I recently read Warranted Christian Belief by philosopher Alvin Plantinga. It's philosophy rather than science and religion, but in the last section of the book, he addressed several alleged "defeaters" of Christian belief. One of those he mentioned was historical-critical Bible scholarship. One type of such scholarship is Troeltschian biblical scholarship, which models itself on the physical sciences.

Unfortunately, they misunderstand the physical sciences to presuppose naturalism, that is, that miracles never happen. So if you begin your study of the Bible by presupposing that miracles never happen, it's not very impressive when you conclude that the miracles in the Bible never happened. Of course you were going to conclude that, regardless of what the evidence is, because it was in your presuppositions.

However, this is an understandable misunderstanding of science, since many scientists and philosophers of science agree that science can only work on the presupposition of naturalism. Plantinga really takes them to task:

A second suggestion, perhaps connected with the plea of inability to do otherwise, is given by the idea that the very practice of science presupposes rejection of the idea of miracle or special divine action in the world. "Science proceeds on the assumption that whatever events occur in the world can be accounted for in terms of other events that also belong within the world," says Macquarrie; perhaps he means to suggest that the very practice of science requires that one reject the idea (e.g.) of God's raising someone from the dead. Of course the argument form
 

If X were true, it would be inconvenient for science; therefore, X is false

is at best moderately compelling. We aren't just given that the Lord has arranged the universe for the comfort and convenience of the National Academy of Science. To think otherwise is to be like the drunk who insisted on looking for his lost car keys under the streetlight, on the grounds that the light was better there. (In fact it would go the drunk one better: it would be to insist that because the keys would be hard to find in the dark, they must be under the light.)

But why think in the first place that we would have to embrace this semideism in order to do science? Many contemporary physicists, for example, believe that Jesus was raised from the dead; this belief seems to do little damage to their physics. To be sure, that's physics; perhaps the problem would be (as Bultmann suggests) with medicine. Is the idea that one couldn't do medical research or prescribe medications if one thought that God has done miracles in the past and might even occasionally do some nowadays? To put the suggestion explicitly is to refute it; there isn't the faintest reason why I couldn't sensibly believe that God raised Jesus from the dead and also engage in medical research into, say, Usher's syndrome or multiple sclerosis, or into ways of staving off the ravages of coronary disease. What would be the problem? That it is always possible that God should do something different, thus spoiling my experiment? But that is possible: God is omnipotent. (Or do we have here a new antitheistic argument? If God exists, he could spoil my experiment; nothing can spoil my experiment; therefore....) No doubt if I thought God often or usually did things in an idiosyncratic way, so that there really aren't much by way discoverable regularities to be found, then perhaps I couldn't sensibly engage in scientific research; the latter presupposes a certain regularity, predictability, stability in the world. But that is an entirely different matter. What I must assume to do science, is only that ordinarily and for the most part these regularities hold. This reason, too, then, is monumentally insufficient as a reason for holding that we are somehow obliged to accept the principles underlying Troeltschian biblical scholarship.