection. More specifically, a biomarker indicates a change in expression or state of a protein that correlates with the risk or progression of a disease, or with the susceptibility of the disease to a given treatment.
+One example of a commonly used biomarker in medicine is prostate-specific antigen (PSA).  This marker can be measured as a proxy of prostate size with rapid changes potentially indicating cancer. The most extreme case would be to detect mutant proteins as cancer specific biomarkers through selected reaction monitoring (SRM), since mutant proteins can only come from an existing tumor, thus providing ultimately the best specificity for medical purposes.
+An example is the traumatic brain injury (TBI) blood-based biomarker test consisted of measuring the levels of neuronal Ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) and  Glial fibrillary acidic protein (GFAP) to aid in the diagnosis of the presence of cranial lesion(s) among moderate to mild TBI patients that is(are) otherwise only diagnosable with the use of a CT scan of the head.
+Another example is KRAS, an oncogene that encodes a GTPase involved in several signal transduction pathways. Biomarkers for precision oncology are typically utilized in the molecular diagnostics of chronic myeloid leukemia, colon, breast, and lung cancer, and in melanoma.
+
+=== Digital ===
+Digital biomarkers are a novel emerging field of biomarkers, mostly collected by smart biosensors. So far, digital biomarkers have been focusing on monitoring vital parameters such as accelerometer data and heartrate but also speech. Novel non-invasive, molecular digital biomarkers are increasingly available recorded by e.g. on-skin sweat analysis (internet-enabled Sudorology), which can be seen as next-generation digital biomarkers. Collecting and tracking digital biomarkers have become more easily available with the advancement of smartphones and wearables. In Parkinson's disease (PD), for example, finger tapping a mobile phone via counting apps have been used as a method of (self-)evaluating bradykinesia and effectiveness of medication.
+Digital biomarkers are currently being used in conjugation with artificial intelligence (A.I.) in order to recognize symptoms for mild cognitive impairment (MCI). One major current use of digital biomarkers involves keeping track of regular brain activity. Specific neural indicators can be measured by devices to evaluate patients for any neuro abnormalities. The data collected can determine the patients disease probability or condition. While patients carryout everyday tasks (IADL), computers are using machine learning to observe and detect any deviation from normal behavior. These markers are used as signs or indicators of cognitive decline.
+
+=== Prognostic ===
+
+A prognostic biomarker provides information about the patients overall outcome, regardless of any treatment or therapeutic intervention. One example of a prognostic biomarkers in clinical research, is the use of mutated PIK3CA in the study of metastatic breast cancer. As illustrated by the graph, the mutation is prognostic since its presence in the patient endure the same outcome regardless of the treatment method used. Women who had the PIK3CA mutation before treatment, had the lowest average survival rate. The decline in the groups containing the mutant occurred quicker and in a much steeper decline. The independent nature of the prognostic factor allows researcher to study the disease or condition in its natural state. This makes it easier to observe these abnormal biological processes and speculate on how to correct them. Prognostic factors are often used in combination with predictive variables in therapeutics studies, to examine how effective different treatments are in curing specific diseases or cancer. As opposed to predictive biomarkers, prognostic do not rely on any explanatory variables, thus allowing for independent examination of the underlying disease or condition.
+
+== Nutrition and diet assessment ==
+Nutritional biomarkers (biochemical markers of intake) are used to estimate dietary intake in nutrition research, in particular nutritional epidemiology, but also in other disciplines such as archaeology where reliable dietary information are required. A nutritional biomarker can be any specimen that reflects intake of dietary constituents and is sufficiently specific. Many biomarkers are derived from compounds found in foods, such as sugar or phytochemicals, or combinations thereof using a metabolomics. Another type of nutritional biomarkers, in particular common in archaeology, are stable isotope ratios.
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+---
+title: "Biomarker"
+chunk: 2/3
+source: "https://en.wikipedia.org/wiki/Biomarker"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:13.536230+00:00"
+instance: "kb-cron"
+---
+
+== Research ==
+Biomarkers for precision medicine are a part of a relatively new behavioral and clinical toolset. In terms of the behavioral toolset, biomarkers are increasingly being used to motivate health behavior change, particularly in diabetes, cardiovascular diseases, and obesity research. Most research to date uses biomarkers that are easily measured, including weight, blood pressure, and glucose; these biomarkers may reflect the impacts of diet, physical activity, and smoking reduction. However, the methods by which feedback from biomarkers are used in intervention research are varied, and their effectiveness remains unclear.
+In reference to the clinical toolset, only two predictive biomarkers are implemented clinically in the case of metastatic colorectal cancer. In this case, the lack of data beyond retrospective studies and successful biomarker-driven approaches may be a factor in using biomarker studies due to the attrition of subjects in clinical trials.
+The field of biomarker research is also expanding to include a combinatorial approach to identifying biomarkers from multiple sources. Combining biomarkers from various data allows for the possibility of developing panels that evaluate treatment response based on many biomarkers at a single time. One such area of expanding research in multiple-factor biomarkers is mitochondrial DNA sequencing. Mutations in mitochondrial DNA have been shown to correlate to risk, progression, and treatment response of head and neck squamous cell carcinoma. In this example, a relatively low cost sequencing pipeline was shown to be able to detect low frequency mutations within tumor-associated cells. This highlights the general snapshot capability of mitochondrial DNA-based biomarkers in capturing heterogeneity amongst individuals.
+
+== Regulatory validation for clinical use ==
+The Early Detection Research Network (EDRN) compiled a list of seven criteria by which biomarkers can be assessed in order to streamline clinical validation.
+
+=== Proof of concept ===
+Previously used to identify the specific characteristics of the biomarker, this step is essential for doing an in situ validation of these benefits. The biologic rationale of a study must be assessed on a small scale before any large scale studies can occur. Many candidates must be tested to select the most relevant ones.
+
+=== Analytical performances validation ===
+One of the most important steps, it serves to identify specific characteristics of the candidate biomarker before developing a routine test. Several parameters are considered including:
+
+sensitivity
+specificity
+robustness
+accuracy
+parallelism
+reproducibility
+practicality
+ethicality
+
+=== Protocol standardization ===
+This optimizes the validated protocol for routine use, including analysis of the critical points by scanning the entire procedure to identify and control the potential risks.
+
+== Ethical issues ==
+In 1997 the National Institute of Health suggested a need for guidelines and legislation development that would regulate the ethical dimensions of biomarker studies.
+Ensuring that all of the participants that are included each step of the project (i.e. planning, implementation, and the compilation of the results) are provided with the protection of ethical principles that are put in place prior to beginning the project. These ethical protections should not only protect the participants in the study, but also the non participants, researchers, sponsors, regulators, and all other persons or groups involved in the study. Some ethical protections could include but are not limited to:
+
+Informed consent of the participant
+Access to participation opportunities independent of race, socio-economic status, gender, sexuality, etc. (within the range allowed by the experimental protocol)
+Scientific integrity
+Confidentiality of data (anonymity)
+Acknowledgement of conflict of interest in terms of funding and sponsorship by given sponsors
+Transparency and recognition of health and legal risks involved in participation
+
+== Cell biology ==
+In cell biology, a biomarker is a molecule that allows the detection and isolation of a particular cell type (for example, the protein Oct-4 is used as a biomarker to identify embryonic stem cells).
+In genetics, a biomarker (identified as genetic marker) is a DNA sequence that causes disease or is associated with susceptibility to disease. They can be used to create genetic maps of whatever organism is being studied.
+
+== Applications in chemistry, geology and astrobiology ==
+
+A biomarker can be any kind of molecule indicating the existence, past or present, of living organisms. In the fields of geology and astrobiology, biomarkers, versus geomarkers, are also known as biosignatures. The term biomarker is also used to describe biological involvement in the generation of petroleum. Biomarkers were used in the geo-chemical investigation of an oil spill in the San Francisco Bay, California in 1988. On April 22–23 around 400,000 gallons of crude oil was accidentally released into the San Joaquin Valley by a refinery and manufacturing complex of the Shell Oil Company. The oil affected many surrounding areas. Samples of the crude oil were collected in the various regions where it had spread and compared to samples that were unreleased in an attempt to distinguish between the spilled oil and the petrogenic background present in the spill area. Mass Spectra was performed to identify biomarkers and cyclic aliphatic hydrocarbons within the samples. Variations in the concentration of constituents of the crude oil samples and sediments were found.
+
+== Ecotoxicology ==
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+---
+title: "Biomarker"
+chunk: 3/3
+source: "https://en.wikipedia.org/wiki/Biomarker"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:13.536230+00:00"
+instance: "kb-cron"
+---
+
+Biomarkers are being used to identify the effects of water contamination on aquatic organisms. Benthic macro-invertebrates reside in the sediment on the bottoms of streams, which is where many contaminants settle. These organisms have high exposure to the contamination, which makes them good study species when detecting pollutant concentrations and pollution impacts on an ecosystem. There are a variety of biomarkers within an aquatic organism that can be measured, depending on the contaminant or the response in question. There are also a variety of contaminants within water bodies. To analyze the impact of a pollutant on an organism, the biomarker must respond to a specific contaminant within a specific time frame or at a certain concentration. The biomarkers used to detect pollution in aquatic organisms can be enzymatic or non-enzymatic.
+Rachel Carson, the author of Silent Spring, raised the issue of using organochlorine pesticides and discussed the possible negative effects that said pesticides have on living organisms. Her book raised ethical issues against chemical corporations that were controlling the general reception of the effect of pesticides on the environment, which pioneered the need for ecotoxicological studies. Ecotoxicologial studies could be considered the precursors to biomarker studies. Biomarkers are used to indicate an exposure to or the effect of xenobiotics which are present in the environment and in organisms. The biomarker may be an external substance itself (e.g. asbestos particles or NNK from tobacco), or a variant of the external substance processed by the body (a metabolite) that usually can be quantified.
+
+== History ==
+The widespread use of the term "biomarker" dates back to as early as 1980.  The manner in which the environment was monitored and studied near the end of the 1980s was still mainly reliant on the study of chemical substances that were considered dangerous or toxic when found in moderate concentrations in water, sediments, and aquatic organisms. The methods used to identify these chemical compounds were chromatography, spectrophotometry, electrochemistry, and radiochemistry. Although these methods were successful in elucidating the chemical makeup and concentrations present in the environment of the contaminants and the compounds in question, the tests did not provide data that was informative on the impact of a certain pollutant or chemical on a living organism or ecosystem. It was proposed that characterizing biomarkers could create a warning system to check in on the well being of a population or an ecosystem before a pollutant or compound could wreak havoc on the system. Now, due to the development of biomarker studies, biomarkers can be used and applied in the fields of human medicine and in the detection of diseases.
+
+=== Definition ===
+The term "biological marker" was introduced in 1950s.
+
+In 1987, biological markers were defined as "indicators signaling events in biological systems or samples" that could be classified into three categories: exposure, effect and susceptibility markers.
+In 1990, McCarthy and Shugart defined biomarkers as, "measurements at the molecular, biochemical, or cellular level in either wild populations from contaminated habitats or in organisms experimentally exposed to pollutants that indicate that the organism has been exposed to toxic chemicals, and the magnitude of the organism's response".
+In 1994, Depledge defined a biomarker as, "a biochemical, cellular, physiological or behavioral change which can be measured in body tissues or fluids or at the level of the whole organism that reveals the exposure at/or the effects of one or more chemical pollutants."
+In 1996, Van Gestel and Van Brummelen attempted to  redefine biomarkers to unambiguously differentiate a biomarker from a bioindicator. According to Van Gestel and Van Brummelen, a biomarker by definition should be used only to describe sublethal biochemical changes resulting from individual exposure to xenobiotics.
+In 1998, the National Institutes of Health Biomarkers Definitions Working Group defined a biomarker as "a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention."
+In 2000, De Lafontaine defined the term biomarker as a "biochemical and/or physiological change(s) in organisms exposed to contaminants, and thus represent initial responses to environmental perturbation and contamination".
+
+== Active biomonitoring ==
+De Kock and Kramer developed the concept of active biomonitoring in 1994. Active biomonitoring is a comparison of the chemical/biological properties of a sample that has been relocated to a new environment that contains different conditions than its original environment.
+
+== See also ==
+
+== References ==
+
+== External links ==
+BiomarkerKB, an open-access knowledge base that integrates and organizes biomarker data from multiple public sources, George Washington University, 2025
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+---
+title: "Biosignal"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Biosignal"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:14.749681+00:00"
+instance: "kb-cron"
+---
+
+A biosignal is any signal in a living organism that can be continually measured and monitored. The term biosignal is often used to refer to bioelectrical signals, but it may refer to both electrical and non-electrical signals. The usual understanding is to refer only to time-varying signals, although spatial parameter variations (e.g. the nucleotide sequence determining the genetic code) are sometimes subsumed as well.
+
+
+== Electrical biosignals ==
+Electrical biosignals, or bioelectrical time signals, usually refers to the change in electric current produced by the sum of an electrical potential difference across a specialized tissue, organ or cell system like the nervous system. Thus, among the best-known bioelectrical signals are:
+
+Electroencephalogram (EEG)
+Electrocardiogram (ECG)
+Electromyogram (EMG)
+Electrooculogram (EOG)
+Electroretinogram (ERG)
+Electrogastrogram (EGG)
+Galvanic skin response (GSR) or electrodermal activity (EDA)
+EEG, ECG, EOG and EMG are measured with a differential amplifier which registers the difference between two electrodes attached to the skin. However, the galvanic skin response measures electrical resistance and the Magnetoencephalography (MEG) measures the magnetic field induced by electrical currents (electroencephalogram) of the brain.
+With the development of methods for remote measurement of electric fields using new sensor technology, electric biosignals such as EEG and ECG can be measured without electric contact with the skin. This can be applied, for example, for remote monitoring of brain waves and heart beat of patients who must not be touched, in particular patients with serious burns.
+Electrical currents and changes in electrical resistances across tissues can also be measured from plants.
+Biosignals may also refer to any non-electrical signal that is capable of being monitored from biological beings, such as mechanical signals (e.g. the mechanomyogram or MMG), acoustic signals (e.g. phonetic and non-phonetic utterances, breathing), chemical signals (e.g. pH, oxygenation) and optical signals (e.g. movements).
+
+
+== Use in artistic contexts ==
+In recent years, the use of biosignals has gained interest amongst an international artistic community of performers and composers who use biosignals to produce and control sound. Research and practice in the field go back decades in various forms and have lately been enjoying a resurgence, thanks to the increasing availability of more affordable and less cumbersome technologies. An entire issue of eContact!, published by the Canadian Electroacoustic Community in July 2012, was dedicated to this subject, with contributions from the key figures in the domain.
+
+
+== See also ==
+Bioindicator
+Biomarker
+Biosignature
+Molecular marker
+Multimedia information retrieval
+
+
+== References ==
+
+
+== Bibliography ==
+Donnarumma, Marco. "Proprioception, Effort and Strain in "Hypo Chrysos": Action art for vexed body and the Xth Sense." eContact! 14.2 — Biotechnological Performance Practice / Pratiques de performance biotechnologique (July 2012). Montréal: CEC.
+Tanaka, Atau. "The Use of Electromyogram Signals (EMG) in Musical Performance: A Personal survey of two decades of practice." eContact! 14.2 — Biotechnological Performance Practice / Pratiques de performance biotechnologique (July 2012). Montréal: CEC.
+Naït-Ali, Amine, ed. (2009). Advanced Biosignal Processing. Berlin, Heidelberg: Springer Berlin Heidelberg. doi:10.1007/978-3-540-89506-0. ISBN 978-3-540-89505-3.
+
+
+== External links ==
+Applications
+
+Using electroencephalograph signals for task classification and activity recognition Microsoft
+NASA scientists use hands-off approach to land passengers jet
+Hardware
+
+University of Vienna : cours Biomedical Engineering, Electromyography (EMG)
+Electroencephalographe, EEG,  sans fil ( Cornell University, Ithaca, NY, USA)
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+---
+title: "Biosignature"
+chunk: 1/6
+source: "https://en.wikipedia.org/wiki/Biosignature"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:15.960639+00:00"
+instance: "kb-cron"
+---
+
+A biosignature is a phenomenon that can be explained by biological processes where all possible abiotic causes of this phenomenon have been eliminated. This term is mainly used in the field of astrobiology in the search for past or present extraterrestrial life, from planets and moons in the Solar System to exoplanets. Candidate biosignatures strongly indicate some of the earliest known life forms, aid studies of the origin of life on Earth as well as the possibility of life on Mars, Venus and elsewhere in the universe.
+
+== History ==
+The term "biosignature" and its definition have evolved over time. In the 1960s, the phrase "life detection" was used as seen in two Nature papers "A physical basis for life detection experiments," by James. E. Lovelock (1965)  and "Signs of Life: Criterion-system of exobiology," by Joshua Lederberg (1965). In 1973, Joon H. Rho used the term "biomarker" in his paper, "A search for porphyrin biomarkers in nonesuch shale and extraterrestrial samples" to describe a fossil organic compound that can be traced back to a specific organism. In medicine, biomarker (medicine) has a different definition. In 1995, the term biosignature was first used by the NASA Exobiology Program office (now the NASA Astrobiology Program) in "An Exobiological Strategy for Mars Exploration." The term has since become widely used in astrobiology.
+The definition of "biosignature" continued to be refined. In 2003, it was described as an object, substance, and/or pattern that unequivocally was originated through a biological process. By 2018, the definition had broadened to a substance or phenomenon that presents evidence of life. In 2023, the astrobiology community further refined the concept, agreeing that a biosignature is a phenomenon that can only be explained by biological processes, with all plausible abiotic explanations having been considered and eliminated.
+
+== Types ==
+Biosignatures can be grouped into ten broad categories:
+
+Isotope patterns: Isotopic evidence or patterns that require biological processes.
+Chemistry: Chemical features that require biological activity.
+Organic matter: Organics formed by biological processes.
+Minerals: Minerals or biomineral-phases whose composition and/or morphology indicate biological activity (e.g., biomagnetite).
+Microscopic structures and textures: Biologically-formed cements, microtextures, microfossils, and films.
+Macroscopic physical structures and textures: Structures that indicate microbial ecosystems, biofilms (e.g., stromatolites), or fossils of larger organisms.
+Temporal variability: Variations in time of atmospheric gases, reflectivity, or macroscopic appearance that indicates life's presence.
+Surface reflectance features: Large-scale reflectance features due to biological pigments.
+Atmospheric gases: Gases formed by metabolic processes, which may be present on a planet-wide scale.
+Technosignatures: Signatures that indicate a technologically advanced civilization.
+
+== Viability ==
+Determining whether an observed feature is a true biosignature is complex. There are three criteria that a potential biosignature must meet to be considered viable for further research: Reliability, survivability, and detectability.
+
+=== Reliability ===
+A biosignature must be able to dominate over all other processes that produce similar physical, spectral, and chemical features. Many forms of life are known to mimic geochemical reactions. One of the theories on the origin of life involves molecules developing the ability to catalyse geochemical reactions to exploit the energy being released by them. These are some of the earliest known metabolisms (see methanogenesis). In such case, scientists might search for a disequilibrium in the geochemical cycle, which would point to a reaction happening more or less often than it should. A disequilibrium such as this could be interpreted as an indication of life. However when looking at disequilibria, it is important to consider the context of the environment, because not all  atmospheric disequilibria has biotic causes. For example, prebiotic environments can have chemical disequilibria due to volcanic activity.
+
+=== Survivability ===
+A biosignature must be able to last for long enough so that a probe, telescope, or human can be able to detect it. A consequence of a biological organism's use of metabolic reactions for energy is the production of metabolic waste. In addition, the structure of an organism can be preserved as a fossil and we know that some fossils on Earth are as old as 3.5 billion years. These byproducts can make excellent biosignatures since they provide direct evidence for life. However, in order to be a viable biosignature, a byproduct must subsequently remain intact so that scientists may discover it.
+
+=== Detectability ===
+A biosignature must be detectable with current technology in order to be considered viable in scientific investigations. Although this may seem straightforward, there are many scenarios in which life may be present on a planet yet remain undetectable due to observational or technological limitations.
+
+==== False positives ====
+Every possible biosignature is associated with its own set of unique false positive mechanisms, in which abiotic processes can mimic the detectable feature of biological activity. An important example is using oxygen as a biosignature. On Earth, most oxygen is produced by photosynthesis and is subsequently used by other life forms. Oxygen is also readily detectable in spectra, with multiple bands across a relatively wide wavelength range, therefore, it makes a very good biosignature. Finding oxygen alone in a planet's atmosphere is not enough to confirm a biosignature because of the false-positive mechanisms associated with it. One possibility is that oxygen can build up abiotically via photolysis if there is a low inventory of non-condensable gasses or if the planet loses a lot of water. Finding and distinguishing a biosignature from its abiotic mechanisms is one of the major challenges of confirming the viability of a biosignature.
+
+==== False negatives ====
+False negative biosignatures occur when life is present, but environmental processes  and/or measurement limitations may obscure or suppress features that would otherwise indicate biological activity. This is another challenge that is a significant focus of ongoing research, especially in preparation for future telescope observations designed to observe exoplanetary atmospheres.
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+---
+title: "Biosignature"
+chunk: 2/6
+source: "https://en.wikipedia.org/wiki/Biosignature"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:15.960639+00:00"
+instance: "kb-cron"
+---
+
+==== Human limitations ====
+Observational or technological limitations may also limit the detectability of a potential biosignature. Telescope resolution maybe insufficient to resolve spectral features needed to distinguish between biological signals and false positives. In addition, observatories and telescopes are designed by multidisciplinary teams, resulting in instrumentation that reflects compromises among a variety of scientific priorities. As a result, optimizing instruments for biosignature detection may requires trade-offs with capabilities aimed at other science goals.
+
+== General examples ==
+
+=== Geomicrobiology ===
+
+The ancient record on Earth provides an opportunity to see what geochemical signatures are produced by microbial life and how these signatures are preserved over geologic time. Some related disciplines such as geochemistry, geobiology, and geomicrobiology often use biosignatures to determine if living organisms are or were present in a sample. These possible biosignatures include: (a) microfossils and stromatolites; (b) molecular structures (biomarkers) and isotopic compositions of carbon, nitrogen and hydrogen in organic matter; (c) multiple sulfur and oxygen isotope ratios of minerals; and (d) abundance relationships and isotopic compositions of redox-sensitive metals (e.g., Fe, Mo, Cr, and rare earth elements).
+For example, the particular fatty acids measured in a sample can indicate which types of bacteria and archaea live in that environment. Another example is the long-chain fatty alcohols with more than 23 atoms that are produced by planktonic bacteria. When used in this sense, geochemists often prefer the term biomarker. Another example is the presence of straight-chain lipids in the form of alkanes, alcohols, and fatty acids with 20–36 carbon atoms in soils or sediments. Peat deposits are an indication of originating from the epicuticular wax of higher plants.
+Life processes may produce a range of biosignatures such as nucleic acids, lipids, proteins, amino acids, kerogen-like material and various morphological features that are detectable in rocks and sediments. Microbes often interact with geochemical processes, leaving features in the rock record indicative of biosignatures. For example, bacterial micrometer-sized pores in carbonate rocks resemble inclusions under transmitted light, but have distinct sizes, shapes, and patterns (swirling or dendritic) and are distributed differently from common fluid inclusions. A potential biosignature is a phenomenon that may have been produced by life, but for which alternate abiotic origins may also be possible.
+
+=== Morphology ===
+Another possible biosignature might be morphology since the shape and size of certain objects may potentially indicate the presence of past or present life. Morphology has sparked debate as it is inconclusive and has resulted in disputed claims of early life on Earth. 
+Stromatolites are difficult to identify chemically and are sometimes claimed based on morphology alone. However geological processes may produce false positive candidates. One case is a 3.7 Ga structure in West Greenland which could be explained by tectonic processes.
+
+=== Chemistry ===
+No single compound will prove life once existed. Rather, it will be distinctive patterns present in any organic compounds showing a process of selection. For example, membrane lipids left behind by degraded cells will be concentrated, have a limited size range, and comprise an even number of carbons. Similarly, life only uses left-handed amino acids. Biosignatures need not be chemical, however, and can also be suggested by a distinctive magnetic biosignature.
+
+Chemical biosignatures include any suite of complex organic compounds composed of carbon, hydrogen, and other elements or heteroatoms such as oxygen, nitrogen, and sulfur, which are found in crude oils, bitumen, petroleum source rock and eventually show simplification in molecular structure from the parent organic molecules found in all living organisms. They are complex carbon-based molecules derived from formerly living organisms. Each biomarker is quite distinctive when compared to its counterparts, as the time required for organic matter to convert to crude oil is characteristic. Most biomarkers also usually have high molecular mass.
+Some examples of biomarkers found in petroleum are pristane, triterpanes, steranes, phytane and porphyrin. Such petroleum biomarkers are produced via chemical synthesis using biochemical compounds as their main constituents. For instance, triterpenes are derived from biochemical compounds found on land angiosperm plants. The abundance of petroleum biomarkers in small amounts in its reservoir or source rock make it necessary to use sensitive and differential approaches to analyze the presence of those compounds. The techniques typically used include gas chromatography and mass spectrometry.
+Petroleum biomarkers are highly important in petroleum inspection as they help indicate the depositional territories and determine the geological properties of oils. For instance, they provide more details concerning their maturity and the source material. In addition to that they can also be good parameters of age, hence they are technically referred to as "chemical fossils". The ratio of pristane to phytane (pr:ph) is the geochemical factor that allows petroleum biomarkers to be successful indicators of their depositional environments.
+Geologists and geochemists use biomarker traces found in crude oils and their related source rock to unravel the stratigraphic origin and migration patterns of presently existing petroleum deposits. The dispersion of biomarker molecules is also quite distinctive for each type of oil and its source; hence, they display unique fingerprints. Another factor that makes petroleum biomarkers more preferable than their counterparts is that they have a high tolerance to environmental weathering and corrosion. Such biomarkers are very advantageous and often used in the detection of oil spillage in the major waterways. The same biomarkers can also be used to identify contamination in lubricant oils. However, biomarker analysis of untreated rock cuttings can be expected to produce misleading results. This is due to potential hydrocarbon contamination and biodegradation in the rock samples.
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+---
+title: "Biosignature"
+chunk: 3/6
+source: "https://en.wikipedia.org/wiki/Biosignature"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:15.960639+00:00"
+instance: "kb-cron"
+---
+
+=== Atmospheric ===
+The atmospheric properties of exoplanets are of particular importance, as atmospheres provide the most likely observables for the near future, including habitability indicators and biosignatures. Over billions of years, the processes of life on a planet would result in a mixture of chemicals unlike anything that could form in an ordinary chemical equilibrium. For example, large amounts of oxygen and small amounts of methane are generated by life on Earth.
+An exoplanet's color—or reflectance spectrum—can also be used as a biosignature due to the effect of pigments that are uniquely biologic in origin such as the pigments of phototrophic and photosynthetic life forms. Scientists use the Earth as an example of this when looked at from far away (see Pale Blue Dot) as a comparison to worlds observed outside of the Solar System. Ultraviolet radiation on life forms could also induce biofluorescence in visible wavelengths that may be detected by the new generation of space observatories under development.
+Some scientists have reported methods of detecting hydrogen and methane in extraterrestrial atmospheres. Habitability indicators and biosignatures must be interpreted within a planetary and environmental context. For example, the presence of oxygen and methane together could indicate the kind of extreme thermochemical disequilibrium generated by life. Two of the top 14,000 proposed atmospheric biosignatures are dimethyl sulfide and chloromethane (CH3Cl). An alternative biosignature is the combination of methane and carbon dioxide.
+
+A disequilibrium in the abundance of gas species in an atmosphere can be interpreted as a biosignature. Life has greatly altered the atmosphere on Earth in a way that would be unlikely for any other processes to replicate. Therefore, a departure from equilibrium is evidence for a biosignature. For example, the abundance of methane in the Earth's atmosphere is orders of magnitude above the equilibrium value due to the constant methane flux that life on the surface emits. Depending on the host star, a disequilibrium in the methane abundance on another planet may indicate a biosignature.
+
+=== Agnostic biosignatures ===
+Because the only known example of life is Earth life, the search for biosignatures is heavily influenced by the products and processes associated with life on Earth. However, life that is fundamentally different from life on Earth may still produce detectable biosignatures, even if its specific biology is unknown. Such indicators are referred to as "agnostic biosignatures," as they do not rely on assumptions about the biochemical nature of the life that generates them. It is widely accepted that all life–no matter how different it is from life on Earth–needs a source of energy to thrive. This must involve a chemical disequilibrium that can support metabolic processes. Geological processes operate independently of biology, and if the geologic state of a planet is well constrained, the expected geochemical equilibrium can be predicted. Departures from this equilibrium may indicate atmospheric disequilibrium and serve as potential agnostic biosignatures.
+
+=== Antibiosignatures ===
+Just as the detection of a biosignature would provide evidence for life, the identification of conditions that strongly indicate the absence of life can be scientifically significant. Such indicators are termed antibiosignatures. All known life relies on redox gradients to obtain energy, so a lifeless environment may accumulate large redox imbalances or significant amounts of unused chemical free energy. When such imbalances persist without evidence of biological processing, they can indicate that no organisms are present to exploit the available energy. In this context, a strong, unutilized chemical disequilibrium can function as an antibiosignature, by implying that biological activity is unlikely.
+
+=== Polyelectrolytes ===
+
+The Polyelectrolyte theory of the gene is a proposed generic biosignature. In 2002, Steven A. Benner and Daniel Hutter proposed that for a linear genetic biopolymer dissolved in water, such as DNA, to undergo Darwinian evolution anywhere in the universe, it must be a polyelectrolyte, a polymer containing repeating ionic charges. Benner and others proposed methods for concentrating and analyzing these polyelectrolyte genetic biopolymers on Mars, Enceladus, and Europa.
+
+== Search for Life ==
+Astrobiological exploration is founded upon the premise that biosignatures encountered in space will be recognizable as extraterrestrial life. The usefulness of a biosignature is determined not only by the probability of life creating it but also by the improbability of non-biological (abiotic) processes producing it. Concluding that evidence of an extraterrestrial life form (past or present) has been discovered requires proving that a possible biosignature was produced by the activities or remains of life. As with most scientific discoveries, discovery of a biosignature will require evidence building up until no other explanation exists.
+
+Possible examples of a biosignature include complex organic molecules or structures whose formation is virtually unachievable in the absence of life:
+
+Cellular and extracellular morphologies
+Biomolecules in rocks
+Bio-organic molecular structures
+Homochirality: uniformity of chirality, or handedness, of biomolecules
+Biogenic minerals
+Biogenic isotope patterns in minerals and organic compounds
+Atmospheric gases
+Photosynthetic pigments
+NASA and other space agencies use versions of a Life Detection Ladder as a planning tool for astrobiology missions. The ladder outlines a hierarchy of biological traits—chemical, structural, and ecological—that robotic instruments might detect, and evaluates how specific each trait is to living processes. By organizing potential biosignatures from least to most diagnostic, the ladder helps researchers design mission strategies, assess measurement credibility, and determine which combinations of evidence would be needed to support a claim of extant life beyond Earth.
+
+== Search for life in the Solar System ==
+
+=== Mars ===
+
+==== Atmosphere of Mars ====
+
+The atmosphere of Mars contains some gases which have been studied as potential biosignatures, most notably putative methane, but also ozone and oxygen.
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+---
+title: "Biosignature"
+chunk: 4/6
+source: "https://en.wikipedia.org/wiki/Biosignature"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:15.960639+00:00"
+instance: "kb-cron"
+---
+
+===== Ozone in the Martian Atmosphere =====
+Mars has traces of ozone (including a seasonal ozone layer over the south pole in winter) and oxygen in its atmosphere both byproducts of life on Earth but explained by photochemistry on Mars. Mariner 7 detected ozone in 1971 and in 1976 by the Viking biological experiments. Significant levels of oxygen were detected in Gale Crater by Curiosity Rover in 2019 with seasonal variability that has not fully been explained. Studies indicate that the Martian atmosphere was once oxygen-rich. Today they are no longer considered valid biosignatures and are proposed to be the result of photodissociation of carbon dioxide.
+
+===== Methane in the Martian Atmosphere =====
+Martian methane is an area of ongoing research. With life being the strongest source of methane on Earth, continued observation of such a disequilibrium could be a viable biosignature. Current photochemical models cannot explain the reported rapid variations in space and time. Neither its fast appearance nor disappearance have been explained. Because of its tendency to be destroyed in the atmosphere by photochemistry, excess methane could indicate that there must be an active source.
+Since 2004 there have been several detection claims of methane in the Mars atmosphere by a variety of instruments onboard orbiters and ground-based landers on the Martian surface as well as Earth-based telescopes. However 2019 measurements put an upper bound on the overall methane abundance at 0.05 p.p.b.v contradicting previous observations.
+The Curiosity rover's Tunable Laser Spectrometer (TLS) has detected methane on the Martian surface. However, this data is inconclusive due to methane leaks in the TLS that have most likely contaminated the methane readings from the surface of Mars.
+To rule out a biogenic origin for the methane, a future probe or lander hosting a mass spectrometer will be needed first to prove its presence, and second, to use the isotopic proportions of carbon-12 to carbon-14 in methane to distinguish between a biogenic and non-biogenic origin, similarly to the use of the δ13C standard for recognizing biogenic methane on Earth.
+
+===== CO and H2 in Martian atmosphere =====
+The Martian atmosphere contains high abundances of photochemically produced CO and H2, which are reducing molecules. Mars' atmosphere is otherwise mostly oxidizing, leading to a source of untapped energy that life could exploit if it used by a metabolism compatible with one or both of these reducing molecules. Because these molecules can be observed, scientists use this as evidence for an antibiosignature. Scientists have used this concept as an argument against life on Mars.
+
+==== Possible Bioorganic Chemistry on Mars ====
+
+Organic chemistry has been discovered on Mars, some of which can be explained by geochemical processes. Chlorobenzene (C6H5Cl), for example, was detected as early as the Viking lander biological experiments and later in sedimentary rocks by Curiosity likely from perchlorate reactions with organic matter. Some abiotic source, such as a Fischer–Tropsch process, could also have produced alkanes.
