In these chapters, Plantinga continues to use a subtractive rhetorical strategy to develop the central theme of The Deep Concord Between Theism and Science. To neutralize the apparent threats science poses to theism, he separates the empirical findings of evolutionary science from the naturalistic interpretations often attached to them. Analyzing theories by Rodney Stark, Scott Atran, and David Sloan Wilson, he addresses concepts such as evolutionary “spandrels” and proposes theoretical modifications, such as “Stark-minus” (142), which strips away explicit claims that no divine creator exists while retaining the underlying evolutionary mechanisms. By demonstrating that the scientific models can function coherently without their atheistic corollaries, he rhetorically downgrades the apparent conflict between science and theism to a mere philosophical disagreement. It should be noted that while presenting his subtractive logic as neutral philosophical reasoning, he continues to argue from a specifically Christian perspective.

The text focuses on the concept of competing evidence bases to explain why scientific consensus does not inherently defeat religious belief. Plantinga defines methodological naturalism as a procedural rule that restricts the scientific evidence base by strictly excluding supernatural explanations. He illustrates this restriction using the analogy of a jury convicting an innocent person based on circumstantial evidence. In this analogy, the verdict is rationally sound based on the limited evidence presented, but it does not defeat the defendant’s independent memory of innocence. This comparison clarifies how a proposition can be highly improbable given a restricted dataset yet remain entirely rational when viewed against a comprehensive dataset. By categorizing naturalism as a limited perspective, Plantinga positions the Christian evidence base, which includes faith, as epistemologically wider. 

To formalize his argument, Plantinga utilizes the language of defeaters and intrinsic warrant. He contends that a new scientific discovery only defeats an existing belief if that contested belief becomes improbable once isolated from its original supporting evidence. However, he asserts this formal test is ultimately insufficient for religious beliefs because they carry an “intrinsic warrant” (188) that operates independently of external argumentation. By comparing faith to basic, reliable cognitive functions like memory or sensory perception, Plantinga elevates religious conviction to the status of knowledge. Consequently, theories positing that religious belief is merely a non-truth-tracking evolutionary adaptation fail to provide a rationality defeater. This effectively insulates religious belief from scientific contradiction. However, secular critics argue this framework immunizes religion from empirical falsification by structurally privileging untestable theological premises over universally accessible data.

Plantinga applies this same epistemological scrutiny to Historical Biblical Criticism, deconstructing its methodologies to reveal inherent philosophical biases. He divides the discipline into two primary camps: Troeltschian criticism, which assumes miracles are impossible, and Duhemian criticism, which relies exclusively on universally agreed-upon secular evidence. Plantinga points out that Troeltschian conclusions against the resurrection naturally follow from their biased starting assumptions. Meanwhile, Duhemian conclusions are structurally guaranteed to be thin and incomplete due to their reliance on only universally agreed-upon data. This categorization exposes the circular logic embedded in secular biblical scholarship. If a discipline methodologically excludes special divine action to maintain its scientific credibility, its subsequent failure to find evidence of divine action is a predetermined artifact of its parameters, not a genuine empirical discovery. Through this rigorous deconstruction, Plantinga challenges the purported neutrality of secular historical methods. Nevertheless, mainstream academic historians maintain that these strict methodological constraints are not driven by ideological hostility toward religion, but are absolutely essential for maintaining an objective, consensus-based standard of scholarly inquiry across diverse belief systems.

The author synthesizes his critique of naturalism by coining the term “Simonian science” to categorize theories fundamentally incompatible with Christian belief. Named after Herbert Simon, whose theory of altruism attributes the self-sacrificing behavior of figures like Mother Teresa to docility and bounded rationality, this label serves as a shorthand for the overreach of evolutionary psychology. By singling out Simon’s theory, Plantinga highlights the reductive nature of evolutionary explanations that attempt to map complex moral and spiritual phenomena entirely onto reproductive fitness. He frames Simonian science as a rigid framework that fundamentally misinterprets the human condition by pathologizing moral goods. This critique is notably at odds with established scientific consensus. While Plantinga views evolutionary accounts of altruism as intellectually impoverished, evolutionary biologists maintain that mechanisms like reciprocal altruism provide robust, empirically verifiable explanations for cooperative behavior without requiring supernatural interpretation.