Consider Dawkins' comment in the first quote: Questions about the existence of the supernatural are actually scientific questions. And then we can ask by what scientific principle this is known? Perhaps the philosopher running beside the locomotive can tell the engineer who, by all appearances has never given this question a moment's thought. No body of knowledge has within itself the competency to examine its own foundations -- although only Mathematics has a rigorous proof that this is so. Physics, which in the original meaning was any knowledge (scientia) of physical bodies, and so includes biology and all the rest, is grounded in metaphysics, which simply means "behind the physics." And that is right where The Metaphysics appears in compilations of Aristotle's works, right after The Physics. It deals with those ontological and epitemological preconditions.This is a point I've often tried to make to the Dawkinsians I know in person (Dawkins, when he comes here, spends a good deal of time with people I know, because they're kindreds or something). Dawkins wants science to replace religion, because he believes that all religious questions are scientific questions, and science has shown itself to be better at answering scientific questions than religion. The latter part of that statement is obviously true: science is better at what it does than any other institution or system we humans have previously invented. That's why we've been able to go to the moon, wipe small pox off the face of the Earth, and talk to each other on the internet, or in our darker hours, flatten Hiroshima and Nagasaki. But the first part of the statement, that all religious questions are scientific questions, is where Dawkins goes wrong in big way. Science isn't built to answer metaphysical questions. That's not what science does. One of the worst (intellectual) things a scientist (or anyone for that matter) can do with science is conclude that it proves the truth of materialism. That's equivalent to saying that linguistics proves that all there is to existence is language, because all linguistics studies is language. There's no way to avoid the circularity of this argument, and it's one that Dawkins and his fans make all of the time.
Science as we know it measures things. Some folks think that because they can measure Stuff really really accurately that they are therefore Experts on Everything from theology to barbeque sauce or even in other branches of science. But to measure is to quantify, and quantification belongs to matter (rather than to form, agency, or finality). Therefore, if you focus exclusively on that-which-can-be-measured, you focus exclusively on that which is matter. Like anyone whose only tool is a hammer, after a while everything starts to look like a nail. But in what way does Dawkins suppose that the "supernatural" (whatever he means by that) is a measurable, material body? Heck. Forget about the existence of the supernatural. The existence of an empirical universe is not a scientific question. It is an a priori assumption necessary if one is to do science in the first place. Even the existence of natural laws is not a scientific question, but an assumption scientists must make before they will look for them.
Now, I don't think anything Flynn says in his post suggests that philosophy of science itself is important to science. Where Dawkins, Myers, and others go wrong is not in their science, to the extent that any of these self-appointed spokespeople for atheism are doing actual science anymore. They go wrong when they try to do philosophy based on what they know about science. It is undoubtedly true that in 2009, science is much more relevant to the doing of philosophy than philosophy is to the doing of science, but science can only answer certain kinds of questions, and can only inform philosophy on those types of questions. Where science leaves off, philosophy is often the best vehicle for continuing on.
I do have to say that I think Flynn is wrong in saying that evolution is not a fact, and thus that Dawkins and Myers are right when they say that it is (even if they don't know why it is, as Myers' quoting of Gould seems to suggest). "Evolution," in its barest biological sense, refers to a set of observable events. Now, I haven't read The Aim and Structure of Physical Theory since I took a philosophy of science course in grad school (and from what I understand, there's a fairly large literature, with which I'm not at all familiar, on how to interpret his philosophy of science anyway), but I'm pretty sure that for Duhem there were different kinds of facts (concrete facts, theoretical facts, practical facts, maybe some others1). It seems reasonable to consider evolution a concrete fact in the Duhemian sense. But Duhem was talking about physics, as the title of the book suggests, so maybe that's not the case. However, in say, a Wittgensteinian sense, evolution is, as a set of observable events, a fact of the world. Theories of evolution are not facts; natural selection is not a fact. These are explanations of facts. Evolution itself, that is the physical, and more specifically genetic, change of organisms and their offspring over time is the set of facts being explained. At the very least, I think this is an arguable position, and it therefore behooves philosophers not to dismiss it out of hand simply because Dawkins is so ignorant of philosophy in general.
1 If I remember correctly, this distinction, specifically the one between theoretical (which are mathematical) facts and practical facts, is very important in his overall discussion of theories and what they do in physics. For example, I'm pretty sure I remember him arguing that there are always a whole bunch of theoretical facts that correspond to a single practical fact, which would have all sorts of implications for how you test theories.
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