+Some discoveries have been found in areas confirmed previously be wet, adding weight to their significance. In 2018 at Gale Crater, Curiosity discovered Thiophene (C4H4S) and polymers (Polythiophene). Natural sulfur reduction has been proposed as a possible abiotic source. Dimethyl sulfide (CH2S) was also detected. In Cheyava Falls discovered by Perseverance in July 2024, organic matter was detected. Also found were millimeter-sized splotches resembling "leopard spots" containing iron and phosphate, elements often associated with microbial life. In 2025, analysis of rocks from Gale Crater by SAM found decane (C10H22), dodecane (C12H26) and undecane (CH3(CH2)9CH3), collectively known as fatty acids, which terrestrial cell membranes are made of. However these have formed on meteorites, which may have delivered them to Mars.
+An analysis of 2020 data from Mary Anning3 (MA3) from SAM TMAH found evidence for more than 20 complex molecules including Nitrogen Heterocyclic compounds considered precursors to RNA and DNA along with many other volatile compounds. Molecules detected included Trimethylbenzene, Tetramethylbenzene, Methyl benzoate, Dihydronaphthalene, Naphthalene, Benzothiophene and Methylnaphthalene. While there is currently no abiotic explanation for the complex organics found, exogenous sources must first be ruled out.
+
+==== Mars Missions ====
+
+===== The Viking missions to Mars =====
+
+The Viking Landers (1976) performed the first in situ biological experiments on Mars, testing for metabolic activity using gas-exchange and labeled-release assays. Although some experiments produced responses initially interpreted as possible metabolic signatures, the absence of organic molecules in Viking’s gas chromatograph–mass spectrometer led to widespread disagreement over the biological interpretation. The results remain inconclusive, and the experiments are often cited as an example of the need for multiple, independent lines of evidence when evaluating biosignatures. The Viking findings also highlighted the importance of characterizing the inorganic chemistry of the environment, as biosignatures cannot be reliably interpreted without understanding the abiotic context in which they may occur.
+
+===== Mars Science Laboratory =====
+
+The Curiosity rover from the Mars Science Laboratory mission, with its Curiosity rover is currently assessing the potential past and present habitability of the Martian environment and is attempting to detect biosignatures on the surface of Mars. Considering the MSL instrument payload package, the following classes of biosignatures are within the MSL detection window: organism morphologies (cells, body fossils, casts), biofabrics (including microbial mats), diagnostic organic molecules, isotopic signatures, evidence of biomineralization and bioalteration, spatial patterns in chemistry, and biogenic gases. The Curiosity rover targets outcrops to maximize the probability of detecting 'fossilized' organic matter preserved in sedimentary deposits.
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+---
+title: "Biosignature"
+chunk: 5/6
+source: "https://en.wikipedia.org/wiki/Biosignature"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:15.960639+00:00"
+instance: "kb-cron"
+---
+
+===== ExoMars Orbiter =====
+The 2016 ExoMars Trace Gas Orbiter (TGO) is a Mars telecommunications orbiter and atmospheric gas analyzer mission. It delivered the Schiaparelli EDM lander and then began to settle into its science orbit to map the sources of methane on Mars and other gases, and in doing so, will help select the landing site for the Rosalind Franklin rover to be launched in 2028. The primary objective of the Rosalind Franklin rover mission is the search for biosignatures on the surface and subsurface by using a drill able to collect samples down to a depth of 2 metres (6.6 ft), away from the destructive radiation that bathes the surface.
+
+===== Mars 2020 =====
+
+The Mars 2020 rover, which launched in 2020, is intended to investigate an astrobiologically relevant ancient environment on Mars, investigate its surface geological processes and history, including the assessment of its past habitability, the possibility of past life on Mars, and potential for preservation of biosignatures within accessible geological materials. In addition, it will cache the most interesting samples for possible future transport to Earth.
+In 2024, Perseverance found a rock, called Cheyava Falls, during its exploration of the Jezero Crater. The rover's instruments detected organic compounds within the rock. According to NASA, Cheyava Falls "possesses qualities that fit the definition of a possible indicator of ancient life".
+On 10 September 2025, NASA reported a "potential biosignature" finding in Cheyava Falls: organic-carbon–bearing mudstones hosting sub-millimetre nodules and millimetre-scale reaction fronts enriched in ferrous iron phosphate and iron sulfide, consistent with vivianite and greigite imply low-temperature, post-depositional redox reactions between organics and Fe–S–P minerals; these textures and chemistries qualify as potential biosignatures but requiring further study and sample return for confirmation. On Earth, vivianite is frequently found in sediments, peat bogs, and around decaying organic matter. Similarly, certain forms of microbial life on Earth can produce greigite. The same organic materials can be produced by non-biological processes which require "hot conditions" like volcanic activity; the rock location suggests that it was underwater, and there is no detected past volcanic activity in that region.
+If confirmed, this biosignature would mean that there were a microbial life on Mars around 3.5 billion years ago. According to geologist Michael Tice:
+
+If the Cheyava Falls results ultimately do lead to the proof of ancient life on Mars ... that means two different planets hosted microbes getting their energy through the same means at about the same time in the distant past. That could suggest that early life learns how to survive in this way regardless of where it originated.
+
+=== Venus ===
+
+==== Atmosphere of Venus ====
+The atmosphere of Venus continues to be investigated for potential biosignatures though abiotic processes have been put forward as explanations.
+
+===== Ammonia in the Venusian Atmosphere =====
+
+Ammonia (NH3) was first detected in the atmosphere by the bromophenol blue chemical sensor of Venera 8 in 1972. Ammonia is essential to life and is both a metabolic input and output, as such it has been explored as having strong potential as a biosignature. Pioneer Venus also detected substantial quantities of the gas. Of particular interest is that unlike the Martian atmosphere where conditions would suit ammonia's presence only transient trace amounts have been detected, on Venus with conditions less conducive to its presence it appears to somehow be replenished. A 2021 paper claimed that it could be a byproduct of life that is in turn providing a stable habitable environment for life to continue in the upper atmosphere. At least one paper puts forward a possible abiotic explanation, proposing that similar processes as nitrogen fixation in early Earth's atmosphere though caused by mantle oxidation due to the planet's water loss. Another has proposed that lightning could be producing it though whether Venus has lightning at all has been extensively debated.
+
+===== Ozone in the Venusian Atmosphere =====
+Ozone (O3) was first detected at concentrations of up to 1 ppm in the night side upper atmosphere by Venus Express in 2011. As a byproduct of living organisms this was once regarded as a candidate biosignature. Known since the 1970s to exists in trace amounts in the Martian atmosphere, Venus in comparison possesses a significant layer similar to but substantially less concentrated than Earth's. Photochemical processes, specifically dissociation of carbon dioxide (CO2) by sunlight, is now offered an explanation for its presence.
+
+===== Phosphine in the Venusian Atmosphere =====
+Phosphine (PH3) was first detected in 2020 by the James Clerk Maxwell Telescope and the Atacama Large Millimeter/submillimeter Array in trace amounts in the upper cloud deck. There was no known abiotic source for the quantities detected. Subsequent analysis and investigation between 2020 and 2015 indicated possible false detection, or a much lower concentration of 1 ppb. However in  September 2024, the preliminary analysis of the JCMT-Venus data confirmed a concentration of 300 ppb at altitude 55 km. Further data processing is still needed to measure phosphine concentration deeper in the Venusian cloud deck.
+
+==== Morning Star Missions to Venus ====
+The Venus Life Finder is a planned mission to Venus, scheduled to launch no earlier than summer of 2026. The goal of these missions is to detecting potential organics, measure acidity, and determine the unknown UV absorber in the clouds of Venus.
+
+=== Icy Moons ===
+
+==== Missions ====
+
+===== Europa Clipper =====
+
+NASA's Europa Clipper probe is designed as a flyby mission to Jupiter's smallest Galilean moon, Europa. The mission launched in October 2024 and is set to reach Europa in April 2030, where it will investigate the potential for habitability on Europa. Europa is one of the best candidates for biosignature discovery in the Solar System because of the scientific consensus that it retains a subsurface ocean, with two to three times the volume of water on Earth. Evidence for this subsurface ocean includes:
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+---
+title: "Biosignature"
+chunk: 6/6
+source: "https://en.wikipedia.org/wiki/Biosignature"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:15.960639+00:00"
+instance: "kb-cron"
+---
+
+Voyager 1 (1979): The first close-up photos of Europa are taken. Scientists propose that a subsurface ocean could cause the tectonic-like marks on the surface.
+Galileo (1997): The magnetometer aboard this probe detected a subtle change in the magnetic field near Europa. This was later interpreted as a disruption in the expected magnetic field due to the current induction in a conducting layer on Europa. The composition of this conducting layer is consistent with a salty subsurface ocean.
+Hubble Space Telescope (2012): An image was taken of Europa which showed evidence for a plume of water vapor coming off the surface.
+The Europa Clipper probe includes instruments to help confirm the existence and composition of a subsurface ocean and thick icy layer. In addition, the instruments will be used to map and study surface features that may indicate tectonic activity due to a subsurface ocean.
+
+===== Dragonfly =====
+NASA's Dragonfly lander/aircraft concept is proposed to launch in 2028 and would seek evidence of biosignatures on the organic-rich surface and atmosphere of Titan, as well as study its possible prebiotic primordial soup. Titan is the largest moon of Saturn and is widely believed to have a large subsurface ocean consisting of a salty brine. In addition, scientists believe that Titan may have the conditions necessary to promote prebiotic chemistry, making it a prime candidate for biosignature discovery.
+
+==== Enceladus ====
+
+Although there are no set plans to search for biosignatures on Saturn's sixth-largest moon, Enceladus, the prospects of biosignature discovery there are exciting enough to warrant several mission concepts that may be funded in the future. Similar to Jupiter's moon Europa, there is much evidence for a subsurface ocean to also exist on Enceladus. Plumes of water vapor were first observed in 2005 by the Cassini mission and were later determined to contain salt as well as organic compounds. In 2014, more evidence was presented using gravimetric measurements on Enceladus to conclude that there is in fact a large reservoir of water underneath an icy surface. Mission design concepts include:
+
+Enceladus Life Finder (ELF)
+Enceladus Life Signatures and Habitability
+Enceladus Organic Analyzer
+Enceladus Explorer (En-Ex)
+Explorer of Enceladus and Titan (E2T)
+Journey to Enceladus and Titan (JET)
+Life Investigation For Enceladus (LIFE)
+Testing the Habitability of Enceladus's Ocean (THEO)
+All of these concept missions have similar science goals: To assess the habitability of Enceladus and search for biosignatures, in line with the strategic map for exploring the ocean-world Enceladus.
+
+=== Meteorites ===
+
+==== Martian Meteorites ====
+
+===== ALH84001 =====
+
+Microscopic magnetite crystals in the Martian meteorite ALH84001 represent one of the longest-standing and most debated potential biosignatures identified in that specimen. Analyses focused on proposed biominerals, including putative microbial microfossils.  These are minute rock-like structures whose morphology was initially suggestive of bacterial shapes. Subsequent studies indicated that these features were likely too small to represent fossilized cells. A broader consensus emerged from these discussions emphasizing that morphological evidence alone is insufficient to substantiate claims of life and must be supported by multiple, independent lines of evidence. Interpretation based solely on morphology are highly subjective and have historically led to numerous misidentifications.
+
+== Search for Life Outside the Solar System ==
+At 4.2 light-years (1.3 parsecs, 40 trillion km, or 25 trillion miles) away from Earth, the closest potentially habitable exoplanet is Proxima Centauri b, which was discovered in 2016. This means it would take more than 18,100 years to get there if a vessel could consistently travel as fast as the Juno spacecraft (250,000 kilometers per hour or 150,000 miles per hour). It is currently not feasible to send humans or even probes to search for biosignatures outside of the Solar System. The only way to search for biosignatures outside of the Solar System is by observing exoplanets with telescopes.
+
+=== Exoplanets ===
+
+==== K2-18b ====
+On September 12, 2023, scientists announced that their investigation into exoplanet K2-18b revealed the possible presence of dimethyl sulfide, noting that it is produced only by biotic processes on Earth. In 2025, another paper was published confirming dimethyl sulfide and dimethyl disulfide on the exoplanet. However, a follow-up study questions the James Webb Space Telescope's instrumentation's ability to differentiate the signature of dimethyl sulfide from methane in the data, which is noisy. Additionally, follow-up studies have identified potential abiotic sources.
+
+=== Telescopes ===
+There have been no plausible or confirmed biosignature detections outside of the Solar System. Despite this, it is a rapidly growing field of research due to the prospects of the next generation of telescopes. The James Webb Space Telescope, which launched in December 2021, will be a promising next step in the search for biosignatures. Although its wavelength range and resolution will not be compatible with some of the more important atmospheric biosignature gas bands like oxygen, it will still be able to detect some evidence for oxygen false positive mechanisms.
+The Habitable Worlds Observatory is a NASA telescope currently in design, expected to launch in the 2040s. It which will specifically target potentially habitable exoplanets, to characterize and observe any potential biosignatures for Earth-like exoplanets.
+The new generation of ground-based 30-meter class telescopes (Thirty Meter Telescope and Extremely Large Telescope) will have the ability to take high-resolution spectra of exoplanet atmospheres at a variety of wavelengths. These telescopes will be capable of distinguishing some of the more difficult false positive mechanisms such as the abiotic buildup of oxygen via photolysis. In addition, their large collecting area will enable high angular resolution, making direct imaging studies more feasible.
+
+== Bibliography ==
+Gaines, Susan M.; Eglinton, Geoffrey; Rullkotter, Jurgen (2008). Echoes of Life: What Fossil Molecules Reveal about Earth History. Oxford University Press. ISBN 978-0-19-517619-3.
+
+== See also ==
+Bioindicator
+Taphonomy
+Technosignature
+
+== References ==
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+---
+title: "Catabiosis"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Catabiosis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:17.204749+00:00"
+instance: "kb-cron"
+---
+
+Catabiosis is the process of growing older, aging and physical degradation.
+The word comes from Greek "kata"—down, against, reverse and "biosis"—way of life and is generally used to describe senescence and degeneration in living organisms and biophysics of aging in general.
+One of the popular catabiotic theories is the entropy theory of aging, where aging is characterized by thermodynamically favourable increase in structural disorder. Living organisms are open systems that take free energy from the environment and offload their entropy as waste. However, basic components of living systems—DNA, proteins, lipids and sugars—tend towards the state of maximum entropy while continuously accumulating damages causing catabiosis of the living structure. 
+Catabiotic force on the contrary is the influence exerted by living structures on adjoining cells, by which the latter are developed in harmony with the primary structures. 
+
+
+== References ==
+
+
+== External links ==
+Onpedia definition of catabiosis
+Catabiotic force
+Dictionary.com - Catabiosis
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+---
+title: "Chemotroph"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Chemotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:18.454829+00:00"
+instance: "kb-cron"
+---
+
+A chemotroph is an organism that obtains energy by the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs, which use photons. Chemotrophs can be either autotrophic or heterotrophic. Chemotrophs can be found in areas where electron donors are present in high concentration, for instance around hydrothermal vents. Some examples of chemotrophic organisms include iron-oxiding bacteria and methanogenic archaea. 
+
+
+== Chemoautotroph ==
+
+Chemoautotrophs are autotrophic organisms that can rely on chemosynthesis, i.e. deriving biological energy from chemical reactions of environmental inorganic substrates and synthesizing all necessary organic compounds from carbon dioxide. Chemoautotrophs can use inorganic energy sources such as hydrogen sulfide, elemental sulfur, ferrous iron, molecular hydrogen, and ammonia or organic sources to produce energy. Most chemoautotrophs are prokaryotic extremophiles, bacteria, or archaea that live in otherwise hostile environments (such as deep sea vents) and are the primary producers in such ecosystems. Chemoautotrophs generally fall into several groups: methanogens, sulfur oxidizers and reducers, nitrifiers, anammox bacteria, and thermoacidophiles. An example of one of these prokaryotes would be Sulfolobus. Chemolithotrophic growth can be very fast, such as Hydrogenovibrio crunogenus with a doubling time around one hour.
+The term "chemosynthesis", coined in 1897 by Wilhelm Pfeffer, originally was defined as the energy production by oxidation of inorganic substances in association with autotrophy — what would be named today as chemolithoautotrophy. Later, the term would include also the chemoorganoautotrophy, that is, it can be seen as a synonym of chemoautotrophy.
+
+
+== Chemoheterotroph ==
+Chemoheterotrophs (or chemotrophic heterotrophs) are unable to fix carbon to form their own organic compounds. Chemoheterotrophs can be chemolithoheterotrophs, utilizing inorganic electron sources such as sulfur, iron, or, much more commonly, chemoorganoheterotrophs, utilizing organic electron sources such as carbohydrates, lipids, and proteins. Most animals and fungi are examples of chemoheterotrophs, as are some halophiles.
+
+
+=== Iron-oxidizing bacteria ===
+
+Iron-oxidizing bacteria are chemotrophic bacteria that derive energy by oxidizing dissolved ferrous iron. They are known to grow and proliferate in waters containing iron concentrations as low as 0.1 mg/L. However, at least 0.3 ppm of dissolved oxygen is needed to carry out the oxidation.
+Iron has many existing roles in biology not related to redox reactions; examples include iron–sulfur proteins, hemoglobin, and coordination complexes. Iron has a widespread distribution globally and is considered one of the most abundant in the Earth's crust, soil, and sediments. Iron is a trace element in marine environments. Its role as the electron donor for some chemolithotrophs is probably very ancient.
+
+
+=== Methanogens ===
+Methanogens are chemotrophic archaea that obtain energy most commonly through CO2 reduction by H2 (hydrogenotrophs) or fermentation of acetate (acetoclastic). They are distinct from other bacteria or archea that do not depend on methane synthesis for energy but produce methane as a byproduct of their other metabolic processes. Methanogens are also different from bacteria and eukarya due to a lack of peptidoglycan in their cell wall, rather methanogens contain either pseudomurein, heteropolysaccharide, or protein-based cell walls. Species that reduce CO2 are chemoautotrophs and fix inorganic carbon, however, a few species use organic carbon in the form of acetate, making them chemoheterotrophs. Methanogens belong to the Methanobacteriota kingdom. Methanogens are a part of an ancient monophyletic lineage, the Methanobacteriati phylum (formerly "Euryarcheota"), and can be classified into three classes, six orders, twelve families and thirty-five genera. Methanogenic metabolic pathways are thought to be present in some of the earliest organisms that occupied the earth. Today, methanogens can be found in a wide range of environments, both oxic and anoxic and both terrestrial and aquatic, especially environments containing low sulfate. Their activity is strongly regulated by temperature, pH, substrate and nutrient availability, as well as competition with other anaerobic microbes, all of which influence their distribution across diverse environments. 
+Methanogenic archaea are involved in the late steps of degradation of organic matter. In many anaerobic environments, methanogens form syntropic relationships with other fermentative bacteria that supply them with substrates such as H2, formate, and acetate. Since the energy yield of methanogenesis is relatively low compared to other processes, methanogenesis does not become the dominant process until the more energy-rich electron acceptors such as O2, NO3-, and SO42- have already been depleted. Due to the absence of these electron acceptors, methanogens can then catalyze the final step of the degradation of organic matter which is essential for anaerobic environments. While different organisms may use different substrates, they all share methane as the final metabolic product, and they are all anaerobic. In addition to CO2 and acetate, methanogens also use formate, methylamine and other small molecules to produce CH4. Regardless of the substrate, all methanogenic archaea utilize the enzyme methyl-coenzyme M reductase, which performs the final step of reducing methyl-coenzyme M to methane. Methanogens also possess several unique coenzymes such as coenzyme F430 and methanopterin, among others. Methanogenic activity contributes to methane that is locked in long-term reservoirs such as permafrost, and as climate warming accelerates thawing of frozen soils, methane production by methanogens is expected increase. As methane has around 25-30 times the global warming potential of CO2, methane is one of the greenhouse gases driving climate change that is a source of concern for climate scientists.
+
+
+== See also ==
+Chemosynthesis
+Lithotroph
+Methanogen (feeds on hydrogen)
+Methanotroph
+RISE project – expedition that discovered high-temperature vent communities
+
+
+== Notes ==
+
+
+== References ==
+1. Katrina Edwards. Microbiology of a Sediment Pond and the Underlying Young, Cold, Hydrologically Active Ridge Flank. Woods Hole Oceanographic Institution.
+2. Coupled Photochemical and Enzymatic Mn(II) Oxidation Pathways of a Planktonic Roseobacter-Like Bacterium. Colleen M. Hansel and Chris A. Francis* Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305-2115. Received 28 September 2005. Accepted 17 February 2006.
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+---
+title: "Earliest known life forms"
+chunk: 1/3
+source: "https://en.wikipedia.org/wiki/Earliest_known_life_forms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:42.867278+00:00"
+instance: "kb-cron"
+---
+
+The earliest known life forms on Earth may be as old as 4.1 billion years (or Ga) according to biologically fractionated graphite inside a single zircon grain in the Jack Hills range of Australia. The earliest evidence of life found in a stratigraphic unit, not just a single mineral grain, is the 3.7 Ga metasedimentary rocks containing graphite from the Isua Supracrustal Belt in Greenland. The earliest direct known life on Earth are stromatolite fossils which have been found in 3.480-billion-year-old geyserite uncovered in the Dresser Formation of the Pilbara Craton of Western Australia. Various microfossils of microorganisms have been found in 3.4 Ga rocks, including 3.465-billion-year-old Apex chert rocks from the same Australian craton region, and in 3.42 Ga hydrothermal vent precipitates from Barberton, South Africa. Much later in the geologic record, likely starting in 1.73 Ga, preserved molecular compounds of biologic origin are indicative of aerobic life. Therefore, the earliest time for the origin of life on Earth is at least 3.5 billion years ago and possibly as early as 4.1 billion years ago—not long after the oceans formed 4.5 billion years ago and after the formation of the Earth 4.54 billion years ago.
+
+== Biospheres ==
+
+Earth is the only place in the universe known to harbor life, where it exists in myriad environments. The origin of life on Earth was at least 3.5 billion years ago, possibly as early as 3.8–4.1 billion years ago. Since its emergence, life has persisted in several geological environments. The Earth's biosphere extends down to at least 10 km (6.2 mi) below the seafloor, up to 41–77 km (25–48 mi) into the atmosphere, and includes soil, hydrothermal vents, and rock. Further, the biosphere has been found to extend at least 914.4 m (3,000 ft; 0.5682 mi) below the ice of Antarctica and includes the deepest parts of the ocean. In July 2020, marine biologists reported that aerobic microorganisms (mainly) in "quasi-suspended animation" were found in organically poor sediment 76.2 m (250 ft) below the seafloor in the South Pacific Gyre (SPG) ("the deadest spot in the ocean"). Microbes have been found in the Atacama Desert in Chile, one of the driest places on Earth. In February 2023, findings of a "dark microbiome" of microbial dark matter of unfamiliar microorganisms in the Atacama Desert were reported. Microbes have also been found in deep-sea hydrothermal vent environments which can reach temperatures over 400 °C. Microbial communities can also survive in cold permafrost conditions down to -25 °C. Under certain test conditions, life forms have been observed to survive in the vacuum of outer space. More recently, studies conducted on the International Space Station found that bacteria could survive in outer space. 
+
+== Geochemical evidence ==
+The age of Earth is about 4.54 billion years; the earliest undisputed evidence of life on Earth dates from at least 3.5 billion years ago according to the stromatolite record. Some computer models suggest life began as early as 4.5 billion years ago. The oldest evidence of life is indirect in the form of isotopic fractionation processes. Microorganisms will preferentially use the lighter isotope of an atom to build biomass, as it takes less energy to break the bonds for metabolic processes. Biologic material will often have a composition that is enriched in lighter isotopes compared to the surrounding rock it's found in. Carbon isotopes, expressed scientifically in parts per thousand difference from a standard as δ13C, are frequently used to detect carbon fixation by organisms and assess if purported early life evidence has biological origins. Typically, life will preferentially metabolize the isotopically light 12C isotope instead of the heavier 13C isotope. Biologic material can record this fractionation of carbon.
+
+The oldest disputed geochemical evidence of life is isotopically light graphite inside a single zircon grain from the Jack Hills in Western Australia. The graphite showed a δ13C signature consistent with biogenic carbon on Earth. Other early evidence of life is found in rocks both from the Akilia Sequence and the Isua Supracrustal Belt (ISB) in Greenland. These 3.7 Ga metasedimentary rocks also contain graphite or graphite inclusions with carbon isotope signatures that suggest biological fractionation.
+The primary issue with isotopic evidence of life is that abiotic processes can fractionate isotopes and produce similar signatures to biotic processes. Reassessment of the Akilia graphite show that metamorphism, Fischer-Tropsch mechanisms in hydrothermal environments, and volcanic processes may be responsible for enrichment lighter carbon isotopes. The ISB rocks that contain the graphite may have experienced a change in composition from hot fluids, i.e., metasomatism, thus the graphite may have been formed by abiotic chemical reactions. However, the ISB's graphite is generally more accepted as biologic in origin after further spectral analysis.
+Metasedimentary rocks from the 3.5 Ga Dresser Formation, which experienced less metamorphism than the sequences in Greenland, contain better preserved geochemical evidence. Carbon isotopes as well as sulfur isotopes found in barite, which are fractionated by microbial metabolisms during sulfate reduction, are consistent with biological processes. However, the Dresser formation was deposited in an active volcanic and hydrothermal environment, and abiotic processes could still be responsible for these fractionations. Many of these findings are supplemented by direct evidence, typically by the presence of microfossils, however.
+
+== Fossil evidence ==
+Fossils are direct evidence of life. In the search for the earliest life, fossils are often supplemented by geochemical evidence. The fossil record does not extend as far back as the geochemical record due to metamorphic processes that erase fossils from geologic units.
+
+=== Stromatolites ===
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+---
+title: "Earliest known life forms"
+chunk: 2/3
+source: "https://en.wikipedia.org/wiki/Earliest_known_life_forms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:42.867278+00:00"
+instance: "kb-cron"
+---
+
+Stromatolites are laminated sedimentary structures created by photosynthetic organisms as they establish a microbial mat on a sediment surface. An important distinction for biogenicity is their convex-up structures and wavy laminations, which are typical of microbial communities who build preferentially toward the sun. A disputed report of stromatolites is from the 3.7 Ga Isua metasediments that show convex-up, conical, and domical morphologies. Further mineralogical analysis disagrees with the initial findings of internal convex-up laminae, a critical criterion for stromatolite identification, suggesting that the structures may be deformation features (i.e. boudins) caused by extensional tectonics in the Isua Supracrustal Belt.
+
+The earliest direct evidence of life are stromatolites found in 3.48 billion-year-old chert in the Dresser formation of the Pilbara Craton in Western Australia. Several features in these fossils are difficult to explain with abiotic processes, for example, the thickening of laminae over flexure crests that is expected from more sunlight. Sulfur isotopes from barite veins in the stromatolites also favor a biologic origin. However, while most scientists accept their biogenicity, abiotic explanations for these fossils cannot be fully discarded due to their hydrothermal depositional environment and debated geochemical evidence.
+Most archean stromatolites older than 3.0 Ga are found in Australia or South Africa. Stratiform stromatolites from the Pilbara Craton have been identified in the 3.47 Ga Mount Ada Basalt. Barberton, South Africa hosts stratiform stromatolites in the 3.46 Hooggenoeg, 3.42 Kromberg and 3.33 Ga Mendon Formations of the Onverwacht Group. The 3.43 Ga Strelley Pool Formation in Western Australia hosts stromatolites that demonstrate vertical and horizontal changes that may demonstrate microbial communities responding to transient environmental conditions. Thus, it is likely anoxygenic or oxygenic photosynthesis has been occurring since at least 3.43 Ga Strelley Pool Formation.
+
+=== Microfossils ===
+
+Claims of the earliest life using fossilized microorganisms (microfossils) are from hydrothermal vent precipitates from an ancient sea-bed in the Nuvvuagittuq Belt of Quebec, Canada. These may be as old as 4.28 billion years, which would make it the oldest evidence of life on Earth, suggesting "an almost instantaneous emergence of life" after ocean formation 4.41 billion years ago. These findings may be better explained by abiotic processes: for example, silica-rich waters, "chemical gardens," circulating hydrothermal fluids, and volcanic ejecta can produce morphologies similar to those presented in Nuvvuagittuq.
+
+The 3.48 Ga Dresser formation hosts microfossils of prokaryotic filaments in silica veins, the earliest fossil evidence of life on Earth, but their origins may be volcanic. 3.465-billion-year-old Australian Apex chert rocks may once have contained microorganisms, although the validity of these findings has been contested. "Putative filamentous microfossils," possibly of methanogens and/or methanotrophs that lived about 3.42-billion-year-old in "a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt, have been identified in South Africa." A diverse set of microfossil morphologies have been found in the 3.43 Ga Strelley Pool Formation including spheroid, lenticular, and film-like microstructures. Their biogenicity are strengthened by their observed chemical preservation. The early lithification of these structures allowed important chemical tracers, such as the carbon-to-nitrogen ratio, to be retained at levels higher than is typical in older, metamorphosed rock units.
+
+=== Molecular biomarkers ===
+
+Biomarkers are compounds of biologic origin found in the geologic record that can be linked to past life. Although they aren't preserved until the late Archean, they are important indicators of early photosynthetic life. Lipids are particularly useful biomarkers because they can survive for long periods of geologic time and reconstruct past environments.
+
+Fossilized lipids were reported from 2.7 Ga laminated shales from the Pilbara Craton and the 2.67 Ga Kaapvaal craton in South Africa. However, the age of these biomarkers and whether their deposition was synchronous with their host rocks were debated, and further work showed that the lipids were contaminants. The oldest "clearly indigenous" biomarkers are from the 1.64 Ga Barney Creek Formation in the McArthur Basin in Northern Australia, but hydrocarbons from the 1.73 Ga Wollogorang Formation in the same basin have also been detected.
+Other indigenous biomarkers can be dated to the Mesoproterozoic era (1.6–1.0 Ga). The 1.4 Ga Hongshuizhuang Formation in the North China Craton contains hydrocarbons in shales that were likely sourced from prokaryotes. Biomarkers were found in siltstones from the 1.38 Ga Roper Group of the McArthur Basin. Hydrocarbons possibly derived from bacteria and algae were reported in 1.37 Ga Xiamaling Formation of the NCC. The 1.1 Ga Atar/El Mreïti Group in the Taoudeni Basin, Mauritania show indigenous biomarkers in black shales.
+
+== Genomic evidence ==
+
+By comparing the genomes of modern organisms (in the domains Bacteria and Archaea), it is evident that there was a last universal common ancestor (LUCA). Another term for the LUCA is the cenancestor and can be viewed as a population of organisms rather than a single entity. LUCA is not thought to be the first life on Earth, but rather the only type of organism of its time to still have living descendants. In 2016, M. C. Weiss and colleagues proposed a minimal set of genes that each occurred in at least two groups of Bacteria and two groups of Archaea. They argued that such a distribution of genes would be unlikely to arise by horizontal gene transfer, and so any such genes must have derived from the LUCA. A molecular clock model suggests that the LUCA may have lived 4.477–4.519 billion years ago, within the Hadean eon.
+
+== RNA replicators ==
+
+Model Hadean-like geothermal microenvironments were demonstrated to have the potential to support the synthesis and replication of RNA and thus possibly the evolution of primitive life.   Porous rock systems, comprising heated air-water interfaces, were shown to facilitate ribozyme catalyzed RNA replication of sense and antisense strands and then subsequent strand-dissociation. This enabled combined synthesis, release and folding of active ribozymes.
+
+== Hypotheses for the origin of life on Earth ==
+
+=== Extraterrestrial origin for early life ===
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+---
+title: "Earliest known life forms"
+chunk: 3/3
+source: "https://en.wikipedia.org/wiki/Earliest_known_life_forms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:42.867278+00:00"
+instance: "kb-cron"
+---
+
+While current geochemical evidence dates the origin of life to possibly as early as 4.1 Ga, and fossil evidence shows life at 3.5 Ga, some researchers speculate that life may have started nearly 4.5 billion years ago. According to biologist Stephen Blair Hedges, "If life arose relatively quickly on Earth ... then it could be common in the universe." The possibility that terrestrial life forms may have been seeded from outer space has been considered. In January 2018, a study found that 4.5 billion-year-old meteorites found on Earth contained liquid water along with prebiotic complex organic substances that may be ingredients for life.
+
+=== Hydrothermal vents ===
+Hydrothermal vents have long been hypothesized to be the grounds from which life originated. The properties of ancient hydrothermal vents, such as the geochemistry, pressure, and temperatures, have the potential to create organic molecules from inorganic molecules. In experiments performed by NASA, it was shown that the organic compounds formate and methane could be created from inorganics in the conditions of ancient hydrothermal vents. The production of organic molecules could have led to the formation of more complex organic molecules, such as amino acids that can eventually form RNA or DNA.
+
+=== Darwin's hypothesis ===
+Charles Darwin is well-known for his theory of evolution via natural selection. His theory for the origin of life was a "warm little pond" that harbored necessary elements for the creation of life such as "ammonia and phosphoric salts, lights, heat, electricity ... so that a protein compound was chemically formed ready to undergo still more complex changes." However, he mentioned that such an environment today would likely have been destroyed faster than it would take to form life. With this, Darwin's ideas are generally regarded as the spontaneous generation hypothesis.
+
+=== Oparin–Haldane hypothesis ===
+In 1924, Alexander Oparin suggested that the early atmosphere on Earth was full of reducing components such as ammonia, methane, water vapor, and hydrogen gas. This was proposed after atmospheric methane was discovered on other planets. Later, in 1929, J. B. S. Haldane published an article that proposed the same conditions for early life on Earth as Oparin suggested. Their hypothesis was later supported by the Miller–Urey experiment.
+
+=== Miller–Urey experiment ===
+
+At the University of Chicago in 1953, a graduate student named Stanley Miller carried out an experiment under his professor, Harold Urey. The method would allow for reducing gases to simulate the atmosphere early on Earth and a spark to simulate lightning. There was a reflux apparatus that would heat water and mix into the atmosphere where it would then cool and run into the "primordial ocean". The gases that were used to mimic the reducing atmosphere were methane, ammonia, water vapor, and hydrogen gas. Within a day of allowing the apparatus to run, the experiment yielded a "brown sludge" which was later tested and found to include the following amino acids: glycine, alanine, aspartic acid, and aminobutyric acid. In the following years, many scientists attempted to replicate the results of the experiment, which is now known as a fundamental approach to the study of abiogenesis. The Miller–Urey experiment was able to simulate the early conditions of Earth's atmosphere and produced essential amino acids that likely contributed to the production of life.
