Theist: You say there is no God.This is the point that philosopher Alvin Plantinga has been making for the last twenty years or so. If we evolved the cognitive faculties we currently possess so as to be better suited for survival back in the stone age what grounds do we have for thinking that those faculties reliably lead to truth, especially truth about metaphysical beliefs like a belief in naturalism?
Theist: Yet belief in God among many (if not most) humans persists.
EM: I cannot deny that.
Theist: How do you explain that?
EM: Religious belief is an evolutionary adaption.
Theist: But you say religious belief is false.
EM: That’s correct.
Theist: Let me get this straight. According to you, religious belief has at least two characteristics: (1) it is false; and (2) evolution selected for it.
EM[looking a little pale now, because he’s just figured out where this is going]: Correct.
Theist: You believe the Neo-Darwinian Synthesis [NDS] is true.
EM: Of course.
Theist: How do you know your belief in NDS is not another false belief that evolution has selected for?
Our materialist friends are invited to fill in the blank.
Consider an example: Suppose in some prehistoric society a belief arises that the more children one has the more richly they'll be rewarded in the afterlife. Suppose, too, that our doxastic inclinations are produced by our genes which are themselves the result of natural selection. If so, people who possess the genes for this belief are likely to have many more children on average than those who don't have it, and the gene that disposes toward the belief will spread rapidly through the population even though the belief is false.
In other words, evolution favors beliefs which have survival value, not necessarily truth value. If we believe ourselves to be solely the products of a natural process like evolution the most we can say about our beliefs about things like naturalism and theism is that they must have survival value or they wouldn't have persisted. A purposeless process like evolution which is geared to promoting survival is indifferent to the actual truth of beliefs. It's only attuned to their utility.
That being so, why should we have any confidence, on naturalism, that our reason is a reliable guide to truth? Indeed, the paradox for the naturalist is that if naturalism is true he can have no confidence that it is. His belief that it's true is the product of cognitive faculties shaped for survival, not for truth.
It's only the theist who believes that his cognitive faculties are designed by God to lead to truth who can have any confidence that those faculties are in fact reliable.