Link: Stanford Encyclopedia of Philosophy
To sort out this debate, let us agree (to what is surely the case) that if you are a methodological naturalist, today you are going to accept evolution and conversely to think that evolution supports your cause. Today, methodological naturalism and evolution are a package deal. Take one, and you take the other. Reject one, and you reject the other. Clearly then, if your theism is one which gets its knowledge of God's actions and purposes from a literal reading of the Bible, you have got a conflict. You cannot accept Genesis literally and evolution. That is a fact. In other words, there can be no accommodation between Creationism and evolution. However, what if you think that theologically speaking there is much to be said for a nice shade of grey? What if you think that much of the Bible, although true, should be interpreted in a metaphorical manner? What if you think you can be an evolutionist, and yet take in the essential heart of the Bible? What price consistency and methodological naturalism then? The answer depends on what you take to be the "essential heart" of the Bible. At a minimum we can say that, to the Christian, this heart speaks of our sinful nature, of God's sacrifice, and of the prospect of ultimate salvation. It speaks of the world as a meaningful creation of God (however caused) and of a foreground drama which takes place within this world. One refers particularly to the original sin, Jesus' life and death, and his resurrection and anything which comes after it. And clearly at once we are plunged into the first of the big problems, namely that of miracles — those of Jesus himself (the turning of water into wine at the marriage at Canna), his return to life on the third day, and (especially if you are a Catholic) such ongoing miracles as transubstantiation and those associated, in response to prayer, with the intervention of saints.
There are a number of options here for the would-be methodological naturalist. You might simply say that such miracles occurred, that they did involve violations of law, but that they are outside your science. They are simply exceptions to the rule. End of argument. A little abrupt, but not flatly inconsistent with calling yourself a theist. Or you might say that miracles occur but that they are compatible with science, or at least not incompatible. Jesus was in a trance and the cure for cancer after the prayers to Saint Bernadette was according to rare, unknown, but genuine laws. This position is less abrupt, although you might worry whether this strategy is truly Christian, in letter or in spirit. It seems a little bit of a cheat to say that the Jesus taken down from the cross was truly not dead, and the marriage at Canna starts to sound like outright fraud. Of course, you can start stripping away at more and more miracles, downgrading them to regular occurrences blown up and magnified by the Apostles, but in the end this rather defeats the whole purpose.