Ever since the Enlightenment philosophers inclined toward a naturalistic worldview had touted their devotion to reason and derided those whose beliefs seemed to them to be irrational. They were convinced that they were occupying the intellectual high ground, but in the latter part of the 20th century many thinkers, both naturalists and theists, noting that a naturalistic view of the world entailed a Darwinian account of the origin of human reason, recognized that on Darwinism there's no good basis for trusting our reason to lead us to truth.
According to naturalism, evolution, unguided by any intelligent agent, has selected for cognitive faculties in human beings that lead to survival, but survival doesn't necessarily require truth. Indeed, survival could just as easily be enhanced by falsehoods as by truths.
Consider, for instance, a prehistoric society in which a gene mutation causes some people to believe that the more children they produce the greater will be their reward in the afterlife. Those who carry the mutation would tend, on average, to generate more children than those who don't, and since the mutant gene would be passed on to offspring the belief would spread through the population. It would have very high survival value despite its being completely false.
As Barry Arrington at Uncommon Descent notes, this is an awkward state of epistemic affairs for naturalists to find themselves in, but, even so, there are lots of examples of naturalists admitting that natural selection, at least naturalistic natural selection, entails precisely the conclusion that reason has evolved to aid our survival not to discover truth, and especially not metaphysical truth.
Arrington offers a sampling of such quotes:
“[Our] brains were shaped for fitness, not for truth. Sometimes truth is adaptive, but sometimes it is not.” Steven PinkerOf course, a further irony in all this is that if the naturalist cannot trust her reason to lead her to truths about her deepest metaphysical beliefs then she has no good grounds for believing that naturalism is true in the first place.
“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
“Improvements in sensorimotor control confer an evolutionary advantage: a fancier style of representing is advantageous so long as it is geared to the organism’s way of life and enhances the organism’s chances of survival. Truth, whatever that is, definitely takes the hindmost.” Patricia Churchland
“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
Anyone interested in reading more about the problem of reconciling naturalism with a belief in the trustworthiness of human reason might check out a book by Alvin Plantinga, one of the foremost philosophers of the 20th century. The book is titled Knowledge and Christian Belief, and it's a more accessible version of his earlier, more technical treatment of the same subject titled Where the Conflict Really Lies: Science, Religion and Naturalism.