+
+=== Clay hypothesis ===
+Cairns-Smith first introduced this hypothesis in 1966, where they proposed that any crystallization process is likely to involve a basic biological evolution. Hartman then added on to this hypothesis by proposing in 1975 that metabolism could have developed from a simple environment such as clays. Clays have the ability to synthesize monomers such as amino acids, nucleotides, and other building blocks and polymerize them to create macromolecules. This makes it possible for nucleic acids like RNA or DNA to be created from clay, and cells could further evolve from there.
+
+== Gallery ==
+
+== See also ==
+
+== References ==
+
+== External links ==
+Vitae (BioLib)
+Biota (Taxonomicon)
+Life (Systema Naturae 2000)
+Wikispecies — a free directory of life
+Life in the Universe — Stephen Hawking (1996)
+Video (24:32): "Migration of Life in the Universe" on YouTube — Gary Ruvkun, 2019.
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+---
+title: "Eukaryote"
+chunk: 1/3
+source: "https://en.wikipedia.org/wiki/Eukaryote"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:19.756158+00:00"
+instance: "kb-cron"
+---
+
+The eukaryotes () are the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes.
+The eukaryotes emerged within the archaeal phylum Promethearchaeota. Ignoring mitochondrial DNA (which is bacterial rather than archaeal), this would imply only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea. Eukaryotes first emerged during the Paleoproterozoic, likely as flagellated cells. The leading evolutionary theory is they were created by symbiogenesis between an anaerobic Promethearchaeota archaeon and an aerobic proteobacterium, which formed the mitochondria. A second episode of symbiogenesis with a cyanobacterium created the plants, with chloroplasts.
+Eukaryotic cells contain membrane-bound organelles such as the nucleus, the endoplasmic reticulum, and the Golgi apparatus. Eukaryotes may be either unicellular or multicellular. In comparison, prokaryotes are typically unicellular. Unicellular eukaryotes are sometimes called protists. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion (fertilization).
+
+== Etymology ==
+The word eukaryote is derived from the Greek words "eu" (εὖ) meaning "true" or "good" and "karyon" (κάρυον) meaning "nut" or "kernel", referring to the nucleus of a cell.
+
+== Diversity ==
+
+Eukaryotes are organisms that range from microscopic single cells, such as picozoans under 3 micrometers across, to animals like the blue whale, weighing up to 190 tonnes and measuring up to 33.6 meters (110 ft) long, or plants like the coast redwood, up to 120 meters (390 ft) tall. Many eukaryotes are unicellular; the informal grouping called protists includes many of these, with some multicellular forms like the giant kelp up to 200 feet (61 m) long. The multicellular eukaryotes include the animals, plants, and fungi, but again, these groups too contain many unicellular species. Eukaryotic cells are typically much larger than those of prokaryotes—the bacteria and the archaea—having a volume of around 10,000 times greater. Eukaryotes represent a small minority of the number of organisms, but, as many of them are much larger, their collective global biomass (468 gigatons) is far larger than that of prokaryotes (77 gigatons), with plants alone accounting for over 81% of the total biomass of Earth.
+The eukaryotes are a diverse lineage, consisting mainly of microscopic organisms. Multicellularity in some form has evolved independently at least 25 times within the eukaryotes. Complex multicellular organisms, not counting the aggregation of amoebae to form slime molds, have evolved within only six eukaryotic lineages: animals, symbiomycotan fungi, brown algae, red algae, green algae, and land plants. Eukaryotes are grouped by genomic similarities, so that groups often lack visible shared characteristics.
+
+== Distinguishing features ==
+
+=== Nucleus ===
+The defining feature of eukaryotes is that their cells have a well-defined, membrane-bound nucleus, distinguishing them from prokaryotes that lack such a structure. Eukaryotic cells have a variety of internal membrane-bound structures, called organelles, and a cytoskeleton which defines the cell's organization and shape. The nucleus stores the cell's DNA, which is divided into linear bundles called chromosomes; these are separated into two matching sets by a microtubular spindle during nuclear division, in the distinctively eukaryotic process of mitosis.
+
+=== Biochemistry ===
+Eukaryotes differ from prokaryotes in multiple ways, with unique biochemical pathways such as sterane synthesis. The eukaryotic signature proteins have no homology to proteins in other domains of life, but appear to be universal among eukaryotes. They include the proteins of the cytoskeleton, the complex transcription machinery, the membrane-sorting systems, the nuclear pore, and some enzymes in the biochemical pathways.
+
+=== Internal membranes ===
+
+Eukaryote cells include a variety of membrane-bound structures, together forming the endomembrane system. Simple compartments, called vesicles and vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. Some cell products can leave in a vesicle through exocytosis.
+The nucleus is surrounded by a double membrane known as the nuclear envelope, with nuclear pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form the endoplasmic reticulum, which is involved in protein transport and maturation. It includes the rough endoplasmic reticulum, covered in ribosomes which synthesize proteins; these enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth endoplasmic reticulum. In most eukaryotes, these protein-carrying vesicles are released and their contents further modified in stacks of flattened vesicles (cisternae), the Golgi apparatus.
+Vesicles may be specialized; for instance, lysosomes contain digestive enzymes that break down biomolecules in the cytoplasm.
+
+=== Mitochondria ===
+
+Mitochondria are organelles in eukaryotic cells. The mitochondrion is commonly called "the powerhouse of the cell", for its function providing energy by oxidizing sugars or fats to produce the energy-storing molecule ATP. Mitochondria have two surrounding membranes, each a phospholipid bilayer, the inner of which is folded into invaginations called cristae where aerobic respiration takes place.
+Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, from which it originated, and which encodes rRNA and tRNA genes that produce RNA which is closer in structure to bacterial RNA than to eukaryote RNA.
+Some eukaryotes, such as the metamonads Giardia and Trichomonas, and the amoebozoan Pelomyxa, appear to lack mitochondria, but all contain mitochondrion-derived organelles, like hydrogenosomes or mitosomes, having lost their mitochondria secondarily. They obtain energy by enzymatic action in the cytoplasm. It is thought that mitochondria developed from prokaryotic cells which became endosymbionts living inside eukaryotes.
+
+=== Plastids ===
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+---
+title: "Eukaryote"
+chunk: 2/3
+source: "https://en.wikipedia.org/wiki/Eukaryote"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:19.756158+00:00"
+instance: "kb-cron"
+---
+
+Plants and various groups of algae have plastids as well as mitochondria. Plastids, like mitochondria, have their own DNA and are developed from endosymbionts, in this case cyanobacteria. They usually take the form of chloroplasts which, like cyanobacteria, contain chlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids probably had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from other eukaryotes through secondary endosymbiosis or ingestion. The capture and sequestering of photosynthetic cells and chloroplasts, kleptoplasty, occurs in many types of modern eukaryotic organisms.
+
+=== Cytoskeletal structures ===
+
+The cytoskeleton provides stiffening structure and points of 
+attachment for motor structures that enable the cell to move, change shape, or transport materials. The motor structures are microfilaments of actin and actin-binding proteins. These include α-actinin, fimbrin, and filamin in submembranous cortical layers and bundles. Motor proteins of microtubules, dynein and kinesin, and myosin of actin filaments, make the network dynamic.
+Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or multiple shorter structures called cilia. These organelles are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin, and are entirely distinct from prokaryotic flagella. They are supported by a bundle of microtubules arising from a centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella may have hairs (mastigonemes), as in many stramenopiles. Their interior is continuous with the cell's cytoplasm.
+Centrioles are often present, even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups that give rise to various microtubular roots. These form a primary component of the cytoskeleton, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles produce the spindle during nuclear division.
+
+=== Cell wall ===
+
+The cells of plants, algae, fungi and most chromalveolates, but not animals, are surrounded by a cell wall. This is a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell.
+The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked together with hemicellulose, embedded in a pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.
+
+=== Sexual reproduction ===
+
+Eukaryotes have a life cycle that involves sexual reproduction, alternating between a haploid phase, where only one copy of each chromosome is present in each cell, and a diploid phase, with two copies of each chromosome in each cell. The diploid phase is formed by fusion of two haploid gametes, such as eggs and spermatozoa, to form a zygote; this may grow into a body, with its cells dividing by mitosis, and at some stage produce haploid gametes through meiosis, a division that reduces the number of chromosomes and creates genetic variability. There is considerable variation in this pattern. Plants have both haploid and diploid multicellular phases. Eukaryotes have lower metabolic rates and longer generation times than prokaryotes, because they are larger and therefore have a smaller surface area to volume ratio.
+The evolution of sexual reproduction may be a primordial characteristic of eukaryotes. Based on a phylogenetic analysis, Dacks and Roger have proposed that facultative sex was present in the group's common ancestor. A core set of genes that function in meiosis is present in both Trichomonas vaginalis and Giardia intestinalis, two organisms previously thought to be asexual. Since these two species are descendants of lineages that diverged early from the eukaryotic evolutionary tree, core meiotic genes, and hence sex, were likely present in the common ancestor of eukaryotes. Species once thought to be asexual, such as Leishmania parasites, have a sexual cycle. Amoebae, previously regarded as asexual, may be anciently sexual; while present-day asexual groups could have arisen recently.
+
+== Evolution ==
+
+=== History of classification ===
+
+In antiquity, the two lineages of animals and plants were recognized by Aristotle and Theophrastus. The lineages were given the taxonomic rank of kingdom by Linnaeus in the 18th century. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom. The various single-cell eukaryotes were originally placed with plants or animals when they became known. In 1818, the German biologist Georg A. Goldfuss coined the word Protozoa to refer to organisms such as ciliates, and this group was expanded until Ernst Haeckel made it a kingdom encompassing all single-celled eukaryotes, the Protista, in 1866. The eukaryotes thus came to be seen as four kingdoms:
+
+Kingdom Protista
+Kingdom Plantae
+Kingdom Fungi
+Kingdom Animalia
+The protists were at that time thought to be "primitive forms", and thus an evolutionary grade, united by their primitive unicellular nature. Understanding of the oldest branchings in the tree of life only developed substantially with DNA sequencing, leading to a system of domains rather than kingdoms as top level rank being put forward by Carl Woese, Otto Kandler, and Mark Wheelis in 1990, uniting all the eukaryote kingdoms in the domain "Eucarya", stating, however, that "'eukaryotes' will continue to be an acceptable common synonym". In 1996, the evolutionary biologist Lynn Margulis proposed to replace kingdoms and domains with "inclusive" names to create a "symbiosis-based phylogeny", giving the description "Eukarya (symbiosis-derived nucleated organisms)".
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+---
+title: "Eukaryote"
+chunk: 3/3
+source: "https://en.wikipedia.org/wiki/Eukaryote"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:19.756158+00:00"
+instance: "kb-cron"
+---
+
+=== Phylogeny ===
+By the early 21st century, a rough consensus started to emerge from phylogenomic studies. The majority of eukaryotes can be placed in one of two large clades dubbed Amorphea (similar in composition to the unikont hypothesis) and the Diphoda (formerly bikonts), which includes plants and most algal lineages. A third major grouping, the Excavata, has been abandoned as a formal group as it was found to be paraphyletic. The proposed phylogeny below includes two groups of excavates (Discoba and Metamonada), and incorporates the 2021 proposal that picozoans are close relatives of rhodophytes. The Provora are a group of microbial predators discovered in 2022. TSAR is a possible clade that would contain Telonemia and the SAR supergroup.
+
+One view of the great kingdoms and their stem groups. The Metamonada are hard to place, being sister possibly to Discoba or to Malawimonadida or being a paraphyletic group external to all other eukaryotes. Eukaryotes are thought to have emerged within the archaeal phylum Promethearchaeota.
+
+=== Origin of eukaryotes ===
+
+The origin of the eukaryotic cell, or eukaryogenesis, is a milestone in the evolution of life, since eukaryotes include all complex cells and almost all multicellular organisms. The last eukaryotic common ancestor (LECA) is the hypothetical origin of all living eukaryotes, and was most likely a biological population, not a single individual. The LECA is believed to have been a protist with a nucleus, at least one centriole and flagellum, facultatively aerobic mitochondria, sex (meiosis and syngamy), a dormant cyst with a cell wall of chitin or cellulose, and peroxisomes.
+An endosymbiotic union between a motile anaerobic archaean and an aerobic alphaproteobacterium gave rise to the LECA and all eukaryotes with mitochondria. A second, much later endosymbiosis with a cyanobacterium gave rise to the ancestor of plants, with chloroplasts.
+The presence of eukaryotic biomarkers in archaea points towards an archaeal origin, except for mitochondrial DNA, which is bacterial in origin. The genomes of Promethearchaeota archaea have plenty of eukaryotic signature protein genes, which play a crucial role in the development of the cytoskeleton and complex cellular structures characteristic of eukaryotes. In 2022, cryo-electron tomography demonstrated that Promethearchaeota archaea have a complex actin-based cytoskeleton, providing the first direct visual evidence of the archaeal ancestry of eukaryotes.
+
+=== Fossils ===
+The timing of the origin of eukaryotes is hard to determine. Multiple different fossils that may be early eukaryotes have been suggested, but remain contested. Fossils that are clearly related to modern groups start appearing an estimated 1.2 billion years ago, in the form of red algae, though fossilized Vindhyan filamentous algae have been suggested to be as much as 1.6 to 1.7 billion years old, rather than Cambrian as previously thought.
+Fossils from the Ruyang Group of China, dating to approximately 1.8-1.6 billion years ago, may be the oldest known eukaryotes. One possible earliest multicellular eukaryote fossil is Qingshania magnifica from North China, which lived 1.635 billion years ago. This would suggest that the crown group eukaryotes originated in the late Paleoproterozoic (Statherian). Other early unicellular eukaryotes, Tappania plana, Shuiyousphaeridium macroreticulatum, Dictyosphaera macroreticulata, Germinosphaera alveolata, and Valeria lophostriata from North China, lived approximately 1.65 billion years ago.
+
+Some acritarchs are known from at least 1.65 billion years ago, and a fossil, Grypania, which may be an alga, is as much as 2.1 billion years old. The "problematic" fossil Diskagma has been found in paleosols 2.2 billion years old. The Neoarchean fossil Thuchomyces shares some similarities with fungi. It especially resembles the problematic fossil Diskagma, with hyphae and multiple differentiated layers. However, it is over 600 million years older than all other possible eukaryotes, and many of its "eukaryote features" are not specific to the clade, meaning it is almost certainly a microbial mat instead.
+Structures proposed to represent "large colonial organisms" have been found in the black shales of the Palaeoproterozoic such as the Francevillian B Formation, in Gabon, dubbed the "Francevillian biota" which is dated at 2.1 billion years old. However, the status of these structures as fossils is contested, with other authors suggesting that they might represent pseudofossils.
+The presence of steranes, eukaryotic-specific biomarkers, in Australian shales previously indicated that eukaryotes were present in these rocks dated at 2.7 billion years old, but these Archaean biomarkers have been rebutted as later contaminants. The oldest valid biomarker records are only around 800 million years old. In contrast, a molecular clock analysis suggests the emergence of sterol biosynthesis as early as 2.3 billion years ago. The nature of steranes as eukaryotic biomarkers is further complicated by the production of sterols by some bacteria.
+Whenever their origins, eukaryotes may not have become ecologically dominant until much later; a massive increase in the zinc composition of marine sediments 800 million years ago has been attributed to the rise of substantial populations of eukaryotes, which preferentially consume and incorporate zinc relative to prokaryotes, approximately a billion years after their origin (at the latest).
+
+== See also ==
+Eukaryote hybrid genome
+List of sequenced eukaryotic genomes
+Parakaryon myojinensis
+
+== References ==
+
+== External links ==
+
+"Eukaryotes" Archived 29 January 2012 at the Wayback Machine (Tree of Life Web Project)
+"Eukaryote". The Encyclopedia of Life.
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+---
+title: "Facilitation cascade"
+chunk: 1/4
+source: "https://en.wikipedia.org/wiki/Facilitation_cascade"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:21.359452+00:00"
+instance: "kb-cron"
+---
+
+A facilitation cascade is a sequence of ecological interactions that occur when a species benefits a second species that in turn has a positive effect on a third species. These facilitative interactions can take the form of amelioration of environmental stress and/or provision of refuge from predation. Autogenic ecosystem engineering species, structural species, habitat-forming species, and foundation species are associated with the most commonly recognized examples of facilitation cascades, sometimes referred to as a habitat cascades. Facilitation generally is a much broader concept that includes all forms of positive interactions including pollination, seed dispersal, and co-evolved commensalism and mutualistic relationships, such as between cnidarian hosts and Symbiodinium in corals, and between algae and fungi in lichens. As such, facilitation cascades are widespread through all of the earth's major biomes with consistently positive effects on the abundance and biodiversity of associated organisms.
+
+== Overview ==
+Facilitation cascades occur when prevalent foundation species, or less abundant but ecologically important keystone species, are involved in a hierarchy of positive interactions and consist of a primary facilitator which positively affects one or more secondary facilitators which support a suite of beneficiary species. Facilitation cascades at a minimum have a primary and secondary facilitator, although tertiary, quaternary, etc. facilitators may be found in some systems.
+A typical example of facilitation cascades in a tropical coastal ecosystem
+
+=== Origin of concept and related terms ===
+The term facilitation cascade was coined by Altieri, Silliman, and Bertness during a study on New England cobblestone beaches to explain the chain of positive interactions that allow a diverse community to exist in a habitat that is otherwise characterized by substrate instability, elevated temperatures, and desiccation stress. Cordgrass is able to establish independently, and then creates a stable and less stressful habitat for mussels which in turn provide hard substrates and damp crevice spaces to facilitates establishment of a community of invertebrates and algal species. Facilitation cascades differ from the facilitation model of succession because species accumulate in the ecosystem due to the direct and indirect effects of the primary and secondary facilitator, whereas in the succession, early species that play a facilitative role are, over time, replaced by later-stage species. The concept emphasizes the hierarchical organization of nature, in which a foundation species creates the basis for an entire community by building a unique habitat, as seen in coral reefs, kelp beds, or hemlock forests, and then secondary interactions (e.g., competition, predation, facilitation) among inhabitants refine community composition and ecological dynamics. The facilitation cascade concept was also foreshadowed by the observation that multiple ecosystem engineers can interact to have emergent synergistic effects.
+Facilitation cascades thus represent a form of indirect interaction occurring over three or more levels, whereby one species impacts another via an intermediate species. Such indirect interactions are an important driver of community structure and ecosystem function that can be as frequent and influential as direct interactions. Facilitation cascades have far-reaching ecological impacts on the diversity and function of the ecosystem as the positive effects of a subset of organisms cascade through the community, as in trophic cascades. The effect size of facilitation cascades can rival or exceed that of trophic cascades, and the main distinction between the indirect positive effects of both facilitation cascades and trophic cascades is that the former is based on positive facilitative interactions whereas the latter is based on negative trophic interactions.
+
+== Classic examples ==
+Facilitation cascades are observed in all of earth's major ecosystem types, and representative examples illustrate their widespread importance as well as the diversity of cascades that arise. The significance of facilitation cascades is often apparent through direct observation, however, experimental manipulations with mimics offer strong evidence for the magnitude of interaction importance. For examples, using artificial mimics as replacements for primary and secondary foundation species allows for isolation of specific mechanisms that are hypothesized to underlie the cascading effects of facilitation on local ecosystem dynamics.
+
+=== Marine ===
+A classic example of facilitation cascades in the marine environment is the relationship between mangroves, seagrasses, and stony corals that are adjacent to one another in a seascape. These foundation species exchange resources and benefit each other by buffering against sedimentation and nutrient inputs from the terrestrial side, and reducing wave energy from the open ocean. This exemplifies how facilitation cascades can occur over a seascape through foundation species that are found adjacent to one another.
+Another common example in marine ecosystems is where seagrass, a primary habitat-forming ecosystem engineer, facilitates bivalves such as mussels by providing them with refuge from predators and stable attachment substrate. In turn, the bivalves act as secondary habitat formers, facilitating epifaunal organisms by providing them with substrate to attach and settle. Since the bivalves can provide nutrient subsidies to the seagrass, this is an example of a common structure of facilitation cascades where the secondary facilitators have a positive effect on primary facilitators, such that there is mutualism within the cascade.
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+---
+title: "Facilitation cascade"
+chunk: 2/4
+source: "https://en.wikipedia.org/wiki/Facilitation_cascade"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:21.359452+00:00"
+instance: "kb-cron"
+---
+
+=== Transitional (intertidal) ===
+On the cobblestone beaches of New England, cordgrasse ameliorates physical stress for the establishment of ribbed mussels which further facilitating increased diversity within the intertidal ecosystem as secondary foundation species. This is the interaction from which the facilitation cascade concept was formed. This complex habitat has also shown how facilitation cascades can increases invasibility because non-native crabs live on and among ribbed mussels, providing a mechanisms to explain positive relationships between native diversity and invasion success, and the co-existence of native and invasive species through differential use of microhabitats associated with the cascade. In salt marshes, the same species of cordgrass and mussels have also been shown to increase biodiversity, multifunctionality, and resilience to disturbance.
+Oyster reefs stabilize the intertidal environment by reducing sediment erosion. This enhances growth of marsh grasses which act as secondary foundation species, facilitating invertebrates including bivalves, insects and birds. The places with oyster reefs and intertidal marshes have been observed to support a higher biodiversity and abundance of inhabitants compared to sites inhabited by only one of those foundation species.
+Mangrove forests along the coast of Australia trap drifting seaweed among their pneumatophores, which this seaweed supports many mollusks through habitat creation and shelter from predation. This example is notable because it involves a foundation species (mangroves) increasing their facilitative effect by aggregating a drifting secondary species from nearby rocky reefs.
+Another example in transitional environments includes the facilitation of seaweed assemblages in soft-bottom shallow lagoons by gardening tube forming polychaetes that actively incorporate seaweed fragments to reduce predation and increase food-supply. The seaweed subsequently provides habitats and supports the high diversity of small epiphytes, invertebrates, and fish in an otherwise bare soft sediment system. This example is notable because the secondary habitat-forming seaweed is invasive in this region.
+
+=== Terrestrial ===
+A classic example of a terrestrial facilitation cascade includes tropical rainforest trees as the facilitating epiphytes which in turn facilitate the abundance of inhabitant invertebrate species by providing a complex, diverse habitat. For example, about half of the invertebrate biomass and abundance of invertebrates was observed to be dependent on secondary epiphyte habitats, suggesting that early estimates of the notably high arthropod diversity in tropical forests may in part be driven by facilitation cascades. This example is notable due to the different taxonomic composition and larger size of insects found in the secondary, intermediate habitat when compared with that of the primary foundation tree species representing the basal habitat. In temperate forests, a similar cascade unfolds in which facilitation of Spanish moss by oak trees increases invertebrate diversity. In this example, the Spanish moss depend on the oak to reduce physical stress and the invertebrates are reliant on the Spanish moss to increase moisture and lower predation stress.
+Another terrestrial facilitation cascade includes trees, mistletoe, and birds, where trees are the primary foundation species that facilitates mistletoe, a secondary foundation species, which then facilitates the nesting and feeding of local and migratory birds. This example has been observed in multiple places around the world from pine forests in southeastern Spain to semi-arid southeastern Zimbabwean savannas. The example is notable because mistletoes can be parasitic and have a negative effect on their tree hosts, which is a reminder that the direction and strength of interactions associated with facilitation cascades can be context-dependent.
+
+=== Freshwater ===
+A classic freshwater facilitation cascade includes freshwater plants facilitating growth of algal filaments which in turn facilitate snails. Here, the plants act as primary foundation species, while the algal filaments, attached by plant holdfasts, are secondary foundation species, facilitating the snail inhabitant. This example is significant due to the chemical signals sent from secondary foundation species to attract the diversity of inhabitant snail to the cascade habitat.
+However, only a few studies appear to have documented freshwater facilitation cascades, and it remains to be determined whether this is a function of the ecosystem structure or simply a reflection of historic research perspectives.
+
+== Scale and ecological feedbacks ==
+
+=== Spatial configuration ===
+The primary and secondary foundation species that make up a facilitation cascade can occur in one of two spatial configurations. First are nested configurations in which the two foundation species are found intermixed or with one facilitator living on another, as in a mangrove pneumatophore providing a surface for oyster colonization. Second are adjacent configurations in which the facilitative species are found segregated across the landscape, as in oyster reefs near salt marshes, or coral reefs adjacent to seagrass. Whether foundation species in a cascade are found in adjacent or nested configurations depends on whether competition for resources at some scale drives one foundation species to displace another. The stress gradient hypothesis has proven useful for predicting which configuration is likely to prevail. In some instances there is scale dependence of the interactions, where competition over short distances leads to zonation of foundation species with distinct borders, and facilitation over longer distances occurs between the organisms in these zones. Facilitation cascades can also be structured as patches on the landscape that arise either because a primary and secondary habitat-forming species co-occur in patches, or a secondary habitat-former exists in patches within a large continuous habitat created by the primary habitat-former.
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+---
+title: "Facilitation cascade"
+chunk: 3/4
+source: "https://en.wikipedia.org/wiki/Facilitation_cascade"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:21.359452+00:00"
+instance: "kb-cron"
+---
+
+=== Temporal variation ===
+The strength of facilitation cascades can also vary across temporal scales. Spatial scale can be influenced by how rapidly a foundation species grows or reproduces, as well as how long the effect of facilitation takes to impact other species within the system. This can be due to the time necessary for a foundation species to reach a minimum individual or patch size to create a facilitative effect for the system, lags in the demographic response in the beneficiary species to the positive effects of a facilitator, or seasonality or some other temporal variability in the stress that the facilitator ameliorates. Phenological matching or mismatching of life cycles may also influence the co-occurrence of participants in a facilitation cascade and therefore the strength of their interaction. For example, hatching of insects that coincides with flowering of the plants they pollinate which are in turn used as habitat for other species later in that year.
+
+=== Dispersal and movement ===
+Movement of organisms can mediate the occurrence and importance of facilitation cascades in three ways. First, movement of a facilitative species to a location with another facilitative species can bring together the components for a facilitation cascade. For examples, algae from a rocky shore that drifts into mangrove root habitat together can facilitate a variety of mobile invertebrates. Second, species that benefit from a facilitation cascade may move beyond the cascade habitat (i.e., spillover) and play an ecologically important role in adjacent habitats. On cobble beaches, for example, an invasive shore crabs utilizes a cordgrass-mussel facilitation cascade as a nursery habitat, but then as adults move into adjacent unvegetated intertidal habitats where they compete with native mud crabs. For highly mobile beneficiary species, such as those with more distant ontogenetic habitat shifts, large foraging ranges, or the capability of long-distance migrations, the reach of the facilitation cascade may be quite extensive. Third, mobile organisms may serve as a facilitative link in a cascade that plays across habitats distantly located on a landscape, as in mangroves that may facilitate coral reefs through the movement of parrotfish that use the mangrove as a nursery habitat and then move to a coral reef where they graze nuisance algae that would otherwise smother corals. More generally, these movements of individuals can serve as a biogeochemical or trophic link between ecosystems, leading to nutrient subsidies and feedbacks that sustain the foundation species that form the basis of facilitation cascades and providing the basis for meta-ecosystems.
+
+== Ecological significance ==
+
+=== Biodiversity ===
+Facilitation cascades have strong positive effects on biodiversity at local or patch scale via direct and indirect facilitation. Within a facilitation cascade, primary and secondary foundation can increase organismal survival, species richness, niche diversity, and habitat complexity, in turn enhancing biodiversity. Primary habitat-formers can provide suitable substrate for colonization by secondary habitat-formers unique traits that contribute to increased heterogeneity enhancement of biodiversity.
+
+=== Ecosystem functioning ===
+Given the close relationship between biodiversity and ecosystem function, facilitation cascades will have strong indirect effect on ecosystem function due their enhancement of biodiversity. Facilitation cascades can also have a strong direct effect on a number of ecological functions that arise through creation of physical structure. The most immediately obvious benefit is the provision of additional habitat that provides living spaces for more and different organisms. The structure, which is typically more complex than areas outside a facilitation cascade habitat can function as a refuge from predation refuge or physical stresses. Other important functions include soil accretion, altered infiltration rates, and translocation of resources. Through these functions, other emergent ecological properties arise such as increased non-trophic species interaction across multiple trophic levels.
+
+== Challenges ==
+
+=== Threats ===
+Facilitation cascades can promote ecosystem stability and resilience through positive species interactions. With increasing stress associated with climate change and other anthropogenic impacts, positive interactions will become increasingly important in maintaining ecosystem stability. However, stresses imposed by a threat may, beyond a certain threshold, have detrimental impacts on foundation species, and thereby lead to breakdown of the facilitation cascade.
+
+==== Natural disasters ====
+Natural disasters, such as earthquakes, natural fires, avalanches and volcanic activities can break down facilitation cascades by killing the foundation species. For example, a seismic uplift in New Zealand associated with the Kaikōura 2016 earthquake caused immediate mortality of both primary and secondary foundation seaweeds followed by cascading destruction of invertebrate biodiversity. These foundation species had not recovered by 2021, and large-scale natural disasters could potentially have legacies on facilitation cascades over decades to centuries as a function of recovery rates of habitat forming organisms.
+
+==== Climate change ====
+Mutualistic relationships and positive interactions that form the basis of facilitation cascades can ameliorate the impact of increased physical stresses such as drought, temperature extremes, and inundation time associated with climate change. For example, the mutualistic interaction between mussels and cordgrass can increase drought resilience in marsh ecosystems. While these facilitative interactions within a cascade may provide relief from increasing abiotic stresses, they are also vulnerable to the impacts of climate change themselves. Due to interspecific differences in thermotolerance and shifting abundances and distributions of species involved in a cascade, alteration or breakdown of the facilitation cascade may occur due to loss of any component in the cascade. For example, in the marine environment, high temperatures result in coral bleaching and disease, disrupting the relationship between coral host and its symbiotic algae and having downstream impacts on the biodiversity of the system.
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+---
+title: "Facilitation cascade"
+chunk: 4/4
+source: "https://en.wikipedia.org/wiki/Facilitation_cascade"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:21.359452+00:00"
+instance: "kb-cron"
+---
+
+==== Pollution ====
+The introduction of harmful or toxic substances into the environment is a threat to facilitation cascades. Nutrient pollution may initially appear to benefit facilitation cascades by stimulating growth of habitat forming species, but ultimately negative effects associated with excess biomass, such as physically smothering and biogeochemical stressors including oxygen depletion and sulfide toxicity, can overwhelm the facilitation cascade. For example, excessive amounts of nutrients can stimulate prolific growth of secondary foundation species such as seaweed in otherwise oligotrophic seagrass systems, resulting in altered competitive hierarchies where the seaweed outcompetes the seagrass. In other instances, eutrophication can lead to an outright replacement of habitat dominants, such as when macroalgae replaces corals on reefs, leading to a change or loss in components of a facilitation cascade and there a shift in the broader community.
+
+==== Disease ====
+Disease prevalence and severity are predicted to increase in response to global changes, though its impacts on facilitation cascades remain relatively understudied. High endemic biodiversity, such as that favored by a facilitation cascade, generally decreases the risk of pathogen transmission. However, disease outbreaks that impact a facilitator can reduce its density or alter its phenotype, thereby reducing habitat complexity which dampens its facilitative effects with negative effects on biodiversity.
+
+==== Overexploitation ====
+Facilitation cascades promote biodiversity and species abundance through positive interactions, which could counteract the consequences of overexploitation. However, harvest of primary or secondary facilitators themselves within the cascade can lead to downstream reductions in species richness, thereby weakening the overexploited species' facilitative effects. For example, harvest of trees can reduce the abundance and diversity of epiphytes that provide shelter and other resources of beneficiary insect communities.
+
+==== Invasive species ====
+The successful establishment of a nonnative species into a new habitat may be expedited by the habitat provisioning and physical stress amelioration of the facilitation cascade that also promotes high native biodiversity. Furthermore, invasive species may be able to better exploit the benefits of facilitation cascades over native species, leading to spillover effects into nearby habitats and further contributing to their invasion success. Invasive species may also be habitat-forming foundation species capable of initiating their own facilitation cascades as in invasive seaweeds incorporated into worm tubes or invasive kelps that co-occur with native mussels.
+
+== Applications in conservation and restoration ==
+
+Positive interactions can play a critical role in the conservation and restoration of natural systems, and a decision framework to guide practitioners in the incorporation of positive interactions to meet project goals and ecosystem services has been developed. This model can be extended to facilitation cascades which can be harnessed to enhance conservation and restoration. For example, the facilitators within a cascade can be identified as focal or indicator species for monitoring and protection in conservation plans given that these species are likely to support elevated biodiversity and species abundance. Furthermore, the species in a facilitation cascade can be candidate species for restoration due to their ability to initiate community assembly and the complex network of species interactions that underlie important ecosystem properties such as resilience. Finally, engineering with facilitating species in a cascade often provides complementary functions that both enhance the performance of one another and lead to beneficial outcomes that might not be possible with any single species. This is apparent, for example, in shoreline stabilization and enhancement projects where oysters are paired with marsh grasses in which oysters reduce wave energy and erosional stress in adjacent cordgrass zone which in turn builds shoreline and accrete elevational gains.
+There are several considerations for practitioners as they incorporate facilitation cascades in their conservation and restoration projects. First, facilitation cascades may occur across multiple habitats through long distance interactions, and so the effectiveness of monitoring and outplanting projects may need to incorporate landscape-scale perspectives or risk failure if essential components of the system are left outside the project scope. Second, while many of the best examples of facilitation cascades in applied contexts come from foundation species or ecosystem engineers that are conspicuous habitat dominants, practitioners should keep in mind that facilitators in a cascade can also include smaller and/or mobile organisms, such as Pollinators that have a positive effect on the reproductive success of habitat-forming vegetation, or mutualists such as Symbiodinium in corals and mycorrhizal fungi in terrestrial plants. Third, facilitation cascades commonly incorporate multiple Trophic levels and/or disparate taxonomic and functional groups, and so restoration projects (or investigations for that matter) need to take a community-wide approach to their design. A 'plant restoration project' is unlikely to meet its management goals without considering the plant interactions with pollinators, invertebrates, epiphytes, etc. Fourth, species mimics may be necessary to jump start a facilitation cascade or replace a living component that may not be practically introduced. Such engineering approaches have already been demonstrated in projects such as seawalls. Finally, the overall importance of facilitation cascades is likely to increase with climate change as associated stressors such as elevated temperature and modified precipitation regimes intensify. Facilitation cascades may suddenly be apparent or important where they were previously undetected, and practitioners may become increasingly dependent on such ecological tools as adaptable and resilient components in their projects.
