Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [71]
E. coli’s genome is not so much a manual as a living palimpsest. E. coli K-12, O157:H7, and all the other strains evolved from a common ancestor that lived dozens of millions of years ago. And that common ancestor itself descended from still older microbes, stretching back over billions of years. The genetic history of E. coli is masked by mutations, duplications, deletions, and insertions. Yet traces of those older layers of text survive in E. coli’s genome, like vestiges of Archimedes.
Until recently, scientists had only crude tools for reading those hidden layers. They struggled like Heiberg with his magnifying glass. They are now getting a much better look at the palimpsest. Like Archimedes’ ancient treatise, they’re finding, E. coli’s genome is a book of wisdom. It offers hints about how life has evolved over billions of years—how complex networks of genes emerge, how evolution can act like an engineer without an engineer’s brain. Nested within E. coli’s genome are clues to the earliest stages of life on Earth, including the world before DNA. Those clues may someday help guide scientists to the origins of life itself.
THE TREE OF LIFE
To read E. coli’s palimpsest, scientists have had to figure out which parts of its genome are new and which are old. The answer can be found in the genealogy of germs. A family tree of the living strains of E. coli indicates that they all descend from a common ancestor that lived some 10 million to 30 million years ago. Even farther back, E. coli shares an ancestor with other species. Reach back far enough, and you ultimately encounter the ancestor E. coli shares with all other living things, ourselves included.
Reconstructing the tree of life—one that includes E. coli and humans and everything else that lives on Earth—has been one of modern biology’s great quests. In 1837, Charles Darwin drew his first version of the tree of life. On a page in his private notebook he sketched a few joined branches, each with a letter at its tip representing a species. Across the top of the page he wrote, “I think.”
The fact that species have common ancestors explains why they share many traits. As different as bats and humans may seem, we are both hairy, warm-blooded, five-fingered mammals. Darwin himself did not try to figure out exactly how all the species alive were related to one another, but within a few years of the publication of The Origin of Species, other naturalists did. The German biologist Ernst Haeckel produced gorgeous illustrations of trees sprouting graceful bark-covered boughs. His trees were accurate in many ways, scientists would later find. But Haeckel marred them with a stupendous anthropocentrism. To Haeckel, the history of life was primarily the history of our own species. His tree looked like a plastic Christmas tree, with branches sticking out awkwardly from a central shaft. He labeled the base of the tree Moneran, the name he used for bacteria and other single-celled organisms. Farther up the tree were branches representing species more and more like ourselves—sponges, lampreys, mice. And atop the tree sat Menschen.
This view of life has been a hard one to shake. It probably had something to do with the decision to split life into prokaryotes and eukaryotes, the supposedly primordial bacteria and the “advanced” species like ourselves that evolved from them. It’s a deeply flawed view. The evolution of life was not a simple climb from low to high. E. coli is a species admirably adapted to warm-blooded creatures that did not emerge for billions of years after life began. It is as modern as we are.
It took a long time for a more accurate picture of the tree of life to take hold. One major obstacle was the lack