The argument which concludes that naturalism is self-refuting goes something like this:
On atheism there is no God. Thus, our reasoning powers must be the product of a purposeless evolutionary process that was geared to survival, not for discovering truth.This is ironic since most atheists argue that atheistic materialism is rational and theism is irrational, but, in fact, the opposite is actually the case.
If that's the case, if we can't trust our reasoning powers to lead us to truth, especially the truth about metaphysical questions, then we have no grounds for believing that atheism is in fact true.
So, although atheism may be true, one cannot rationally believe that it is.
Theism is the more rational worldview since the belief that we are endowed with a trustworthy reasoning faculty which can reliably lead us to truth only makes sense if theism is true.
Thus, the theist has grounds for believing that reason is trustworthy and is therefore rational in trusting his reason to lead him to truth, whereas the naturalist is irrational to believe that naturalism is true since she has no grounds for believing that her reason has led her to the truth about naturalism.
Numerous naturalists have acknowledged in one way or another that this is a problem. To illustrate the point here's a baker's dozen of quotations culled from philosophers and scientists, most of whom, so far as I know, are atheistic materialists:
- "Our brains were shaped for fitness, not for truth. Sometimes truth is adaptive sometimes not." Steven Pinker
- Evolution selects for survival and 'Truth, whatever that is, definitely takes the hindmost.' Patricia Churchland
- "Modern [naturalism] is the faith that through science humankind can know the truth and so be free. But if Darwin's theory of natural selection is true this is impossible. The human mind serves evolutionary success, not truth." John Gray
- "Our highly developed brains, after all, were not evolved under the pressure of discovering scientific truths but only to enable us to be clever enough to survive." Francis Crick
- “With me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy.” Charles Darwin
- “Sometimes you are more likely to survive and propagate if you believe a falsehood than if you believe the truth.” Eric Baum
- “According to evolution by natural selection, an organism that sees reality as it is will never be more fit than an organism of equal complexity that sees none of reality but is just tuned to fitness. Never.” Donald Hoffman
- "We are anything but a mechanism set up to perceive the truth for its own sake. Rather, we have evolved a nervous system that acts in the interest of our gonads, and one attuned to the demands of reproductive competition. If fools are more prolific than wise men, then to that degree folly will be favored by selection. And if ignorance aids in obtaining a mate, then men and women will tend to be ignorant." Michael Ghiselin
- “[N]atural selection does not care about truth; it cares only about reproductive success” Stephen Stich
- “We are jumped-up apes, and our brains were only designed to understand the mundane details of how to survive in the stone-age African savannah.” Richard Dawkins
- “Our brains aren’t wired for accuracy. They’re wired to keep us alive.” Lisa Feldman Barrett
- “If my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true… and hence I have no reason for supposing my brain to be composed of atoms.” J.B.S. Haldane
- "Supposing there was no intelligence behind the universe, no Creative Mind. In that case, nobody designed my brain for the purpose of thinking. It is merely that when atoms inside my skull happen, for physical or chemical reasons, to arrange themselves in a certain way, this gives me, as a by-product, the sensation I call thought. But, if so, how can I trust my own thinking to be true?.... Unless I believe in God, I cannot believe in thought: so I can never use thought to disbelieve in God." C.S. Lewis