Jerry Coyne has posted his thoughts on the subject of methodological naturalism. Here’s a sample:
I am a methodological naturalist, but I don’t think that all supernatural claims defy scientific analysis. Moreover, I don’t see that the methodological/philosophical distinction has a lot to do with the dissonance between faith and science. The real dissonance, as I have repeatedly emphasized, is between the scientific acceptance of only those claims adjudicated by empirical investigation, and the religious acceptance of “truth” claims that are discovered by revelation (or instruction by one’s parents) and are unfalsifiable. These are two fundamentally different and incompatible ways of ascertaining “truth.” In fact, I don’t see that religion has any way at all of ascertaining “truth,” since its claims cannot be falsified. The fact that the major “truths” of different religions are in permanent and irresolvable conflict testifies to this difference between science and faith.
Lot’s of food for thought. Go read the whole thing.