On the particular argument, you might want to take a look at the Wikipedia article: http://en.wikipedia.org/wiki/Evolutionary_argument_against_naturalism

The "evolutionary argument against naturalism" seems to go back to CS Lewis, and Alvin Plantina attempted to formulate it in Bayesian terms. There is a rather devastating response from Fitelson and Sober. In particular:

For the fact of the matter is that our cognitive mechanisms are reliable on some subjects, unreliable on others, and of unknown reliability on still others. We should divide our beliefs into categories and associate a characteristic degree of reliability with each of them. Perhaps certain simple perceptual beliefs are very reliable, while beliefs about other subjects are less so...

Once we decompose ... into a conjunction of claims, it is far from obvious that evolutionary theory does a worse job of predicting this conjunction than traditional theism does. Plantinga says the traditional theist “believes that God is the premier knower and has created us human beings in his image, an important part of which involves his endowing them with a reflection of his powers as a knower (p. 237).” However, an influential point of view in cognitive science asserts that human reasoning is subject to a variety of biases. It isn’t just that people occasionally make mistakes, but that the human reasoning faculty seems to follow heuristics that lead to systematic error (Kahnemann, Tversky, and Slovic 1982). It would be no surprise, from an evolutionary point of view, if human beings had highly reliable devices for forming beliefs about practical issues that affect survival and reproduction, but are rather less gifted when it comes to matters of philosophy, theology, and theoretical science. Does traditional theology also predict this result? No doubt, a theology can be specified that makes any prediction one wants. However, it is not at all clear that Plantinga’s traditional theology does a good job predicting the varying levels of reliability that the human mind exhibits. Plantinga must address the same problem that Paley’s design argument faces: Why would an omniscient, omnipotent, and benevolent deity produce organisms who seem to be so manifestly imperfect in the adaptations they exhibit (Sober 1993)?