Chapters 6 and 7, on “Difficulties on Theory” and “Instinct,” are the fulcrum of Darwin’s Origin of Species. They come at the center of the work, after the first five chapters that explicate the theory of natural selection and outline the causes and effects of the mysterious laws of variation on which Darwin’s argument for natural selection depends. These two chapters sustain the narrative drive that Darwin had been building through the first five chapters and introduce new scientific and emotional dimensions, particularly in his treatment of the theory’s larger implications for the religious context in which he was writing.

“Difficulties on Theory” and “Instinct” take on two classes of what Darwin describes as “a crowd of difficulties [that] will have occurred to the reader … [l]ong before having arrived at this part of my work” (Origin, 171). The first class of problems, covered largely in Chapter Six, deals with the apparent lack of transitional forms, wide variation within taxa, organs of apparently small importance, and, most importantly, the difficulty of giving a wholly materialist explanation for the evolution of structures and organs of extreme perfection, such as the vertebrate eye. The second class, covered in Chapter Seven, deals with the evolution of behavior and instinct, phenomena for which the physical basis was quite unknown (as with the laws of variation), and which thus presented particular problems for a materialist explanation.