tgb comments on Justifiable Erroneous Scientific Pessimism - Less Wrong Discussion
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I posted the following in a quotes page a few months back. I don't know how justifiable these were, and these are only questionably pessimism, but there may be some interesting examples in this. In particular, my light knowledge of the subject suggests that there really were extremely compelling reasons to disregard Feynman's formulation of QED for many years after it was first introduced.
[Footnote to: "This was a most disturbing result. Niels Bohr (not for the first time) was ready to abandon the law of conservation of energy". The disturbing result refers to the observations of electron energies in beta-decay prior to hypothesizing the existence of neutrinos.]
-David Griffiths, Introduction to Elementary Particles, 2008 page 24