Darwin does a much better job of analyzing the relationships between species through their differences in variation. He illustrates his case for descent with modification by explaining how developed organs in particular species are highly variable compared to the undeveloped organs in similar species, and by describing how modification can separate species over time. Darwin’s discussion of the reversion to characteristics from previous species shows evidence of how one species can be related to—or, in his terms, descended from—a parent species through the reappearance of characteristics from the parent species in subsequent generations. Although Darwin still does not explain how variations occur, his analysis of hereditary variation helps to bolster the theory of natural selection by explaining how variations link separate species through heredity. Here, Darwin the scientist is at his best, using particular facts and examples to draw conclusions that create broad scientific principles (an effective usage of inductive reasoning) and showing the ways variations help to prove the relationship between species.

Darwin also uses this analysis to attack the separate creation of species theory. Somewhat paradoxically, he invokes religion to bolster his own theory of the origin of species. He argues that some naturalists who might ignore his theory and cling to the notion of the separate creation of species are making a “mockery” of the “work of God.” Darwin challenges natural theologians—those naturalists who believe that the natural world shows the beauty of God’s independent creation of each species—by suggesting that their theory of independent creation is not the only one that can invoke the greatness of God. Implicitly, Darwin argues that the system of natural selection is just as brilliant and wondrous as a system of independently created species. Darwin implies that religion must not turn its back on scientific reasoning. Facts and analysis have led him to his theory, and the evidence cannot simply be ignored because of devotion to a set dogma, be it religious or scientific in nature. Anticipating the resistance to his theory, Darwin emphasizes that a shift in scientific and theological reasoning must occur before his theory can be accepted as scientifically valid.