+
+== References ==
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+---
+title: "Facultative"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Facultative"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:22.612139+00:00"
+instance: "kb-cron"
+---
+
+Facultative means "optional" or "discretionary" (antonym obligate), and is used mainly in biology.  It is seen in topics including:
+
+Facultative anaerobe, an organism that can use oxygen but also has anaerobic methods of energy production.
+Facultative biotroph, an organism, often a fungus, that can live as a saprotroph but also form mutualisms with other organisms at different times of its life cycle.
+Facultative biped, an animal that is capable of walking or running on two legs as well as walking or running on four limbs or more, as appropriate
+Facultative carnivore, a carnivore that does not depend solely on animal flesh for food but also can subsist on non-animal food. Compare this with the term omnivore
+Facultative heterochromatin, tightly packed but non-repetitive DNA in the form of Heterochromatin, but which can lose its condensed structure and become transcriptionally active
+Facultative lagoon, a type of stabilization pond used in biological treatment of industrial and domestic wastewater
+Facultative necrophage, an animal that feeds on carrion but retains the traits needed to find and consume other food sources
+Facultative parasite, a parasite that can complete its life cycle without depending on a host
+Facultative photoperiodic plant, a plant that will eventually flower regardless of night length but is more likely to flower under appropriate light conditions.
+Facultative saprophyte, lives on dying, rather than dead, plant material
+Wetland indicator status for plants can include facultative (FAC), facultative wetland (FACW), and facultative upland (FACU) to distinguish types that appear in multiple regions
+
+
+== See also ==
+(antonym) Obligate
+Opportunism (Biology)
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+---
+title: "Flux (biology)"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Flux_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:23.812857+00:00"
+instance: "kb-cron"
+---
+
+In general, flux in biology relates to movement of a substance between compartments. There are several cases where the concept of flux is important.
+
+The movement of molecules across a membrane: in this case, flux is defined by the rate of diffusion or transport of a substance across a permeable membrane.  Except in the case of active transport, net flux is directly proportional to the concentration difference across the membrane, the surface area of the membrane, and the membrane permeability constant.
+In ecology, flux is often considered at the ecosystem level – for instance, accurate determination of carbon fluxes using techniques like eddy covariance (at a regional and global level) is essential for modeling the causes and consequences of global warming.
+Metabolic flux refers to the rate of flow of metabolites through a biochemical network, along a linear metabolic pathway, or through a single enzyme. A calculation may also be made of carbon flux or flux of other elemental components of biomolecules (e.g. nitrogen). The general unit of flux is chemical mass /time (e.g., micromole/minute; mg/kg/minute). Flux rates are dependent on a number of factors, including: enzyme concentration; the concentration of precursor, product, and intermediate metabolites; post-translational modification of enzymes; and the presence of metabolic activators or repressors. Metabolic flux in biologic systems can refer to biosynthesis rates of polymers or other macromolecules, such as proteins, lipids, polynucleotides, or complex carbohydrates, as well as the flow of intermediary metabolites through pathways. Metabolic control analysis and flux balance analysis provide frameworks for understanding metabolic fluxes and their constraints.
+
+
+== Measuring movement ==
+Flux is the net movement of particles across a specified area in a specified period of time. The particles may be ions or molecules, or they may be larger, like insects, muskrats or cars. The units of time can be anything from milliseconds to millennia. Flux is not the same as velocity or speed nor is it the same as density or concentration. Movement itself is not enough.
+
+
+== References ==
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+---
+title: "Glossary of invasion biology terms"
+chunk: 1/4
+source: "https://en.wikipedia.org/wiki/Glossary_of_invasion_biology_terms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:25.112976+00:00"
+instance: "kb-cron"
+---
+
+The need for a clearly defined and consistent invasion biology terminology has been acknowledged by many sources. Invasive species, or invasive exotics, is a nomenclature term and categorization phrase used for flora and fauna, and for specific restoration-preservation processes in native habitats. Invasion biology is the study of these organisms and the processes of species invasion. 
+The terminology in this article contains definitions for invasion biology terms in common usage today, taken from accessible publications.  References for each definition are included.  Terminology relates primarily to invasion biology terms with some ecology terms included to clarify language and phrases on linked articles.
+
+== Introduction ==
+Definitions of "invasive non-indigenous species have been inconsistent", which has led to confusion both in literature and in popular publications (Williams and Meffe 2005).  Also, many scientists and managers feel that there is no firm definition of non-indigenous species, native species, exotic species, "and so on, and ecologists do not use the terms consistently." (Shrader-Frechette 2001)  Another question asked is whether current language is likely to promote "effective and appropriate action" towards invasive species through cohesive language (Larson 2005).  Biologists today spend more time and effort on invasive species work because of the rapid spread, economic cost, and effects on ecological systems, so the importance of effective communication about invasive species is clear. (Larson 2005)
+Controversy in invasion biology terms exists because of past usage and because of preferences for certain terms.  Even for biologists, defining a species as native may be far from being a straightforward matter of biological classification based on the location or the discipline a biologist is working in (Helmreich 2005).  Questions often arise as to what exactly makes a species native as opposed to non-native, because some non-native species have no known negative effects (Woods and Moriarty 2001).  Natural biological invasions, generally considered range expansions, and introductions involving human activities are important and could be considered a normal ecological process (Vermeij 2005).  Non-native and native species may be sometimes considered invasive, and these invasions often follow human-induced landscape changes, with subsequent damage to existing landscapes a value judgment (Foster and Sandberg 2004).  As a result, many important terms relevant to invasion biology, such as invasive, weed, or transient, include qualities that are "open to subjective interpretation" (Colautti and MacIsaac 2004).  Sometimes one species can have both beneficial and detrimental effects, such as the Mosquito fish (Gambusia affinis), which has been widely introduced because of its suppression of larval mosquitoes, although it also has negative impacts on native species of insects, fish and amphibians (Colautti and MacIsaac 2004).
+The large number and current complexity of terms makes interpretation of some of the invasion biology literature challenging and intimidating.  Exotic, alien, transplanted, introduced, non-indigenous, and invasive are all words that have been used to describe plants and animals that have been moved beyond their native ranges by humans (Williams and Meffe 2005), along with other terms such as foreign, injurious, aquatic nuisance, pest, non-native, all with a particular implication.  Even the use of what seem to be simple, basic terms to articulate ecological concepts "can confuse ideological debates and undermine management efforts" (Colautti and MacIsaac 2004).  Attempts to redefine commonly used terms in invasion biology have been difficult because many authors and biologists are particular to a favorite definition (Colautti and MacIsaac 2004).  Also, the status and identification of any species as an invader, a weed, or an exotic are "conditioned by cultural and political circumstances." (Robbins 2004)
+
+== Terminology ==
+Where words in a sentence are also defined elsewhere in this article, they appear in italics.
+
+Adventive species (see casual)A species (usually a plant), that is introduced in a new environment and successfully reproduces without human intervention, but does not necessarily formed sustained populations.
+Alien species (See Introduced species)
+Less commonly used in scientific literature but often included in population publications, public information displays, and educational literature. This term refers to species that spread beyond their native range, not necessarily harmful, or species introduced to a new range that establish themselves and spread; similar terms include exotic species, foreign species, introduced species, non indigenous species, and non native species (Jeschke and Strayer 2005).
+Aquatic nuisance species
+Less commonly used in most literature.
+A nonindigenous species that threatens the diversity or abundance of native species or the ecological stability of infested waters, or commercial, agricultural, aquacultural or recreational activities dependent on such waters (EPA 1990).
+Aquatic species that causes economic or environmental harm to humans (Heutte and Bella 2003).
+An aquatic species with adverse effects on humans, either directly (e.g. species that produce toxins that are harmful to humans) or indirectly (e.g. species that infest nature reserves) (Colautti and MacIsaac 2004).
+Biological control or biocontrol (See Biological pest control)
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+---
+title: "Glossary of invasion biology terms"
+chunk: 2/4
+source: "https://en.wikipedia.org/wiki/Glossary_of_invasion_biology_terms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:25.112976+00:00"
+instance: "kb-cron"
+---
+
+In general, the control of the numbers of one organism as a result of natural predation by another or others. Specifically, the human use of natural predators for the control of pests or weeds. Also applied to the introduction of large numbers of sterilized males of the pest species, whose matings result in the laying of infertile eggs (Allaby 1998).
+The release of one species to control another (Carlton 2001).
+The management of weeds using introduced herbivores (often insects) as biological control agents (Booth et al. 2003).
+Biological invasion or bioinvasion
+A broad term for both human-assisted introductions and natural range expansions (Carlton 2001).
+Biological diversity (See biodiversity)
+Used to describe species richness, ecosystem complexity, and genetic variation (Allaby 1998).
+Biological control (See Biological pest control)
+Control method involving a biological control agent that is a natural enemy of a target pest (Heutte and Bella 2003).
+Bioregion (See Ecoregion)
+A biological subdivision of the earth's surface delineated by the flora and fauna of the region (Allaby 1998).
+Biota
+The organisms (plants, animals, fungi, bacteria, algae, etc.) of a specific region or period, or the total aggregation of organisms in the biosphere (Allaby 1998).
+Casual species (see adventive)
+This term is becoming less common in usage. A non native species that does not form self-replacing populations (Booth et al. 2003). Similar terms include introduced species, non indigenous species, and non native species.
+Chemical control
+Control method that employs herbicides to control exotic plants (Heutte and Bella 2003).
+Community
+Any grouping of populations of different organisms that live together in a particular environment (Allaby 1998).
+Cryptogenic species
+Species that are neither clearly native nor exotic (Cohen and Carlton 1988).
+Cultivar
+A variety of a plant produced and maintained by horticultural techniques and not normally found in wild populations (Allaby 1998).
+Disturbance
+An event or change in the environment that alters the composition and successional status of a biological community and may deflect succession onto a new trajectory, such as a forest fire or hurricane, glaciation, agriculture, and urbanization (Art 1993).
+Ecosystem
+A discrete unit, or community of organisms and their physical environment (living and non-living parts), that interact to form a stable system (Allaby 1998).
+Endemic
+A species or taxonomic group that is restricted to a particular geographic region because of such factors as isolation or response to soil or climatic conditions; this species is said to be endemic to the region (Allaby 1998).
+Exotic species (See Introduced species)
+This term is commonly used in publications and literature, and is similar to the terms alien species, foreign species, introduced species, non indigenous species, and non native species (Heutte and Bella 2003). Other definitions include:
+An introduced, non native species, or a species that is the result of direct or indirect, deliberate or accidental introduction of the species by humans, and for which introduction permitted the species to cross a natural barrier to dispersal (Noss and Cooperrider 1994).
+In North America, often refers to those species not present in a bioregion before the entry of Europeans in the 16th century, or present in later parts of that region and later introduced to an ecosystem by human-mediated mechanisms (Cohen and Carlton 1988).
+Fauna
+The animal life of a region or geological period (Allaby 1998).
+Foreign species (See Introduced species)
+A species introduced to a new area or country. Similar terms include alien species, exotic species, introduced species, non indigenous species, and non native species.
+Flora
+Plant or bacterial life forms of a region or geological period (Allaby 1998).
+Habitat
+The place, including physical and biotic conditions, where a plant or an animal usually occurs (Allaby 1998).
+Herbicide
+Pesticide that specifically targets vegetation (Heutte and Bella 2003).
+Hybridization
+Production of novel genotypes, through mating between distinct species or ecotypes. Novel genotypes may be more invasive than parental genotypes.
+Indigenous (See Indigenous species)
+A species that occurs naturally in an area; a synonym for native species (Allaby 1998).
+Injurious species
+An introduced species that causes economic or environmental harm to humans. Similar terms include aquatic nuisance species, noxious weed, and invasive species (Heutte and Bella 2003).
+Intentional introduction
+A species that is brought to a new area, country, or bioregion for a specific purpose, such as for a garden or lawn; a crop species; a landscaping species; a species that provides food; a groundcover species; for soil stabilization or hydrological control; for aesthetics or familiarity of the species; or other purposeful reasons (Booth et al. 2003).
+Introduced species
+This term, along with the terms introduced species and nonindigenous species, is one of the most commonly used terms to describe a plant or animal species that is not originally from the area in which it occurs. This terms means those species that have been transported by human activities, either intentionally or unintentionally, into a region in which they did not occur in historical time and are now reproducing in the wild (Carlton 2001). Similar terms include alien species, exotic species, foreign species, non indigenous species, and non native species.
+Invasibility
+The ease with which a habitat is invaded (Booth et al. 2003).
+Invasion (See Introduced species and Invasive species)
+The expansion of a species into an area not previously occupied by it (Booth et al. 2003).
+Invasive species
+Generally, this term refers to a subset of plants or animals that are introduced to an area, survive, and reproduce, and expand beyond the original area of introduction. This is the biological definition. Practical definitions add that they cause harm economically or environmentally within the new area of introduction.
+An alien species whose introduction does or is likely to cause economic or environmental harm or harm to human health (Executive Order 1999).
+An adjective for non native or nonindigenous species that have colonized natural areas;
+Discrimination of nonindigenous species established in cultivated habitats (as 'noninvasive') from those established in natural habitats;
+Nonindigenous species that are widespread; or 5. Widespread nonindigenous species that have adverse effects on the invaded habitat (Colautti and MacIsaac 2004).
+Other definitions include the following: 
+Integrated pest management
+IPM focuses on long-term prevention or suppression of pests. The integrated approach to weed management incorporates the best suited cultural, biological and chemical controls that have minimum impact on the environment and on people (Heutte and Bella 2003).
+Manual control
+Removal that involves the use of tools such as shovels, axes, rakes, grubbing hoes, and hand clippers to expose, cut, and remove flowers, fruits, stems, leaves, and/or roots from target plants (Heutte and Bella 2003).
+Mechanical control
+Removal that involves the use of motorized equipment such as mowers, "weed-whackers", and tractor-mounted plows, disks, and sweepers. Burning is also categorized here (Heutte and Bella 2003).
+Native range
+The ecosystem that a species inhabits (Booth et al. 2003).
+Native species (See Indigenous (ecology))
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+---
+title: "Glossary of invasion biology terms"
+chunk: 3/4
+source: "https://en.wikipedia.org/wiki/Glossary_of_invasion_biology_terms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:25.112976+00:00"
+instance: "kb-cron"
+---
+
+A synonym for indigenous species
+A species that occurs naturally in an area, and has not been introduced by humans either intentionally or unintentionally (Allaby 2005).
+In North America, a species established before the year 500 (Jeschke and Strayer 2005)
+Native weed (invasive native)
+A species that is native to an area or bioregion that has increased in number dramatically. In cases of disturbance or change to a landscape, a ruderal species can increase in cover and compete with other native plants, threatening the diversity of a community. In other cases, landscape level changes can cause the increase of the population of a species, such as white-tailed deer in the northeastern part of the United States, which are at the highest levels historically and cause damage to humans, crops, and structures, suffer high disease levels, and pose threats to humans through interactions on roads (Foster and Sandberg 2004).
+Naturalized species (See Introduced species)
+
+A species that was originally introduced from a different country, a different bioregion, or a different geographical area, but now behaves like a native species in that it maintains itself without further human intervention and now grows and reproduces in native communities (Allaby 1998).
+A non native species that forms self-sustaining populations but is not necessarily an invasive species (Booth et al. 2003).
+Neobiota
+An umbrella term for the entirety of all non-native species, independently of their taxonomic rank, naturalization status or time of introduction, without defining these by a negation (non-native) or by an evaluative approach (Kowarik 2002.
+Niche opportunity
+Defines conditions that promote invasions in terms of resources, natural enemies, the physical environment, interactions between these factors, and the manner in which they vary in time and space (Shea and Chesson 2002).
+Nonindigenous species
+This is a common term used along with non native species and introduced species in current literature and publications; other similar terms include alien species, exotic species, and foreign species.
+Any species or other viable biological material that enters an ecosystem beyond its historic range, including any such organism transferred from one country into another (EPA 1990).
+A plant or animal that is not native to the area in which it occurs which was either intentionally or unintentionally introduced (Williams and Meffe 2005).
+Non native species
+This term, along with the terms introduced species and nonindigenous species, is one of the most commonly used terms to describe a plant or animal species that is not originally from the area in which it occurs. Similar terms also include alien species, exotic species, and foreign species. This term has also been defined as:
+A species whose presence is due to intentional or unintentional introduction as a result of human activity (Booth et al. 2003).
+A species that has been introduced to an area or bioregion (Heutte and Bella 2003).
+Noxious weed
+This term is frequently a legal term in state code, denoting a special status of the plant as, for example, prohibited or restricted.
+Native or non-native plants, or plant products, that injure or cause damage to interests of agriculture, irrigation, navigation, natural resources, public health, or the environment (Heutte and Bella 2003).
+Implies a species' adverse effects on humans, either directly (e.g. species that produce toxins that are harmful to humans) or indirectly (e.g. species that infest nature reserves) (Colautti and MacIsaac 2004).
+Any species of plants, either annual, biennial, or perennial; reproduced by seed, root, underground stem, or bulblet; which when established is or may become destructive and difficult to control by ordinary means of cultivation or other farm practices (Heutte and Bella 2003).
+Pathway (See Path)
+
+Used to mean vector, purpose (the reason why a species is moved), and route (the geographic corridor from one point to another) (Carlton 2001). 2. Mode by which a species establishes and continues to exist in a new environment (Heutte and Bella 2003).
+Pest
+
+An animal that competes with humans by consuming or damaging food, fiber, or other materials intended for human consumption or use, such as an insect consuming a cropfield (Allaby 1998)
+Synonymous to invasive species (Jeschke and Strayer 2005).
+Pesticide
+A chemical or biological agent intended to prevent, destroy, repel, or mitigate plant or animal life and any substance intended for use as a plant regulator, defoliant, or desiccant, including insecticides, fungicides, rodenticides, herbicides, nematocides, and biocides (Heutte and Bella 2003).
+Population
+A group of potentially inter-breeding individuals of the same species found in the same place at the same time (Booth et al. 2003).
+Prohibited weed
+A specific legal term applied to a plant or plant part that may not be brought into a state (Heutte and Bella 2003).
+Restricted weed
+A specific legal term applied to a plant or plant part that may only be brought into a state in limited quantities (Heutte and Bella 2003).
+Ruderal species
+A plant associated with human dwellings, construction, or agriculture, that usually colonizes disturbed or waste ground. Ruderals are often weeds which have high demands for nutrients and are intolerant of competition. See also native weed or invasive native (Allaby 1998).
+Seed bank
+Seeds that become incorporated into the soil (Booth et al. 2003).
+Species
+A group of organisms formally recognized as distinct from other groups; the taxon rank in the hierarchy of biological classification below genus; the basic unit of biological classification, defined by the reproductive isolation of the group from all other groups of organisms (Allaby 1998).
+Tens rule
+
+Describes how approximately ten percent of species pass through each transition from being imported to becoming casual to becoming established, and finally becoming a weed (Booth et al. 2003).
+Ten percent of the introduced species establish themselves in the non native continent and ten percent of these, in turn, spread or are pests although many exceptions to this rule have been noted (Jeschke and Strayer 2005).
+Time lag
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+---
+title: "Glossary of invasion biology terms"
+chunk: 4/4
+source: "https://en.wikipedia.org/wiki/Glossary_of_invasion_biology_terms"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:25.112976+00:00"
+instance: "kb-cron"
+---
+
+Time between introduction, establishment, and spread of a species (Jeschke and Strayer 2005).
+The time between when a species is introduced and when its population growth explodes (Booth et al. 2003).
+Unintentional introduction
+An introduction of nonindigenous species that occurs as the result of activities other than the purposeful or intentional introduction of the species involved, such as the transport of nonindigenous species in ballast or in water used to transport fish, mollusks or crustaceans for aquaculture or other purposes (EPA 1990).
+Vector (See Vector (epidemiology))
+The physical means or agent by which a species is transported, such as ballast water, ships' hulls, boats, hiking boats, cars, vehicles, packing material, or soil in nursery stock (Carlton 2001). See also pathway.
+Weed
+
+A plant in the wrong place, being one that occurs opportunistically on land or in water that has been disturbed by human activities (see also ruderal species and native weed or invasive native), or on cultivated land, where it competes for nutrients, water, sunlight, or other resources with cultivated plants such as food crops. Under different circumstances the weed plant itself may be cultivated for different purposes (Allaby 1998).
+A native or introduced species that has a perceived negative ecological or economic effect on agricultural or natural ecosystems (Booth et al. 2003).
+A plant growing in an area where it is not wanted (Royer and Dickinson 1999).
+
+=== Legal definitions ===
+Invasive species (United States)
+Executive Order 13112 (1999) defines this term as an alien species whose introduction does or is likely to cause economic or environmental harm or harm to human health. Website: [1]
+Introduction (United States)
+Executive Order 13112 (1999) defines this term as the intentional or unintentional escape, release, dissemination, or placement of a species into an ecosystem as a result of human activity. Website: [2]
+Native species (United States)
+Executive Order 13112 (1999) defines this term as a species with respect to a particular ecosystem that historically occurred or currently occurs in that ecosystem rather than as a result of an introduction. Website: [3]
+Nonindigenous species (United States)
+The Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 (Public Law 101-646, 16 USC 4701-4741) defines this term as any species or other viable biological material that enters an ecosystem beyond its historic range, including any such organism transferred from one country into another. [Website: http://www.epa.gov/owow/invasive_species/nanpca90.pdf]
+Species (United States)
+Executive Order 13112 (1999) defines this term as a group of organisms, all of which have a high degree of physical and genetic similarity, generally interbreed only among themselves, and show persistent differences from members of allied groups of organisms. Website: [4]
+Unintentional introduction (United States)
+The Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 (Public Law 101-646, 16 USC 4701-4741) defines this term as an introduction of nonindigenous species that occurs as the result of activities other than the purposeful or intentional introduction of the species involved, such as the transport of nonindigenous species in ballast or in water used to transport fish, mollusks or crustaceans for aquaculture or other purposes. Website: [5]
+
+== See also ==
+Neophyte
+Archaeophyte
+Columbian Exchange
+
+== References ==
+
+Allaby, M. 1998.  Oxford Dictionary of Ecology.  New York, NY: Oxford University Press.
+Art, H. W.  1993.  The Dictionary of Ecology and Environmental Science.  New York, NY: Henry Holt and Company.
+Booth, B. D., S. D. Murphy, and C. J. Swanton.  2003.  Weed Ecology in Natural and Agricultural Systems.  Cambridge, MA: CABI Publishing.
+Carlton, J.T.  2001.  Introduced Species in U.S. Coastal Waters: Pew Oceans Commissions Report.  Pew Oceans Commissions: Washington, DC.
+Clearwater S.J., Hickey C.W. & Martin M.L. 2008. Overview of potential piscicides and molluscicides for controlling aquatic pest species in New Zealand. Science for Conservation 283. p 74. Published by Department of Conservation, New Zealand. [6]
+Cohen, A. H., and J. T. Carlton.  1998. Accelerating invasion rate in a highly invaded estuary.  Science 279: 555–58.
+Colautti, R. I., and H. J. MacIsaac.  2004.  A neutral terminology to define 'invasive' species.  Diversity and Distributions 10: 134–41.
+Executive Presidential Order.  1999.  Executive Order 13112 of February 3, 1999: Invasive Species.  Federal Register 64 (25):6183-6186.
+Foster, J., and L. A. Sandberg.  2004. Friends or foe?  Invasive species and public green space in Toronto.  The Geographical Review 94(2): 178–98.
+Helmreich, S.  2005.  How scientists think; about 'natives', for example.  A problem of taxonomy among biologists of alien species in Hawaii.  Journal of the Royal Anthropological Institute 11:107-28.
+Heutte, T., and E. Bella.  2003. Invasive plants and exotic weeds of Southeast Alaska.  Anchorage, AK: USDA Forest Service.  Website: [7]
+Jeschke, J. M., and D. L. Strayer.  2005. Invasion success of vertebrates in Europe and North America.  Proceedings of the National Academy of Sciences 102(20):7198-202.
+Kowarik, I. 2002. Biologische Invasionen in Deutschland: zur Rolle nichteinheimischer Pflanzen. NeoBiota 1:5-24.
+Larson, B. M. H. 2005.  The war of the roses: demilitarizing invasion biology. Frontiers in Ecology and the Environment 3(9):495-500.
+Noss, R. F., and A. Y. Cooperrider.  1994. Saving Nature's Legacy: Protecting and Restoring Biodiversity.  Washington, DC: Island Press.
+Robbins, P.  2005.  Comparing invasive networks: cultural and political biographies of invasive species. The Geographical Review 94(20):139-56.
+Royer, F., and R. Dickinson.  1999.  Weeds of the northern U.S. and Canada.  Edmonton, AB: Lone Pine Press.
+Shea, K., and P. Chesson.  2002.  Community ecology theory as a framework for biological invasions.  Trends in Ecology and the Environment 17(4):170-176.
+Shrader-Frechette, K.  2001. Non-indigenous species and ecological explanation.  Biology and Philosophy 16:507-19.
+United States Environmental Protection Agency (EPA).  1990.  Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990.  Washington, DC.
+Vermeij, G. J. 2005. Invasion as Expectation: A historical fact of life.  Pages 315–339 in D. F. Sax, J. J. Stachowicz, and S. D. Gaines, editors.  Species invasions: insights into ecology, evolution and biogeography.  Sinauer Associates, Inc., Sunderland, MA.
+Williams, J. D., and G. K. Meffe.  2005.  Status and trends of the nation's biological resources: Nonindigenous species.  Washington, DC: US Geological Survey.
+Woods, M., and P. V. Moriarty.  2001.  Strangers in a strange land: The problem of exotic species.  Environmental Values 10:163-91.
+
+== External links ==
+Global Invasive Species Database
+Global Invasive Species Programme (GISP)
+The Nature Conservancy Global Invasive Species Initiative
+Union of Concerned Scientists Invasive Species
+Africa
+Forest Invasive Species Network for Africa – FISNA Archived 2022-07-12 at the Wayback Machine
+DST-NRF Centre of Excellence for Invasion Biology
+Australia and New Zealand
+Australian Government Department of Climate Change, Energy, the Environment and Water, Invasive Species page
+CSIRO Australian Weeds
+Queensland Government Weeds & Pest Animal Management
+Tasmanian Government Pests and Diseases
+Weeds Australia
+Biosecurity New Zealand
+Europe
+Regional Biological Invasions Centre (Europe)
+NEOBIOTA - The European Group on Biological Invasions
+United States (including Hawaii)
+Hawaiian Ecosystems at Risk project (HEAR) Archived 2021-02-21 at the Wayback Machine
+United States Executive Order 13112 (1999)
+United States Federal Interagency Committee for the Management of Noxious and Exotic Weeds (FICMNEW)
+United States Invasive Species Government site (Invasivespecies.gov)
+United States Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990
+Weed Science Society of America
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+---
+title: "Gracility"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Gracility"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:26.372103+00:00"
+instance: "kb-cron"
+---
+
+Gracility is slenderness, the condition of being gracile, which means slender. It derives from the Latin adjective gracilis (masculine or feminine), or gracile (neuter), which in either form means slender, and when transferred for example to discourse takes the sense of "without ornament", "simple" or various similar connotations.
+In Glossary of Botanic Terms, B. D. Jackson speaks dismissively of an entry in earlier dictionary of A. A. Crozier as follows: "Gracilis (Lat.), slender. Crozier has the needless word 'gracile'". However, his objection would be hard to sustain in current usage; apart from the fact that gracile is a natural and convenient term, it is hardly a neologism. The Shorter Oxford English Dictionary gives the source date for that usage as 1623 and indicates the word is misused (through association with grace) for "gracefully slender". This misuse is unfortunate at least, because the terms gracile and grace are unrelated: the etymological root of grace is the Latin word gratia from gratus, meaning 'pleasing', and has nothing to do with slenderness or thinness.
+
+
+== In biology ==
+In biology, the term is in common use, whether as English or Latin:
+
+The term gracile and its opposite, robust—occur in discussion of the morphology of various hominids for example.
+The gracile fasciculus is a particular bundle of axon fibres in the spinal cord
+The gracile nucleus is a particular structure of neurons in the medulla oblongata
+"GRACILE syndrome", is associated with a BCS1L mutation
+The gracilis muscle is a thin, flat muscle of the medial thigh
+In biological taxonomy, gracile is the specific name or specific epithet for various species. Where the gender is appropriate, the form is gracilis. Examples include:
+
+Campylobacter gracilis, a species of bacterium implicated in foodborne disease
+Ctenochasma gracile, a late Jurassic pterosaur
+Eriophorum gracile, a species of sedge, Cyperaceae
+Euglena gracilis, a unicellular flagellate protist
+Hydrophis gracilis, a species of sea snakes
+Melampodium gracile, a flowering plant species
+Moeritherium gracile, an Eocene mammal species
+The same root appears in the names of some genera and higher taxa:
+
+Gracilaria is a genus of red algae in the order Gracilariales
+Gracillaria is a genus of leaf miner moths in the superfamily Gracillarioidea
+
+
+== See also ==
+ 
+Buckling, for the slenderness ratio in engineering
+Grace (disambiguation)
+Gracilis (disambiguation), a Latin adjective in several species names –  as remarked above, the meanings are the same as for gracile, except for their grammatical gender
+Somatotype and constitutional psychology
+
+
+== References ==
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diff --git a/data/en.wikipedia.org/wiki/Haplotype_block-0.md b/data/en.wikipedia.org/wiki/Haplotype_block-0.md
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+---
+title: "Haplotype block"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Haplotype_block"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:27.632738+00:00"
+instance: "kb-cron"
+---
+
+In genetics, a haplotype block is a region of an organism's genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes. According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one another by numerous recombination events. The boundaries of haplotype blocks cannot be directly observed; they must instead be inferred indirectly through the use of algorithms. However, some evidence suggests that different algorithms for identifying haplotype blocks give very different results when used on the same data, though another study suggests that their results are generally consistent. The National Institutes of Health funded the HapMap project to catalog haplotype blocks throughout the human genome.
+
+
+== Definition ==
+There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). In 2001, Patil et al. proposed the following definition of the term: "Suppose we have a number of haplotypes consisting of a set of consecutive SNPs. A segment of consecutive SNPs is a block if at least α percent of haplotypes are represented more than once".
+
+
+== References ==
\ No newline at end of file
diff --git a/data/en.wikipedia.org/wiki/Heterotroph-0.md b/data/en.wikipedia.org/wiki/Heterotroph-0.md
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+---
+title: "Heterotroph"
+chunk: 1/4
+source: "https://en.wikipedia.org/wiki/Heterotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:28.864372+00:00"
+instance: "kb-cron"
+---
+
+A heterotroph (; from Ancient Greek ἕτερος (héteros), meaning "other", and τροφή (trophḗ), meaning "nourishment") is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly matter from other organisms. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers. Living organisms that are heterotrophic include most animals, all fungi, some bacteria and protists, and many parasitic plants. The term heterotroph arose in microbiology in 1946 as part of a classification of microorganisms based on their type of nutrition. The term is now used in many fields, such as ecology, in describing the food chain. Heterotrophs occupy the second and third trophic levels of the food chain while autotrophs occupy the first trophic level.
+Heterotrophs may be subdivided according to their energy source. If the heterotroph uses chemical energy, it is a chemoheterotroph (e.g., humans and mushrooms). If it uses light for energy, then it is a photoheterotroph (e.g., haloquadratum walsbyi and green non-sulfur bacteria).
+Heterotrophs represent one of the two mechanisms of nutrition (trophic levels), the other being autotrophs (auto = self, troph = nutrition). Autotrophs use energy from sunlight (photoautotrophs) or oxidation of inorganic compounds (lithoautotrophs) to convert inorganic carbon dioxide to organic carbon compounds and energy to sustain their life. Comparing the two in basic terms, heterotrophs (such as animals) eat either autotrophs (such as plants) or other heterotrophs, or both.
+Detritivores are heterotrophs which obtain nutrients by consuming detritus (decomposing plant and animal parts as well as feces). Saprotrophs (also called lysotrophs) are chemoheterotrophs that use extracellular digestion in processing decayed organic matter. The process is most often facilitated through the active transport of such materials through endocytosis within the internal mycelium and its constituent hyphae.
+
+== Types ==
+Heterotrophs can be organotrophs or lithotrophs.
+
+Organoheterotrophs exploit reduced carbon compounds (organics) as electron sources, such as carbohydrates, fats, and proteins from plants and animals.
+Lithoheterotrophs, on the other hand, use inorganic compounds such as ammonium, nitrite, or sulfur, to obtain electrons.
+Another way of classifying different heterotrophs is by assigning them as chemotrophs or phototrophs. Phototrophs utilize light to obtain energy and carry out metabolic processes, whereas chemotrophs use the energy obtained by the oxidation of chemicals from their environment.
+
+Photoorganoheterotrophs, such as Rhodospirillaceae and purple non-sulfur bacteria synthesize organic compounds using sunlight coupled with oxidation of organic substances. They use organic compounds to build structures. They do not fix carbon dioxide and apparently do not have the Calvin cycle.
+Chemolithoheterotrophs like Oceanithermus profundus obtain energy from the oxidation of inorganic compounds, including hydrogen sulfide, elemental sulfur, thiosulfate, and molecular hydrogen.
+Mixotrophs (or facultative chemolithotroph) can use either carbon dioxide or organic carbon as the carbon source, meaning that mixotrophs have the ability to use both heterotrophic and autotrophic methods. Although mixotrophs have the ability to grow under both heterotrophic and autotrophic conditions, C. vulgaris have higher biomass and lipid productivity when growing under heterotrophic compared to autotrophic conditions.
+Heterotrophs, by consuming reduced carbon compounds, are able to use all the energy that they obtain from food for growth and reproduction, unlike autotrophs, which must use some of their energy for carbon fixation. Both heterotrophs and autotrophs alike are usually dependent on the metabolic activities of other organisms for nutrients other than carbon, including nitrogen, phosphorus, and sulfur, and can die from lack of food that supplies these nutrients. This applies not only to animals and fungi but also to bacteria.
