I have a question: Out of all the problems that science has tried to solve in the last few hundred years, which scientific problems exactly has any form of supernaturalism solved? Science uses methodological naturalism because otherwise the scientist can just throw up his hands at any time & say "goddidit" & go home. So, when in the history of science has "goddidit" ever advanced science or answered any scientific question?
I think you can see from my post just above to Steve, that I am not opposed to methodological naturalism. I don't know of anybody who pronounces "goddidit" and goes home. I'm sure there IS someone like that, it's just that I've never come across them.
That makes it hard to answer your last Q about "when has godidit ever advanced science?", but I have a little story for you that might help:
When I was a 12-year-old, back in 1960, My Dad took me on a trip to Yellowstone Park, where we came upon a formation named "Specimen Ridge." The explanatory plaque there informed us that at Specimen Ridge there are 27 different petrified forests resting one atop the other. My father, a plumber, a fundamentalist with an 8th grade education, studied this for a while. Then he said, "Do they have any idea what the odds of that are? This is bunk."
His attitude toward evolution (what you would probably call "godidit") enabled him to not only doubt, but to seek rational argument in mathematics. My father, with his 8th grade fundamentalism was thinking critically, while the worlds's "experts," with their U/Chicago and Harvard PhD's, were uncritically amazed at the explanatory power of "modern science." It turns out my Dad was right. The scientific establishment was wrong, though they did come around to his view (not that they ever heard of him!).