To be fair to her, the speech consisted mainly of an attack on Intelligent Design theory, claiming that it is not scientific. I more or less agree with this, though not necessarily for precisely the same reasons. For me, it's enough that ID theory has no genuine research program, is contrived to reach a predetermined outcome, and therefore lacks the very rigorous standards of intellectual honesty that we expect of scientists, etc. It is more like legal advocacy than science - it attempts to put the most persuasive case for a conclusion that is decided in advance. There's nothing wrong with that, in its place, but it's not science. ID's conclusions can in no way be characterised as conclusions with scientific credibility, and the claim that they are can never be relied upon by a public school system that wishes to teach them or to offer them as an alternative to genuine evolutionary biology.
That, however, is not how Scott put it. Still, she must be given credit for what she was trying to do, and she did make some similar points in her own way. In any event, it was the first part of the speech that worried me. This emphasised the claim that science (Scott said "science", not "reason") is only one way of knowing. The others that she mentioned were personal insight and authority (I don't think she was saying that these three are the only "ways of knowing"). She appeared to be happy to count all sorts of ideas gained from personal insight, perhaps assisted by rituals or drugs, as "knowledge", which is rather odd, since knowledge is, at the least, justified belief. She counted revelation, including the words of holy books, as a sub-set of authority, and explained that the problem is when empirical claims are based on revelation.
Scott also said that science is a limited way of knowing because it can only investigate natural phenomena, and can only offer natural explanations for them, and so cannot deal with supernatural claims. She offered no argument for this claim. Indeed, she gave an example of scientific study of truth claims that appeared to refute it. This was a description of a controlled experiment to see whether people really can perform better than chance at dowsing for water. Clearly, if the claim "I can perform better than chance at dowsing for water" is refuted by scientific investigation, it follows, a fortiori, that the claim "I can perform better than chance at dowsing for water by using supernatural means" is also refuted.
The fact is that science has reached a point where it is bad form for scientists to postulate supernatural explanations for phenomena. This is mainly because such explanations have such an unimpressive historical track record (think of preformationist theories of reproduction that depend on an original divine miracle to create an infinite set of tiny homunculi within homunculi, or of diluvian theories of geology that explain rock formation in terms of Noah's flood). So-called "methodological naturalism" is a useful rule of thumb adopted by modern science, and a contemporary scientist who did not adopt it when postulating causes would now be laughed at by colleagues. However, there is no reason why science cannot offer supernatural explanations. In earlier times, reputable scientists often did this; methodological naturalism was never essential to the definition of "science".
Moreover, although modern scientists are (quite correctly) unwilling to postulate supernatural explanations, that does not mean that they are unable to test supernatural explanations when postulated by others. The fact that supernatural explanations have a poor record when tested is (at least part of) the reason why scientists are now so unwilling to postulate them.
Scott's speech was rather long, with no time for questions. It went down well with the audience, and much of its content justified this, but I'd have liked to have seen some challenges to its simplistic claims about scientific epistemology. (She told people with a background in this area of philosophy to "deal [with it]", since she could not give all the detail, but that is hardly satisfactory.) Alas, none of the speech acknowledged that the problems created by religious thinking - and the acceptance of religious leaders, religious organisations, and holy books as having authority - go FAR beyond those caused when empirical claims are based on scriptural revelation. Of course, those are the problems that Scott is required to deal with at the NCSE, but they are far from the only ones or necessarily the most important. Any suggestion that they are is most unfortunate.
This is why, with some regret, I find myself talking about "appeasement". Such speeches effectively say to religious organisations, "You can have all the authority you want (to lobby for banning of RU-486 or whatever your latest problem is) as long as you don't oppose the teaching of evolution." I know that many rational people don't like the implied comparison of religion, or of particular religions, to Nazism, or the suggestion that goodwilled folks such as Eugenie Scott are selling out to something as evil as Nazism. Nazism was and is a particularly vicious quasi-religious belief system. But the great organised religions are, collectively, a bigger problem than Nazism these days.
When a religious organisation such as the Catholic Church is welcomed as an ally of the cause of reason merely because it takes the right side on one issue, that looks like a form of appeasement. The Vatican hierarchs are not our allies merely because they don't oppose evolutionary theory. The Vatican is the same organisation that teaches that the use of the contraceptive pill, masturbation, homosexual acts, etc., are all very serious "sins". It is anti-rational and authoritarian. It doesn't hesitate to try to get the coercive power of the state to ban whichever of these "sins" it can, wherever and whenever it can. It is a kind of opportunistic predator in that respect. Most recently, RU-486 was legalised in Italy only in the face of strong Vatican opposition. The Church continually does all it can to interfere in personal decisions about how we live our lives, and especially about bioethical issues at the beginning and end of life. It does not merely preach its benighted moral views to the faithful, but tries to get governments to enshrine those views in legislation, thus getting them imposed on us by force. In short, the Catholic Church is a far greater menace to our liberties than a motley bunch of American fundamentalists whose immediate goal is to undermine the teaching of biological evolution in American schools.
Of course, organisations such as the Discovery Institute have a much broader theocratic agenda, but this is precisely what Eugenie Scott will never criticise them for. The only problem, apparently, is that they make empirical claims based in scriptural revelation. No, that is not the only problem, or the greatest problem. The far larger problem is the epistemic, moral, and above all political authority claimed by many religious organisations. This most definitely includes the Catholic Church, which Scott obviously sees as an ally - even employing a Catholic priest to head the NCSE's faith outreach program.
That said, I am not suggesting that the NCSE enlarge its remit to attack religion more generally. That is not its raison d'etre at all. But it can be neutral about such questions as whether science undermines a large amount of religious thinking, far beyond the claims of creationism and Intelligent Design. It can stop relying on an unnecessarily narrow (and very dubious) view of scientific epistemology, designed to leave as much authority with religion as possible. It can stop promoting Gould's intellectually bankrupt principle of Non-Overlapping Magisteria on its website.
It's a pity that Scott's talk left no time to debate any of this. Perhaps next year the Dragon*Con organisers will provide space in their program for challenges to the more dubious and dangerous epistemological claims that Scott was trying to sell to us yesterday. Maybe Jerry Coyne would be a good speaker for next year. Put your hand up, Jerry!