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It was these RNA viruses, Forterre argues, that invented DNA. For viruses, DNA might have offered a powerful, immediate benefit. It would have allowed them to ward off attacks by their hosts by combining pairs of single-stranded RNA into double-stranded DNA. The vulnerable bases carrying the virus’s genetic information were now nestled on the inside of the double helix while a strong backbone faced outward.

Early DNA viruses probably evolved a range of relationships with their hosts. E. coli’s viruses are good to keep in mind here: the lethal ones that make the microbe explode with hundreds of viral offspring, the quiet ones that cause trouble only in times of stress, and the beneficial ones that have become fused seamlessly to their hosts. Forterre argues that on several occasions, DNA viruses became permanently established in their RNA hosts. As they became domesticated, they lost the genes they had used to escape and make protein shells. They became nothing more than naked DNA, encoding genes for their own replication.

Only at that point, Forterre argues, could RNA-based life have made the transition to DNA. From time to time, mutations caused genes from the RNA chromosome to be pasted on the virus’s DNA chromosome. The transferred genes could then enjoy all the benefits of DNA-based replication. They were more stable and less prone to devastating mutations. Natural selection favored organisms that carried more genes in DNA than in RNA. Over time, the RNA chromosome shriveled while the DNA chromosome grew. Eventually the organism became completely DNA based. Even the genes for riboswitches and other relics of the RNA world were converted to DNA. Forterre proposes that this viral takeover occurred three times. Each infection gave rise to one of the three domains of life.

Forterre argues that his scenario can account for the deep discord between the genes that all three domains share and the ones that are different. Forterre started his scientific career studying the enzymes E. coli uses to build DNA. Related versions of those enzymes exist in other species of bacteria, but they are nowhere to be found in archaea or eukaryotes. The difference, Forterre argues, lies in the fact that the ancestors of E. coli and other bacteria got their DNA-building enzymes from one strain of virus and the eukaryotes and archaea didn’t.

Once the three domains split, they followed different trajectories. Our own ancestors, the early eukaryotes, may have acquired their nucleus and other traits from other viruses. Eukaryotes grew to be larger than bacteria or archaea, and as a result their populations grew smaller. In small populations it’s easier for slightly harmful mutations to spread, thanks merely to chance. It may have been only then that the eukaryote genome began to expand. Interspersing noncoding DNA within genes may have been harmful at first, but over time it may have given eukaryotes the ability to shuffle segments of their genes to encode different proteins. We humans have 18,000 genes, but we can make 100,000 proteins out of them.

Forterre’s proposal is as radical as the suggestion in 1968 that life was once based on RNA. It will demand just as much research to test. In the meantime, it is intriguing to think about what it would mean if Forterre is right. The differences between the elephant and E. coli would actually be the sign of yet another fundamental similarity: we—all living things—are different only because we got sick from different viruses.

Ten

PLAYING NATURE

PORTRAIT IN PROTOPLASM

IN CHRISTOPHER VOIGT’S LABORATORY at the University of California, San Francisco, you can have your picture taken by E. coli. Voigt will place a photograph of you before a hooded contraption. The reflected light from the picture strikes a tray covered with a thin, gummy layer of E. coli. It’s a special strain that Voigt and his colleagues created in 2005. They inserted genes into the bacteria, some of which let the bacteria detect