Darwin addresses some of the flaws in his theory of natural selection. He tackles two major questions: First, if species have gradually descended from other species, why do clearly defined, separate species exist, instead of numerous intermediate forms of species? Second, can natural selection really produce highly complex organs, such as the eye, from species lacking anything remotely similar to such complex organs?

To answer the first question, Darwin argues that natural selection requires that intermediate varieties become extinct. Since natural selection urges species to become perfectly adapted to their environments, certain environments favor some characteristics and other environments favor others, allowing species to diverge based on their separate environments. The favored characteristics in these respective environments would become more advantageous than any intermediate characteristics, causing the intermediate species to become extinct. Darwin addresses the question of whether an intermediate species would exist in an intermediate geological area between the two different environments. He argues that intermediate environments are so geographically small that intermediate species in those areas would not be able to reproduce sufficiently to perpetuate themselves and survive and would eventually become extinct. Therefore, we only see small numbers of intermediate species in these intermediate geographical zones.

Darwin is not as confident about the answer to his second question as he is about the answer to his first. He admits that it is difficult to explain how new structures, such as the wings of a bat, are created when a species descends from one that lacks such structures. He does give examples from other species, in which modifications develop from existing structures instead of sprouting anew, such as the species of flying squirrels with broad tails that allow them to parachute through the air, a tail modified from existing tails in other squirrel species. He also explains that scientists are unable to see a clear line of organ modification because of gaps in the development of these structures (for example, squirrel tails that are not yet fully adapted for flying). These gaps come about when the intermediate species have become extinct. Examples of explainable models, such as the flying squirrel’s tail, can help an observer imagine the development of more complex organs, such as the wings of the bat or the eye. Over time, gradual developments of structures and nerves become more complex with modifications, until finally the most perfect eye organ develops. Darwin compares the eye to a telescope: Over time and through its development, the telescope has become more and more advanced, replacing older versions. While the mechanism of change for the telescope is technological advancement, for the eye it is natural selection.

Darwin also discusses the existence of undeveloped and useless organs. In contrast to highly complex organs that are clearly products of natural selection, undeveloped and useless organs indicate that some traits might have been advantageous at one point and eventually waned in importance over time. Primarily, Darwin argues that science cannot always assume the importance or unimportance of a particular variation. Some organs, transmitted to a species but useless to it, may have been useful to a distant ancestor. Moreover, some modifications that seem important to us may not be important at all. For example, if only green woodpeckers existed, scientists would assume that the color green was important to the woodpecker’s survival. However, many different colors of woodpeckers exist, so color must be a result of sexual selection, which is relatively unimportant for species’ survival. The perpetuation of useless or random variations illustrates one of the principles of natural selection: that selection of advantageous characteristics makes a species better than those before it but does not create immediate perfection in a species. Leftover characteristics may remain, as long as they cause no harm to the species. Ultimately, these leftover characteristics serve as reminders of the very slightness of change that occurred by natural selection over time. The goal of natural selection is to make each species better, not to produce perfection right away. Only over time do species become perfectly adapted to their environments.


In attempting to address some of the gaps in his theory of natural selection, Darwin once again shows the power of inductive reasoning. He acknowledges the unknowns inherent in his own theory and accepts that he simply cannot answer certain questions, such as how a bat develops its wings or how the eye develops its immensely complex structure. However, by using examples that demonstrate how modification might occur in some species, Darwin creates principles of modification that can be applied to the development of other species, even if he can’t explicitly prove that the principles hold true for these particular species. This is precisely how scientific theories develop—through the creation of models that can be applied to similar situations. In Chapter VI, Darwin highlights the uncertainty inherent in scientific theorizing and the inductive reasoning and modeling that allow theories to survive despite these uncertainties.

By defending his theory with inductive reasoning, Darwin once again implicitly attacks natural theologians who believe that the complex structure of each species proves that God created them independently. Darwin’s comparison of the eye to a telescope singles out natural theologian William Paley, who used the telescope analogy to suggest that God reveals his plan in the complexity and purpose of the organs he designs. Darwin turns the telescope example on its head. He asks, If millions of years of modification have shaped the eye to its perfected state, could the eye be even more perfect than the telescope? And doesn’t the perfection of the eye show the power of natural selection, regardless of whether God or nature controls the process? Darwin challenges natural theology on its own terms. He argues that natural selection provides the requisite explanations for the development of species. He also acknowledges the brilliance of creation, leaving room for God in the theory of natural selection.