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+---
+title: "Heterotroph"
+chunk: 2/4
+source: "https://en.wikipedia.org/wiki/Heterotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:28.864372+00:00"
+instance: "kb-cron"
+---
+
+== Origin and diversification ==
+The chemical origin of life hypothesis suggests that life originated in a prebiotic soup with heterotrophs. The summary of this theory is as follows: early Earth had a highly reducing atmosphere and energy sources such as electrical energy in the form of lightning, which resulted in reactions that formed simple organic compounds, which further reacted to form more complex compounds and eventually resulted in life. Alternative theories of an autotrophic origin of life contradict this theory.
+The theory of a chemical origin of life beginning with heterotrophic life was first proposed in 1924 by Alexander Ivanovich Oparin, and eventually published "The Origin of Life." It was independently proposed for the first time in English in 1929 by John Burdon Sanderson Haldane. While these authors agreed on the gasses present and the progression of events to a point, Oparin championed a progressive complexity of organic matter prior to the formation of cells, while Haldane had more considerations about the concept of genes as units of heredity and the possibility of light playing a role in chemical synthesis (autotrophy).
+Evidence grew to support this theory in 1953, when Stanley Miller conducted an experiment in which he added gasses that were thought to be present on early Earth – water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2) – to a flask and stimulated them with electricity that resembled lightning present on early Earth. The experiment resulted in the discovery that early Earth conditions were supportive of the production of amino acids, with recent re-analyses of the data recognizing that over 40 different amino acids were produced, including several not currently used by life. This experiment heralded the beginning of the field of synthetic prebiotic chemistry, and is now known as the Miller–Urey experiment.
+On early Earth, oceans and shallow waters were rich with organic molecules that could have been used by primitive heterotrophs. This method of obtaining energy was energetically favorable until organic carbon became more scarce than inorganic carbon, providing a potential evolutionary pressure to become autotrophic. Following the evolution of autotrophs, heterotrophs were able to utilize them as a food source instead of relying on the limited nutrients found in their environment. Eventually, autotrophic and heterotrophic cells were engulfed by these early heterotrophs and formed a symbiotic relationship. The endosymbiosis of autotrophic cells is suggested to have evolved into the chloroplasts while the endosymbiosis of smaller heterotrophs developed into the mitochondria, allowing the differentiation of tissues and development into multicellularity. This advancement allowed the further diversification of heterotrophs. Today, many heterotrophs and autotrophs also utilize mutualistic relationships that provide needed resources to both organisms. One example of this is the mutualism between corals and algae, where the former provides protection and necessary compounds for photosynthesis while the latter provides oxygen.
+However this hypothesis is controversial as CO2 was the main carbon source at the early Earth, suggesting that early cellular life were autotrophs that relied upon inorganic substrates as an energy source and lived at alkaline hydrothermal vents or acidic geothermal ponds. Simple biomolecules transported from space was considered to have been either too reduced to have been fermented or too heterogeneous to support microbial growth. Heterotrophic microbes likely originated at low H2 partial pressures. Bases, amino acids, and ribose are considered to be the first fermentation substrates.
+Heterotrophs are currently found in each domain of life: Bacteria, Archaea, and Eukarya. Domain Bacteria includes a variety of metabolic activity including photoheterotrophs, chemoheterotrophs, organotrophs, and heterolithotrophs. Within Domain Eukarya, kingdoms Fungi and Animalia are entirely heterotrophic, though most fungi absorb nutrients through their environment. Most organisms within Kingdom Protista are heterotrophic while Kingdom Plantae is almost entirely autotrophic, except for myco-heterotrophic plants. Lastly, Domain Archaea varies immensely in metabolic functions and contains many methods of heterotrophy.
+
+== Flowchart ==
+
+Autotroph
+Chemoautotroph
+Photoautotroph
+Heterotroph
+Chemoheterotroph
+Photoheterotroph
+
+== Ecology ==
\ No newline at end of file
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+---
+title: "Heterotroph"
+chunk: 3/4
+source: "https://en.wikipedia.org/wiki/Heterotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:28.864372+00:00"
+instance: "kb-cron"
+---
+
+Many heterotrophs are chemoorganoheterotrophs that use organic carbon (e.g. glucose) as their carbon source, and organic chemicals (e.g. carbohydrates, lipids, proteins) as their electron sources. Heterotrophs function as consumers in food chain: they obtain these nutrients from saprotrophic, parasitic, or holozoic nutrients. They break down complex organic compounds (e.g., carbohydrates, fats, and proteins) produced by autotrophs into simpler compounds (e.g., carbohydrates into glucose, fats into fatty acids and glycerol, and proteins into amino acids). They release the chemical energy of nutrient molecules by oxidizing carbon and hydrogen atoms from carbohydrates, lipids, and proteins to carbon dioxide and water, respectively.
+They can catabolize organic compounds by respiration, fermentation, or both. Fermenting heterotrophs are either facultative or obligate anaerobes that carry out fermentation in low oxygen environments, in which the production of ATP is commonly coupled with substrate-level phosphorylation and the production of end products (e.g. alcohol, CO2, sulfide). These products can then serve as the substrates for other bacteria in the anaerobic digestion, and be converted into CO2 and CH4, which is an important step for the carbon cycle for removing organic fermentation products from anaerobic environments. Heterotrophs can undergo respiration, in which ATP production is coupled with oxidative phosphorylation. This leads to the release of oxidized carbon wastes such as CO2 and reduced wastes like H2O, H2S, or N2O into the atmosphere. Heterotrophic microbes' respiration and fermentation account for a large portion of the release of CO2 into the atmosphere, making it available for autotrophs as a source of nutrient and plants as a cellulose synthesis substrate.
+Respiration in heterotrophs is often accompanied by mineralization, the process of converting organic compounds to inorganic forms. When the organic nutrient source taken in by the heterotroph contains essential elements such as N, S, P in addition to C, H, and O, they are often removed first to proceed with the oxidation of organic nutrient and production of ATP via respiration. S and N in organic carbon source are transformed into H2S and NH4+ through desulfurylation and deamination, respectively. Heterotrophs also allow for dephosphorylation as part of decomposition. The conversion of N and S from organic form to inorganic form is a critical part of the nitrogen and sulfur cycle. H2S formed from desulfurylation is further oxidized by lithotrophs and phototrophs while NH4+ formed from deamination is further oxidized by lithotrophs to the forms available to plants. Heterotrophs' ability to mineralize essential elements is critical to plant survival.
+Most opisthokonts and prokaryotes are heterotrophic; in particular, all animals and fungi are heterotrophs. Some animals, such as corals, form symbiotic relationships with autotrophs and obtain organic carbon in this way. Furthermore, some parasitic plants have also turned fully or partially heterotrophic, while carnivorous plants consume animals to augment their nitrogen supply while remaining autotrophic.
+Animals are classified as heterotrophs by ingestion, fungi are classified as heterotrophs by absorption.
+
+== Heterotroph Impacts on Biogeochemical Cycles ==
+Heterotrophs, organisms that obtain energy and carbon by consuming organic matter, are vital parts of Earth's biogeochemical cycles particularly in the carbon, nitrogen, and sulfur cycles. Their metabolic activities impact the processing and cycling of elements through ecosystems and the biosphere.
+Heterotrophs are key players in the carbon cycle, acting as both consumers and decomposers. They release carbon dioxide (CO2) into the atmosphere through respiration, contributing to a large portion of carbon dioxide emissions. This process makes carbon available for autotrophs, who can fix carbon through photosynthesis or chemosynthesis. This circulation supports the continuous cycling of carbon between organic and inorganic forms.
+Heterotrophic organisms contribute to key processes in the nitrogen cycle like ammonification, the conversion of organic nitrogen to ammonia, and denitrification, the reduction of nitrate and the release of nitrogen gas to the atmosphere. These processes can be known as secondary metabolism in heterotrophs. Heterotrophic microorganisms are essential in the mineralization of organic compounds containing nitrogen. Through deamination, they convert organic nitrogen to ammonium (NH4+), which can be further oxidized by lithotrophs into forms available to plants. Similarly, desulfurylation by heterotrophs transforms organic sulfur into hydrogen sulfide (H2S), which is then oxidized by lithotrophs and phototrophs, contributing to the sulfur cycle.
+The ability of heterotrophs to break down complex organic compounds is fundamental to nutrient cycling in ecosystems. By decomposing dead organic matter, they release essential elements like phosphorus through dephosphorylation, making these nutrients available for other organisms. This process is critical for maintaining soil fertility and supporting plant growth. Heterotrops connect the flow of energy and organic matter across ecosystems. Their biological processes link with atmospheric, chemical and geological systems.
+Heterotrophs form intricate relationships with autotrophs in ecosystems. While they depend on autotrophs for energy-rich organic compounds, heterotrophs support autotrophic growth by releasing minerals and carbon dioxide (CO2). This interdependence is exemplified in symbiotic relationships, such as those between corals and algae, where nutrient exchange benefits both partners. Their metabolic processes depend on each other and traces of organic compounds.
+The biogeochemical activities of heterotrophs are thus integral to ecosystem functioning, influencing the availability of nutrients, the composition of the atmosphere, and the productivity of both terrestrial and aquatic environments.
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+---
+title: "Heterotroph"
+chunk: 4/4
+source: "https://en.wikipedia.org/wiki/Heterotroph"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:28.864372+00:00"
+instance: "kb-cron"
+---
+
+== Impacts on Biogeochemical Cycles ==
+Heterotrophs, organisms that obtain energy and carbon by consuming organic matter, are vital parts of Earth's biogeochemical cycles particularly in the carbon, nitrogen, and sulfur cycles. Their metabolic activities impact the processing and cycling of elements through ecosystems and the biosphere.
+Heterotrophs are key players in the carbon cycle, acting as both consumers and decomposers. They release carbon dioxide (CO2) into the atmosphere through respiration, contributing to a large portion of carbon dioxide emissions. This process makes carbon available for autotrophs, who can fix carbon through photosynthesis or chemosynthesis. This circulation supports the continuous cycling of carbon between organic and inorganic forms.
+Heterotrophic organisms contribute to key processes in the nitrogen cycle like ammonification, the conversion of organic nitrogen to ammonia, and denitrification, the reduction of nitrate and the release of nitrogen gas to the atmosphere. Heterotrophic microorganisms are essential in the mineralization of organic compounds containing nitrogen. Through deamination, they convert organic nitrogen to ammonium (NH4+), which can be further oxidized by lithotrophs into forms available to plants. Similarly, desulfurylation by heterotrophs transforms organic sulfur into hydrogen sulfide (H2S), which is then oxidized by lithotrophs and phototrophs, contributing to the sulfur cycle.
+The ability of heterotrophs to break down complex organic compounds is fundamental to nutrient cycling in ecosystems. By decomposing dead organic matter, they release essential elements like phosphorus through dephosphorylation, making these nutrients available for other organisms. This process is critical for maintaining soil fertility and supporting plant growth. Heterotrops connect the flow of energy and organic matter across ecosystems. Their biological processes link with atmospheric, chemical and geological systems.
+Heterotrophs form intricate relationships with autotrophs in ecosystems. While they depend on autotrophs for energy-rich organic compounds, heterotrophs support autotrophic growth by releasing minerals and carbon dioxide (CO2). This interdependence is exemplified in symbiotic relationships, such as those between corals and algae, where nutrient exchange benefits both partners.
+The biogeochemical activities of heterotrophs are thus integral to ecosystem functioning, influencing the availability of nutrients, the composition of the atmosphere, and the productivity of both terrestrial and aquatic environments.
+
+== References ==
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diff --git a/data/en.wikipedia.org/wiki/Hindgut_fermentation-0.md b/data/en.wikipedia.org/wiki/Hindgut_fermentation-0.md
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+---
+title: "Hindgut fermentation"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Hindgut_fermentation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:30.125848+00:00"
+instance: "kb-cron"
+---
+
+Hindgut fermentation is a digestive process seen in monogastric herbivores (animals with a simple, single-chambered stomach).   Cellulose is digested with the aid of symbiotic microbes including bacteria, archaea, and eukaryotes. The microbial fermentation occurs in the digestive organs that follow the small intestine: the cecum and large intestine.  Examples of hindgut fermenters include proboscideans and large odd-toed ungulates such as horses and rhinos, as well as small animals such as rodents, rabbits and koalas.
+In contrast, foregut fermentation is the form of cellulose digestion seen in ruminants such as cattle which have a four-chambered stomach, as well as in sloths, macropodids, some monkeys, and one bird, the hoatzin.
+
+
+== Cecum ==
+
+Hindgut fermenters generally have a cecum and large intestine that are much larger and more complex than those of a foregut fermenter. Research on small cecum fermenters such as flying squirrels, rabbits and lemurs has revealed these mammals to have a GI tract about 10-13 times the length of their body.  This is due to the high intake of fiber and other hard to digest compounds that are characteristic to the diet of monogastric herbivores.
+Easily digestible food is processed in the gastrointestinal tract & expelled as regular feces.  But in order to get nutrients out of hard to digest fiber, some smaller hindgut fermenters, like lagomorphs (rabbits, hares, pikas), ferment fiber in the cecum (at the small and large intestine junction) and then expel the contents as cecotropes, which are reingested (cecotrophy).  The cecotropes are then absorbed in the small intestine to utilize the nutrients.
+This process is also beneficial in allowing for restoration of the microflora population, or gut flora. These microbes are found in the gastrointestinal tract and can act as protective agents that strengthen the immune system. Small hindgut fermenters have the ability to expel their microflora, which is useful during the acts of hibernation, estivation and torpor.
+
+
+== Efficiency ==
+While foregut fermentation is generally considered more efficient, and monogastric animals cannot digest cellulose as efficiently as ruminants, hindgut fermentation allows animals to consume small amounts of low-quality forage all day long and thus survive in conditions where ruminants might not be able to obtain nutrition adequate for their needs. While ruminants require a good deal of time resting between meals, hindgut fermenters are able to take in smaller meals more frequently, allowing them to eat and move more readily.  The large hindgut fermenters are bulk feeders: they ingest large quantities of low-nutrient food, which they process more rapidly than would be possible for a similarly sized foregut fermenter. The main food in that category is grass, and grassland grazers move over long distances to take advantage of the growth phases of grass in different regions.
+
+
+== Speed ==
+The ability to process food more rapidly than foregut fermenters gives hindgut fermenters an advantage at very large body size, as they are able to accommodate significantly larger food intakes. The largest extant and prehistoric megaherbivores, elephants and indricotheres (a type of rhino), respectively, have been hindgut fermenters. Study of the rates of evolution of larger maximum body mass in different terrestrial mammalian groups has shown that the fastest growth in body mass over time occurred in hindgut fermenters (perissodactyls, rodents  and proboscids).
+
+
+== Types ==
+Hindgut fermenters are subdivided into two groups based on the relative size of various digestive organs in relationship to the rest of the system: colonic fermenters tend to be larger species such as horses, and cecal fermenters are smaller animals such as rabbits and rodents. However, in spite of the terminology, colonic fermenters such as horses make extensive use of the cecum to break down cellulose. Also, colonic fermenters typically have a proportionally longer large intestine than small intestine, whereas cecal fermenters have a considerably enlarged cecum compared to the rest of the digestive tract.
+
+
+== Swine ==
+Among mammals, pigs are classified as hindgut fermenters. They possess a relatively large cecum, which provides substantial space for fermentation. This fermentation occurs through interactions between the cecal digesta and the cecal microbiota. The composition of the cecal digesta reflects dietary composition, because the residues that reach the cecum are those that were not digested in the ileum and subsequently passed into the cecum.
+The major components of cecal digesta are typically fibers that cannot be digested by the pig's endogenous enzymes, although some other nutrients also remain. Similarly, the composition of the cecal microbiota is largely influenced by the dietary composition. Briefly, when pigs consume a high-protein diet, the amount of undigested protein entering the cecum increases, which can elevate the abundance of ammonia-producing bacteria. In contrast, when pigs consume high-fiber diets, more fiber reaches the cecum, resulting in an increased relative abundance of fiber-degrading bacteria.
+The major metabolites produced by cecal bacteria are short-chain fatty acids and ammonia. The short-chain fatty acids are primiarly generated from the fermentation of dietary fiber, whereas ammonia is produced through the fermentation of protein and amino acids. Short-chain fatty acids can serve as an energy source for enterocytes and help prevent the proliferation of pathogenic bacteria by lowering the cecal pH. In contrast, ammonia can increase the luminal pH and promote the growth of pathogenic bacteria, which may cause intestinal inflammation.
+
+
+== Insects ==
+In addition to mammals, several insects are also hindgut fermenters, the best studied of which are the termites, which are characterised by an enlarged "paunch" of the hindgut that also houses the bulk of the gut microbiota. Digestion of wood particles in lower termites is accomplished inside the phagosomes of gut flagellates, but in the flagellate-free higher termites, this appears to be accomplished by fibre-associated bacteria.
+
+
+== See also ==
+Foregut fermentation
+Pseudoruminants
+Ruminants
+Cecotrope
+
+
+== References ==
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+title: "Homeostasis"
+chunk: 1/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+In biology, homeostasis (British also homoeostasis;  HOH-mee-ə-STAY-sis) is the state of steady internal physical and chemical conditions maintained by living organisms. This is the condition of optimal functioning for the organism and includes many variables, such as body temperature and fluid balance, being kept within certain pre-set limits (homeostatic range). Other variables include the pH of extracellular fluid, the concentrations of sodium, potassium, and calcium ions, as well as the blood sugar level, and these need to be regulated despite changes in the environment, diet, or level of activity. Each of these variables is controlled by one or more regulators or homeostatic mechanisms, which together maintain life.
+Homeostasis is brought about by a natural resistance to change when already in its optimal conditions, and equilibrium is maintained by many regulatory mechanisms; it is thought to be the central motivation for all organic action. All homeostatic control mechanisms have at least three interdependent components for the variable being regulated: a receptor, a control center, and an effector. The receptor is the sensing component that monitors and responds to changes in the environment, either external or internal. Receptors include thermoreceptors and mechanoreceptors. Control centers include the respiratory center and the renin-angiotensin system. An effector is the target acted on, to bring about the change back to the normal state. At the cellular level, effectors include nuclear receptors that bring about changes in gene expression through up-regulation or down-regulation and act in negative feedback mechanisms. An example of this is in the control of bile acids in the liver.
+Some centers, such as the renin–angiotensin system, control more than one variable. When the receptor senses a stimulus, it reacts by sending action potentials to a control center. The control center sets the maintenance range—the acceptable upper and lower limits—for the particular variable, such as temperature. The control center responds to the signal by determining an appropriate response and sending signals to an effector, which can be one or more muscles, an organ, or a gland. When the signal is received and acted on, negative feedback is provided to the receptor that stops the need for further signaling.
+The cannabinoid receptor type 1, located at the presynaptic neuron, is a receptor that can stop stressful neurotransmitter release to the postsynaptic neuron; it is activated by endocannabinoids such as anandamide (N-arachidonoylethanolamide) and 2-arachidonoylglycerol via a retrograde signaling process in which these compounds are synthesized by and released from postsynaptic neurons, and travel back to the presynaptic terminal to bind to the CB1 receptor for modulation of neurotransmitter release to obtain homeostasis.
+The polyunsaturated fatty acids are lipid derivatives of omega-3 (docosahexaenoic acid, and eicosapentaenoic acid) or of omega-6 (arachidonic acid). They are synthesized from membrane phospholipids and used as precursors for endocannabinoids to mediate significant effects in the fine-tuning adjustment of body homeostasis.
+
+== Etymology ==
+The word homeostasis ( hoh-mee-oh-STAY-sis) uses combining forms of homeo- and -stasis, Neo-Latin from Greek: ὅμοιος homoios, "similar" and στάσις stasis, "standing still", yielding the idea of "staying the same".
+
+== History ==
+The concept of the regulation of the internal environment was described by French physiologist Claude Bernard in 1849, and the word homeostasis was coined by Walter Bradford Cannon in 1926. In 1932, Joseph Barcroft, a British physiologist, was the first to say that higher brain function required the most stable internal environment. Thus, to Barcroft homeostasis was not only organized by the brain—homeostasis served the brain. Homeostasis is an almost exclusively biological term, referring to the concepts described by Bernard and Cannon, concerning the constancy of the internal environment in which the cells of the body live and survive. The term cybernetics is applied to technological control systems such as thermostats, which function as homeostatic mechanisms but are often defined much more broadly than the biological term of homeostasis.
+
+== Overview ==
+The metabolic processes of all organisms can only take place in very specific physical and chemical environments. The conditions vary with each organism, and also with whether the chemical processes take place inside the cell or in the interstitial fluid bathing the cells. The best-known homeostatic mechanisms in humans and other mammals are regulators that keep the composition of the extracellular fluid (or the "internal environment") constant, especially with regard to the temperature, pH, osmolality, and the concentrations of sodium, potassium, glucose, carbon dioxide, and oxygen. However, a great many other homeostatic mechanisms, encompassing many aspects of human physiology, control other entities in the body. Where the levels of variables are higher or lower than those needed, they are often prefixed with hyper- and hypo-, respectively such as hyperthermia and hypothermia or hypertension and hypotension.
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+title: "Homeostasis"
+chunk: 2/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+If an entity is homeostatically controlled it does not imply that its value is necessarily absolutely steady in health. Core body temperature is, for instance, regulated by a homeostatic mechanism with temperature sensors in, amongst others, the hypothalamus of the brain. However, the set point of the regulator is regularly reset. For instance, core body temperature in humans varies during the course of the day (i.e. has a circadian rhythm), with the lowest temperatures occurring at night, and the highest in the afternoons. Other normal temperature variations include those related to the menstrual cycle. The temperature regulator's set point is reset during infections to produce a fever. Organisms are capable of adjusting somewhat to varied conditions such as temperature changes or oxygen levels at altitude, by a process of acclimatisation.
+Homeostasis does not govern every activity in the body. For instance, the signal (be it via neurons or hormones) from the sensor to the effector is, of necessity, highly variable in order to convey information about the direction and magnitude of the error detected by the sensor.  Similarly, the effector's response needs to be highly adjustable to reverse the error – in fact it should be very nearly in proportion (but in the opposite direction) to the error that is threatening the internal environment. For instance, arterial blood pressure in mammals is homeostatically controlled and measured by stretch receptors in the walls of the aortic arch and carotid sinuses at the beginnings of the internal carotid arteries. The sensors send messages via sensory nerves to the medulla oblongata of the brain indicating whether the blood pressure has fallen or risen, and by how much. The medulla oblongata then distributes messages along motor or efferent nerves belonging to the autonomic nervous system to a wide variety of effector organs, whose activity is consequently changed to reverse the error in the blood pressure. One of the effector organs is the heart whose rate is stimulated to rise (tachycardia) when the arterial blood pressure falls, or to slow down (bradycardia) when the pressure rises above the set point. Thus the heart rate (for which there is no sensor in the body) is not homeostatically controlled but is one of the effector responses to errors in arterial blood pressure. Another example is the rate of sweating. This is one of the effectors in the homeostatic control of body temperature, and therefore highly variable in rough proportion to the heat load that threatens to destabilize the body's core temperature, for which there is a sensor in the hypothalamus of the brain.
+
+== Controls of variables ==
+
+=== Core temperature ===
+
+Mammals regulate their core temperature using input from thermoreceptors in the hypothalamus, brain, spinal cord, internal organs, and great veins. Apart from the internal regulation of temperature, a process called allostasis can come into play that adjusts behaviour to adapt to the challenge of very hot or cold extremes (and to other challenges). These adjustments may include seeking shade and reducing activity, seeking warmer conditions and increasing activity, or huddling.
+Behavioral thermoregulation takes precedence over physiological thermoregulation since necessary changes can be affected more quickly and physiological thermoregulation is limited in its capacity to respond to extreme temperatures.
+When the core temperature falls, the blood supply to the skin is reduced by intense vasoconstriction. The blood flow to the limbs (which have a large surface area) is similarly reduced and returned to the trunk via the deep veins which lie alongside the arteries (forming venae comitantes). This acts as a counter-current exchange system that short-circuits the warmth from the arterial blood directly into the venous blood returning into the trunk, causing minimal heat loss from the extremities in cold weather. The subcutaneous limb veins are tightly constricted, not only reducing heat loss from this source but also forcing the venous blood into the counter-current system in the depths of the limbs.
+The metabolic rate is increased, initially by non-shivering thermogenesis, followed by shivering thermogenesis if the earlier reactions are insufficient to correct the hypothermia.
+When core temperature rises are detected by thermoreceptors, the sweat glands in the skin are stimulated via cholinergic sympathetic nerves to secrete sweat onto the skin, which, when it evaporates, cools the skin and the blood flowing through it. Panting is an alternative effector in many vertebrates, which cools the body also by the evaporation of water, but this time from the mucous membranes of the throat and mouth.
+
+=== Blood glucose ===
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+title: "Homeostasis"
+chunk: 3/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+Blood sugar levels are  regulated within fairly narrow limits. In mammals, the primary sensors for this are the beta cells of the pancreatic islets. The beta cells respond to a rise in the blood sugar level by secreting insulin into the blood and simultaneously inhibiting their neighboring alpha cells from secreting glucagon into the blood. This combination (high blood insulin levels and low glucagon levels) act on effector tissues, the chief of which is the liver, fat cells, and muscle cells. The liver is inhibited from producing glucose, taking it up instead, and converting it to glycogen and triglycerides. The glycogen is stored in the liver, but the triglycerides are secreted into the blood as very low-density lipoprotein (VLDL) particles which are taken up by adipose tissue, there to be stored as fats. The fat cells take up glucose through special glucose transporters (GLUT4), whose numbers in the cell wall are increased as a direct effect of insulin acting on these cells. The glucose that enters the fat cells in this manner is converted into triglycerides (via the same metabolic pathways as are used by the liver) and then stored in those fat cells together with the VLDL-derived triglycerides that were made in the liver. Muscle cells also take glucose up through insulin-sensitive GLUT4 glucose channels, and convert it into muscle glycogen.
+A fall in blood glucose, causes insulin secretion to be stopped, and glucagon to be secreted from the alpha cells into the blood. This inhibits the uptake of glucose from the blood by the liver, fats cells, and muscle. Instead the liver is strongly stimulated to manufacture glucose from glycogen (through glycogenolysis) and from non-carbohydrate sources (such as lactate and de-aminated amino acids) using a process known as gluconeogenesis. The glucose thus produced is discharged into the blood correcting the detected error (hypoglycemia). The glycogen stored in muscles remains in the muscles, and is only broken down, during exercise, to glucose-6-phosphate and thence to pyruvate to be fed into the citric acid cycle or turned into lactate. It is only the lactate and the waste products of the citric acid cycle that are returned to the blood. The liver can take up only the lactate, and, by the process of energy-consuming gluconeogenesis, convert it back to glucose.
+
+=== Iron levels ===
+
+Iron homeostasis is a crucial physiological process that regulates iron levels in the body, ensuring that this essential nutrient is available for vital functions while preventing potential toxicity from excess iron. The primary site for iron absorption is the duodenum, where dietary iron exists in two forms: heme iron, sourced from animal products, and non-heme iron, found in plant foods. Heme iron is more efficiently absorbed than non-heme iron, which requires factors like vitamin C for optimal uptake. Once absorbed, iron enters the bloodstream bound to transferrin, a transport protein that delivers it to various tissues and organs. Cells uptake iron through transferrin receptors, making it available for critical processes such as oxygen transport and DNA synthesis. Excess iron is stored in the liver, spleen, and bone marrow as ferritin and hemosiderin. The regulation of iron levels is primarily controlled by the hormone hepcidin, produced by the liver, which adjusts intestinal absorption and the release of stored iron based on the body's needs. Disruptions in iron homeostasis can lead to conditions such as iron deficiency anemia or iron overload disorders like hemochromatosis, highlighting the importance of maintaining the delicate balance of this vital nutrient for overall health.
+
+=== Copper regulation ===
+
+Copper is absorbed, transported, distributed, stored, and excreted in the body according to complex homeostatic processes which ensure a constant and sufficient supply of the micronutrient while simultaneously avoiding excess levels. If an insufficient amount of copper is ingested for a short period of time, copper stores in the liver will be depleted. Should this depletion continue, a copper health deficiency condition may develop. If too much copper is ingested, an excess condition can result. Both of these conditions, deficiency and excess, can lead to tissue injury and disease. However, due to homeostatic regulation, the human body is capable of balancing a wide range of copper intakes for the needs of healthy individuals.
+Many aspects of copper homeostasis are known at the molecular level. Copper's essentiality is due to its ability to act as an electron donor or acceptor as its oxidation state fluxes between Cu1+ (cuprous) and Cu2+ (cupric). As a component of about a dozen cuproenzymes, copper is involved in key redox (i.e., oxidation-reduction) reactions in essential metabolic processes such as mitochondrial respiration, synthesis of melanin, and cross-linking of collagen. Copper is an integral part of the antioxidant enzyme copper-zinc superoxide dismutase, and has a role in iron homeostasis as a cofactor in ceruloplasmin.
+
+=== Levels of blood gases ===
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+title: "Homeostasis"
+chunk: 4/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+Changes in the levels of oxygen, carbon dioxide, and plasma pH are sent to the respiratory center, in the brainstem where they are regulated.
+The partial pressure of oxygen and carbon dioxide in the arterial blood is monitored by the peripheral chemoreceptors (PNS) in the carotid artery and aortic arch. A change in the partial pressure of carbon dioxide is detected as altered pH in the cerebrospinal fluid by central chemoreceptors (CNS) in the medulla oblongata of the brainstem. Information from these sets of sensors is sent to the respiratory center which activates the effector organs – the diaphragm and other muscles of respiration. An increased level of carbon dioxide in the blood, or a decreased level of oxygen, will result in a deeper breathing pattern and increased respiratory rate to bring the blood gases back to equilibrium.
+Too little carbon dioxide, and, to a lesser extent, too much oxygen in the blood can temporarily halt breathing, a condition known as apnea, which freedivers use to prolong the time they can stay underwater.
+The partial pressure of carbon dioxide is more of a deciding factor in the monitoring of pH. However, at high altitude (above 2500 m) the monitoring of the partial pressure of oxygen takes priority, and hyperventilation keeps the oxygen level constant. With the lower level of carbon dioxide, to keep the pH at 7.4 the kidneys secrete hydrogen ions into the blood and excrete bicarbonate into the urine. This is important in acclimatization to high altitude.
+
+=== Blood oxygen content ===
+The kidneys measure the oxygen content rather than the partial pressure of oxygen in the arterial blood. When the oxygen content of the blood is chronically low, oxygen-sensitive cells secrete erythropoietin (EPO) into the blood. The effector tissue is the red bone marrow which produces red blood cells (RBCs, also called erythrocytes). The increase in RBCs leads to an increased hematocrit in the blood, and a subsequent increase in hemoglobin that increases the oxygen carrying capacity. This is the mechanism whereby high altitude dwellers have higher hematocrits than sea-level residents, and also why persons with pulmonary insufficiency or right-to-left shunts in the heart (through which venous blood by-passes the lungs and goes directly into the systemic circulation) have similarly high hematocrits.
+Regardless of the partial pressure of oxygen in the blood, the amount of oxygen that can be carried, depends on the hemoglobin content. The partial pressure of oxygen may be sufficient for example in anemia, but the hemoglobin content will be insufficient and subsequently as will be the oxygen content. Given enough supply of iron, vitamin B12 and folic acid, EPO can stimulate RBC production, and hemoglobin and oxygen content restored to normal.
+
+=== Arterial blood pressure ===
+
+The brain can regulate blood flow over a range of blood pressure values by vasoconstriction and vasodilation of the arteries.
+High pressure receptors called baroreceptors in the walls of the aortic arch and carotid sinus (at the beginning of the internal carotid artery) monitor the arterial blood pressure. Rising pressure is detected when the walls of the arteries stretch due to an increase in blood volume. This causes heart muscle cells to secrete the hormone atrial natriuretic peptide (ANP) into the blood. This acts on the kidneys to inhibit the secretion of renin and aldosterone causing the release of sodium, and accompanying water into the urine, thereby reducing the blood volume.
+This information is then conveyed, via afferent nerve fibers, to the solitary nucleus in the medulla oblongata. From here motor nerves belonging to the autonomic nervous system are stimulated to influence the activity of chiefly the heart and the smallest diameter arteries, called arterioles. The arterioles are the main resistance vessels in the arterial tree, and small changes in diameter cause large changes in the resistance to flow through them. When the arterial blood pressure rises the arterioles are stimulated to dilate making it easier for blood to leave the arteries, thus deflating them, and bringing the blood pressure down, back to normal. At the same time, the heart is stimulated via cholinergic parasympathetic nerves to beat more slowly (called bradycardia), ensuring that the inflow of blood into the arteries is reduced, thus adding to the reduction in pressure, and correcting the original error.
+Low pressure in the arteries, causes the opposite reflex of constriction of the arterioles, and a speeding up of the heart rate (called tachycardia). If the drop in blood pressure is very rapid or excessive, the medulla oblongata stimulates the adrenal medulla, via "preganglionic" sympathetic nerves, to secrete epinephrine (adrenaline) into the blood. This hormone enhances the tachycardia and causes severe vasoconstriction of the arterioles to all but the essential organs in the body (especially the heart, lungs, and brain). These reactions usually correct the low arterial blood pressure (hypotension) very effectively.
+
+=== Calcium levels ===
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+title: "Homeostasis"
+chunk: 5/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+The plasma ionized calcium (Ca2+) concentration is very tightly controlled by a pair of homeostatic mechanisms. The sensor for the first one is situated in the parathyroid glands, where the chief cells sense the Ca2+ level by means of specialized calcium receptors in their membranes. The sensors for the second are the parafollicular cells in the thyroid gland. The parathyroid chief cells secrete parathyroid hormone (PTH) in response to a fall in the plasma ionized calcium level; the parafollicular cells of the thyroid gland secrete calcitonin in response to a rise in the plasma ionized calcium level.
+The effector organs of the first homeostatic mechanism are the bones, the kidney, and, via a hormone released into the blood by the kidney in response to high PTH levels in the blood, the duodenum and jejunum. Parathyroid hormone (in high concentrations in the blood) causes bone resorption, releasing calcium into the plasma. This is a very rapid action which can correct a threatening hypocalcemia within minutes. High PTH concentrations cause the excretion of phosphate ions via the urine. Since phosphates combine with calcium ions to form insoluble salts (see also bone mineral), a decrease in the level of phosphates in the blood, releases free calcium ions into the plasma ionized calcium pool. PTH has a second action on the kidneys. It stimulates the manufacture and release, by the kidneys, of calcitriol into the blood. This steroid hormone acts on the epithelial cells of the upper small intestine, increasing their capacity to absorb calcium from the gut contents into the blood.
