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On 4 September 1939, the day after the UK declared war on Germany, Turing reported to Bletchley Park, the wartime station of GC&CS. Like all others who came to Bletchley, he was required to sign the Official Secrets Act, in which he agreed not to disclose anything about his work at Bletchley, with severe legal penalties for violating the Act. Specifying the bombe was the first of five major cryptanalytical advances that Turing made during the war. The others were: deducing the indicator procedure used by the German navy; developing a statistical procedure dubbed Banburismus for making much more efficient use of the bombes; developing a procedure dubbed Turingery for working out the cam settings of the wheels of the Lorenz SZ 40/42 (Tunny) cipher machine and, towards the end of the war, the development of a portable secure voice scrambler at Hanslope Park that was codenamed Delilah. By using statistical techniques to optimise the trial of different possibilities in the code breaking process, Turing made an innovative contribution to the subject. He wrote two papers discussing mathematical approaches, titled The Applications of Probability to Cryptography and Paper on Statistics of Repetitions, which were of such value to GC&CS and its successor GCHQ that they were not released to the UK National Archives until April 2012, shortly before the centenary of his birth. A GCHQ mathematician, "who identified himself only as Richard," said at the time that the fact that the contents had been restricted under the Official Secrets Act for some 70 years demonstrated their importance, and their relevance to post-war cryptanalysis:

[He] said the fact that the contents had been restricted "shows what a tremendous importance it has in the foundations of our subject". ... The papers detailed using "mathematical analysis to try and determine which are the more likely settings so that they can be tried as quickly as possible". ... Richard said that GCHQ had now "squeezed the juice" out of the two papers and was "happy for them to be released into the public domain". Turing had a reputation for eccentricity at Bletchley Park. He was known to his colleagues as "Prof" and his treatise on Enigma was known as the "Prof's Book". According to historian Ronald Lewin, Jack Good, a cryptanalyst who worked with Turing, said of his colleague:

In the first week of June each year he would get a bad attack of hay fever, and he would cycle to the office wearing a service gas mask to keep the pollen off. His bicycle had a fault: the chain would come off at regular intervals. Instead of having it mended he would count the number of times the pedals went round and would get off the bicycle in time to adjust the chain by hand. Another of his eccentricities is that he chained his mug to the radiator pipes to prevent it being stolen. Peter Hilton recounted his experience working with Turing in Hut 8 in his "Reminiscences of Bletchley Park" from A Century of Mathematics in America:

It is a rare experience to meet an authentic genius. Those of us privileged to inhabit the world of scholarship are familiar with the intellectual stimulation furnished by talented colleagues. We can admire the ideas they share with us and are usually able to understand their source; we may even often believe that we ourselves could have created such concepts and originated such thoughts. However, the experience of sharing the intellectual life of a genius is entirely different; one realizes that one is in the presence of an intelligence, a sensibility of such profundity and originality that one is filled with wonder and excitement. Alan Turing was such a genius, and those, like myself, who had the astonishing and unexpected opportunity, created by the strange exigencies of the Second World War, to be able to count Turing as colleague and friend will never forget that experience, nor can we ever lose its immense benefit to us. While working at Bletchley, Turing, who was a talented long-distance runner, occasionally ran the 40 miles (64 km) to London when he was needed for meetings, and he was capable of world-class marathon standards. Turing tried out for the 1948 British Olympic team, but he was hampered by an injury. His tryout time for the marathon was only 11 minutes slower than British silver medallist Thomas Richards' Olympic race time of 2 hours 35 minutes. He was Walton Athletic Club's best runner, a fact discovered when he passed the group while running alone. When asked why he ran so hard in training he replied:

I have such a stressful job that the only way I can get it out of my mind is by running hard; it's the only way I can get some release. Due to the challenges answering questions concerning what an outcome would have been if a historical event did or did not occur (the realm of counterfactual history), it is hard to estimate the precise effect Ultra intelligence had on the war. However, official war historian Harry Hinsley estimated that this work shortened the war in Europe by more than two years. He added the caveat that this did not account for the use of the atomic bomb and other eventualities. At the end of the war, a memo was sent to all those who had worked at Bletchley Park, reminding them that the code of silence dictated by the Official Secrets Act did not end with the war but would continue indefinitely. Thus, even though Turing was appointed an Officer of the Order of the British Empire (OBE) in 1946 by King George VI for his wartime services, his work remained secret for many years.