I finally got around to listening to Alvin Plantinga's torpedo to naturalism (downloadable here), where he takes a doubt toyed with by the later Darwin, and shows it to be a weapon, not a toy.
In short, the argument is that there may be apparent, surface discontinuities between theism and science, but these overlie much deeper, systemic continuities (i.e. the trustworthiness of knowledge). Conversely, there may be apparent, surface continuities between naturalism and science, but these overlie much deeper systemic discontinuities (i.e. the untrustworthiness of knowledge). If, as a naturalist would argue, our cognitive faculties are merely a product of evolutionary drives (concatenations of the mating urge), what possible trust can we put in them to be reliable when it comes to abstract scientific questions? If materialism is true, are not "arguments" one more verbal cocktail intended to propagate the species? What matters, from a naturalist's perspective, is survival, not scientific accuracy.
On the contrary, Plantinga shows evolutionary theory to be something the theist is in best position to affirm. Of course, this doesn't mean that secular scientists can't continue to do good work, only that that if such scientists insist on the ideology of naturalism, their conclusions will be self-referentially incoherent.
Next thing you know someone will write a respected book about how the entire project of reason itself, and hence science, is not a product of the supposed Age of Reason, but that it lies on a theological foundation secured in the Middle Ages, without which the Age of Reason would have been impossible. Oh wait, that already happened.