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In 1859 he finally delivered his revolutionary book. Although it was hefty and substantive at 490 pages, he considered The Origin of Species just a quick-and-dirty "abstract" of the huge volume he had been working on until interrupted by an alarming event. (In fact, he'd wanted to title it An Abstract of an Essay on the Origin of Species and Varieties Through Natural Selection, but his publisher found that insufficiently catchy.) The alarming event was his receiving a letter and an enclosed manuscript from Alfred Wallace, whom he knew only as a distant pen pal. Wallace's manuscript sketched out the same great idea—evolution by natural selection—that Darwin considered his own. Wallace had scribbled this paper and (unaware of Darwin's own evolutionary thinking, which so far had been kept private) mailed it to him from the Malay Archipelago, along with a request for reaction and help. Darwin was horrified. After two decades of painstaking effort, now he'd be scooped. Or maybe not quite. He forwarded Wallace's paper toward publication, though managing also to assert his own prior claim by releasing two excerpts from his unpublished work. Then he dashed off The Origin, his "abstract" on the subject. Unlike Wallace, who was younger and less meticulous, Darwin recognized the importance of providing an edifice of supporting evidence and logic.

The evidence, as he presented it, mostly fell within four categories: biogeography, paleontology, embryology, and morphology. Biogeography is the study of the geographical distribution of living creatures—that is, which species inhabit which parts of the planet and why. Paleontology investigates extinct life-forms, as revealed in the fossil record. Embryology examines the revealing stages of development (echoing earlier stages of evolutionary history) that embryos pass through before birth or hatching; at a stretch, embryology also concerns the immature forms of animals that metamorphose, such as the larvae of insects. Morphology is the science of anatomical shape and design. Darwin devoted sizable sections of The Origin of Species to these categories.

Biogeography, for instance, offered a great pageant of peculiar facts and patterns. Anyone who considers the biogeographical data, Darwin wrote, must be struck by the mysterious clustering pattern among what he called "closely allied" species—that is, similar creatures sharing roughly the same body plan. Such closely allied species tend to be found on the same continent (several species of zebras in Africa) or within the same group of oceanic islands (dozens of species of honeycreepers in Hawaii, 13 species of Galápagos finch), despite their species-by-species preferences for different habitats, food sources, or conditions of climate. Adjacent areas of South America, Darwin noted, are occupied by two similar species of large, flightless birds (the rheas, Rhea americana and Pterocnemia pennata), not by ostriches as in Africa or emus as in Australia. South America also has agoutis and viscachas (small rodents) in terrestrial habitats, plus coypus and capybaras in the wetlands, not—as Darwin wrote—hares and rabbits in terrestrial habitats or beavers and muskrats in the wetlands. During his own youthful visit to the Galápagos, aboard the survey ship Beagle, Darwin himself had discovered three very similar forms of mockingbird, each on a different island.

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