According to a panel at the American Association for the Advancement of Science, this isn't a failure of medical research; it's a failure of statistics, and one that is becoming more common in fields ranging from genomics to astronomy. The problem is that our statistical tools for evaluating the probability of error haven't kept pace with our own successes, in the form of our ability to obtain massive data sets and perform multiple tests on them. Even given a low tolerance for error, the sheer number of tests performed ensures that some of them will produce erroneous results at random.
You would also be well advised to read Taleb's "The Black Swan", which addresses a host of other epistemological and statistical problems with many of the models we use.
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