The answer to the second question is 'both.' My primary problem with Mooney is that he seems to believe (indeed, the whole context of the article is) that science is the only source of knowledge. This is scientism; indeed, this is what's known as 'strong' scientism, as opposed to a weaker, slightly more reasonable (but still flawed) epistemology. And in the particular case of whether vaccination can trigger autism, this demonstrably illogical view leads him to an unfounded (and wrong) conclusion. In both his epistemology--scientism--and the wrong conclusions to which it leads, Mooney's basic problem is a lack of understanding of science itself.
Now, to be sure, if the question were, 'what percentage of autism diagnoses appear to be associated with (triggered by) vaccination?', that would require some sort of 'scientific' testing, whether that were a questionnaire or actually some sort of experimentation. But Mooney's claim is that since 'science' stepped in and hasn't discovered a link, we can dismiss as goofy the claims of those parents who believe (on the basis of mere eyewitness evidence) that vaccination triggered autism in their child.
All of this underscores a basic problem with the degree of authority with which we invest scientists. (And this gets back to the first question, 'what is the definition of science?') It turns out that scientists like Mooney are not the experts on what constitutes science, and he betrays his naivete by talking as though scientism is true. Further, the mistake he makes with regard to the specific case of vaccination-induced autism is rather a freshman error. That is, he seems unaware of a basic understanding in the philosophy of science. Let me explain. Jordan wrote,
In the case of the Autism-Vaccine link, do you think science can say conclusively one way or the other? I would think that given the right experiment(s) science should be able to detect a correlation if it exists.The correct answer, according to philosophers of science (and scientists with some basic understanding of same) is that science should be able to say conclusively one way, but not the other. In other words, if there is a link, science might (or perhaps should) be able to discover it. But if science fails to discover such a link, it is illegitimate to claim (as Mooney does) that no such link exists.
Put simply, it's impossible to prove a universal negative. To prove the claim that there is no extraterrestrial life anywhere in the universe would require searching every inch of it. Likewise, science can prove a link between vaccination and autism but cannot prove that no such link exists. And what we have here is a scientist (Mooney) who lacks philosophical understanding basic to his science claiming that science has proved a universal negative. What's worse, he makes this absurd claim in spite of a good deal of counterevidence, evidence he dismisses because of his mistaken belief in scientism.
So what is science? Well, that's a profound question that really requires years of study (in philosophy and history, not in any science discipline per se). Let me just say this for now... While we often know science when we see it, there is no line of demarcation--no set of necessary and sufficient criteria--that separates science from non-science. And whereas it has thus far proved impossible to adequately define science, it is quite simple to demonstrate that the view known as scientism--the idea that so-called science is the only true source of knowledge--is logically absurd.
(A common mistake is to equate any knowledge gained through our senses with scientific knowledge. Such a definition of science is recognized as much too broad to have any value. People have always used, and continue to use, their senses at every moment of their lives, yet we do not think of ourselves as continually engaged in science.)