Difficulties for the theory
Chapter VI begins by saying the next three chapters will address possible objections to the theory, the first being that often no intermediate forms between closely related species are found, though the theory implies such forms must have existed. As Darwin noted, "Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion, instead of the species being, as we see them, well defined?" Darwin attributed this to the competition between different forms, combined with the small number of individuals of intermediate forms, often leading to extinction of such forms.
Another difficulty, related to the first one, is the absence or rarity of transitional varieties in time. Darwin commented that by the theory of natural selection "innumerable transitional forms must have existed," and wondered "why do we not find them embedded in countless numbers in the crust of the earth?" (For further discussion of these difficulties, see Speciation#Darwin's dilemma: Why do species exist? and Bernstein et al. and Michod.)
The chapter then deals with whether natural selection could produce complex specialised structures, and the behaviours to use them, when it would be difficult to imagine how intermediate forms could be functional. Darwin said:
Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some animal with wholly different habits? Can we believe that natural selection could produce, on the one hand, organs of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, organs of such wonderful structure, as the eye, of which we hardly as yet fully understand the inimitable perfection?
His answer was that in many cases animals exist with intermediate structures that are functional. He presented flying squirrels, and flying lemurs as examples of how bats might have evolved from non-flying ancestors. He discussed various simple eyes found in invertebrates, starting with nothing more than an optic nerve coated with pigment, as examples of how the vertebrate eye could have evolved. Darwin concludes: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case."
In a section on "organs of little apparent importance", Darwin discusses the difficulty of explaining various seemingly trivial traits with no evident adaptive function, and outlines some possibilities such as correlation with useful features. He accepts that we "are profoundly ignorant of the causes producing slight and unimportant variations" which distinguish domesticated breeds of animals, and human races. He suggests that sexual selection might explain these variations:
I might have adduced for this same purpose the differences between the races of man, which are so strongly marked; I may add that some little light can apparently be thrown on the origin of these differences, chiefly through sexual selection of a particular kind, but without here entering on copious details my reasoning would appear frivolous.
Chapter VII (of the first edition) addresses the evolution of instincts. His examples included two he had investigated experimentally: slave-making ants and the construction of hexagonal cells by honey bees. Darwin noted that some species of slave-making ants were more dependent on slaves than others, and he observed that many ant species will collect and store the pupae of other species as food. He thought it reasonable that species with an extreme dependency on slave workers had evolved in incremental steps. He suggested that bees that make hexagonal cells evolved in steps from bees that made round cells, under pressure from natural selection to economise wax. Darwin concluded:
Finally, it may not be a logical deduction, but to my imagination it is far more satisfactory to look at such instincts as the young cuckoo ejecting its foster-brothers, —ants making slaves, —the larvæ of ichneumonidæ feeding within the live bodies of caterpillars, —not as specially endowed or created instincts, but as small consequences of one general law, leading to the advancement of all organic beings, namely, multiply, vary, let the strongest live and the weakest die.
Chapter VIII addresses the idea that species had special characteristics that prevented hybrids from being fertile in order to preserve separately created species. Darwin said that, far from being constant, the difficulty in producing hybrids of related species, and the viability and fertility of the hybrids, varied greatly, especially among plants. Sometimes what were widely considered to be separate species produced fertile hybrid offspring freely, and in other cases what were considered to be mere varieties of the same species could only be crossed with difficulty. Darwin concluded: "Finally, then, the facts briefly given in this chapter do not seem to me opposed to, but even rather to support the view, that there is no fundamental distinction between species and varieties."
In the sixth edition Darwin inserted a new chapter VII (renumbering the subsequent chapters) to respond to criticisms of earlier editions, including the objection that many features of organisms were not adaptive and could not have been produced by natural selection. He said some such features could have been by-products of adaptive changes to other features, and that often features seemed non-adaptive because their function was unknown, as shown by his book on Fertilisation of Orchids that explained how their elaborate structures facilitated pollination by insects. Much of the chapter responds to George Jackson Mivart's criticisms, including his claim that features such as baleen filters in whales, flatfish with both eyes on one side and the camouflage of stick insects could not have evolved through natural selection because intermediate stages would not have been adaptive. Darwin proposed scenarios for the incremental evolution of each feature.
