Darwin discusses how the classification system was developed by naturalists and is supported by his theory of descent with modification. Naturalists have already developed complicated schemes for grouping species, genera (groups of related species), and families (groups of related genera), into arrangements that show the similarities and physical relationships between existing species. Though Darwin notes that the separation between family, genus, and species is just as arbitrary as the separation between species and varieties, he uses the rules by which scientists organize species into these classifications to help bolster his theory of descent with modification. External structures (those that relate to everyday habits or physical appearance) turn out to be the least important way of classifying species, as many unrelated species—such as whales and fish—have adapted similar characteristics. These “adaptive” or “analogous” characteristics appear in numerous animals and have the same physiological importance (that is, they serve the same biological function from one to the next) but cannot explain descent relationships, as the structures were adapted by different species simultaneously rather than passed down through heredity. Naturalists acknowledge that external appearance is not basis enough to develop a classificatory scheme that would explain which species are descended from the same parent species. Instead, naturalists rely on internal structures, such as reproductive systems and patterns in embryonic development, to classify species into families and genera. Darwin uses these classifications to illustrate chains of descent with modification.

One of the first places that naturalists look when determining classification of species is morphology, which is the study of the underlying structural relationships between physical organs of separate species. Several species share similar bone and placement structures for physical organs, even though these organs are shaped externally for each animal’s particular “habits of life.” For example, a human being’s hand shares a bone and placement structure with the front legs of a mole, the paddle-shaped limbs of a porpoise, and the wings of a bat. Natural selection explains these similar structures, in that the physical adaptations seen in each species have been naturally selected for that particular species’ use. The hands of a human have been selected for grasping objects, the front legs of a mole have been selected for digging, and the wings of a bat have been selected for flying. This homology, or correspondence of bone structures, is also seen within organs of the same individual organism. The bones of the skull, for example, are homologous with the neighboring vertebrae in the neck and spine, which suggests that the skull may have developed as a modified structure from the neck of a former species. These homologous structures show how organs developed within a species and from one species to the next.

The development of embryos also illustrates how species have descended from common ancestry. Darwin notes that many embryos of different species appear initially to be similar, with species-specific differences developing only as the embryo (or young) matures. The development of the embryo mirrors the development of divergent characteristics in each species. If a particular adaptation in a species appears at a certain time in its development and causes its divergence from the parent species, that adaptation will appear during the developmental stage in its offspring. Darwin notes that this same phenomenon can be observed in the offspring of humans. Infants will not take on their inherited characteristics of eye or hair color, height, or body type until they grow older. Since inherited modifications occur later in life, the embryos of related species look alike at their beginning stages and can therefore help naturalists determine relationships of descent between species. Embryology, the study of embryos, allows naturalists to observe the modifications that have caused species divergences throughout time, providing clues about the arrangement of species in classifications, which illustrate their descent with modification from one another.

Also important for classification schemes are “rudimentary organs”—organs that are left over from previous species and unimportant physiologically. Sometimes, naturalists can easily tell which rudimentary organs correspond to a past species. Leftover membranes on the backs of insects, for example, clearly represent wings. Other rudimentary organs are harder to classify, especially if an organ once used for one purpose is now used for another, such as swim bladders in fish that were once used for buoyancy but are now used for breathing. These organs can reveal chains of descent, even if divergent species remain completely unalike except for their one shared rudimentary part. The existence of these rudimentary organs deals another blow to natural theology, which claims that each species was independently, perfectly created. Rudimentary organs reveal that the current state of species is far from perfect: Useless organs have been rendered such by disuse and therefore bolster the theory that species have descended from one another.


Darwin makes a brilliant argument by linking existing classification systems to his scheme of descent with modification. Naturalists had already recognized the structural and physiological similarities between different species and had created sophisticated ways of grouping species based on their similarities. Although naturalists had developed intricate rules governing these classifications, they had not explained why species should be grouped together in the first place. Natural theology, which was the leading scientific explanation for the origin of species at the time, argued that each species was independently created and that any physical or physiological similarities in species were either random or the brilliant design of their creator. Darwin takes the existing classification system and uses it as proof of his theory of descent with modification. Species can be classified into genera and families, he says, because species descended from one another, and the existing rules of classification provide patterns that illustrate how this descent occurred.

By showing the imperfection of species, Darwin again argues against natural theologians’ notion that species were created individually. Natural theology hypothesizes that the perfect adaptations of organisms to their environment is due to their independent creation by a creator. Darwin points to the existence of rudimentary organs to expose inconsistencies in this theory. If species were created to be perfectly suited to their environment, he asks, why would their creator endow some species with useless organs?

The theory of natural selection, in contrast, provides the perfect explanation for rudimentary organs. Only variations advantageous to the species are naturally selected. But natural selection weeds out only those variations or organs that cause the species harm. It does not bother getting rid of unimportant variations or organs. Advantageous variation causes the divergence of new species but does not rid species of now-unusable organs from their predecessors. Thus, rudimentary organs from predecessor species remain, rendering species somewhat imperfect in structure. Although this argument refutes natural theologians’ theory of the individual creation of perfect species, it does not contradict Darwin’s notion that natural selection creates perfectly adapted species. As noted in previous chapters, natural selection does not automatically create perfect species. Each new species becomes slightly more complex in its adaptability to its environment, resulting in the seemingly perfect species seen today. Natural selection explains both perfections and imperfections in species in the natural world.

Darwin invites controversy by bringing human beings into the classification system. When he compares the structure of hands to similar organs in bats, moles, and porpoises, he is essentially claiming that humans evolved from other species the same way animals did. He implies, for example, that the hands of human beings were a variation of the front legs of the mole and were “naturally selected” in the human population because they helped humans grasp rather than dig. This argument remains one of the most controversial aspects of Darwin’s theory, as well as of evolutionary theory in general.

In addition, in his discussion of classification rules, Darwin uses the example of physical similarities of the Hottentot group (an ethnic group discovered in Africa in the 17th century) to the “Negro race” to explain how physical similarities relate to classification. It was widely assumed among scientists in 19th-century Europe that “Negroes” were ancestors of the Hottentot, and although Darwin does not specifically say that different races of human beings evolved from one another, his use of the Hottentot/Negro example implies that all races of human beings are evolutionarily linked. According to some readings of Darwin, the implication is one of evolutionary human hierarchy: The theory that some humans have progressed further evolutionarily than others. Social theorists would later construct human hierarchies based on Darwin’s theory of evolution to justify discrimination, repression, and even genocide.