Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [87]
AU REVOIR, MON ÉLÉPHANT
In many ways, Jacques Monod was far more right than he realized when he uttered his famous words about E. coli and the elephant. We share with E. coli a basic genetic code and many proteins essential for getting energy from food. E. coli and our own cells face many of the same challenges. They both need to keep a boundary with the outside world intact yet not too rigid. E. coli has to keep its DNA neatly folded and yet accessible for speed-reading. It has to keep track of its inner geography. It needs to organize its thousands of genes into a network that can respond in a coordinated way to changes in the outside world. Its network has to remain rugged and robust despite the fact that it is swamped with noise. E. coli communicates with other members of its species, allies with some, fights with others, gives up its life. Like us, it grows old.
Some of these similarities are the result of a common heritage reaching back to the earliest stages of life on Earth. Others are the result of two evolutionary paths that converged on the same solution. Yet even the cases of convergence strengthen Monod’s insight. They are evidence that despite 4 billion years of separate history, we and E. coli are still deeply sculpted by the same evolutionary forces.
I have met some scientists, however, who simply hate Monod’s quip. It tramples over some fundamental differences between the elephant and E. coli. Elephants—and humans and lichens and all other eukaryotes—have vastly larger genomes than E. coli. Our own genome, for example, has about five times as many genes. It’s also padded with a lot of DNA that does not encode proteins. Another major difference can be found in the proteins we use to replicate DNA. They do not show any clear relationship to the proteins used by E. coli or other bacteria. Eukaryotes do swap a few genes, but much more rarely than E. coli does. We do not shake hands with friends and take up their genes for blue eyes. As animals, we have a way of reproducing that couldn’t be more different from E. coli’s. Only a tiny fraction of the cells in our bodies have the potential to carry our genes successfully to the next generation, and our genomes carry the information necessary for the stately development of a new trillion-celled body complete with 200 cell types and dozens of organs.
These differences are indeed great and genuine, and yet scientists have surprisingly little idea of how they came to be. Why we’re not more like E. coli is, in some ways, an open question. The answer must be lurking in the early history of life on Earth. Scientists are agreed that life split into three branches very early on, and the differences among them—particularly those that divide eukaryotes from bacteria and archaea—are profound. Yet at the moment, experts are contemplating some radically different explanations for how those divisions emerged. Some have claimed that eukaryotes originated from archaea that swallowed oxygen-breathing bacteria. Others claim that the split occurred long before that, before life crossed into the DNA world.
I find one explanation particularly intriguing. It comes from Patrick Forterre, an evolutionary biologist at Monod’s Pasteur Institute. He proposes that the profound split between us and E. coli is the work of viruses.
Forterre’s scenario begins in the RNA world, before the three great divisions of life had yet emerged. RNA-based organisms were promiscuously swapping genes. Some of these genes began to specialize, becoming parasites. They no longer built their own gene-replicating machinery but invaded other organisms to use theirs. These were the first viruses, and they are still