There are a few more interesting posts over at Letters From Babylon regarding science - one from John Zimmer and another from Joshua Davey, one of his several talented co-bloggers. Both generally examine the implications of a strictly defined understanding of science for our larger epistemological structure, on a theoretical as well as on a practical level.
Regarding the possibility that natural and supernatural explanations of an event will conflict, John remarks that automatically defering to the 'scientific' explanation typically entails -
believing "that science in general is a more foolproof and reliable way of knowing—that science as an invented human construct is more trustworthy for correspondence to truth than the supernatural alternative. It is this latter idea that needs debunking. [debunking is pretty strong here, but I am still with him - mw2] Science is wonderful. It is very useful and enlightening. I like it very much. But it is absolutely not infallible or foolproof. It is only a model."
Josh adds to the conversation a set of questions regarding the overcompartmentalization of knowledge because such compartmentalization is an inaccurate description of our functioning epistemology - of which he is quite right. Practical considerations affect how, why and what we believe in addition to the raw power and coherence of the ideas themselves. The question of how we integrate different ways of knowing is critical particularly given that this very compartmentalization that John and I are endorsing (though I don't particularly like the use of that term) has brought about the situation in which we currently find ourselves - the privileging of naturalistic knowledge over other types. If we compartmentalize, how do you prevent one compartment from taking over - as has essentially happened with naturalism being equated with knowledge. He's right, there's a weakness here. Several rough thoughts come to mind.
One is to acknowledge that to some degree we already have this problem - science doesn't really inform us about aesthetics, ethics, and similar fields.
The second is the analogy of the Incarnation. God became man. Its a powerful image that allows us to embrace the overlap between the supernatural and the natural. God can bring about results that are extraordinary through ordinary means. There is more here than I can really explain because there is more here than I really understand.