+The second homeostatic mechanism, with its sensors in the thyroid gland, releases calcitonin into the blood when the blood ionized calcium rises. This hormone acts primarily on bone, causing the rapid removal of calcium from the blood and depositing it, in insoluble form, in the bones.
+The two homeostatic mechanisms working through PTH on the one hand, and calcitonin on the other can very rapidly correct any impending error in the plasma ionized calcium level by either removing calcium from the blood and depositing it in the skeleton, or by removing calcium from it. The skeleton acts as an extremely large calcium store (about 1 kg) compared with the plasma calcium store (about 180 mg). Longer term regulation occurs through calcium absorption or loss from the gut.
+Another example are the most well-characterised endocannabinoids like anandamide (N-arachidonoylethanolamide; AEA) and 2-arachidonoylglycerol (2-AG), whose synthesis occurs through the action of a series of intracellular enzymes activated in response to a rise in intracellular calcium levels to introduce homeostasis and prevention of tumor development through putative protective mechanisms that prevent cell growth and migration by activation of CB1 and/or CB2 and adjoining receptors.
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+title: "Homeostasis"
+chunk: 6/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+=== Sodium concentration ===
+ 
+The homeostatic mechanism which controls the plasma sodium concentration is rather more complex than most of the other homeostatic mechanisms described on this page.
+The sensor is situated in the juxtaglomerular apparatus of kidneys, which senses the plasma sodium concentration in a surprisingly indirect manner. Instead of measuring it directly in the blood flowing past the juxtaglomerular cells, these cells respond to the sodium concentration in the renal tubular fluid after it has already undergone a certain amount of modification in the proximal convoluted tubule and loop of Henle. These cells also respond to rate of blood flow through the juxtaglomerular apparatus, which, under normal circumstances, is directly proportional to the arterial blood pressure, making this tissue an ancillary arterial blood pressure sensor.
+In response to a lowering of the plasma sodium concentration, or to a fall in the arterial blood pressure, the juxtaglomerular cells release renin into the blood. Renin is an enzyme which cleaves a decapeptide (a short protein chain, 10 amino acids long) from a plasma α-2-globulin called angiotensinogen. This decapeptide is known as angiotensin I.  It has no known biological activity. However, when the blood circulates through the lungs a pulmonary capillary endothelial enzyme called angiotensin-converting enzyme (ACE) cleaves a further two amino acids from angiotensin I to form an octapeptide known as angiotensin II.  Angiotensin II is a hormone which acts on the adrenal cortex, causing the release into the blood of the steroid hormone, aldosterone. Angiotensin II also acts on the smooth muscle in the walls of the arterioles causing these small diameter vessels to constrict, thereby restricting the outflow of blood from the arterial tree, causing the arterial blood pressure to rise. This, therefore, reinforces the measures described above (under the heading of "Arterial blood pressure"), which defend the arterial blood pressure against changes, especially hypotension.
+The angiotensin II-stimulated aldosterone released from the zona glomerulosa of the adrenal glands has an effect on particularly the epithelial cells of the distal convoluted tubules and collecting ducts of the kidneys. Here it causes the reabsorption of sodium ions from the renal tubular fluid, in exchange for potassium ions which are secreted from the blood plasma into the tubular fluid to exit the body via the urine. The reabsorption of sodium ions from the renal tubular fluid halts further sodium ion losses from the body, and therefore preventing the worsening of hyponatremia. The hyponatremia can only be corrected by the consumption of salt in the diet. However, it is not certain whether a "salt hunger" can be initiated by hyponatremia, or by what mechanism this might come about.
+When the plasma sodium ion concentration is higher than normal (hypernatremia), the release of renin from the juxtaglomerular apparatus is halted, ceasing the production of angiotensin II, and its consequent aldosterone-release into the blood. The kidneys respond by excreting sodium ions into the urine, thereby normalizing the plasma sodium ion concentration. The low angiotensin II levels in the blood lower the arterial blood pressure as an inevitable concomitant response.
+The reabsorption of sodium ions from the tubular fluid as a result of high aldosterone levels in the blood does not, of itself, cause renal tubular water to be returned to the blood from the distal convoluted tubules or collecting ducts. This is because sodium is reabsorbed in exchange for potassium and therefore causes only a modest change in the osmotic gradient between the blood and the tubular fluid. Furthermore, the epithelium of the distal convoluted tubules and collecting ducts is impermeable to water in the absence of antidiuretic hormone (ADH) in the blood. ADH is part of the control of fluid balance. Its levels in the blood vary with the osmolality of the plasma, which is measured in the hypothalamus of the brain. Aldosterone's action on the kidney tubules prevents sodium loss to the extracellular fluid (ECF). So there is no change in the osmolality of the ECF, and therefore no change in the ADH concentration of the plasma. However, low aldosterone levels cause a loss of sodium ions from the ECF, which could potentially cause a change in extracellular osmolality and therefore of ADH levels in the blood.
+
+=== Potassium concentration ===
+
+High potassium concentrations in the plasma cause depolarization of the zona glomerulosa cells' membranes in the outer layer of the adrenal cortex. This causes the release of aldosterone into the blood.
+Aldosterone acts primarily on the distal convoluted tubules and collecting ducts of the kidneys, stimulating the excretion of potassium ions into the urine. It does so, however, by activating the basolateral Na+/K+ pumps of the tubular epithelial cells. These sodium/potassium exchangers pump three sodium ions out of the cell, into the interstitial fluid and two potassium ions into the cell from the interstitial fluid. This creates an ionic concentration gradient which results in the reabsorption of sodium (Na+) ions from the tubular fluid into the blood, and secreting potassium (K+) ions from the blood into the urine (lumen of collecting duct).
+
+=== Fluid balance ===
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+title: "Homeostasis"
+chunk: 7/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+The total amount of water in the body needs to be kept in balance. Fluid balance involves keeping the fluid volume stabilized, and also keeping the levels of electrolytes in the extracellular fluid stable. Fluid balance is maintained by the process of osmoregulation and by behavior. Osmotic pressure is detected by osmoreceptors in the median preoptic nucleus in the hypothalamus. Measurement of the plasma osmolality to give an indication of the water content of the body, relies on the fact that water losses from the body, (through unavoidable water loss through the skin which is not entirely waterproof and therefore always slightly moist, water vapor in the exhaled air, sweating, vomiting, normal feces and especially  diarrhea) are all hypotonic, meaning that they are less salty than the body fluids (compare, for instance, the taste of saliva with that of tears. The latter has almost the same salt content as the extracellular fluid, whereas the former is hypotonic with respect to the plasma. Saliva does not taste salty, whereas tears are decidedly salty). Nearly all normal and abnormal losses of body water therefore cause the extracellular fluid to become hypertonic. Conversely, excessive fluid intake dilutes the extracellular fluid causing the hypothalamus to register hypotonic hyponatremia conditions.
+When the hypothalamus detects a hypertonic extracellular environment, it causes the secretion of an antidiuretic hormone (ADH) called vasopressin which acts on the effector organ, which in this case is the kidney. The effect of vasopressin on the kidney tubules is to reabsorb water from the distal convoluted tubules and collecting ducts, thus preventing aggravation of the water loss via the urine. The hypothalamus simultaneously stimulates the nearby thirst center causing an almost irresistible (if the hypertonicity is severe enough) urge to drink water. The cessation of urine flow prevents the hypovolemia and hypertonicity from getting worse; the drinking of water corrects the defect.
+Hypo-osmolality results in very low plasma ADH levels. This results in the inhibition of water reabsorption from the kidney tubules, causing high volumes of very dilute urine to be excreted, thus getting rid of the excess water in the body.
+Urinary water loss, when the body water homeostat is intact, is a compensatory water loss, correcting any water excess in the body. However, since the kidneys cannot generate water, the thirst reflex is the all-important second effector mechanism of the body water homeostat, correcting any water deficit in the body.
+
+=== Blood pH ===
+
+The plasma pH can be altered by respiratory changes in the partial pressure of carbon dioxide; or altered by metabolic changes in the carbonic acid to bicarbonate ion ratio. The bicarbonate buffer system regulates the ratio of carbonic acid  to bicarbonate to be equal to 1:20, at which ratio the blood pH is 7.4 (as explained in the Henderson–Hasselbalch equation). A change in the plasma pH gives an acid–base imbalance.
+In acid–base homeostasis there are two mechanisms that can help regulate the pH. Respiratory compensation a mechanism of the respiratory center, adjusts the partial pressure of carbon dioxide by changing the rate and depth of breathing, to bring the pH back to normal. The partial pressure of carbon dioxide also determines the concentration of carbonic acid, and the bicarbonate buffer system can also come into play. Renal compensation can help the bicarbonate buffer system.
+The sensor for the plasma bicarbonate concentration is not known for certain. It is very probable that the renal tubular cells of the distal convoluted tubules are themselves sensitive to the pH of the plasma. The metabolism of these cells produces carbon dioxide, which is rapidly converted to hydrogen and bicarbonate through the action of carbonic anhydrase. When the ECF pH falls (becoming more acidic) the renal tubular cells excrete hydrogen ions into the tubular fluid to leave the body via urine. Bicarbonate ions are simultaneously secreted into the blood that decreases the carbonic acid, and consequently raises the plasma pH.  The converse happens when the plasma pH rises above normal: bicarbonate ions are excreted into the urine, and hydrogen ions released into the plasma.
+When hydrogen ions are excreted into the urine, and bicarbonate into the blood, the latter combines with the excess hydrogen ions in the plasma that stimulated the kidneys to perform this operation. The resulting reaction in the plasma is the formation of carbonic acid which is in equilibrium with the plasma partial pressure of carbon dioxide.  This is tightly regulated to ensure that there is no excessive build-up of carbonic acid or bicarbonate. The overall effect is therefore that hydrogen ions are lost in the urine when the pH of the plasma falls. The concomitant rise in the plasma bicarbonate mops up the increased hydrogen ions (caused by the fall in plasma pH) and the resulting excess carbonic acid is disposed of in the lungs as carbon dioxide. This restores the normal ratio between bicarbonate and the partial pressure of carbon dioxide and therefore the plasma pH.
+The converse happens when a high plasma pH stimulates the kidneys to secrete hydrogen ions into the blood and to excrete bicarbonate into the urine.  The hydrogen ions combine with the excess bicarbonate ions in the plasma, once again forming an excess of carbonic acid which can be exhaled, as carbon dioxide, in the lungs, keeping the plasma bicarbonate ion concentration, the partial pressure of carbon dioxide and, therefore, the plasma pH, constant.
+
+=== Cerebrospinal fluid ===
+Cerebrospinal fluid (CSF) allows for regulation of the distribution of substances between cells of the brain, and neuroendocrine factors, to which slight changes can cause problems or damage to the nervous system. For example, high glycine concentration disrupts temperature and blood pressure control, and high CSF pH causes dizziness and syncope.
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+---
+title: "Homeostasis"
+chunk: 8/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+=== Neurotransmission ===
+Inhibitory neurons in the central nervous system play a homeostatic role in the balance of neuronal activity between excitation and inhibition. Inhibitory neurons using GABA, make compensating changes in the neuronal networks preventing runaway levels of excitation. An imbalance between excitation and inhibition is seen to be implicated in a number of neuropsychiatric disorders.
+
+=== Neuroendocrine system ===
+
+The neuroendocrine system is the mechanism by which the hypothalamus maintains homeostasis, regulating metabolism, reproduction, eating and drinking behaviour, energy utilization, osmolarity and blood pressure.
+The regulation of metabolism, is carried out by hypothalamic interconnections to other glands.
+Three endocrine glands of the hypothalamic–pituitary–gonadal axis (HPG axis) often work together and have important regulatory functions. Two other regulatory endocrine axes are the hypothalamic–pituitary–adrenal axis (HPA axis) and the hypothalamic–pituitary–thyroid axis (HPT axis).
+The liver also has many regulatory functions of the metabolism. An important function is the production and control of bile acids. Too much bile acid can be toxic to cells and its synthesis can be inhibited by activation of FXR a nuclear receptor.
+
+=== Gene regulation ===
+
+At the cellular level, homeostasis is carried out by several mechanisms including transcriptional regulation that can alter the activity of genes in response to changes.
+
+=== Energy balance ===
+
+The amount of energy consumed through dietary intake must align closely with the amount of energy expended by the body in order to maintain overall energy balance, a state known as energy homeostasis. This critical process is managed through the regulation of appetite, which is influenced by two key hormones: ghrelin and leptin. Ghrelin is known as the hunger hormone, as it plays a significant role in stimulating feelings of hunger, thereby prompting individuals to seek out and consume food. On the other hand, leptin serves a different function; it signals satiety, or the feeling of fullness, telling the body that it has consumed enough food.
+In a comprehensive review conducted in 2019 that examined various weight-change interventions—including dieting, exercise, and instances of overeating—it was determined that the body's mechanisms for regulating weight homeostasis are not capable of precisely correcting for energetic errors. These energetic errors refer to the notable loss or gain of calories that can occur in the short term. This research highlights the complexity of energy balance, showing that the body may struggle to adjust rapidly to fluctuations in calorie intake or expenditure, thereby complicating the process of maintaining a stable body weight in response to immediate changes in energy consumption and usage.
+
+== Clinical significance ==
+Many diseases are the result of a homeostatic failure. Almost any homeostatic component can malfunction either as a result of an inherited defect, an inborn error of metabolism, or an acquired disease. Some homeostatic mechanisms have inbuilt redundancies,  which ensures that life is not immediately threatened if a component malfunctions; but sometimes a homeostatic malfunction can result in serious disease, which can be fatal if not treated. A well-known example of a homeostatic failure is shown in type 1 diabetes mellitus. Here blood sugar regulation is unable to function because the beta cells of the pancreatic islets are destroyed and cannot produce the necessary insulin. The blood sugar rises in a condition known as hyperglycemia.
+The plasma ionized calcium homeostat can be disrupted by the constant, unchanging, over-production of parathyroid hormone by a parathyroid adenoma resulting in the typically features of hyperparathyroidism, namely high plasma ionized Ca2+ levels and the resorption of bone, which can lead to spontaneous fractures. The abnormally high plasma ionized calcium concentrations cause conformational changes in many cell-surface proteins (especially ion channels and hormone or neurotransmitter receptors) giving rise to lethargy, muscle weakness, anorexia, constipation and labile emotions.
+The body water homeostat can be compromised by the inability to secrete ADH in response to even the normal daily water losses via the exhaled air, the feces, and insensible sweating. On receiving a zero blood ADH signal, the kidneys produce huge unchanging volumes of very dilute urine, causing dehydration and death if not treated.
+As organisms age, the efficiency of their control systems becomes reduced. The inefficiencies gradually result in an unstable internal environment that increases the risk of illness, and leads to the physical changes associated with aging.
+Various chronic diseases are kept under control by homeostatic compensation, which masks a problem by compensating for it (making up for it) in another way.  However, the compensating mechanisms eventually wear out  or are disrupted by a new complicating factor (such as the advent of a concurrent acute viral infection), which sends the body reeling through a new cascade of events.  Such decompensation unmasks the underlying disease, worsening its symptoms. Common examples include decompensated heart failure, kidney failure, and liver failure according to Fan et al. (2011).
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+---
+title: "Homeostasis"
+chunk: 9/9
+source: "https://en.wikipedia.org/wiki/Homeostasis"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:31.436253+00:00"
+instance: "kb-cron"
+---
+
+== Biosphere ==
+In the Gaia hypothesis, James Lovelock stated that the entire mass of living matter on Earth (or any planet with life) functions as a vast homeostatic superorganism that actively modifies its planetary environment to produce the environmental conditions necessary for its own survival. In this view, the entire planet maintains several homeostasis (the primary one being temperature homeostasis). Whether this sort of system is present on Earth is open to debate. However, some relatively simple homeostatic mechanisms are generally accepted. For example, it is sometimes claimed that when atmospheric carbon dioxide levels rise, certain plants may be able to grow better and thus act to remove more carbon dioxide from the atmosphere. However, warming has exacerbated droughts, making water the actual limiting factor on land. When sunlight is plentiful and the atmospheric temperature climbs, it has been claimed that the phytoplankton of the ocean surface waters, acting as global sunshine, and therefore heat sensors, may thrive and produce more dimethyl sulfide (DMS). The DMS molecules act as cloud condensation nuclei, which produce more clouds, and thus increase the atmospheric albedo, and this feeds back to lower the temperature of the atmosphere. However, rising sea temperature has stratified the oceans, separating warm, sunlit waters from cool, nutrient-rich waters. Thus, nutrients have become the limiting factor, and plankton levels have actually fallen over the past 50 years, not risen. As scientists discover more about Earth, vast numbers of positive and negative feedback loops are being discovered,, that, together, maintain a metastable condition, sometimes within a very broad range of environmental conditions.
+
+== Predictive ==
+Predictive homeostasis is an anticipatory response to an expected challenge in the future, such as the stimulation of insulin secretion by gut hormones which enter the blood in response to a meal. This insulin secretion occurs before the blood sugar level rises, lowering the blood sugar level in anticipation of a large influx into the blood of glucose resulting from the digestion of carbohydrates in the gut. Such anticipatory reactions are open loop systems which are based, essentially, on "guess work", and are not self-correcting. Anticipatory responses always require a closed loop negative feedback system to correct the 'over-shoots' and 'under-shoots' to which the anticipatory systems are prone.
+
+== Other fields ==
+The term has come to be used in other fields, for example:
+
+=== Risk ===
+
+An actuary may refer to risk homeostasis, where (for example) people who have anti-lock brakes have no better safety record than those without anti-lock brakes, because the former unconsciously compensate for the safer vehicle via less-safe driving habits. Previous to the innovation of anti-lock brakes, certain maneuvers involved minor skids, evoking fear and avoidance: Now the anti-lock system moves the boundary for such feedback, and behavior patterns expand into the no-longer punitive area. It has also been suggested that ecological crises are an instance of risk homeostasis in which a particular behavior continues until proven dangerous or dramatic consequences actually occur.
+
+=== Stress ===
+Sociologists and psychologists may refer to stress homeostasis, the tendency of a population or an individual to stay at a certain level of stress, often generating artificial stresses if the "natural" level of stress is not enough.
+Jean-François Lyotard, a postmodern theorist, has applied this term to societal 'power centers' that he describes in The Postmodern Condition, as being 'governed by a principle of homeostasis,' for example, the scientific hierarchy, which will sometimes ignore a radical new discovery for years because it destabilizes previously accepted norms.
+
+=== Technology ===
+Familiar technological homeostatic mechanisms include:
+
+A thermostat operates by switching heaters or air-conditioners on and off in response to the output of a temperature sensor.
+Cruise control adjusts a car's throttle in response to changes in speed.
+An autopilot operates the steering controls of an aircraft or ship in response to deviation from a pre-set compass bearing or route.
+Process control systems in a chemical plant or oil refinery maintain fluid levels, pressures, temperature, chemical composition, etc. by controlling heaters, pumps and valves.
+The centrifugal governor of a steam engine, as designed by James Watt in 1788, reduces the throttle valve in response to increases in the engine speed, or opens the valve if the speed falls below the pre-set rate.
+
+=== Society and culture ===
+The use of sovereign power, codes of conduct, religious and cultural practices and other dynamic processes in a society can be described as a part of an evolved homeostatic system of regularizing life and maintaining an overall equilibrium that protects the security of the whole from internal and external imbalances or dangers. Healthy civic cultures can be said to have achieved an optimal homeostatic balance between multiple contradictory concerns such as in the tension between respect for individual rights and concern for the public good, or that between governmental effectiveness and responsiveness to the interests of citizens.
+
+== See also ==
+
+== References ==
+
+== Further reading ==
+
+== External links ==
+
+Homeostasis Archived 15 August 2017 at the Wayback Machine
+Walter Bradford Cannon, Homeostasis (1932)
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+---
+title: "Hybrid (biology)"
+chunk: 1/5
+source: "https://en.wikipedia.org/wiki/Hybrid_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:32.895326+00:00"
+instance: "kb-cron"
+---
+
+In biology, a hybrid is the offspring resulting from combining the qualities of two organisms of different varieties, subspecies, species or genera through sexual reproduction. Generally, it means that each cell has genetic material from two different organisms, whereas an individual where some cells are derived from a different organism is called a chimera. Hybrids are not always intermediates between their parents such as in blending inheritance (a now discredited theory in modern genetics by particulate inheritance), but can show hybrid vigor, sometimes growing larger or taller than either parent. The concept of a hybrid is interpreted differently in animal and plant breeding, where there is interest in the individual parentage. In genetics, attention is focused on the numbers of chromosomes. In taxonomy, a key question is how closely related the parent species must be for their offspring to be classified as a hybrid, since crosses between species within the same genera are often treated differently from crosses between more distantly related taxa.
+Species are reproductively isolated by strong barriers to hybridization, which include genetic and morphological differences, differing times of fertility, mating behaviors and cues, and physiological rejection of sperm cells or the developing embryo. Some act before fertilization and others after it. Similar barriers exist in plants, with differences in flowering times, pollen vectors, inhibition of pollen tube growth, somatoplastic sterility, cytoplasmic-genic male sterility and the structure of the chromosomes. A few animal species and many plant species, however, are the result of hybrid speciation, including important crop plants such as wheat, where the number of chromosomes has been doubled.
+A form of often intentional human-mediated hybridization is the crossing of wild and domesticated species. This is common in both traditional horticulture and modern agriculture; many commercially useful fruits, flowers, garden herbs, and trees have been produced by hybridization. One such flower, Oenothera lamarckiana, was central to early genetics research into mutationism and polyploidy. It is also more occasionally done in the livestock and pet trades; some well-known wild × domestic hybrids are beefalo and wolfdogs. Human selective breeding of domesticated animals and plants has also resulted in the development of distinct breeds (usually called cultivars in reference to plants); crossbreeds between them (without any wild stock) are sometimes also imprecisely referred to as "hybrids".   
+Hybrid humans existed in prehistory. For example, Neanderthals and anatomically modern humans are thought to have interbred as recently as 40,000 years ago. Mythological hybrids appear in human culture in forms as diverse as the Minotaur, blends of animals, humans and mythical beasts such as centaurs and sphinxes, and the Nephilim of the Biblical apocrypha described as the wicked sons of fallen angels and attractive women.
+
+== Significance ==
+
+=== In evolution ===
+
+Hybridization between species plays an important role in evolution, though there is much debate about its significance. Roughly 25% of plants and 10% of animals are known to form hybrids with at least one other species. One example of an adaptive benefit to hybridization is that hybrid individuals can form a "bridge" transmitting potentially helpful genes from one species to another when the hybrid backcrosses with one of its parent species, a process called introgression. Hybrids can also cause speciation, either because the hybrids are genetically incompatible with their parents and not each other, or because the hybrids occupy a different niche than either parent. 
+Hybridization is a particularly common mechanism for speciation in plants, and is now known to be fundamental to the evolutionary history of plants. Plants frequently form polyploids, individuals with more than two copies of each chromosome. Whole genome doubling has occurred repeatedly in plant evolution. When two plant species hybridize, the hybrid may double its chromosome count by incorporating the entire nuclear genome of both parents, resulting in offspring that are reproductively incompatible with either parent because of different chromosome counts.
+
+=== In conservation ===
+Human impact on the environment has resulted in an increase in the interbreeding between regional species, and the proliferation of introduced species worldwide has also resulted in an increase in hybridization. This has been referred to as genetic pollution out of concern that it may threaten many species with extinction. Similarly, genetic erosion from monoculture in crop plants may be damaging the gene pools of many species for future breeding. 
+The conservation impacts of hybridization between species are highly debated. While hybridization could potentially threaten rare species or lineages by "swamping" the genetically "pure" individuals with hybrids, hybridization could also save a rare lineage from extinction by introducing genetic diversity. It has been proposed that hybridization could be a useful tool to conserve biodiversity by allowing organisms to adapt, and that efforts to preserve the separateness of a "pure" lineage could harm conservation by lowering the organisms' genetic diversity and adaptive potential, particularly in species with low populations. While endangered species are often protected by law, hybrids are often excluded from protection, resulting in challenges to conservation. 
+
+== Etymology ==
+
+The term hybrid is derived from Latin hybrida, used for crosses such as of a tame sow and a wild boar. The term came into popular use in English in the 19th century, though examples of its use have been found from the early 17th century.
+Conspicuous hybrids are popularly named with portmanteau words, starting in the 1920s with the breeding of tiger–lion hybrids (liger and tigon). Examples of this include the cama, pumapard, sturddlefish, and wholphin.
+
+== As seen by different disciplines ==
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+---
+title: "Hybrid (biology)"
+chunk: 2/5
+source: "https://en.wikipedia.org/wiki/Hybrid_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:32.895326+00:00"
+instance: "kb-cron"
+---
+
+=== Animal and plant breeding ===
+From the point of view of animal and plant breeders, there are several kinds of hybrid formed from crosses within a species, such as between different breeds. Single cross hybrids result from the cross between two true-breeding organisms which produces an F1 hybrid (first filial generation). The cross between two different homozygous lines produces an F1 hybrid that is heterozygous; having two alleles, one contributed by each parent and typically one is dominant and the other recessive. Typically, the F1 generation is also phenotypically homogeneous, producing offspring that are all similar to each other.
+Double cross hybrids result from the cross between two different F1 hybrids (i.e., there are four unrelated grandparents).
+Three-way cross hybrids result from the cross between an F1 hybrid and an inbred line. Triple cross hybrids result from the crossing of two different three-way cross hybrids. Top cross (or "topcross") hybrids result from the crossing of a top quality or pure-bred male and a lower quality female, intended to improve the quality of the offspring, on average.
+ Population hybrids result from the crossing of plants or animals in one population with those of another population. These include interspecific hybrids or crosses between different breeds. In biology, the result of crossing of two populations is called a synthetic population.
+In horticulture, the term stable hybrid is used to describe an annual plant that, if grown and bred in a small monoculture free of external pollen (e.g., an air-filtered greenhouse) produces offspring that are "true to type" with respect to phenotype; i.e., a true-breeding organism.
+
+=== Biogeography ===
+
+Hybridization can occur in the hybrid zones where the geographical ranges of species, subspecies, or distinct genetic lineages overlap. For example, the butterfly Limenitis arthemis has two major subspecies in North America, L. a. arthemis (the white admiral) and L. a. astyanax (the red-spotted purple). The white admiral has a bright, white band on its wings, while the red-spotted purple has cooler blue-green shades. Hybridization occurs between a narrow area across New England, southern Ontario, and the Great Lakes, the "suture region". It is at these regions that the subspecies were formed. Other hybrid zones have formed between described species of plants and animals.
+
+=== Genetics ===
+
+From the point of view of genetics, several different kinds of hybrid can be distinguished.
+A genetic hybrid carries two different alleles of the same gene, where for instance one allele may code for a lighter coat colour than the other. A structural hybrid results from the fusion of gametes that have differing structure in at least one chromosome, as a result of structural abnormalities. A numerical hybrid results from the fusion of gametes having different haploid numbers of chromosomes. A permanent hybrid results when only the heterozygous genotype occurs, as in Oenothera lamarckiana, because all homozygous combinations are lethal. In the early history of genetics, Hugo de Vries supposed these were caused by mutation.
+
+=== Genetic complementation ===
+Genetic complementation is a hybridization test widely used in genetics to determine whether two separately isolated mutants that have the same (or similar) phenotype are defective in the same gene or in different genes (see complementation).  If a hybrid organism containing the genomes of two different mutant parental organisms displays a wild type phenotype, it is ordinarily considered that the two parental mutant organisms are defective in different genes.  If the hybrid organism displays a distinctly mutant phenotype, the two mutant parental organisms are  considered to be defective in the same gene.  However, in some cases the hybrid organism may display a phenotype that is only weakly (or partially) wild-type, and this may reflect intragenic (interallelic) complementation.
+
+=== Taxonomy ===
+
+From the point of view of taxonomy, hybrids differ according to their parentage.
+Hybrids between different subspecies (such as between the dog and Eurasian wolf) are called intra-specific hybrids. Interspecific hybrids are the offspring from interspecies mating; these sometimes result in hybrid speciation. Intergeneric hybrids result from matings between different genera, such as between sheep and goats. Interfamilial hybrids, such as between chickens and guineafowl or pheasants, are reliably described but extremely rare. Interordinal hybrids (between different orders) are few, but have been engineered between the sea urchin Strongylocentrotus purpuratus (female) and the sand dollar Dendraster excentricus (male).
+
+== Biology ==
+
+=== Expression of parental traits ===
+
+When two distinct types of organisms breed with each other, the resulting hybrids typically have intermediate traits (e.g., one plant parent has red flowers, the other has white, and the hybrid, pink flowers). Commonly, hybrids also combine traits seen only separately in one parent or the other (e.g., a bird hybrid might combine the yellow head of one parent with the orange belly of the other).
+
+=== Mechanisms of reproductive isolation ===
+
+Interspecific hybrids are bred by mating individuals from two species, normally from within the same genus. The offspring display traits and characteristics of both parents, but are often sterile, preventing gene flow between the species. Sterility is often attributed to the different number of chromosomes between the two species. For example, donkeys have 62 chromosomes, horses have 64 chromosomes, and mules or hinnies have 63 chromosomes. Mules, hinnies, and other normally sterile interspecific hybrids cannot produce viable gametes, because differences in chromosome structure prevent appropriate pairing and segregation during meiosis, meiosis is disrupted, and viable sperm and eggs are not formed. However, fertility in female mules has been reported with a donkey as the father.
+A variety of mechanisms limit the success of hybridization, including the large genetic difference between most species. Barriers include morphological differences, differing times of fertility, mating behaviors and cues, and physiological rejection of sperm cells or the developing embryo. Some act before fertilization; others after it.
+In plants, some barriers to hybridization include blooming period differences, different pollinator vectors, inhibition of pollen tube growth, somatoplastic sterility, cytoplasmic-genic male sterility and structural differences of the chromosomes.
+
+=== Speciation ===
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+---
+title: "Hybrid (biology)"
+chunk: 3/5
+source: "https://en.wikipedia.org/wiki/Hybrid_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:32.895326+00:00"
+instance: "kb-cron"
+---
+
+A few animal species are the result of hybridization. The Lonicera fly is a natural hybrid. The American red wolf appears to be a hybrid of the gray wolf and the coyote, although its taxonomic status has been a subject of controversy. The European edible frog is a semi-permanent hybrid between pool frogs and marsh frogs; its population requires the continued presence of at least one of the parent species. Cave paintings indicate that the European bison is a natural hybrid of the aurochs and the steppe bison.
+Plant hybridization is more commonplace compared to animal hybridization. Many crop species are hybrids, including notably the polyploid wheats: some have four sets of chromosomes (tetraploid) or six (hexaploid), while other wheat species have (like most eukaryotic organisms) two sets (diploid), so hybridization events likely involved the doubling of chromosome sets, causing immediate genetic isolation.
+Hybridization may be important in speciation in some plant groups. However, homoploid hybrid speciation (not increasing the number of sets of chromosomes) may be rare: by 1997, only eight natural examples had been fully described. Experimental studies suggest that hybridization offers a rapid route to speciation, a prediction confirmed by the fact that early generation hybrids and ancient hybrid species have matching genomes, meaning that once hybridization has occurred, the new hybrid genome can remain stable.
+Many hybrid zones are known where the ranges of two species meet, and hybrids are continually produced in great numbers. These hybrid zones are useful as biological model systems for studying the mechanisms of speciation. Recently DNA analysis of a bear shot by a hunter in the Northwest Territories confirmed the existence of naturally occurring and fertile grizzly–polar bear hybrids.
+
+=== Hybrid vigour ===
+
+Hybridization between reproductively isolated species often results in hybrid offspring with lower fitness than either parental. However, hybrids are not, as might be expected, always intermediate between their parents (as if there were blending inheritance), but are sometimes stronger or perform better than either parental lineage or variety, a phenomenon called heterosis, hybrid vigour, or heterozygote advantage. This is most common with plant hybrids. A transgressive phenotype is a phenotype that displays more extreme characteristics than either of the parent lines. Plant breeders use several techniques to produce hybrids, including line breeding and the formation of complex hybrids. An economically important example is hybrid maize (corn), which provides a considerable seed yield advantage over open pollinated varieties. Hybrid seed dominates the commercial maize seed market in the United States, Canada and many other major maize-producing countries.
+In a hybrid, any trait that falls outside the range of parental variation (and is thus not simply intermediate between its parents) is considered heterotic. Positive heterosis produces more robust hybrids, they might be stronger or bigger; while the term negative heterosis refers to weaker or smaller hybrids. Heterosis is common in both animal and plant hybrids. For example, hybrids between a lion and a tigress ("ligers") are much larger than either of the two progenitors, while "tigons" (lioness × tiger) are smaller. Similarly, the hybrids between the common pheasant (Phasianus colchicus) and domestic fowl (Gallus gallus) are larger than either of their parents, as are those produced between the common pheasant and hen golden pheasant (Chrysolophus pictus). Spurs are absent in hybrids of the former type, although present in both parents.
+
+== Human influence ==
+
+=== Anthropogenic hybridization ===
+Hybridization is greatly influenced by human impact on the environment, through effects such as habitat fragmentation and species introductions. Such impacts make it difficult to conserve the genetics of populations undergoing introgressive hybridization. Humans have introduced species worldwide to environments for a long time, both intentionally for purposes such as biological control, and unintentionally, as with accidental escapes of individuals. Introductions can drastically affect populations, including through hybridization.
+
+=== Management ===
+
+There is a kind of continuum with three semi-distinct categories dealing with anthropogenic hybridization: hybridization without introgression, hybridization with widespread introgression (backcrossing with one of the parent species), and hybrid swarms (highly variable populations with much interbreeding as well as backcrossing with the parent species). Depending on where a population falls along this continuum, the management plans for that population will change. Hybridization is currently an area of great discussion within wildlife management and habitat management. Global climate change is creating other changes such as difference in population distributions which are indirect causes for an increase in anthropogenic hybridization.
