Saw Eugenie Scott speak last week. Most of what she had to say was not new to me (although she put it well) but she finally explained the whole "methodological naturalism"/"philosophical naturalism" thing.
It's interesting to see what Phillip Johnson has to say about defeating materialistic science. Methodolical naturalism (= methodological materialism) is the basis of science - that you have to limit yourself to "materialistic" explanations in science. It doesn't matter whether you believe in the supernatural or not - as a scientist you need to limit yourself to known or knowable physical processes. Sure, you can propose new processes, hopefully they will be something you can measure (which is the problem with string theory, of course, because there may not be any way to measure strings). But if you move beyond methodological materialism, into the type of science Johnson wants, you create irrefutable hypotheses. Which means, you have no science, no medicine, know way to distinguishing truth from fiction.
Imagine your doctor including the supernatural in his diagnosis. If you can't rule out demonic possession, or a curse, you need to attack the matter on all fronts. Which means, I suspect, that every hospital would have to hire a few pundits (given the number of Hindu doctors). If Johnson was serious about this, he should be advocating this. I'd love to see that.