Reading my explanations above, you might suppose that I think of atheists as deliberately deceptive: that they have an a priori commitment to naturalism and understand it as such, but use sophistry to disguise that premise as a conclusion.
This is not actually the case. I don't think that atheists, generally, (or people, generally, for that matter) are entirely clear about the logical relations between premises and conclusions. Aristotle went out of fashion quite some time ago as a subject for teaching in school, and they threw out the good stuff with the bad, sadly. The trouble with atheists, such as Richard Dawkins, who claim science as their grounds, is that they believe themselves to be particularly rational people, and thus disinclined to doubt the rigorousness of their own arguments. Further, they often think that science itself is the heart and soul of reason, such that being a scientist makes one a member of the class of people most in touch with truth. The upshot of this is that Richard Dawkins frequently talks about the virtues of "critical thinking", and considers himself an expert in the subject because he's a scientist, without realising that he desperately needs some training in the subject himself. He's never likely to obtain it, however, because the teachers are in the philosophy department, which is considered "arts", not "science".
For a slight change of pace, then, without going off-topic, I'd like to explain how naturalistic thinking can come to permeate scientific thought, with the effect that most scientists treat naturalism as a strict requirement of science. This argument is meant to sound reasonable without being rigorously logical, and it's that kind of argument which is most seductive to those who relish in reason without understanding the full difficulties of producing a coherent argument.
Let's start with the idea that supernatural explanations do not explain, which was seen in the quotation from The God Delusion that I cited earlier. Without being too rigorous about the analysis (as rigour would expose flaws), what is the basis of this claim?
One of the key ideas behind this claim is what we might call the "supernatural lameness principle": the idea that supernatural explanations are the sort that simply says, "because God wills it". Clearly, if you can answer every scientific question with "because God wills it", you will have a fairly useless kind of science: all the questions have answers, but none of the answers are useful. A cursory analysis suggests that the problem lies in the fact that "because God wills it" is a teleological explanation: one which explains in terms of purpose and intention. What would be preferable is a mechanistic explanation: one which explains how things are happening, which is an aspect of the problem not addressed by "God wills it". Thus, useful science is necessarily mechanistic in its outlook. It won't do to ascribe God as the mechanism, either, because that would just be allowing the lame explanations back in through a semantic loophole.
With this idea elucidated, one can then see the appeal of another popular doctrine, which we might call the "replacement principle". This is the idea that because mechanistic explanations are better than supernatural ones, the former naturally supersede the latter, and thus science forever encroaches on the territory of religion, always replacing it and never yielding any territory back. Taking a long-term view of this, we see science perpetually on the rise, producing ever-more useful explanations of a broader range of things, and religion on the decline as its lame explanations are superseded.
So, let me now answer your earlier question, while playing Devil's Advocate. "Hasn't the term, supernatural, throughout history, always been definitially mutable from one discovery to the next?" No. The history of (useful) science has been to replace supernatural explanations with natural ones. "Supernatural" is merely a synonym for "not understood". As we come to understand the mechanisms behind the behaviour that we study, we replace lame supernatural explanations with superior mechanistic ones. Granted, it's often the case that the first such explanation is lacking in some regards, but it is still superior to the lame explanation that it displaced, and it may in turn be displaced by a better mechanistic explanation. The only sense in which "supernatural" is mutable is in the sense that our increased understanding of a subject (through mechanistic explanations, i.e. science) typically brings to our attention "new" areas of ignorance. They aren't really new, given that we have always been ignorant of them, but scientific progress makes us newly aware of this ignorance.
So there you have it: an attempt at playing Devil's Advocate. As I've said, I think that this line of reasoning is full of holes due to its lack of rigour, but I hope that I've managed to make the point of view look somewhat reasonable, and say the kind of things that Richard Dawkins would approve of. Nowhere in the argument do I profess an a priori commitment to naturalism -- but you can probably see that the banishment of the supernatural and the dedication to mechanistic explanations (which I have tried to present as necessary) entails a commitment to naturalism.
Not everyone will notice this relationship without it being pointed out to them, and attitudes towards the entailment can vary. That said, many people subscribe to the idea that "science disproves God" without realising that it is the definition of science (as I have presented it), not the products of science, that exclude God. When God is excluded at the root (the definition), it is quite simply inevitable that He will not be found in the fruit (the products). The fact that an inherently Godless science produces no evidence for God should come as a surprise to nobody.
_________________ The Famous Brett Watson -- brett.watson@gmail.com
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