Yes, science is hard. Especially when you are dealing with extremely complex phenomena with multiple variables, it can be extremely difficult to demonstrate the validity of a hypothesis (I detest the word "prove" in science, which we don't do, and we know it; Lehrer should, too). What the decline effect demonstrates, when it occurs, is that just maybe the original hypothesis was wrong. This shouldn't be disturbing, depressing, or troubling at all, except, as we see in his article, when we have scientists who have an emotional or profit-making attachment to an idea.
That's all this fuss is really saying. Sometimes hypotheses are shown to be wrong, and sometimes if the support for the hypothesis is built on weak evidence or a highly derived interpretation of a complex data set, it may take a long time for the correct answer to emerge. So? This is not a failure of science, unless you're somehow expecting instant gratification on everything, or confirmation of every cherished idea.
But those last few sentences, where Lehrer dribbles off into a delusion of subjectivity and essentially throws up his hands and surrenders himself to ignorance, is unjustifiable. Early in any scientific career, one should learn a couple of general rules: science is never about absolute certainty, and the absence of black & white binary results is not evidence against it; you don't get to choose what you want to believe, but instead only accept provisionally a result; and when you've got a positive result, the proper response is not to claim that you've proved something, but instead to focus more tightly, scrutinize more strictly, and test, test, test ever more deeply. It's unfortunate that Lehrer has tainted his story with all that unwarranted breast-beating, because as a summary of why science can be hard to do, and of the institutional flaws in doing science, it's quite good.
But science works. That's all that counts. One could whine that we still haven't "proven" cell theory, but who cares? Cell and molecular biologists have found it a sufficiently robust platform to dive ever deeper into how life works, constantly pushing the boundaries of uncertainty. - PZ Myers
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