Plantinga’s central argument for a “deep conflict” between science and naturalism culminates in his Evolutionary Argument Against Naturalism (EAAN). Here, he contends that a rational person cannot consistently accept both naturalism and the modern theory of evolution. The core of his argument is that this conjunction of beliefs is self-referentially incoherent, as it provides its adherents with a powerful, undefeated reason to doubt the reliability of their own cognitive faculties. If one’s mind is untrustworthy, then all of its products—including the beliefs in naturalism and evolution themselves—are undermined. This internal contradiction, Plantinga argues, reveals a fundamental incompatibility between the quasi-religion of naturalism and a key pillar of modern science.

The first premise of the EAAN is that the conditional probability of our cognitive faculties being reliable, given naturalism and evolution, is low—a thesis Plantinga calls “Darwin’s doubt.” He finds support for this in Darwin’s own writings, where Darwin expressed a “horrid doubt […] 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” (316). Plantinga argues that natural selection favors adaptive behavior for survival and reproduction, not true beliefs. On a materialist view of the mind (which he takes as part of naturalism), beliefs are neural structures that cause behavior via their neurophysiological properties, not their content. Whether the content of a belief is true or false is irrelevant to its evolutionary fitness, so long as the underlying neurology produces the right actions. Thus, evolution would have no reason to select truth-tracking faculties, making it highly improbable that a mind produced under these conditions would be reliable.

From this low probability, Plantinga builds his second step: Anyone who accepts naturalism and evolution (N&E) and grasps this argument acquires a defeater (a reason to abandon a belief) for the conviction that their cognitive faculties are reliable (R). By accepting N&E, the naturalist accepts a worldview that implies their own mind is probably untrustworthy. This realization functions like learning one has ingested a drug known to cause cognitive malfunction; it gives one a powerful reason to suspend belief in the reliability of one’s own reasoning. This defeater for R cannot be defeated by arguing for the reliability of one’s faculties, as any such argument would necessarily rely on the very faculties now in doubt, resulting in vicious circularity.

The final step of Plantinga’s argument shows that the defeater for R is global, spreading to every belief produced by one’s cognitive faculties. As Plantinga states, “Anyone who has a defeater for R has a defeater for any other belief she thinks she has, including N&E itself” (343). The defeater neutralizes the naturalist’s justification for holding any belief, including the belief in N&E that generated the defeater in the first place. The position is therefore self-defeating and cannot be rationally held. This, for Plantinga, locates the real conflict between science and naturalism, which, when paired with evolution, leads to a skepticism so profound it consumes itself. At the same time, it supports the concord between science and theism: a worldview that presupposes a God who creates us with reliable cognition capable of accurately interpreting the world.