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"Mutual Affinities of Organic Beings; Morphology; Embryology; Rudimentary Organs" is the thirteenth chapter of On the Origin of Species by Means of Natural Selection by Charles Darwin and Darwin's Ghost by Steve Jones. In this long-titled chapter, Darwin covers several related topics that have not yet come up in Origin of Species. He begins, "From the first dawn of life, all organic groups are found to resemble each other in descending degrees, so that they can be classed in groups under groups. This classification is evidently not arbitrary like the grouping of the stars in constellations." Indeed, the ways in which these species are related suggest that they have descended from fewer, older species. The "mutual affinities of organic beings" fit the arguments of evolution; natural history is evidenced in today’s species.

Before Darwin, most biologists saw themselves as classifying species mostly on resemblance. "I believe that something more is included," Darwin wrote, "and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications." In other words, we do not define creatures as being closely related because they are similar; rather, they are similar because they are, in the actual history of the Earth, closely related. Indeed, Linnaeus, the inventor of our current system of classification, recognized this relation. Darwin paraphrased him in this way: "the characters do not give the genus, but the genus gives the characters."

Darwin also notes that classification takes place a bit differently than one might think. "It might be thought," he writes, "(and was in ancient times thought) that those parts of the structure which determined the habits of life, and the general place of each being in the economy of nature, would be of very high importance in classification. Nothing can be more false." Because habits of a species can change relatively quickly through natural selection, Darwin writes that "the less any part of the organization is concerned with special habits, the more important it becomes for classification." For instance, a whale resembles a fish in habit and basic appearance, but they are only very distant relatives. By studying other qualities of the whale, we can see that it is in fact more closely related to the hippopotamus, but that the whale has, living in a different environment from a hippo, picked up many different habits and appearances.

Jones states these ideas a little more generally. "To classifiers, of whatever persuasion," he writes, "relatedness is always more important than mere appearance." For instance, males and females of the same species are always classified together, even though they may look dramatically different from each other. The same is true of old and young members of the same species. In fact, Darwin adds, some naturalists have argued that the youngest members of a species, the embryos, are the most useful for the classification of that species. Darwin adds that we will come back to this topic later in this chapter when we reach the subject of embryology.

Meanwhile, we can come back to Jones. Jones begins a section of his chapter, "Evolution can sometimes hide a true pedigree. It would be foolish to classify flies and bats as the same because both have wings. Their similarity comes not from shared descent but from separate answers to the same problem." This convergence of solutions to a problem among different, unrelated species has an even more dramatic example: the Antarctic perch and the Arctic cod. The perch and the cod split forty million years ago, "long before the Antarctic froze," Jones notes. Yet both the Antarctic perch and the Arctic cod have, in the time since, evolved the same protein, a protein that functions as an antifreeze and allows them to live in water two degrees below freezing, Celsius.

Moving on again is this chapter, we come to the topic of morphology, the study of the similarities and differences between the "several parts and organs" of various species. Darwin has one particularly interesting observation in this section. He writes, "Naturalists frequently speak of the skull as formed of metamorphosed vertebrae: the jaws of crabs as metamorphosed legs; the stamens and pistils of flowers as metamorphosed leaves; but it would in these cases probably be more correct, as Professor Huxley has remarked, to speak of both skull and vertebrae, both jaws and legs, &c.,—as having been metamorphosed, not one from the other, but from some common element." He continues that naturalists actually use the word metamorphosed in this context "only in a metaphorical sense," yet adds that in his opinion "these words may be used literally," because, over many generations, these organs do actually evolve into different ones.

Now we reach the aforementioned section on embryology. Darwin begins this section by writing that "certain organs in the individual, which when mature become widely different and serve for different purposes, are in the embryo exactly alike. The embryos, also, of distinct animals within the same class are often strikingly similar: a better proof of this cannot be given, than a circumstance mentioned by Agassiz, namely, that having forgotten to ticket the embryo of some vertebrate animal, he cannot now tell whether it be that of a mammal, bird, or reptile." Later, Darwin continues, "The points of structure, in which the embryos of widely different animals of the same class resemble each other, often have no direct relation to their conditions of existence." In other words, embryos of different species are often very similar, because, being inactive their mothers’ wombs, they are not much acted on by natural selection. "Whatever influence long-continued exercise or use on the one hand, and disuse on the other, may have in modifying an organ," Darwin writes a few pages later, "such influence will mainly affect the mature animal, which has come to its full powers of activity and has to gain its own living; and the effects thus produced will be inherited at a corresponding mature age."

While embryos are important evidence of an animal’s history, some biologists have suggested that they are more than that. To quote Jones, "In 1866 Haeckel came up with his 'biogenetic law': new forms are, he said, the result of extra stages added on to the development of those that went before. He published sketches of the embryos of birds, reptiles, and mammals (somewhat doctored to support the idea) that seemed to prove his case." Unfortunately, embryos do not show an exact lineage of an animal as they grow, but they do suggest some relations with other species.

Jones sums up this idea nicely: "For eyes, ears, limbs, and deciding which way is up [the genes influencing a vertebrate’s back are the same that effect an invertebrate’s stomach], the embryo is left as a sort of picture, preserved by nature, of the ancient and less modified condition of each animal. Its image is proof of the course of evolution from a time older than the earliest fossil."

Darwin also includes one more section in this chapter: "Rudimentary, atrophied, or aborted organs." He begins this section with a number of examples, including the mammary glands of male mammals, lungs and legs of snakes, teeth of fetal whales, and wings of flightless insects. Darwin notes that rudimentary organs sometimes maintain the potential for use, but are not developed. The main example of this is the male mammae, which are actually capable of excreting milk under certain conditions. Other organs, "serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose," Darwin writes, "and remain perfectly efficient for the other."

Rudimentary organs vary in unusual ways. Members of the same species are "very liable," Darwin writes, to have organs that vary in degree of development. These organs vary even more among closely related species. In addition, many rudimentary organs are visible in an embryo, but disappear later in an animal’s development.

The existence of rudimentary organs, including our own tailbone, fits well with the idea of evolution. Indeed, it is hard to explain in any other way, as Darwin argues. "In works on natural history," he writes, "rudimentary organs are generally said to have been created 'for the sake of symmetry,' or in order 'to complete the scheme of nature;' but this seems to me no explanation, merely a restatement of the fact. Would it be thought sufficient to say that because planets revolve in elliptic orbits round the sun, satellites follow the same course round the planets, for the sake of symmetry, and to complete the scheme of nature?"

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