+Conservationists disagree on when is the proper time to give up on a population that is becoming a hybrid swarm, or to try and save the still existing pure individuals. Once a population becomes a complete mixture, the goal becomes to conserve those hybrids to avoid their loss. Conservationists treat each case on its merits, depending on detecting hybrids within the population. It is nearly impossible to formulate a uniform hybridization policy, because hybridization can occur beneficially when it occurs "naturally", and when hybrid swarms are the only remaining evidence of prior species, they need to be conserved as well.
+
+=== Genetic mixing and extinction ===
+
+Regionally developed ecotypes can be threatened with extinction when new alleles or genes are introduced that alter that ecotype. This is sometimes called genetic mixing. Hybridization and introgression, which can happen in natural and hybrid populations, of new genetic material can lead to the replacement of local genotypes if the hybrids are more fit and have breeding advantages over the indigenous ecotype or species. These hybridization events can result from the introduction of non-native genotypes by humans or through habitat modification, bringing previously isolated species into contact. Genetic mixing can be especially detrimental for rare species in isolated habitats, ultimately affecting the population to such a degree that none of the originally genetically distinct population remains.
+
+=== Effect on biodiversity and food security ===
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+---
+title: "Hybrid (biology)"
+chunk: 4/5
+source: "https://en.wikipedia.org/wiki/Hybrid_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:32.895326+00:00"
+instance: "kb-cron"
+---
+
+In agriculture and animal husbandry, the Green Revolution's use of conventional hybridization increased yields by breeding high-yielding varieties. The replacement of locally indigenous breeds, compounded with unintentional cross-pollination and crossbreeding (genetic mixing), has reduced the gene pools of various wild and indigenous breeds resulting in the loss of genetic diversity. Since the indigenous breeds are often well-adapted to local extremes in climate and have immunity to local pathogens, this can be a significant genetic erosion of the gene pool for future breeding. Therefore, commercial plant geneticists strive to breed "widely adapted" cultivars to counteract this tendency.
+
+== Different taxa ==
+
+=== In animals ===
+
+==== Mammals ====
+
+Familiar examples of equid hybrids are the mule, a cross between a female horse and a male donkey, and the hinny, a cross between a female donkey and a male horse. Pairs of complementary types like the mule and hinny are called reciprocal hybrids. Polar bears and brown bears are another case of a hybridizing species pairs, and introgression among non-sister species of bears appears to have shaped the Ursidae family tree. Among many other mammal crosses are hybrid camels, crosses between a bactrian camel and a dromedary. There are many examples of felid hybrids, including the liger. The oldest-known animal hybrid bred by humans is the kunga equid hybrid produced as a draft animal and status symbol 4,500 years ago in Umm el-Marra, present-day Syria.
+
+The first known instance of hybrid speciation in marine mammals was discovered in 2014. The clymene dolphin (Stenella clymene) is a hybrid of two Atlantic species, the spinner and striped dolphins. In 2019, scientists confirmed that a skull found 30 years earlier was a hybrid between the beluga whale and narwhal, dubbed the narluga.
+
+==== Birds ====
+
+Hybridization between species is common in birds. Hybrid birds are purposefully bred by humans, but hybridization is also common in the wild. Waterfowl have a particularly high incidence of hybridization, with at least 60% of species known to produce hybrids with another species. Among ducks, mallards widely hybridize with many other species, and the genetic relationships between ducks are further complicated by the widespread gene flow between wild and domestic mallards.
+One of the most common interspecific hybrids in geese occurs between Greylag and Canada geese (Anser anser x Branta canadensis). One potential mechanism for the occurrence of hybrids in these geese is interspecific nest parasitism, where an egg is laid in the nest of another species to be raised by non-biological parents. The chick imprints upon and eventually seeks a mate among the species that raised it, instead of the species of its biological parents. 
+Cagebird breeders sometimes breed bird hybrids known as mules between species of finch, such as goldfinch × canary.
+
+==== Amphibians ====
+Among amphibians, Japanese giant salamanders and Chinese giant salamanders have created hybrids that threaten the survival of Japanese giant salamanders because of competition for similar resources in Japan.
+
+==== Fish ====
+Among fish, a group of about 50 natural hybrids between Australian blacktip shark and the larger common blacktip shark was found by Australia's eastern coast in 2012.
+Russian sturgeon and American paddlefish were hybridized in captivity when sperm from the paddlefish and eggs from the sturgeon were combined, unexpectedly resulting in viable offspring. This hybrid is called a sturddlefish.
+
+==== Cephalochordates ====
+The two genera Asymmetron and Branchiostoma are able to produce viable hybrid offspring, even if none have lived into adulthood so far, despite the parents' common ancestor living tens of millions of years ago.
+
+==== Insects ====
+Among insects, so-called killer bees were accidentally created during an attempt to breed a strain of bees that would both produce more honey and be better adapted to tropical conditions. It was done by crossing a European honey bee and an African bee.
+The Colias eurytheme and C. philodice butterflies have retained enough genetic compatibility to produce viable hybrid offspring. Hybrid speciation may have produced the diverse Heliconius butterflies, but that is disputed.
+The two closely related harvester ant species Pogonomyrmex barbatus and Pogonomyrmex rugosus have evolved to depend on hybridization. When a queen fertilizes her eggs with sperm from males of her own species, the offspring is always new queens. And when she fertilizes the eggs with sperm from males of the other species, the offspring is always sterile worker ants (and because ants are haplodiploid, unfertilized eggs become males). Without mating with males of the other species, the queens are unable to produce workers, and will fail to establish a colony of their own.
+
+=== In plants ===
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+---
+title: "Hybrid (biology)"
+chunk: 5/5
+source: "https://en.wikipedia.org/wiki/Hybrid_(biology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:32.895326+00:00"
+instance: "kb-cron"
+---
+
+Plant species hybridize more readily than animal species, and the resulting hybrids are fertile more often. Many plant species are the result of hybridization, combined with polyploidy, which duplicates the chromosomes. Chromosome duplication allows orderly meiosis and so viable seed can be produced.
+Plant hybrids are generally given names that include an "×" (not in italics), such as Platanus × hispanica for the London plane, a natural hybrid of P. orientalis (oriental plane) and P. occidentalis (American sycamore). The parent's names may be kept in their entirety, as seen in Prunus persica ×  Prunus americana, with the female parent's name given first, or if not known, the parent's names given alphabetically.
+Plant species that are genetically compatible may not hybridize in nature for various reasons, including geographical isolation, differences in flowering period, or differences in pollinators. Species that are brought together by humans in gardens may hybridize naturally, or hybridization can be facilitated by human efforts, such as altered flowering period or artificial pollination. Hybrids are sometimes created by humans to produce improved plants that have some of the characteristics of each of the parent species. Much work is now being done with hybrids between crops and their wild relatives to improve disease resistance or climate resilience for both agricultural and horticultural crops.
+Some crop plants are hybrids from different genera (intergeneric hybrids), such as Triticale, × Triticosecale, a wheat–rye hybrid. Most modern and ancient wheat breeds are themselves hybrids; bread wheat, Triticum aestivum, is a hexaploid hybrid of three wild grasses. Several commercial fruits including loganberry (Rubus × loganobaccus) and grapefruit (Citrus × paradisi) are hybrids, as are garden herbs such as peppermint (Mentha × piperita), and trees such as the London plane (Platanus × hispanica). Among many natural plant hybrids is Iris albicans, a sterile hybrid that spreads by rhizome division, and Oenothera lamarckiana, a flower that was the subject of important experiments by Hugo de Vries that produced an understanding of polyploidy.
+
+Sterility in a non-polyploid hybrid is often a result of chromosome number; if parents are of differing chromosome pair number, the offspring will have an odd number of chromosomes, which leaves them unable to produce chromosomally balanced gametes. While that is undesirable in a crop such as wheat, for which growing a crop that produces no seeds would be pointless, it is an attractive attribute in some fruits. Triploid bananas and watermelons are intentionally bred because they produce no seeds and are also parthenocarpic.
+
+=== In fungi ===
+Hybridization between fungal species is common and well established, particularly in  yeast. Yeast hybrids are widely found and used in human-related activities, such as brewing and winemaking. The production of lager beers for instance are known to be carried out by the yeast Saccharomyces pastorianus, a cryotolerant hybrid between Saccharomyces cerevisiae and Saccharomyces eubayanus, which allows fermentation at low temperatures. 
+
+=== In humans ===
+
+There is evidence of hybridization between modern humans and other species of the genus Homo. In 2010, the Neanderthal genome project showed that 1–4% of DNA from all people living today, apart from most Sub-Saharan Africans, is of Neanderthal heritage. Analyzing the genomes of 600 Europeans and East Asians found that combining them covered 20% of the Neanderthal genome that is in the modern human population. Ancient human populations lived and interbred with Neanderthals, Denisovans, and at least one other extinct Homo species. Thus, Neanderthal and Denisovan DNA has been incorporated into human DNA by introgression.
+In 1998, a complete prehistorical skeleton found in Portugal, the Lapedo child, had features of both anatomically modern humans and Neanderthals. Some ancient human skulls with especially large nasal cavities and unusually shaped braincases represent human-Neanderthal hybrids. A 37,000- to 42,000-year-old human jawbone found in Romania's Oase cave contains traces of Neanderthal ancestry from only four to six generations earlier. All genes from Neanderthals in the current human population are descended from Neanderthal fathers and human mothers.
+
+== Mythology ==
+
+Folk tales and myths sometimes contain mythological hybrids; the Minotaur was the offspring of a human, Pasiphaë, and a white bull. More often, they are composites of the physical attributes of two or more kinds of animals, mythical beasts, and humans, with no suggestion that they are the result of interbreeding, as in the centaur (man/horse), chimera (goat/lion/snake), hippocamp (fish/horse), and sphinx (woman/lion). The Old Testament mentions a first generation of half-human hybrid giants, the Nephilim, while the apocryphal Book of Enoch describes the Nephilim as the wicked sons of fallen angels and attractive women.
+
+== See also ==
+
+== Notes ==
+
+== References ==
+
+== External links ==
+
+Artificial Hybridisation Archived 8 March 2021 at the Wayback Machine – Artificial Hybridisation in orchids
+Domestic Fowl Hybrids
+Scientists Create Butterfly Hybrid – Creation of new species through hybridization was thought to be common only in plants, and rare in animals (archived 3 December 2008)
+What is a human admixed embryo? (archived 25 February 2012)
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+---
+title: "Hybrid incompatibility"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Hybrid_incompatibility"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:34.128889+00:00"
+instance: "kb-cron"
+---
+
+Hybrid incompatibility is a phenomenon in plants and animals, wherein offspring produced by the mating of two different species or populations have reduced viability and/or are less able to reproduce. Examples of hybrids include mules and ligers from the animal world, and subspecies of the Asian rice crop Oryza sativa from the plant world. Multiple models have been developed to explain this phenomenon. Recent research suggests that the source of this incompatibility is largely genetic, as combinations of genes and alleles prove lethal to the hybrid organism. Incompatibility is not solely influenced by genetics, however, and can be affected by environmental factors such as temperature.  The genetic underpinnings of hybrid incompatibility may provide insight into factors responsible for evolutionary divergence between species.
+
+
+== Background ==
+Hybrid incompatibility occurs when the offspring of two closely related species are not viable or suffer from infertility. Charles Darwin posited that hybrid incompatibility is not a product of natural selection, stating that the phenomenon is an outcome of the hybridizing species diverging, rather than something that is directly acted upon by selective pressures. The underlying causes of the incompatibility can be varied: earlier research focused on things like changes in ploidy in plants. More recent research has taken advantage of improved molecular techniques and has focused on the effects of genes and alleles in the hybrid and its parents.
+
+
+=== Dobzhansky-Muller model ===
+The first major breakthrough in the genetic basis of hybrid incompatibility is the Dobzhansky-Muller model, a combination of findings by Theodosius Dobzhansky and Joseph Muller between 1937 and 1942. The model provides an explanation as to why a negative fitness effect like hybrid incompatibility is not selected against. By hypothesizing that the incompatibility arose from alterations at two or more loci, rather than one, the incompatible alleles are in one hybrid individual for the first time rather than throughout the population - thus, hybrids that are infertile can develop while the parent populations remain viable. The negative fitness effects of infertility are not present in the original population. In this way, hybrid infertility contributes in some part to speciation by ensuring that gene flow between diverging species remains limited. Further analysis of the issue has supported this model, although it does not include conspecific genic interactions, a potential factor that more recent research has begun to look in to.
+
+
+=== Gene identification ===
+Decades after the research of Dobzhansky and Muller, the specifics of hybrid incompatibility were explored by Jerry Coyne and H. Allen Orr. Using introgression techniques to analyze the fertility in Drosophila hybrid and non-hybrid offspring, specific genes that contribute to sterility were identified; a study by Chung-I Wu which expanded on Coyne and Orr's work found that the hybrids of two Drosophila species were made sterile by the interaction of around 100 genes. These studies widened the scope of the Dobzhansky-Muller model, who thought it likely that more than two genes would be responsible. The ubiquity of Drosophila as a model organism has allowed many of the sterility genes to be sequenced in the years since Wu's study.
+
+
+== Modern directions ==
+With modern molecular techniques, researchers have been able to more accurately identify the underlying genetic causes of hybrid incompatibility. This has led to both the development of expansions to the Dobzhansky-Muller model. Recent research has also explored the possibility of external influences on sterility as well.
+
+
+=== The "snowball effect" ===
+An extension of the Dobzhansky-Muller model is the "snowball effect"; an accumulation of incompatible loci due to increased species divergence. Since the model posits that sterility is due to negative allelic interaction between the hybridizing species, as species become more diverged it follows that more negative interactions should develop. The snowball effect states that the number of these incompatibilities will increase exponentially over the time of divergence, particularly when more than two loci contribute to the incompatibility. This concept has been exhibited in tests with the flowering plant genus Solanum, with the findings supporting the genetic underpinnings of Dobzhansky-Muller: "Overall, our results indicate that the accumulation of sterility loci follows a different trajectory from the accumulation of loci for other quantitative species differences, consistent with the unique genetic basis expected to underpin species reproductive isolating barriers. ...In doing so, we uncover direct empirical support for the Dobzhansky-Muller model of hybrid incompatibility, and the snowball prediction in particular."
+
+
+=== Environmental influences ===
+Though the primary causes of hybrid incompatibility appear to be genetic, external factors may play a role as well. Studies focused primarily on model plants have found that the viability of hybrids can be dependent on environmental influence. Several studies on rice and Arabidopsis species identify temperature as an important factor in hybrid viability; generally, low temperatures seem to cause negative hybrid symptoms to be expressed while high temperatures suppress them, although one rice study found the opposite to be true. There has also been evidence in an Arabidopsis species that in poor environmental conditions (in this case, high temperatures), hybrids did not express negative symptoms and are viable with other populations. When environmental conditions return to normal, however, the negative symptoms are expressed and the hybrids are once again incompatible with other populations.
+
+
+=== Lynch-Force model ===
+Though a multitude of evidence supports the Dobzhansky-Muller model of hybrid sterility and speciation, this does not rule out the possibility that other situations besides the inviable combination of benign genes can lead to hybrid incompatibility. One such situation is incompatibility by way of gene duplication, or the Lynch and Force model (put forth by Michael Lynch and Allan Force in 2000). When gene duplication occurs, there is a possibility that a redundant gene can be rendered non-functional over time by mutations. From Lynch and Force's paper:"The divergent resolution of genomic redundancies, such that one population loses function from one copy while the second population loses function from a second copy at a  different chromosomal location, leads to chromosomal repatterning such that gametes produced by hybrid individuals can be completely lacking in functional genes for a duplicate pair." This hypothesis is relatively recent compared to Dobzhansky-Muller, but has support as well.
+
+
+=== Epigenetic influences ===
+A possible contributor to hybrid incompatibility that fits with the Lynch and Force model better than the Dobzhansky-Muller model is epigenetic inheritance. Epigenetics broadly refers to heritable elements that affect offspring phenotype without adjusting the DNA sequence of the offspring. When a particular allele has been epigenetically modified, it is referred to as an epiallele A study found that an Arabidopsis gene is not expressed because it is a silent epiallele, and when this epiallele is inherited by hybrids in combination with a mutant gene at the same locus, the hybrid is inviable. This fits with the Lynch and Force model because the heritable epiallele, ordinarily not an issue in non-hybrid populations with non-epiallele copies of the gene, becomes problematic when it is the only copy of the gene in the hybrid population.
+Study in Capsella shows that dosage of maternal small-interfering RNAs can contribute to hybrid incompatibility between closely related plant species.
+
+
+== See also ==
+Hybrid inviability
+
+
+== References ==
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+---
+title: "Individuation"
+chunk: 1/3
+source: "https://en.wikipedia.org/wiki/Individuation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:35.415660+00:00"
+instance: "kb-cron"
+---
+
+The principle of individuation, or principium individuationis, describes the manner in which a thing is identified as distinct from other things.
+The concept appears in numerous fields and is encountered in works of Leibniz, Carl Jung, Gunther Anders, Gilbert Simondon, Bernard Stiegler, Friedrich Nietzsche, Arthur Schopenhauer, David Bohm, Henri Bergson, Gilles Deleuze, and Manuel DeLanda.
+
+== Usage ==
+The word individuation occurs with different meanings and connotations in different fields.
+
+=== In philosophy ===
+
+Philosophically, "individuation" expresses the general idea of how a thing is identified as an individual thing that "is not something else". This includes how an individual person is held to be different from other elements in the world and how a person is distinct from other persons. By the seventeenth century, philosophers began to associate the question of individuation or what brings about individuality at any one time with the question of identity or what constitutes sameness at different points in time.
+
+=== In Jungian psychology ===
+
+In analytical psychology, individuation is the process by which the individual self develops out of an undifferentiated unconscious – seen as a developmental psychic process during which innate elements of personality, the components of the immature psyche, and the experiences of the person's life become, if the process is more or less successful, integrated over time into a well-functioning whole. Other psychoanalytic theorists describe it as the stage where an individual transcends group attachment and narcissistic self-absorption.
+
+=== In the news industry ===
+The news industry has begun using the term individuation to denote new printing and on-line technologies that permit mass customization of the contents of a newspaper, a magazine, a broadcast program, or a website so that its contents match each user's unique interests. This differs from the traditional mass-media practice of producing the same contents for all readers, viewers, listeners, or on-line users.
+Communications theorist Marshall McLuhan alluded to this trend when discussing the future of printed books in an electronically interconnected world in the 1970s and 1980s.
+
+=== In privacy and data protection law ===
+From around 2016, coinciding with increased government regulation of the collection and handling of personal data, most notably the GDPR in European Union law, individuation has been used to describe the "singling out" of a person from a crowd – a threat to privacy, autonomy and dignity.    
+Most data protection and privacy laws turn on the identifiability of an individual as the threshold criterion for when data subjects will need legal protection. However, privacy advocates argue that privacy harm can also arise from the ability to disambiguate or "single out" a person. Doing so allows the person, at an individual level, to be tracked, profiled, targeted, contacted, or subject to a decision or action which impacts them - even if their civil or legal identity is not known (or knowable).  
+In some jurisdictions the wording of the relevant statute already includes the concept of individuation, for example the California Consumer Privacy Act of 2018 (CCPA). In other jurisdictions, regulatory guidance has suggested that the concept of 'identification' includes individuation - i.e., the process by which an individual can be 'singled out' or distinguished from all other members of a group.     
+However, where privacy and data protection statutes use only the word "identification" or "identifiability", varying court decisions mean that there is not necessarily a consensus about whether the legal concept of identification already encompasses individuation or not.
+Rapid advances in technologies including artificial intelligence, and video surveillance coupled with facial recognition systems have now altered the digital environment to such an extent that ‘not identifiable by name’ is no longer an effective proxy for ‘will suffer no privacy harm’. Many data protection laws may require redrafting to give adequate protection to privacy interests, by explicitly regulating individuation as well as identification of individual people.
+
+=== In physics ===
+Two quantum entangled particles cannot be understood independently. Two or more states in quantum superposition, e.g., as in Schrödinger's cat being simultaneously dead and alive, is mathematically not the same as assuming the cat is in an individual alive state with 50% probability. The Heisenberg's uncertainty principle says that complementary variables, such as position and momentum, cannot both be precisely known – in some sense, they are not individual variables. A natural criterion of individuality has been suggested.
+
+== Arthur Schopenhauer ==
+For Schopenhauer, the principium individuationis is constituted of time and space, being the ground of multiplicity. In his view, the mere difference in location suffices to make two systems different, with each of the two states having its own real physical state, independent of the state of the other.
+This view influenced Albert Einstein. Schrödinger put the Schopenhaurian label on a folder of papers in his files “Collection of Thoughts on the physical Principium individuationis.”
+
+== Carl Jung ==
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+---
+title: "Individuation"
+chunk: 2/3
+source: "https://en.wikipedia.org/wiki/Individuation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:35.415660+00:00"
+instance: "kb-cron"
+---
+
+According to Jungian psychology, individuation (German: Individuation) is a process of psychological integration. "In general, it is the process by which individual beings are formed and differentiated [from other human beings]; in particular, it is the development of the psychological individual as a being distinct from the general, collective psychology."
+Individuation is a process of transformation whereby the personal and collective unconscious are brought into consciousness (e.g., by means of dreams, active imagination, or free association) to be assimilated into the whole personality. It is a completely natural process that is necessary for the integration of the psyche. Individuation has a holistic healing effect on the person, both mentally and physically.
+In addition to Jung's theory of complexes, his theory of the individuation process forms conceptions of an unconscious filled with mythic images, a non-sexual libido, the general types of extraversion and introversion, the compensatory and prospective functions of dreams, and the synthetic and constructive approaches to fantasy formation and utilization.
+"The symbols of the individuation process . . . mark its stages like milestones, prominent among them for Jungians being the shadow, the wise old man . . . and lastly the anima in man and the animus in woman." Thus, "There is often a movement from dealing with the persona at the start . . . to the ego at the second stage, to the shadow as the third stage, to the anima or animus, to the Self as the final stage. Some would interpose the Wise Old Man and the Wise Old Woman as spiritual archetypes coming before the final step of the Self."
+"The most vital urge in every being, the urge to self-realize, is the motivating force behind the individuation process. With the internal compass of our very nature set toward self-realization, the thrust to become who and what we are derives its power from the instincts. On taking up the study of alchemy, Jung realized his long-held desire to find a body of work expressive of the psychological processes involved in the overarching process of individuation."
+
+== Gilbert Simondon ==
+
+In L'individuation psychique et collective, Gilbert Simondon developed a theory of individual and collective individuation in which the individual subject is considered as an effect of individuation rather than a cause. Thus, the individual atom is replaced by a never-ending ontological process of individuation.
+Simondon also conceived of "pre-individual fields" which make individuation possible. Individuation is an ever-incomplete process, always leaving a "pre-individual" left over, which makes possible future individuations. Furthermore, individuation always creates both an individual subject and a collective subject, which individuate themselves concurrently. Like Maurice Merleau-Ponty, Simondon believed that the individuation of being cannot be grasped except by a correlated parallel and reciprocal individuation of knowledge.
+
+== Bernard Stiegler ==
+
+The philosophy of Bernard Stiegler draws upon and modifies the work of Gilbert Simondon on individuation and also upon similar ideas in Friedrich Nietzsche and Sigmund Freud. During a talk given at the Tate Modern art gallery in 2004, Stiegler summarized his understanding of individuation. The essential points are the following:
+
+The I, as a psychic individual, can only be thought in relationship to we, which is a collective individual. The I is constituted in adopting a collective tradition, which it inherits and in which a plurality of I ’s acknowledge each other’s existence.
+This inheritance is an adoption, in that I can very well, as the French grandson of a German immigrant, recognize myself in a past which was not the past of my ancestors but which I can make my own. This process of adoption is thus structurally factual.
+The I is essentially a process, not a state, and this process is an in-dividuation — it is a process of psychic individuation. It is the tendency to become one, that is, to become indivisible.
+This tendency never accomplishes itself because it runs into a counter-tendency with which it forms a metastable equilibrium. (It must be pointed out how closely this conception of the dynamic of individuation is to the Freudian theory of drives and to the thinking of Nietzsche and Empedocles.)
+The we is also such a process (the process of collective individuation). The individuation of the I is always inscribed in that of the we, whereas the individuation of the we takes place only through the individuations, polemical in nature, of the I ’s which constitute it.
+That which links the individuations of the I and the we is a pre-individual system possessing positive conditions of effectiveness that  belong to what Stiegler calls retentional apparatuses. These retentional apparatuses arise from a technical system which is the condition of the encounter of the I and the we — the individuation of the I and the we is, in this respect, also the individuation of the technical system.
+The technical system is an apparatus which has a specific role wherein all objects are inserted — a technical object exists only insofar as it is disposed within such an apparatus with other technical objects (this is what Gilbert Simondon calls the technical group).
+The technical system is also that which founds the possibility of the constitution of retentional apparatuses, springing from the processes of grammatization growing out of the process of individuation of the technical system. And these retentional apparatuses are the basis for the dispositions between the individuation of the I and the individuation of the we in a single process of psychic, collective, and technical individuation composed of three branches, each branching out into process groups.
+This process of triple individuation is itself inscribed within a vital individuation which must be apprehended as:
+the vital individuation of natural organs
+the technological individuation of artificial organs
+and the psycho-social individuation of organizations linking them together
+In the process of individuation, wherein knowledge as such emerges, there are individuations of mnemo-technological subsystems which overdetermine, qua specific organizations of what Stiegler calls tertiary retentions, the organization, transmission, and elaboration of knowledge stemming from the experience of the sensible.
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+---
+title: "Individuation"
+chunk: 3/3
+source: "https://en.wikipedia.org/wiki/Individuation"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:35.415660+00:00"
+instance: "kb-cron"
+---
+
+== In collectivistic cultures ==
+Research indicates that individuation is culturally mediated: in collectivist societies, expressions of individuation "take the lead" or "seek attention" rather than follow a singular independent pattern. Concepts like "integrative individuation" emphasize maintaining relational bonds rather than complete separation. Collectivist norms tend to discourage standing out, meaning individuation is often constrained or reshaped according to cultural values.
+
+== See also ==
+
+Akrasia
+Deindividuation
+Identical particles
+Identity formation
+Indiscernibles
+Individualistic culture
+Nekyia
+Positive disintegration
+Principle of individuation
+Rationalization (sociology)
+Self-actualization
+
+== References ==
+
+== Bibliography ==
+
+Gilbert Simondon, Du mode d'existence des objets techniques (Méot, 1958; Paris: Aubier, 1989, second edition). (in French)
+Gilbert Simondon, On the Mode of Existence of Technical Objects, Part 1, link to PDF of 1980 translation.
+Gilbert Simondon, L'individu et sa genèse physico-biologique (l'individuation à la lumière des notions de forme et d'information) (Paris: PUF, 1964; J.Millon, coll. Krisis, 1995, second edition). (in French)
+Gilbert Simondon, The Individual and Its Physico-Biological Genesis, Part 1, Part 2, links to HTML files of unpublished 2007 translation.
+Gilbert Simondon, L'Individuation psychique et collective (1964; Paris: Aubier, 1989). (in French)
+Bernard Stiegler, Acting Out.
+Bernard Stiegler, Temps et individuation technique, psychique, et collective dans l’oeuvre de Simondon. (in French)
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+---
+title: "Infraspecific name"
+chunk: 1/2
+source: "https://en.wikipedia.org/wiki/Infraspecific_name"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:36.651923+00:00"
+instance: "kb-cron"
+---
+
+In botany, an infraspecific name is the scientific name for any taxon below the rank of species, i.e. an infraspecific taxon or infraspecies. The scientific names of botanical taxa are regulated by the International Code of Nomenclature for algae, fungi, and plants (ICN). As specified by the ICN, the name of an infraspecific taxon is a combination of the name of a species and an infraspecific epithet, separated by a connecting term that denotes the rank of the taxon. An example of an infraspecific name is Astrophytum myriostigma subvar. glabrum, the name of a subvariety of the species Astrophytum myriostigma (bishop's hat cactus). In the previous example, glabrum is the infraspecific epithet.
+Names below the rank of species of animals and of cultivated plants are regulated by different codes of nomenclature and are formed somewhat differently.
+
+== Construction of infraspecific names ==
+Article 24 of the ICN describes how infraspecific names are constructed. The order of the three parts of an infraspecific name is:
+
+genus name, specific epithet, connecting term indicating the rank (not part of the name, but required), infraspecific epithet.
+It is customary to italicize all three parts of such a name, but not the connecting term. For example:
+
+Acanthocalycium klimpelianum var. macranthum
+genus name = Acanthocalycium, specific epithet = klimpelianum, connecting term = var. (short for "varietas" or variety), infraspecific epithet = macranthum
+Astrophytum myriostigma subvar. glabrum
+genus name = Astrophytum, specific epithet = myriostigma, connecting term = subvar. (short for "subvarietas" or subvariety), infraspecific epithet = glabrum
+The recommended abbreviations for ranks below species are:
+
+subspecies - recommended abbreviation: subsp. (but "ssp." is also in use although not recognised by Art 26)
+varietas (variety) - recommended abbreviation: var.
+subvarietas (subvariety) -  recommended abbreviation: subvar.
+forma (form) -  recommended abbreviation: f.
+subforma (subform) -  recommended abbreviation: subf.
+Although the connecting terms mentioned above are the recommended ones, the ICN allows for other connecting terms in validly published infraspecific taxa.  It specifically mentions that Greek letters α, β, γ, etc. can be used in this way in the original document and further ranks may be added without limit.  Names that use these connecting terms are now deprecated (though still legal), but they have an importance because they can be basionyms of current species.  The commonest cases use "β" and "b"; examples mentioned in the ICN are Cynoglossum cheirifolium β Anchusa (lanata) and Polyporus fomentarius β applanatus whilst other examples (coming from the fungus database Index Fungorum) are Agaricus plexipes b fuliginaria and Peziza capula ß cernua.  The ICN allows the possibility that a validly published name could have no defined rank and uses "[unranked]" as the connecting term in such cases.
+
+== Abbreviation of infraspecific names ==
+Like specific epithets, infraspecific epithets cannot be used in isolation as names. Thus the name of a particular species of Acanthocalycium is Acanthocalycium klimpelianum, which can be abbreviated to A. klimpelianum where the context makes the genus clear. The species cannot be referred to as just klimpelianum. In the same way, the name of a particular variety of Acanthocalycium klimpelianum is Acanthocalycium klimpelianum var. macranthum, which can be abbreviated to A. k. var. macranthum where the context makes the species clear. The variety cannot be referred to as just macranthum.
+Sometimes more than three parts will be given; strictly speaking, this is not a name, but a classification. The ICN gives the example of Saxifraga aizoon var. aizoon subvar. brevifolia f. multicaulis subf. surculosa; the name of the subform would be Saxifraga aizoon subf. surculosa.
+
+== Legitimate infraspecific names ==
+For a proposed infraspecific name to be legitimate it must be in accordance with all the rules of the ICN. Only some of the main points are described here.
+A key concept in botanical names is that of a type. In many cases the type will be a particular preserved specimen stored in a herbarium, although there are other kinds of type. Like other names, an infraspecific name is attached to a type. Whether a plant should be given a particular infraspecific name can then be decided by comparing it to the type.
+There is no requirement for a species to be divided into infraspecific taxa, of whatever rank; in other words, a species does not have to have subspecies, varieties, forms, etc. However, if infraspecific ranks are created, then the name of the type of the species must repeat the specific epithet as its infraspecific epithet. The type acquires this name automatically as soon as any infraspecific rank is created. As an example, consider Poa secunda J.Presl, whose type specimen is in the Wisconsin State Herbarium.
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+---
+title: "Infraspecific name"
+chunk: 2/2
+source: "https://en.wikipedia.org/wiki/Infraspecific_name"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:36.651923+00:00"
+instance: "kb-cron"
+---
+
+As soon as a subspecies of Poa secunda  was created, then the type specimen of P. secunda  immediately became the type specimen of Poa secunda subsp. secunda. The name "Poa secunda subsp. secunda" was automatically created (it is an "autonym"). Soreng created the subspecies Poa secunda subsp. juncifolia (whose type specimen is also in the Wisconsin State Herbarium), thereby making the type specimen of P. secunda also the type specimen of Poa secunda subsp. secunda.
+If in addition to the subspecies any variety of Poa secunda were to be created, then the type specimen of P. secunda  would automatically become the type specimen of Poa secunda var. secunda. The type specimen would then have the classification Poa secunda subsp. secunda var. secunda.
+The same epithet can be used again within a species, at whatever level, only if the names with the re-used epithet are attached to the same type. Thus there can be a form called Poa secunda f. juncifolia as well as the subspecies Poa secunda subsp. juncifolia if, and only if, the type specimen of Poa secunda f. juncifolia is the same as the type specimen of Poa secunda subsp. juncifolia (in other words, if there is a single type specimen whose classification is Poa secunda subsp. juncifolia f. juncifolia).
+If two infraspecific taxa which have different types are accidentally given the same epithet, then a homonym has been created. The earliest published name is the legitimate one and the other must be changed.
+
+== Specifying authors ==
+When indicating authors for infraspecific names, it is possible to show either just the author(s) of the final, infraspecific epithet, or the authors of both the specific and the infraspecific epithets, as is demonstrated throughout the ICN. Examples:
+
+Adenia aculeata subsp. inermis de Wilde
+This identifies de Wilde as the author who published this name for the subspecies (i.e. who created the epithet inermis). Note that here it was decided not to indicate authority for the species.
+Pinus nigra J.F.Arnold subsp. salzmannii (Dunal) Franco
+Here, J.F.Arnold is the author who gave the species, European black pine, its botanical name Pinus nigra; Dunal is the author who was the first to publish the epithet salzmanii for this taxon (as the species Pinus salzmanii); Franco is the author who reduced the taxon to a subspecies of Pinus nigra.
+
+== Difference from zoological nomenclature ==
+In zoological nomenclature, names of taxa below species rank are formed somewhat differently, using a trinomen or 'trinomial name'. No connecting term is required as there is only one rank below species, the subspecies.
+
+== Difference from prokaryotic nomenclature ==
+The Prokaryotic Code was split from the ICN in 1975. This nomenclature only governs one infraspecific rank, the subspecies, but allows a number of infrasubspecific subdivisions to be used. The authorship is to be specified in the form "Bacillus subtilis subsp. spizizenii Nakamura et al. 1999.", i.e. with only the infraspecific author.
+Authors may still choose to use ungoverned ranks such as sv. (serovar) and pv. (pathovar).
