At the end of Chapter 4, Darwin summarizes his argument thus far with an extended simile and a metaphor comparing the evolution of life on earth to the growth of an old tree:
As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications.
Darwin describes earlier in the passage how early life was like the early stages of tree growth: a single species shot up like a sapling and then branched into a few "budding" species, like little offshoots. Like the new growth on a maturing tree, species have fought one another to establish themselves as "branches" on the metaphorical "Tree of Life." Only some species make it, and often new species beat out older ones. The species that go extinct fall to the ground like "dead and broken branches." Darwin has some fun here with the way his simile slides neatly into metaphor: the "dead and broken branches," he writes, incorporate into the "crust of the earth." Technically, dead tree branches on the ground do decompose into the ground and become part of the very top layer of the earth's crust. What Darwin is getting at, though, is the fossil record. Species that have fallen off the "Tree of Life" have turned into the fossils that humans have unearthed and begun studying as records of natural history. The species still alive today are the living branches and buds on the Tree of Life, but eventually many of them, too, will fall to the ground and turn into fossils.
Darwin's Tree of Life simile is an interesting counterpoint to some of his other similes and metaphors comparing natural selection to war and other forms of fierce and brutal competition. While he does emphasize the way buds and branches are always fighting to "overtop" one another, ultimately the tree is a single organism. Darwin refers elsewhere to the "division of physiological labor," the notion that different kinds of tissue perform different functions within a single organism. The branches of the Tree of Life compete with one another to accomplish their own ends, but each of them is also working to keep the tree itself standing. In fact, the more competition there is, the more the tree flourishes.
In Chapter 6, Darwin refutes the counterargument that his theory is unreasonable because there aren't enough fossils representing all the intermediate species he believes have existed over time. He uses a metaphor comparing the earth's crust to "a vast museum":
The crust of the earth is a vast museum; but the natural collections have been imperfectly made, and only at long intervals of time.
Darwin's metaphor implies that nature has placed all the fossils we have on display in the earth's crust so that modern-day scientists can peruse the collection. A museum can never contain every artifact pertaining to the society, time, or idea it aims to represent. Rather, it contains a sampling of objects to give attendees a curated sense of that society, time, or idea. Even the best museum collections are "imperfectly made" because curators are only human. Darwin suggests that nature is a bit of a haphazard and neglectful curator who is not terribly concerned with the careful preservation of objects at every turn.
This is just one example of Darwin's use of metaphor to explain natural phenomena. Knowing that his readers are Victorians, he turns to cultural comparisons he knows will ring true to them. The museum metaphor is especially apt for his readers who are professionally invested in science and the history of science. These readers would have been engaged in conversations about how to represent and interpret things like the fossil record, and many of them would have felt a (sometimes egotistical) responsibility to inform "the masses." The idea that the earth's crust is not an objective source of truth but rather a sloppy museum displaying the fossil record would tap into their understanding that evidence needs to be carefully interpreted and presented, and that not all sources of "authority" should be trusted. They would then see Darwin's careful questioning of the fossil record not as a rejection of evidence, but rather as responsible scientific thinking.
