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For example, there were small errors in the Met Office's climate change software that I detected. The scientific papers were correct, but the translation into code was not. This could have happened here and it would be better if they released the code.
http://blog.jgc.org/2010/02/something-odd-in-crutem3-station...
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That said, a brief search turned up this paper ( https://facultystaff.richmond.edu/~ebunn/vanelburg.pdf ) which argues that that explanation is faulty (i.e., the paper made a mistake, and when corrected, the original researchers' results stand).
(Disclaimer: although I once read a book on this stuff, I shouldn't be confused with an expert, and I have no idea who's right and who's wrong. But it is exciting.)
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1) The distance between the labs is smaller than they think
2) Tachyonic neutrinos (not likely)
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I have seen Apache ignore updated PHP files, and serving old code, which should never happen. This a real bitch to debug.
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But it is an important step towards understanding what's happening, and it's great that the OPERA group were able to put together this followup experiment so quickly.