Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [66]
It’s a bizarre coincidence that just as scientists were discovering the evolutionary importance of viruses, computer engineers were creating a good metaphor for their effect. In the late 1990s, a group of American engineers became frustrated by the slow pace of software development. Corporations would develop new programs but make it impossible for anyone on the outside to look at the code. Improvements could come only from within—and they came slowly, if at all. In 1998, these breakaway engineers issued a manifesto for a different way of developing programs, which they called open-source software. They began to write programs with fully accessible code. Other programmers could tinker with the program, or merge parts of different programs to create new ones. The open-source software movement predicted that this uncontrolled code swapping would make better programs faster. Studies have also shown that software can be debugged faster if it is open source than if it is private. Open-source software has now gone from manifesto to reality. Even big corporations such as Microsoft are beginning to open up some of their programs to the world’s inspection.
In 2005, Anne O. Summers, a microbiologist at the University of Georgia, and her colleagues coined a new term for evolution driven by horizontal gene transfer: open-source evolution. Vertical gene transfer and natural selection act like an in-house team of software developers, hiding the details of their innovations from the community. Horizontal gene transfer allows E. coli to grab chunks of software and test them in its own operating system. In some cases, the combination is a disaster. Its software crashes, and it dies. But in other cases, the fine-tuning of natural selection allows the combination to work well. The improved patch may later end up in the genome of another organism, where it can be improved even more. If E. coli is any guide, the open-source movement has a bright future.
ASSEMBLING ASSASSINS
Among its many accomplishments, open-source evolution has produced a lot of ways for us to get sick. When Kiyoshi Shiga discovered Shigella, he believed it was a distinct species, and so did generations of scientists who followed him. But when scientists began to examine the genes of Shigella in the 1990s, they realized it was just a particularly vicious form of E. coli. More detailed comparisons revealed that Shigella is actually many separate strains. Many of them are more closely related to harmless strains of E. coli than they are to other strains of Shigella. In other words, Shigella is not a species. It is not even a single strain. It is more a state of being, one that has been achieved by several lineages of E. coli.
Shigella strains typically evolved from less sophisticated parasites. Their ancestors sat on top of the cells of the intestinal wall, injecting molecules into host cells to make them pump out fluids. (Many strains of E. coli still make this sort of living today.) Shigella’s ancestors acquired new genes that allowed them to invade and move inside cells, to escape the immune system and manipulate it. These innovations did not happen in a single lineage of E. coli. They evolved many times over.
Just as important as the genes Shigella gained were the ones it lost. Flagella are wonderful for swimming in the gut, but they are useless inside the crammed interior of a host cell. No Shigella strain can make flagella, although they all still carry disabled copies of