Notable atheist and Oxford biologist Richard Dawkins once remarked to A.J. Ayer at an Oxford college dinner that he couldn’t imagine being an atheist before 1859, the year Darwin’s Origins of the Species was published: “[A]lthough atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.” However, according to one argument by Christian philosopher Alvin Plantinga, this statement (in a certain sense) may actually not be true.
First, just what do we mean by naturalism? In short, naturalism “eschews or rejects appeal to the supernatural, and traces our origins back to blind and uncaring forces” . Thus, physical reality is all that exists; no supernatural or personal forces lie beyond the scope of the universe. As Plantinga says, “to be a naturalist is not to believe anything special – e.g., that there aren’t any fairies, or angels, or gods; to be a naturalist is to adopt a certain attitude, an attitude involving among other things an exclusive commitment to science in guiding one’s opinions” .
Plantinga’s argument has three relevant areas of concern:
- (1) Theism: the belief that a wholly good, all powerful and all knowing person exists: one who has beliefs (or knowledge), aims and intentions and acts to accomplish them.
- (2) Naturalism: As Plantinga interestingly says: “The theistic picture minus God.”
- (3) Cognitive Faculties: The powers or faculties of capacities whereby we have knowledge or form belief: memory, perception, reason, and maybe others.
Plantinga’s argument can be stated as such: Given the acceptance of our belief in naturalism, what is the reliability of that belief given our arisal through successive evolutionary history via blind and uncaring forces? or, as Ernest Sosa further explains: “[T]he probability that our cognitive faculties are reliable must be either quite low or at best inscrutable. This defeats any belief we may have in the reliability of our faculties. Absent such belief, finally, we are deprived also of epistemic warrant (Authority, justification) for all beliefs deriving from such faculties” . The thrust of the argument however, is its devastating conclusion: “But among those beliefs is the very belief in naturalism, which therefore defeats itself” . Consider Plantinga’s further explanation:
[I] argue that (1) if naturalism were true, there would be no such thing as proper function, and therefore also no such thing as malfunction or dysfunction. Hence there would be no such thing as health or sickness, sanity or madness; further, and in this epistemological context crucial, there would be no such thing as knowledge. That’s bad enough, but there’s worse to follow: [I] argue (2) that the naturalist is committed to the sort of deep and debilitating skepticism according to which he can’t trust his cognitive faculties to furnish him with any true beliefs; he has a defeater for whatever he believes, including naturalism itself. 
Consider the probability function P(R/N&E). N stands for Metaphysical Naturalism – N excludes the existence of God as understood under traditional theism; E stands for the arisal of our cognitive faculties by way of evolution; R is the claim that our cognitive faculties are reliable. Now, what is the probability of R, given N&E? First, consider a few things regarding the matter of conditional probability.
Take for example that we have some given factor H, which means that an individual will live a healthy lifestyle passed the age of 75. So, what is the probability of H on the condition that an individual never exercises, doesn’t eat right, and has high blood pressure? Well, the obvious answer seems to be that the probability of H given those factors would be considerably low. However, the probability of H will be much higher on the condition that if the individual exercises, eats right, and does have a lower blood pressure.
In a likewise fashion, what is the probability of R given metaphysical naturalism (N) and the arisal of our faculties by way of evolution (E)? According to Charles Darwin himself, he might consider the probability of R to be fairly low. As he once wrote in his Autobiography, “But then arises the doubt, can the mind of man, which has, as I fully believe, been developed from a mind as low as that possessed by the lowest animals, be trusted when it draws such grand conclusions?”  Then, there is Patricia Churchland’s take on the probability of R:
Boiled down to essentials, a nervous system enables the organism to succeed in the four F’s: feeding, fleeing, fighting, and reproducing. The principle chore of nervous systems is to get the body parts where they should be in order that the organism may survive [ … ] 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. 
Thus, the thrust of the probability of R packs a weak punch. Since the naturalist contends that our faculties derive from brute forces, it seems that we cannot rationally hold to our “implicit trusts” of the reliability of our faculties. However, if we cannot trust our faculties, then we cannot rationally trust anything that is a deliverance of those faculties. Naturalism is a deliverance from our faculties, therefore, we cannot rationally hold on to that belief. Consider the thrust of this conclusion:
Consider now any subjects who face the question whether their faculties are reliable, and realize that if they do have reliable faculties, this is a contingent matter, and that they cannot just assume so and let it go at that. Given the contingency of the reliability of their faculties, what assurance is there that though they might be unreliable, in fact they are reliable? Wouldn’t the inability to give a rational, nonarbitrary answer to this question itself constitute a problem? 
The contingent nature of our cognitive faculties constitutes that they are one particular way and could have possibly been another, but aren’t; thus, the naturalist ignoring this question seems to catch himself in a bit of a problem. To end with Plantinga: “The conclusion to be drawn, therefore, is that the conjunction of naturalism with evolutionary theory is self-defeating: it provides for itself an undefeated defeater.”
-  Ernest Sosa, “Natural Theology and Natural Atheology” in Alvin Plantinga, ed. Deane-Peter Baker (Cambridge University Press: 2007) p. 95
-  Alvin Plantinga and Michael Tooley, Knowledge of God (Blackwell Publishing: 2008) p. 18 – emphasis Plantinga’s.
-  Sosa, 95
-  Ibid.
-  Plantinga (2008), p. 1 – emphasis his.
-  Charles Darwin, “Autobiography” in Portable Atheist, ed. Christoper Hitchens (Da Capo: 2007) p. 96
-  See lecture outline – emphasis Churchland’s.
-  Sosa, 101
- [a] http://www.calvin.edu/academic/philosophy/virtual_library/articles/plantinga_alvin/an_evolutionary_argument_against_naturalism.pdf