+
+== Cultivated plants ==
+The ICN does not regulate the names of cultivated plants, of cultivars, i.e. plants specifically created for use in agriculture or horticulture. Such names are regulated by the International Code of Nomenclature for Cultivated Plants (ICNCP).
+Although logically below the rank of species (and hence "infraspecific"), a cultivar name may be attached to any scientific name at the genus level or below. The minimum requirement is to specify a genus name. For example, Achillea 'Cerise Queen' is a cultivar; Pinus nigra 'Arnold Sentinel' is a cultivar of the species P. nigra (which is propagated vegetatively, by cloning).
+
+== See also ==
+International Code of Zoological Nomenclature
+International Code of Nomenclature for Cultivated Plants
+Cultivar
+Strain (biology)
+Race (biology)
+Variant (biology)
+Forma specialis, an informal naming system for parasites that is included in the botanical code of nomenclature
+Pathovar, a system for naming parasitic bacteria
+
+== References ==
+
+== Bibliography ==
+Turland, N.J.; et al., eds. (2017), International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017, vol. Regnum Vegetabile 154 (electronic ed.), Glashütten: International Association for Plant Taxonomy, retrieved 2019-02-21
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+---
+title: "Klepton"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Klepton"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:37.873011+00:00"
+instance: "kb-cron"
+---
+
+In biology, a klepton (abbreviated kl.) and synklepton (abbreviated sk.) is a species that requires input from another biological taxon (normally from a species which is closely related to the kleptonic species) to complete its reproductive cycle. Specific types of kleptons are zygokleptons, which reproduce by zygogenesis; gynokleptons which reproduce by gynogenesis, and tychokleptons, which reproduce by a combination of both systems.
+Kleptogenic reproduction results in three potential outcomes:
+
+A unisexual female may simply activate cell division in the egg through the presence of a male's sperm without incorporating any of his genetic material—this results in the production of clonal offspring.
+The female may also incorporate the male's sperm into her egg, but can do so without excising any of her genetic material. This results in increased ploidy levels that range from triploid to pentaploid in wild individuals.
+Finally, the female also has the option of replacing some of her genetic material with that of the male's, resulting in a "hybrid" of sorts without increasing ploidy.
+
+
+== Etymology ==
+The term is derived from the (Ancient or Modern) Greek κλέπτ(ης), klépt(ēs), 'thief' + -on, after taxon, or kleptein, 'to steal'. A klepton "steals" from an exemplar of another species in order to reproduce. In a paper entitled "Taxonomy of Parthenogenetic Species of Hybrid Origin", Charles J. Cole argues that the thief motif closely parallels the behaviour of certain reptiles.
+
+
+== Examples ==
+
+
+=== Salamander species ===
+In the wild, five species of Ambystoma salamanders contribute to a unisexual complex that reproduces via a combination of gynogenesis and kleptogenesis: A. tigrinum, A. barbouri, A. texanum, A. jeffersonium, and A. laterale. Over twenty genomic combinations have been found in nature, ranging from "LLJ" individuals (two A. laterale and an A. jeffersonium genome) to "LJTi" individuals (an A. laterale, A. jeffersonium, and an A. tigrinum genome). Every combination, however, contains the genetic information from the A. laterale species, and analysis of mitochondrial DNA has indicated that these unisexual species most likely diverged from an A. barbouri individual some 5 million years ago, making them the oldest known unisexual vertebrate species.
+
+The fact that these salamanders have persisted for so long is remarkable, as it contradicts the notion that a majority of asexual lineages arise when the conditions are right and quickly disappear. It has been argued that this persistence is very much due to the aforementioned "genome replacement" strategy that accompanies kleptogenic reproduction—replacing a portion of the maternal genome with paternal DNA in offspring has allowed unisexual individuals to "refresh" their genetic material through time. This facet of kleptogenesis was recently ascertained from genetic research that indicates there is no ancestral A. laterale genome that is maintained from one unisexual to the next, and that there is not a specific "L" genome that is found more often than others. "L" genetic material found in these salamanders has also not evolved to be substantially unique from sexual genomes.
+In 2007 Bogart et al found that, within a population, unisexual and sexual individuals are able to co-exist; that the genetic makeup of the unisexuals is highly variable; and that unisexual individuals share alleles with sexual individuals.
+
+
+=== Frog species ===
+Other species exhibiting the property include European water frogs of the genus Pelophylax.
+
+
+=== Fish species ===
+The Amazon Molly (Poecilia formosa) exhibits gynogenesis.
+
+
+== See also ==
+Eukaryotes, which can be unisexual or asexual
+Gametophytic apomixis, a phenomenon in plants that requires fertilization of the endosperm, but reproduction is clonal
+Gynogenesis
+
+
+== References ==
+
+Dubois, A.; Günther, R. (1982), "Klepton and synklepton: two new evolutionary systematics categories in zoology", Zoologische Jahrbücher, Abteilung für Systematik, Ökologie & Biologie der Tiere, 109: 290–305
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+---
+title: "Landrace"
+chunk: 1/3
+source: "https://en.wikipedia.org/wiki/Landrace"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:39.109121+00:00"
+instance: "kb-cron"
+---
+
+A landrace is a domesticated, locally adapted, often traditional variety of a species of animal or plant that has developed over time, through adaptation to its natural and cultural environment of agriculture and pastoralism, and due to isolation from other populations of the species. Landraces are distinct from cultivars and from standard breeds.|
+Landrace dogs are commonly referenced. They typically have distinct ecological and behavioral characteristics that evolutionally developed in certain nations and locales, especially those with a history of colonization.
+A significant proportion of farmers around the world grow landrace crops, and most plant landraces are associated with traditional agricultural systems. Landraces of many crops have probably been grown for millennia. Increasing reliance upon modern plant cultivars that are bred to be uniform has led to a reduction in biodiversity, because most of the genetic diversity of domesticated plant species lies in landraces and other traditionally used varieties. Some farmers using scientifically improved varieties also continue to raise landraces for agronomic reasons that include better adaptation to the local environment, lower fertilizer requirements, lower cost, and better disease resistance. Cultural and market preferences for landraces include culinary uses and product attributes such as texture, color, or ease of use.
+Plant landraces have been the subject of more academic research, and the majority of academic literature about landraces is focused on botany in agriculture, not animal husbandry. Animal landraces are distinct from ancestral wild species of modern animal stock, and are also distinct from separate species or subspecies derived from the same ancestor as modern domestic stock. Not all landraces derive from wild or ancient animal stock; in some cases, notably dogs and horses, domestic animals have escaped in sufficient numbers in an area to breed feral populations that form new landraces through evolutionary pressure.
+
+== Characteristics ==
+There are differences between authoritative sources on the specific criteria which describe landraces, although there is broad consensus about the existence and utility of the classification. Individual criteria may be weighted differently depending on a given source's focus (e.g., governmental regulation, biological sciences, agribusiness, anthropology and culture, environmental conservation, pet-keeping and -breeding, etc.). Additionally, not all cultivars agreed to be landraces exhibit every characteristic of a landrace. General features that characterize a landrace may include:
+
+It is morphologically distinctive and identifiable (i.e., has particular and recognizable characteristics or properties), yet remains "dynamic".
+It is genetically adapted to, and has a reputation for being able to withstand, the conditions of the local environment, including climate, disease and pests, even cultural practices.
+It is not the product of formal (governmental, organizational, or private) breeding programs, and may lack systematic selection, development and improvement by breeders.
+It is maintained and fostered less deliberately than a standardized breed, with its genetic isolation principally a matter of geography acting upon whatever animals that happened to be brought by humans to a given area.
+It has a historical origin in a specific geographic area, will usually have its own local name(s), and will often be classified according to intended purpose.
+Where yield (e.g. of a grain or fruit crop) can be measured, a landrace will show high stability of yield, even under adverse conditions, but a moderate yield level, even under carefully managed conditions.
+At the level of genetic testing, its heredity will show a degree of integrity, but still some genetic heterogeneity (i.e. genetic diversity).
+
+== Terminology ==
+
+Landrace literally means 'country-breed' (German: Landrasse) and close cognates of it are found in various Germanic languages. The first known reference to the role of landraces as genetic resources was made in 1890 at an agriculture and forestry congress in Vienna, Austria. The term was first defined by Kurt von Rümker in 1908, and more clearly described in 1909 by U. J. Mansholt, who wrote that landraces have more stable characteristics and better resistance to adverse conditions, but have lower production capacity than cultivars, and are apt to change genetically when moved to another environment. Hans Kiessling added in 1912 that a landrace is a mixture of phenotypic forms despite relative outward uniformity, and a great adaptability to its natural and human environment.
+The word landrace entered non-academic English in the early 1930s, by way of the Danish Landrace pig, a particular breed of lop-eared swine. Many other languages do not use separate terms, like landrace and breed, but instead rely on extended description to convey such distinctions. Spanish is one such language.
+Geneticist D. Phillip Sponenberg described animal breeds within these classes: the landrace, the standardized breed, modern "type" breeds, industrial strains, and feral populations. He describes landraces as an early stage of breed development, created by a combination of founder effect, isolation, and environmental pressures. Human selection for production goals is also typical of landraces.
+As discussed in more detail in breed, that term itself has several definitions from various scientific and animal husbandry perspectives. Some of those senses of breed relate to the concept of landraces. A Food and Agriculture Organization of the United Nations (FAO) guideline defines landrace and landrace breed as "a breed that has largely developed through adaptation to the natural environment and traditional production system in which it has been raised." This is in contrast to its definition of a standardized breed: "a breed of livestock that was developed according to a strict programme of genetic isolation and formal artificial selection to achieve a particular phenotype."
+In various domestic species (including pigs, goats, sheep and geese) some standardized breeds include "Landrace" in their names, but do not meet widely used definitions of landraces. For example, the British Landrace pig is a standardized breed, derived from earlier breeds with "Landrace" names.
+Farmers' variety, usually applied to local cultivars, or seen as intermediate between a landrace and a cultivar, may also include landraces when referring to plant varieties not subjected to formal breeding programs.
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+---
+title: "Landrace"
+chunk: 2/3
+source: "https://en.wikipedia.org/wiki/Landrace"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:39.109121+00:00"
+instance: "kb-cron"
+---
+
+=== Autochthonous and allochthonous landraces ===
+A landrace native to, or produced for a long time within the agricultural system in which it is found is referred to as an autochthonous landrace, while a more recently introduced one is termed an allochthonous landrace.
+Within academic agronomy, the term autochthonous landrace is sometimes used with a more technical, productivity-related definition, synthesized by A. C. Zeven from previous definitions beginning with Mansholt's: "an autochthonous landrace is a variety with a high capacity to tolerate biotic and abiotic stress, resulting in a high yield stability and an intermediate yield level under a low input agricultural system."
+The terms autochthonous and allochthonous are most often applied to plants, with animals more often being referred to as indigenous or native. Examples of references in sources to long-term local landraces of livestock include constructions such as "indigenous landraces of sheep", and "Leicester Longwool sheep were bred to the native landraces of the region".  Some usage of autochthonous does occur in reference to livestock, e.g. "autochthonous races of cattle such as the Asturian mountain cattle – Ratina and Casina – and Tudanca cattle."
+
+== Biodiversity and conservation ==
+
+A significant proportion of farmers around the world grow landrace crops. However, as industrialized agriculture spreads, cultivars, which are selectively bred for high yield, rapid growth, disease and drought resistance, and other commercial production values, are supplanting landraces, putting more and more of them at risk of extinction.
+In 1927 at the International Agricultural Congress, organized by the predecessor of the FAO, an extensive discussion was held on the need to conserve landraces. A recommendation that members organize nation-by-nation landrace conservation did not succeed in leading to widespread conservation efforts.
+Landraces are often free from many intellectual property and other regulatory encumbrances. However, in some jurisdictions, a focus on their production may result in missing out on some benefits afforded to producers of genetically selected and homogenous organisms, including breeders' rights legislation, easier availability of loans and other business services, even the right to share seed or stock with others, depending on how favorable the laws in the area are to high-yield agribusiness interests.
+As Regine Andersen of the Fridtjof Nansen Institute (Norway) and the Farmers' Rights Project puts it, "Agricultural biodiversity is being eroded. This trend is putting at risk the ability of future generations to feed themselves. In order to reverse the trend, new policies must be implemented worldwide. The irony of the matter is that the poorest farmers are the stewards of genetic diversity." Protecting farmer interests and protecting biodiversity is at the heart of the International Treaty on Plant Genetic Resources for Food and Agriculture (the "Plant Treaty" for short), under the Food and Agriculture Organization of the United Nations (FAO), though its concerns are not exclusively limited to landraces.
+Landraces played a basic role in the development of the standardized breeds but are today threatened by the market success of the standardized breeds. In developing countries, landraces still play an important role, especially in traditional production systems. Specimens within an animal landrace tend to be genetically similar, though more diverse than members of a standardized or formal breed.
+
+=== In situ and ex situ landrace conservation ===
+Two approaches have been used to conserve plant landraces:
+
+in situ where the landrace is grown and conserved by farmers on farms.
+ex situ where the landrace is conserved in an artificial environment such as a gene-bank, using controls such as laminated packets kept frozen at −18 °C (0 °F).
+As the amount of agricultural land dedicated to growing landrace crops declines, such as in the example of wheat landraces in the Fertile Crescent, landraces can become extinct in cultivation. Therefore ex situ landrace conservation practices are considered a way to avoid losing the genetic diversity completely. Research published in 2020 suggested that existing ways of cataloging diversity within ex situ genebanks fall short of cataloging the appropriate information for landrace crops.
+An in situ conservation effort to save the Berrettina di Lungavilla squash landrace made use of participatory plant breeding practices in order to incorporate the local community into the work.
+
+=== Preserving cereal landraces ===
+Preservation efforts for cereal strains are ongoing including in situ and in online-searchable germplasm collections (seed banks), coordinated by Biodiversity International and the National Institute of Agricultural Botany (NIAB, UK). However, more may need to be done, because plant genetic variety, the source of crop health and seed quality, depends on a diversity of landraces and other traditionally used varieties. Efforts (as of 2008) were mostly focused on Iberia, the Balkans, and European Russia, and dominated by species from mountainous areas. Despite their incompleteness, these efforts have been described as "crucial in preventing the extinction of many of these local ecotypes".
+An agricultural study published in 2008 showed that landrace cereal crops began to decline in Europe in the 19th century such that cereal landraces "have largely fallen out of use" in Europe. Landrace cultivation in central and northwest Europe was almost eradicated by the early 20th century, due to economic pressure to grow improved, modern cultivars. While many in the region are already extinct, some have survived by being passed from generation to generation, and have also been revived by enthusiasts outside Europe to preserve European agriculture and food culture elsewhere. These survivals are usually for specific uses, such as thatch, and traditional European cuisine and craft beer brewing.
+
+== Plants ==
+
+=== Plant landrace development ===
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+---
+title: "Landrace"
+chunk: 3/3
+source: "https://en.wikipedia.org/wiki/Landrace"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:39.109121+00:00"
+instance: "kb-cron"
+---
+
+The label landrace includes regional cultigens that are genetically heterogeneous, but with enough characteristics in common to permit their recognition as a group. These characteristics are used by farmers to manage diversity and purity within landraces.
+In some cultures, the development of new landraces is typically limited to members of specific social groups, such as women or shaman. Maintaining existing landraces, like developing new landraces, requires that farmers be able to identify crop-specific characteristics and that those characteristics are passed on to following generations.
+Over time, the process of identifying the distinguishing characteristic or features of a new landrace is reinforced by cultivation processes; for example, descendants of a plant that is notably drought tolerant may become iteratively more so through selective breeding as farmers regard it as better for dry areas and prioritize planting it in those locations. This is one way in which farming systems can develop a portfolio of landraces over time that have specific ecological niches and uses.
+Conversely, modern cultivars can also be developed into a landrace over time when farmers save seed and practice selective breeding.
+Although landraces are often discussed once they have become endemic to a particular geographical region, landraces have always been moved over long and short distances. Some landraces can adapt to various environments, while others only thrive within specific conditions. Self-fertilizing and vegetatively populated species adapt by changing the frequencies of phenotypes. Outbreeding crops absorb new genotypes through intentional and unintentional hybridization, or through mutation.
+A clear example of vegetal landrace would consist in the diverse adaptations of wheat to differential artificial selection constraints.
+
+=== Cultivars developed from landraces ===
+Members of a landrace variety, selected for uniformity with regards to a unique feature over a period of time, can be developed into a farmers' variety or cultivar. Traits from landraces are valuable for incorporation into elite lines. Crop disease resistance genes from landraces can provide eternally-needed resistances to more widely used, modern varieties.
+
+=== Examples of plant landraces ===
+
+==== Beans ====
+
+==== Carrots ====
+
+==== Maize ====
+
+==== Okra ====
+
+==== Peas ====
+
+==== Peppers ====
+
+==== Rice ====
+
+==== Squash ====
+
+==== Tomatillo ====
+
+==== Tomatoes ====
+
+==== Wheat ====
+
+== Animals ==
+
+=== Animal landrace development ===
+Some standardized animal breeds originate from attempts to make landraces more consistent through selective breeding, and a landrace may become a more formal breed with the creation of a breed registry or publication of a breed standard. In such a case, one may think of the landrace as a "stage" in breed development. However, in other cases, formalizing a landrace may result in the genetic resource of a landrace being lost through crossbreeding.
+While many landrace animals are associated with farming, other domestic animals have been put to use as modes of transportation, as companion animals, for sporting purposes, and for other non-farming uses, so their geographic distribution may differ. For example, horse landraces are less common because human use of them for transport has meant that they have moved with people more commonly and constantly than most other domestic animals, reducing the incidence of populations locally genetically isolated for extensive periods of time.
+
+=== Examples of animal landraces ===
+
+==== Cats ====
+Many standardized breeds have rather recently (within a century or less) been derived from landraces. Examples, often called natural breeds, include Arabian Mau, Egyptian Mau, Korat, Kurilian Bobtail, Maine Coon, Manx, Norwegian Forest Cat, Siberian, and Siamese.
+In some cases, such as the Turkish Angora and Turkish Van breeds and their possible derivation from the Van cat landrace, the relationships are not entirely clear.
+
+==== Cattle ====
+
+==== Dogs ====
+
+Dog landraces and the selectively bred dog breeds that follow breed standards vary widely depending on their origins and purpose.
+Landraces are distinguished from dog breeds which have breed standards, breed clubs and registries.
+Landrace dogs have more variety in their appearance than do standardized dog breeds. An example of a dog landrace with a related standardized breed with a similar name is the collie. The Scotch Collie is a landrace, while the Rough Collie and the Border Collie are standardized breeds. They can be very different in appearance, though the Rough Collie in particular was developed from the Scotch Collie by inbreeding to fix certain highly desired traits. In contrast to the landrace, in the various standardized Collie breeds, purebred individuals closely match a breed-standard appearance but might have lost other useful characteristics and have developed undesirable traits linked to inbreeding.
+The ancient landrace dogs of the Fertile Crescent that led to the Saluki breed excels in running down game across open tracts of hot desert, but conformation-bred individuals of the breed are not necessarily able to chase and catch desert hares.
+
+==== Goats ====
+Some standardized breeds that are derived from landraces include the Dutch Landrace, Swedish Landrace and Finnish Landrace goats. The Danish Landrace is a modern mix of three different breeds, one of which was a "Landrace"-named breed.
+
+==== Sheep ====
+
+==== Horses ====
+The wild progenitor of the domestic horse is extinct. It is rare for landraces among domestic horses to remain isolated, due to human use of horses for transportation, thus causing horses to move from one local population to another.
+The heavy 'draft' type of domestic horse, developed in Europe, has differentiated into many separate landraces or breeds. Examples of horse landraces also include insular populations in Greece and Indonesia, and, on a broader scale, New World populations derived from the founder stock of Colonial Spanish horse.
+The Yakutian and Mongolian Horses of Asia have "unimproved" characteristics.
+
+==== Pigs ====
+The standardized swine breeds named "Landrace" are often not actually landraces or derived from landraces. The Danish Landrace pig breed, pedigreed in 1896 from an actual local landrace, is the principal ancestor of the American Landrace (1930s). In this way, the Swedish Landrace is derived from the Danish and from other Scandinavian breeds, as is the British Landrace breed.
+
+==== Chicken ====
+
+==== Ducks ====
+
+==== Geese ====
+Many standardized goose breeds named "Landrace", e.g. the Twente Landrace goose, are not actually true landraces, but may be derived from them.
+
+==== Rabbits ====
+
+== See also ==
+
+== References ==
+
+== External links ==
+
+Short DIVERSEEDS video on crop wild relatives and landraces in the fertile crescent in Israel
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diff --git a/data/en.wikipedia.org/wiki/Landscape_limnology-0.md b/data/en.wikipedia.org/wiki/Landscape_limnology-0.md
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+---
+title: "Landscape limnology"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Landscape_limnology"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:40.323130+00:00"
+instance: "kb-cron"
+---
+
+Landscape limnology is the spatially explicit study of lakes, streams, and wetlands as they interact with freshwater, terrestrial, and human landscapes to determine the effects of pattern on ecosystem processes across temporal and spatial scales. Limnology is the study of inland water bodies inclusive of rivers, lakes, and wetlands; landscape limnology seeks to integrate all of these ecosystem types.
+The terrestrial component represents spatial hierarchies of landscape features that influence which materials, whether solutes or organisms, are transported to aquatic systems; aquatic connections represent how these materials are transported; and human activities reflect features that influence how these materials are transported as well as their quantity and temporal dynamics.
+Bremigan. 2009. The lake landscape-context framework: linking aquatic connections, terrestrial features and human effects at multiple spatial scales.
+Verhandlungen Internationale Vereinigung für theoretische und angewandte Limnologie. 30:695-700
+
+
+== Foundation ==
+The core principles or themes of landscape ecology provide the foundation for landscape limnology. These ideas can be synthesized into a set of four landscape ecology themes that are broadly applicable to any aquatic ecosystem type, and that consider the unique features of such ecosystems.
+A landscape limnology framework begins with the premise of Thienemann (1925). Wiens (2002): freshwater ecosystems can be considered patches. As such, the location of these patches and their placement relative to other elements of the landscape is important to the ecosystems and their processes. Therefore, the four main themes of landscape limnology are:
+
+Patch characteristics: The characteristics of a freshwater ecosystem include its physical morphometry, chemical, and biological features, as well as its boundaries. These boundaries are often more easily defined for aquatic ecosystems than for terrestrial ecosystems (e.g., shoreline, riparian zones, and emergent vegetation zone) and are often a focal point for important ecosystem processes linking terrestrial and aquatic components.
+Patch context: The freshwater ecosystem is embedded in a complex terrestrial mosaic (e.g., soils, geology, and land use/cover) that has been shown to drive many within-ecosystem features and processes such as water chemistry, species richness, and primary and secondary productivity.
+Patch connectivity and directionality: The complex freshwater mosaic is connected to the particular patch of interest and defines the degree to which materials and organisms move across the landscape through freshwater connections. For freshwater ecosystems, these connections often display a strong directionality component that must be explicitly considered. For example, a specific wetland can be connected through groundwater to other wetlands or lakes, or through surface water connections directly to lakes and rivers, or both, and the directionality of those connections will strongly impact the movement of nutrients and biota.
+Spatial scale and hierarchy: Interactions among terrestrial and freshwater elements occur at multiple spatial scales that must be considered hierarchically. The explicit integration of hierarchy into landscape limnology is important because (a) many freshwater ecosystems are hierarchically organized and controlled by processes that are hierarchically organized, (b) most freshwater ecosystems are managed at multiple spatial scales, from policy set at the national level, to land management conducted at local scales, and (c) the degree of homogeneity among freshwater ecosystems can change in relation to the scale of observation.
+
+
+== Contributions to other fields ==
+Findings from landscape limnology research are contributing to many facets of aquatic ecosystem research, management, and conservation. Landscape limnology is especially relevant for geographical areas with thousands of ecosystems (i.e. lake-rich regions of the world), in situations with a range of human disturbances, or when considering lakes, streams, and wetlands that are connected to other such ecosystems.
+For example, landscape limnology perspectives have contributed to the development of nutrient criteria for lakes, formation of classification systems that can be used to monitor the health of aquatic ecosystems, understanding ecosystem responses to environmental stressors, or explaining biogeographic patterns of community composition.
+
+
+== See also ==
+Deposition (geology)
+Ecology
+Ecoregions
+Landscape ecology
+Limnology
+
+
+== Notes ==
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diff --git a/data/en.wikipedia.org/wiki/Liana-0.md b/data/en.wikipedia.org/wiki/Liana-0.md
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+---
+title: "Liana"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Liana"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:41.589127+00:00"
+instance: "kb-cron"
+---
+
+A liana ( lee-ANN-ə, also  -⁠AH-nə) is a long-stemmed  woody vine that is rooted in the soil at ground level and uses trees, as well as other means of vertical support, to climb up to the canopy in search of direct sunlight. The word liana does not refer to a taxonomic grouping, but rather a habit of plant growth—much like tree or shrub. It comes from standard French liane, itself from an Antilles French dialect word meaning 'to sheave'.
+
+
+== Ecology ==
+Lianas are characteristic of tropical moist broadleaf forests (especially seasonal forests), but may be found in temperate rainforests and temperate deciduous forests. There are also temperate lianas, for example the members of the Clematis or Vitis (wild grape) genera. Lianas can form bridges in the forest canopy, providing arboreal animals—including ants and many other invertebrates, lizards, rodents, sloths, monkeys, and lemurs—with paths through the forest. For example, in the Eastern tropical forests of Madagascar many lemurs achieve higher mobility from the web of lianas draped among the vertical tree species. Many lemurs prefer trees with lianas because of their roots.
+Lianas are parasitic, they do not derive nutrients directly from host trees, but live on and indirectly derive nutrients at their expense. Specifically, their growth may greatly reduce their hosts' growth and tree reproduction, greatly increase tree mortality, prevent tree seedlings from establishing, alter the course of regeneration in forests, and ultimately decrease tree population growth rates. For example, forests without lianas grow 150% more fruit, and trees with lianas have twice the probability of dying.
+Lianas are uniquely adapted to living in forests as they use host trees, for stability, to reach to top of the canopy. Lianas directly damage their hosts by mechanical abrasion and strangulation, render hosts more susceptible to ice and wind damage, and increase the probability that the host tree falls. Lianas also provide support for weaker trees when strong winds blow by laterally anchoring them to stronger trees. However, this anchoring can also be destructive because when one tree falls, the connections made by the lianas can cause many other trees to fall. Because of these negative effects, trees that remain free of lianas are at an advantage; some species have evolved characteristics which help them avoid or shed lianas. 
+Some lianas attain great length, such as Bauhinia sp. in Surinam which has grown as long as 600 m (2,000 ft). Hawkins has accepted a length of 1.5 km (1 mile) for an Entada phaseoloides. The longest monocot liana is Calamus manan  (or Calamus ornatus) at 240 m (787 ft).  One way of distinguishing lianas from trees and shrubs is their stiffness, specifically, the Young's modulus of various parts of the stem. Trees and shrubs have young twigs and smaller branches that are quite flexible and older growth such as trunks and large branches that are stiffer. A liana often has stiff young growths and older, more flexible growth at the base of the stem. Because of these stresses, some lianas grow flat ribbon-like stems which are very flexible, including certain Bauhinia species, Entada species, some Tetrastigma species, as well as Serjania  icthyoctonia  and Thinonia scandens,  both in the Sapindaceae. These last two go still further and the ribbon divides into parallel strands.
+
+
+== Examples ==
+Some examples of taxa with lianas include:
+
+
+== References ==
+
+
+== External links ==
+Lianas and Climbing Plants of the Neotropics
+Lianas and Climbing Plants of the Neotropics: Family Treatments
+'Vines and Lianas' by Rhett Butler, at http://rainforests.mongabay.com/0406.htm
+"Lianas" . The New Student's Reference Work . 1914.
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diff --git a/data/en.wikipedia.org/wiki/Live_crown-0.md b/data/en.wikipedia.org/wiki/Live_crown-0.md
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+---
+title: "Live crown"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Live_crown"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:15:44.042313+00:00"
+instance: "kb-cron"
+---
+
+The live crown is the top part of a tree, the part that has green leaves (as opposed to the bare trunk, bare branches, and dead leaves). The ratio of the size of a tree's live crown to its total height is used in estimating its health and its level of competition with neighboring trees. This is referred to as the Live Crown Ratio (LCR).
+
+
+== References ==
\ No newline at end of file
diff --git a/data/en.wikipedia.org/wiki/Virtual_archaeology-0.md b/data/en.wikipedia.org/wiki/Virtual_archaeology-0.md
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+++ b/data/en.wikipedia.org/wiki/Virtual_archaeology-0.md
@@ -0,0 +1,21 @@
+---
+title: "Virtual archaeology"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Virtual_archaeology"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:14:58.279288+00:00"
+instance: "kb-cron"
+---
+
+Virtual archaeology is a subfield of digital archeology that creates and use virtual models and simulations of archaeological sites, artifacts, and processes. It makes use of 3D modeling, virtual reality (VR), augmented reality (AR), and other technologies to recreate or visualize archaeological findings.
+
+
+== Etymology ==
+It is a term introduced in 1990 by archaeologist and computer scientist Paul Reilly to describe the use of computer based simulations of archaeological excavations. Since that time, scientific results related to virtual archaeology were annually discussed, among others, at  Computer Applications and Quantitative Methods in Archaeology (CAA). The keyword "visualization" defined the aim of the virtual archaeology in the London Charter Initiative:
+
+It should be made clear to users what a computer-based visualization seeks to represent, for example the existing state, an evidence-based restoration or an hypothetical reconstruction of a cultural heritage object or site, and the extent and nature of any factual uncertainty.
+Since its introduction, the focus of the term has been extended to explore methods that increase the visibility and accessibility of archaeology. Today it serves as an integration paradigm that allows many modern three-dimensional datasets to be analysed together, taking account preliminary reconstructions of archaeological sites and guiding further investigations, for example through archaeological prospection, historical research or excavation. In this iterative and incremental process, the interpretation and virtual representation of results is only one, albeit important, outcome. Consequently, by using 3D printing technologies, results may even be created as physical reality. Such a development was discussed at the first international conference on virtual archaeology, organized by the Department of Eastern Europe and Siberian Archaeology of the State Hermitage Museum, which took place in Saint Petersburg in 2012. A second meeting was held at the State Hermitage Museum in 2015, resulting in a new edited volume, and then in 2018. Next meeting with motto "Revealing the Past, Enriching the Present and Shaping the Future Languages in 2021 was transferred to the Siberian Federal University in Krasnoyarsk.
+
+
+== References ==
\ No newline at end of file
diff --git a/data/en.wikipedia.org/wiki/Waterlogging_(archaeology)-0.md b/data/en.wikipedia.org/wiki/Waterlogging_(archaeology)-0.md
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+++ b/data/en.wikipedia.org/wiki/Waterlogging_(archaeology)-0.md
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+---
+title: "Waterlogging (archaeology)"
+chunk: 1/1
+source: "https://en.wikipedia.org/wiki/Waterlogging_(archaeology)"
+category: "reference"
+tags: "science, encyclopedia"
+date_saved: "2026-05-05T07:14:59.422773+00:00"
+instance: "kb-cron"
+---
+
+In archaeology, waterlogging is the long-term exclusion of air by groundwater, which creates an anaerobic environment that can preserve artifacts perfectly. Such waterlogging preserves perishable artifacts. Thus, in a site which has been waterlogged since the archaeological horizon was deposited, exceptional insight may be obtained by study of artifacts made of leather, wood, textile or similar materials. 75-90% of the archaeological remains at wetland sites are found to be organic material. Tree rings found from logs that have been preserved allow archaeologists to accurately date sites. Wetland sites include all those found in lakes, swamps, marshes, fens, and peat bogs.
+Peat bogs, nearly all of which occur in northern latitudes, are some of the most important environments for wetland archaeology. Peat bogs have likewise preserved many wooden trackways, including the world's oldest road, which is a 6,000-year-old one-mile stretch of track.
+
+Bog bodies are the best-known finds from the peat bogs of northwest Europe, with most of them dating from the Iron Age. Most corpses that were found were individuals that met a violent death and were probably either executed as criminals or killed as a sacrifice before thrown into the bog. For example, the Old Croghan Man was stabbed, decapitated, mutilated, and tied down to the bottom of a bog pool. His body is an amazing display of how splendidly waterlogging can preserve a body, as his hands, skin, fingernails, and stomach were amazingly intact. Another example of a waterlogging artifact or mummy was Ötzi, found by two tourists near the border of Austria and Italy. Ötzi is now displayed in Bolzano, Italy, in the South Tyrol Museum of Archaeology.
+Occasionally, waterlogged conditions can occur inside burial mounds. The oak-coffin burials of Bronze Age northern Europe, and most notably those of Denmark, date to about 1000 BC. These coffins had an inner core of stones packed round the tree-trunk coffin, with a round barrow built above. Water then infiltrated the inside of the mound and by combining with tannin exuding from the tree trunks, set up acidic conditions which destroyed the skeleton but preserved the skin, hair, ligaments, and clothing of the individuals.
+Perhaps the most interesting wetland archaeological find was the Ozette site. In 1750, a huge mudslide buried a whale-hunting settlement on the coast of Washington, which protected the organic artifacts from the oxygen that would lead to their deterioration. Over 50,000 artifacts were found in a fine state of preservation, with almost half of them being wood or plant material. The most fascinating thing they found was a meter-high block of cedar that was carved in the shape of a whale's dorsal fin.
+The major archaeological problem with waterlogged finds, particularly wood, is that they deteriorate rapidly when they are uncovered, beginning to dry and crack almost at once. They therefore need to be kept wet until treated in a laboratory. Conservation measures explain why wet archaeology costs around four times as much as dry archaeology.
+
+
+== See also ==
+Wetland settlement
+
+
+== References ==
+
+Renfrew, Collin (2008). Archaeology: Theories, Minds, and Practice. New York, New York: Thames&Hudson. pp. 62–72. ISBN 9780500287132.
+Barnes, Trevor (2004). Archaeology. Boston: Kingfisher.
+Lobell, Jarret (May–June 2010). "Clonycavan and Old Croghan Men". Archaeology. Retrieved 2016-08-08.
+Weisenberg, Adam (July 2011). "Waterlogging". {{cite journal}}: Cite journal requires |journal= (help)
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