This chapter shows Darwin at his most rigorous and rhetorically masterful. Aware of the controversy surrounding his theory, Darwin opens by confronting its potential weaknesses directly. In his Autobiography, he described a golden rule he had followed for decades: to make immediate note of all serious objections and recalcitrant facts. In Chapter 6, this habit becomes a strength. Rather than dodging critique, Darwin anticipates the strongest objections his readers might raise and addresses them systematically, using examples from natural history, comparative anatomy, behavior, and the fossil record.
He acknowledges up front that there are grave difficulties confronting the theory of natural selection. Some, he notes, will be treated in later chapters: Particularly those relating to instincts and hybridism. Here, he focuses on two specific challenges: the absence or rarity of transitional forms in nature and the origin of peculiar habits and complex structures. These are not minor issues. The first challenges the gradualism at the heart of natural selection. The second questions whether natural selection could account for structures so perfect and habits so specialized that they seem to defy incremental development.
Darwin begins with the absence of transitional varieties. If species evolve gradually from one another, why do we not see countless intermediate forms in the fossil record or in the natural world today? Why, he asks, does nature not appear chaotic and full of fluid forms, instead of cleanly delineated species? This is one of the most common and intuitively powerful criticisms of his theory. Darwin’s response is grounded in the imperfection of the geological record. The crust of the Earth, he writes, is like a vast but incomplete museum. Its collections were not made continuously but at intervals immensely remote in time. Fossilization is rare, destruction is common, and much of the record remains inaccessible.
He also points out that many regions are geologically unexplored or eroded, and most fossils that do exist have yet to be discovered. Even within the known record, the fine gradations between forms may not be preserved or easily recognizable. Darwin thus turns the objection around: the real question is not why we see so few transitional fossils, but why we would expect to see many in the first place, given the nature of geological processes.
Darwin then turns to peculiar structures and habits, those features that seem too specialized or too perfectly adapted to have arisen gradually. He asks, rhetorically: how could an animal with the structure and habits of a bat have descended from one with completely different behavior? Could natural selection really produce an organ as perfect as the eye? Darwin does not downplay these questions. In fact, he admits that to suppose the eye, with all its subtle adaptations for adjusting focus, light levels, and correcting optical aberrations, could have evolved through natural selection seems, I freely confess, absurd in the highest possible degree.
But instead of retreating, Darwin responds by emphasizing that such complex organs do not appear out of nowhere. They arise through small, incremental changes, each of which confers a slight advantage. He points to animals that possess only basic light-sensitive spots, and others with more complex visual systems. These gradations, he argues, reveal the stages through which an organ like the eye could evolve. Later research would confirm that light-sensitive structures have evolved independently many times (at least forty), across the animal kingdom, supporting Darwin’s intuition that complexity can emerge through gradual steps.
Darwin also illustrates his argument with examples of partial or transitional structures. Flying squirrels, for example, do not truly fly but glide clumsily, suggesting an intermediate state between terrestrial mammals and bats. The flying lemur “Galeopithecus” is an even more efficient glider and was once misclassified as a bat. Birds provide even more dramatic examples. Their wings, Darwin notes, have been co-opted for entirely different uses: as paddles in the steamer duck, as fins in penguins, as balance rudders for running ostriches, or as shading devices in the kiwi. The same structure can evolve for very different functions, depending on selective pressures.
This leads into one of the chapter’s most insightful themes: the conversion of organs from one function to another. Darwin highlights his own studies of barnacles to make the point. In pedunculated cirripedes, the folds of skin that hold eggs have also taken on a respiratory role. These structures were eventually transformed, through selection, into the true gills of sessile cirripedes. If the pedunculated forms had gone extinct, we would never have imagined this transformation. Yet the continuity becomes evident when both forms are studied side by side. Modern DNA analysis has confirmed Darwin’s conclusion that sessile barnacles evolved from pedunculated ancestors.
This reinforces a broader principle: natural selection cannot make leaps: “Natura non facit saltum” (nature does not jump). Complex structures evolve step by step. Every intermediate form must be functional. Natural selection acts only on slight, successive variations, and always moves gradually. If special creation were responsible for life’s diversity, Darwin asks, why do we observe so many half-formed structures, rudiments, and functionally ambiguous organs? Why wouldn’t a Creator leap directly from one perfected form to the next? The existence of transitional forms makes far more sense under descent with modification than under separate creation.
Darwin’s view on the relationship between behavior and structure is also worth noting. He seems to favor the idea that behavior changes first, and structure follows. That is, when an organism adopts a new habit, say, burrowing, gliding, or nocturnal foraging. It sets up selection pressures that lead to morphological changes. This aligns with a concept later called the Baldwin effect, where behavioral flexibility creates new conditions for natural selection to act. Ernst Mayr later summarized this as behavior is the pacemaker of evolution. Darwin provides several examples of species whose habits differ sharply from those of their close relatives, suggesting that shifts in behavior can drive anatomical innovation.
In his summary, Darwin once again admits that serious objections exist. But he insists that these difficulties are not fatal to the theory. Rather, they are challenges to be met with observation, experimentation, and further inquiry. He argues that natural selection remains the best explanation for complex adaptations, and that the theory of special creation fails to explain transitional forms, rudimentary organs, and the variety of structures we observe across related species.
The power of this chapter lies not just in its content, but in its tone. Darwin does not offer certainty, but reasoned confidence. He treats objections with respect and curiosity, not defensiveness. And he shows, again and again, that apparent problems often become sources of insight when viewed through the lens of natural selection. The effectiveness of this chapter is underscored by the fact that it was the only one in the Origin to spawn a sequel. In the sixth edition, Darwin added an additional chapter titled Miscellaneous Objections, which continued the work begun here.
Chapter 6 reveals Darwin not only as a scientist, but as a careful and persuasive thinker. By engaging directly with the weaknesses of his theory, he strengthens it. And by doing so in clear, empirical, and humble prose, he invites the reader to examine the evidence with him: Not as a dogma, but as an unfolding discovery.