Three philosophers talk about an argument C.S. Lewis once made in his little book Miracles to the effect that one can embrace metaphysical naturalism or one can believe that reason leads us to truth, but one cannot do both. Naturalism, in other words, is incompatible with a confidence in reason:
This is ironic since naturalists pride themselves on their reasonableness and often emphasize that their reliance on reason as a means of gaining knowledge is much superior to other ways of knowing, such as religious faith. Yet the naturalist must accept the trustworthiness of reason by faith, and indeed he can't argue that reason is trustworthy without presupposing that it is trustworthy. He has to use reason in order to argue that reason is reliable. This is called begging the question.
Philosopher Alvin Plantinga has convincingly demonstrated that since the evolutionary story accepted by naturalists maintains that traits evolve based on their survival value and not upon whether they lead to truth, human reason would have evolved because it somehow equipped early man to survive in his environment and would only coincidentally have had anything to do with truth.
For example, primitive cognitive faculties that produced a belief that one's reward in the afterlife depended upon how many children one had in this life would have spread through a population of prehistoric humans like rumors of a White House sex scandal among a gaggle of journalists. But although those cognitive faculties would have conferred enormous evolutionary advantages, they would've had nothing to do with truth.
Thus the argument from reason poses a serious problem for naturalism. Victor Reppert, one of the philosophers in the video, writes about it in his book C.S. Lewis' Dangerous Idea, and Alvin Plantinga explains it in his book Where the Conflict Really Lies. Both are excellent reads for the philosophically-minded.