Over the last several decades a number of theistic philosophers have developed a powerful argument the conclusion of which is that naturalism - the view that material nature is all there is - is self-refuting. They argue that if we believe naturalism is true then we must believe that none of our beliefs, including our belief in naturalism, is trustworthy.
The foremost proponent of this argument has been Alvin Plantinga who presents a lecture on it here. The lecture is in six parts and is perhaps too long for those with limited time so as an alternative interested readers might check out this short summary:
Lest one criticize the video for its theistic bias against naturalism it might be mentioned that a lot of naturalists have implicitly and explicitly agreed with the thesis of the video.
Naturalist philosopher Thomas Nagel in his book Mind and Cosmos acknowledges that materialist versions of evolution simply can't explain cognition, value, or consciousness.
Evolutionary cognitive psychologist Steven Pinker has written that “Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not.”
As an example of how a false belief may have survival value, at least for our genes, imagine a prehistoric society in which arises a genetic mutation inclining the possessor of the mutation toward the belief that the more children one has the greater will be one's reward in the afterlife. Such a belief would be expected to produce large numbers of progeny, and the factors responsible for it, if they're genetic, will, over the course of time, eventually dominate in the society. Yet the belief is false.
As Plantinga says, one can believe in natural selection or one can believe in naturalism, but one can't believe in both. If natural selection has produced our cognitive faculties in a way consonant with naturalism then those faculties evolved to promote survival not to ascertain truth. Thus we have no good reason to think that our belief in naturalism is true.
On the other hand, if natural selection was superintended by an intelligent agent then we have reason to think that the process shaped our cognitive faculties to discern truth. That allows us to still believe in natural selection, but, of course, the existence of the intelligent agent means that the basic metaphysical assumption of naturalism, that nature is all there is, is false.
Naturalism appears to be a philosophical dead end. Followed to its logical conclusion it results in epistemological and moral nihilism.