Joe Carter at Evangelical Outpost has summarized what is becoming a popular philosophical argument against naturalism or, more precisely, against physicalism (the belief that all that exists is comprised solely of matter, energy and physical force).
One version of the argument is essentially this: If we are naturalists, i.e. we believe that physical nature is all there is, what do we base this belief upon? Most naturalists would reply that they believe it based upon the dictates of their reason. But what is reason? It might be replied that it is the ability to draw conclusions or inferences from facts. But how do we know we can trust this faculty of reason to give us truth? At this point the naturalist would offer some argument or another in support of the general trustworthiness of reason, but in so doing he must use reason to demonstrate the trustworthiness of reason. In other words, he must assume the truth of the very thing he seeks to demonstrate the truth of. This is called begging the question, and it's logically fallacious.
This is perhaps not necessarily fatal to naturalism since lots of beliefs, if taken far enough, have the same problem. The special difficulty it presents for naturalism, however, is that naturalism offers itself as a more rational or reasonable alternative to theism. Naturalism, we are told, dispenses with irrational constructs like faith, but this is manifestly not true. Naturalism places a great deal of confidence in the reliability of reason, a reliability it is unable to rationally demonstrate and which must therefore be accepted on faith.
Philosopher Victor Reppart has written a book titled C.S.Lewis's Dangerous Idea upon which Carter relies for his post. Reppart, following Lewis's argument in his classic work Miracles, asks where our faculty of reason comes from. The physicalist replies that it comes from non-rational matter, energy, and forces which over time produce brains that possess the ability to draw inferences from facts. This means that all of our beliefs (inferences), including our belief that naturalism is true, are ultimately the product of non-rational causes.
However, Reppart argues, no belief that is fully explained in terms of non-rational causes can be rationally arrived at. Thus, if physicalism is true, none of our beliefs are rational. They may be true by coincidence, but they're not rationally justified. Any thesis that entails the conclusion that no belief is rationally justified is self-referentially incoherent, i.e. it refutes itself, and should be rejected. Therefore, physicalism, Reppart concludes, should be rejected.
Reppart is not alone in his "Argument from Reason", of course, since Alvin Plantinga and others have offered similar arguments in recent years, but he draws out the implications of Lewis's thinking in a way that is devastating to naturalism. There's much more to his argument than what we can discuss here. To get a fuller picture go here and scroll down to the post titled C.S.Lewis's Dangerous Idea: Physicalism and the Argument from Reason then work your way up. Carter has six brief posts on the argument elucidating six different aspects of it.
Readers who are interested in Reppart's thinking might also wish to go here to read an interview with him.