One of the things that impressed me most while I was training to be a patent attorney I found from Paul Cole's book "Fundamentals of Patent Drafting" (which can be ordered from CIPA here). On page 2 of the introduction is a footnote referencing an article titled "Cargo Cult Science" by the physicist Richard Feynman. Paul Cole identified this as being required reading, so I duly went away and bought the book, although it turns out the article in question is also freely available on the internet (here). The book is certainly worth buying anyway, because it is full of all sorts of strange and funny stories from Feynman's life, including how he picked the safes holding the secrets of the atomic bomb while working on the Manhattan project.
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The philosopher Karl Popper considered that the way in which science must work was that any scientific theory must be falsifiable for it to be a theory at all (see here for more), otherwise it was just useless. The theory of gravity is a valid theory not just because all everyday observations support it but more importantly because it could be disproved by, for example, something falling (or not falling) contrary to what the theory predicted. The theory of evolution, which has great explanation power for how life forms change over time, could also be disproved, for example by the existence of rabbits in the precambrian. Other ideas, however, cannot be properly classified as scientific theories if there is no way they could be disproved, or are so vague as to be able to cover every eventuality, especially if they do so retrospectively (astrology, for example). Such theories are useless, largely because they have no predictive power and explain nothing. Another philosopher Bertrand Russell came up with the idea of a celestial teapot as an example of a theory that could not be disproved because no matter where you looked it could always be said that you hadn't yet found it. The burden of proof for any such non-falsifiable theories must therefore fall on those who make such claims, and not on those who consider them to be false.
In what I think of as effectively an update on Feynman's cargo cult speech, Matt Ridley (author of the excellent book The Rational Optimist) recently presented a lecture on 'scientific heresies' at the RSA in Edinburgh. This lecture has been reproduced here and here (with pictures), and has been noted on Richard Dawkins' website here (although Dawkins does not necessarily agree with Ridley's conclusions). It is also available, with images, in the form of a pdf here. I cannot underestimate, or overemphasise, how important it is for anyone who thinks they know how science works to read this. If there is only one thing you read about the subject in question (and after reading it I doubt that this will remain the case), then this should be it. Once you have read it in full, please feel free to come back and tell me why, and how, he is wrong.