Plantinga turns from cosmological to biological arguments for the world’s design, focusing on Michael Behe’s work. In Darwin’s Black Box (1996), Behe states that systems such as the bacterial flagellum, cilia, and the biochemistry of vision are “irreducibly complex”—meaning that removing any single component renders the entire system nonfunctional. Based on this observation, Behe claims that random mutation cannot account for such biological complexity, making a case for an intelligent guiding force behind evolution. Plantinga notes that Behe’s conclusions are not universally accepted. The philosopher Paul Draper argues that Behe does not prove that his examples fully satisfy the definition of irreducible complexity. Furthermore, Behe’s theory does not rule out indirect evolutionary pathways, in which a precursor system serving one function later acquires additional parts to serve a new function. 

Plantinga agrees that Behe’s case is not deductively airtight. For instance, in The Edge of Evolution (2007), Behe makes a quantitative argument based on the malaria parasite: Across more than 10²⁰ replication events under drug pressure, no novel protein-protein interactions arose, suggesting that assembling the complex protein machines inside cells by unguided selection is prohibitively improbable. At the same time, Plantinga contends that many critics of Behe fail to engage accurately with his actual claims. He contends that reviews by prominent evolutionary biologists such as Richard Dawkins and Jerry Coyne are often marked by ridicule of the notion of an “intelligent designer” of life rather than careful analysis. Plantinga acknowledges that some criticisms are more substantive, such as the possibility that Behe's evidence is drawn from atypical host-parasite systems or that complex biological structures could evolve through a series of individually advantageous intermediate steps. However, he maintains that these objections require further empirical investigation rather than dismissal.

Drawing on William Paley’s observations on the intricacy of design in the natural world, Plantinga suggests that perception alone may be a valid method of recognizing intelligent design. For instance, it is possible to identify a mountain goat on sight, without analyzing its characteristics or proving the point scientifically. Similarly, we instinctively perceive when another person is angry without consciously analyzing their facial expression and gestures. Plantinga argues that many beliefs—perceptual, memorial, social—are formed in this non-inferential “basic way” and carry significant warrant without requiring argumentative support. Darwin himself reportedly admitted to a strong perceptual impression of design in nature.

Within this model, Plantinga suggests that Behe is not primarily constructing proofs but directing attention to phenomena that trigger design perception. Such perceptual beliefs can be defeated—either rebutted (directly contradicted) or undercut (the basis for the belief is removed). However, Plantinga argues that evolutionary biology has done neither at the molecular level and provides only a weak, partial defeater at the level of gross anatomy. A theist’s prior belief acts as a defeater-deflector, preventing Darwinian considerations from dislodging the design belief. The chapter concludes that Behe’s design discourses offer genuine but difficult-to-quantify support for theism.

In this chapter, Plantinga argues for a deep concord between Christian theism and science. He contends that Christian theism provides a framework within which the very success of science is intelligible, whereas naturalism cannot explain it. He observes that modern Western science arose exclusively within Christian culture and that its founders, from Copernicus to Newton to Boyle, were sincere believers. Plantinga cites the physicist C. F. von Weizsäcker’s description of science as “a legacy of Christianity” (266). He argues that Christian theism provides a natural explanation for several assumptions that underpin modern science.

First, the author points to the doctrine of the image of God (imago dei). Because God is rational and created humans in his image, there is a deep correspondence between our cognitive faculties and the structure of reality. We understand the world because our minds were designed to do so. Naturalism, by contrast, offers no explanation for this fit. 

Second, science relies on the assumption that nature is governed by laws. Plantinga contends that this expectation fits naturally with the Christian conviction that a rational God governs creation consistently. Drawing on the work of Alfred North Whitehead, he notes that medieval philosophers such as Thomas Aquinas emphasized God’s rationality and predictability, fostering the idea that the world would be governed by stable laws rather than by capricious divine whims.

Third, theism makes the necessity of natural laws intelligible: They cannot be violated by created beings, while remaining contingent on God’s free choice, and God is not bound by them himself. 

Fourth, Plantinga refers to the mathematician Eugene Wigner’s observation that mathematics is remarkably effective at describing the physical world. From a theistic view, mathematical objects such as numbers and sets can be understood as reflecting God’s rational mind, while our ability to grasp them stems from our being made in the imago dei. 

Fifth, Plantinga argues that the reliability of inductive reasoning (our assumption that patterns observed in the past will continue into the future) is difficult to justify on purely naturalistic grounds. Following David Hume, he notes that induction cannot be proved without circular reasoning. Theism, however, explains that inductive reasoning is successful because a rational God created an orderly world and reliable cognitive faculties. 

Sixth, science’s preference for simple, elegant theories to describe the world. Plantinga sees this as further evidence of a fit between the human mind and the structure of reality. 

Finally, Plantinga argues that the very empirical character of science is grounded in the theological doctrine of creation's contingency. Because God freely chose to create this particular world, its specific laws could not be deduced in advance but must be discovered through observation and experiment. He notes that the mathematician Roger Cotes made this connection explicit in his Preface to Newton’s Principia Mathematica. 

Plantinga closes by noting that naturalism is not merely neutral on all these points but is in deep tension with them.