Methodological Naturalism

UPDATE: This post no longer reflects my opinion on this subject. I now believe that science is not bound by methodological naturalism. Science as a way of knowing is free to investigate claims of the supernatural. [Is Science Restricted to Methodologial Naturalism?] [Accommodationism in Dover] [Methodological Naturalism].

In a comment on The Neville Chamberlain Atheists thread "slc" repeats a claim that he/she has been making for several months. I started to reply on that thread but the comment grew too long so I'm making it into a separate posting.
"slc" says,

As I have commented on this and other blogs, Prof. Morans' position, along with Myers and Dawkins is that philosophical naturalism is science and therefore science == atheism.

Indeed, I've seen you make that claim several dozen times. I'm glad it makes you happy.
For the record, I am an atheist so naturally I'm a philosophical naturalist. (Duh!) But I do not claim that good science requires philosophical naturalism. I claim that methodological naturalism is a requirement.
Most of my arguments [e.g. Theistic Evolution: The Fallacy of the Middle Ground] are based on the idea that methodological naturalism is the foundation of science and that, therefore, science is effectively atheistic in practice. I've been trying to show that methodological naturalism all by itself is capable of highlighting all of the important conflicts between science and religion. In my opinion, it's simply not true that the only conflicts that arise are when you make the leap to philosophical naturalism.
In this sense—and this sense only—I'm defending the concept of non-overlapping magisteria (NOMA) promoted by Stephen Jay Gould. As long as religion sticks to it's proper domain (magisterium) and stays out of science then it's okay (e.g., I have no problem with Deism and most versions of Buddhism). The problem is that most believers want to violate the rules of methodological naturalism and still be praised for being good scientists. One of the ways they rationalize this obvious conflict is to try and equate methodological naturalism with philosophical naturalism. They claim that it's okay to allow a little bit of religion into science because science is not the same as atheism. We see an example of that in "slc"'s attempt to dismiss what many of us are saying about the conflict between science and religion.
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