Human reason poses an interesting problem for metaphysical naturalists of both a modern and a postmodern inclination. Metaphysical naturalists hold that only nature exists and that human beings are simply the product of impersonal forces. Naturalists who embrace a modern or Enlightenment worldview argue that reason is our most trustworthy guide to truth while postmoderns assert that reason is an inadequate guide to truth.
Yet both must employ reason in order to make their respective cases. The modern has to assume reason is trustworthy in order to argue that it's trustworthy, which is surely question-begging, and the postmodern has to assume reason is trustworthy in order to conclude that it's not trustworthy at all, which is surely self-refuting.
In neither case can it be said that the modern or the postmodern is thinking rationally. We can have confidence that our reason generally leads us to truth, especially metaphysical truth, only on the assumption that God exists, is Himself rational, and has created us in his image.
If we join the naturalist in assuming God does not exist then we must conclude that our rational faculties are the product of processes which have evolved those faculties to suit us for survival, not for the attainment of true beliefs. As Harvard's Steven Pinker puts it, "Our brains were shaped for fitness, not for truth. Sometimes truth is adaptive sometimes not."
Here's philosopher Patricia Churchland on the same subject: "Evolution selects for survival and “Truth, whatever that is, definitely takes the hindmost.”
And philosopher John Gray: "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."
Each of these thinkers embraces metaphysical naturalism, but on that view there's no basis for thinking that their reason is a trustworthy guide to truth which makes their claim that reason isn't a trustworthy guide to truth itself untrustworthy. What a muddle.
Anyway, a trio of philosophers discuss the conundrum in which naturalists finds themselves in this video:
The same argument is an integral part of philosopher Alvin Plantinga's Evolutionary Argument Against Naturalism which he discusses in this video: