The Flagellum After Dover

It was a delicious coincidence that the Dover trial, which brought E. coli's flagellum to the world's attention, took place right around the time scientists were starting to get a good look at the flagellum's evolution. They began to trace the history of its genes by finding related genes both in E. coli and in other microbes. Together those genealogies are beginning to add up to a history of the flagellum—and an illustration of how life can produce a complex trait.

The most important lesson of this new research is that it's absurd for creationists to talk of the flagellum. From species to species there's a huge amount of variation in flagella. Even within a single species different populations of microbes may make different kinds of flagella.

Flagella vary at all levels, from their finest features to their biggest. Take flagellin, the protein that E. coli uses to build the tail of its flagella. Scientists have identified forty kinds of flagellin in various strains of E. coli, and they expect to find many more as they expand their survey. And from species to species, flagellins vary even more. In 2003, a ship of microbiologists and geneticists trawled microbes in the Sargasso Sea and analyzed their genes. They discovered 300 genes for flagellins.

These patterns make eminent sense in light of evolution. A single ancestral flagellin gave rise to many new flagellins through gene duplication and mutations. As different species adapted to different environments—from feeding inside the human gut to swimming the Sargasso Sea—their flagellins evolved as well. After E. coli emerged tens of millions of years ago, its flagellins continued to evolve. The variation in its flagellins was probably driven by the need to evade the immune system of its host, which recognizes intruders by the proteins on their surface, such as flagellin. If a mutation makes the outer surface of flagellin harder for an immune system to recognize, it may be favored by natural selection. And just as you'd expect, the most variation found in flagellins in E. coli lies in the parts that face outward. The parts that face inward—and have to lock neatly into the other flagellins—are much more similar to one another. Natural selection does not look kindly on mutations that disturb their tight fit.

Flagella also vary in other ways. E. coli drives its motors with protons, but some species use sodium ions. E. coli spins its flagella through a fluid. Other species make flagella for slithering across surfaces. Scientists have observed some species of bacteria that can make either kind, depending on what sort of swimming they have to do.

In 2005, Mark Pallen of the University of Birmingham in England and his colleagues discovered a set of genes for building slithering flagella in an unexpected place: the genome of E. coli. E. coli cannot actually build these slithering flagella, because the switch that turns on the genes was disabled by a mutation. In some strains, scientists have found all forty-four genes necessary for building all the parts of the slithering flagellum—its hooks, its rings, its filament. In other strains, some of the genes have disappeared entirely. In K-12 only two badly degraded genes remain.

Pallen's discovery makes ample sense if flagella are the product of evolution, and it makes no sense at all if they are the result of intelligent design. A complex feature evolves and is passed down from ancestors to descendants. In some lineages it falls apart. Darwin described many rudimentary organs, from the flesh-covered eyes of a cave fish to the stubby wings of ostriches. If natural selection no longer favored their use, Darwin argued, individuals would be able to survive well enough even if the organs no longer served their original function. E. coli carries vestiges as well, like ancient passages hidden in a palimpsest.

E. coli also carries clues to how its flagellum evolved in the first place. As Kenneth Miller pointed out in the Dover trial, the needle that delivers flagellin across the microbe's membrane corresponds, protein for protein, to the type III secretion system for injecting toxins and other molecules. The resemblance speaks to a common ancestry. The type III secretion system is far from the only structure that is related to parts of flagella. Proteins in the motor, for example, are related to proteins found in other motors that E. coli and other bacteria use to pump out molecules from their interior.

Scientists are now developing hypotheses from this evidence to explain how flagella evolved. Pallen and Nicholas Matzke, now a graduate student at the University of California, Berkeley, offered one hypothesis in 2006. Before there were flagella, Pallen and Matzke argued, there were simpler parts carrying out other functions. Gene duplication made extra copies of those parts, and mutations caused the copies to be combined into the evolving flagellum. Today flagella serve one main function: to swim. But their parts did not start out that way.

The flagellum's syringe may have begun as a simple pore that allowed molecules to slip through the inner membrane. A proton-driving motor became linked to it, allowing it to push out big molecules. This primitive system may have allowed ancient bacteria to release signals or toxins. Two kinds of structures eventually evolved from it: the type III secretion system and the needle that injects pieces of the flagellum across the membrane.

The next step in the evolution of flagella may have come when the needle began squirting out sticky proteins. Instead of floating away, these proteins clumped around the pore. Bacteria could have used these sticky proteins as many species do today, to allow them to grip surfaces. The microbes added more proteins to produce hairs, which could reach out farther to find purchase.

In the next step, this sticky hair began to move. A second type of motor became linked to it, which could make the hair quiver. Now the microbe could move. Its crude, random movement may have allowed it to disperse during times of stress. Over time this protoflagellum became fine-tuned. Gene duplication allowed the proteins making up the filament to become a flexible hook at the base and stiff, twisted fibers along the shaft. And finally bacteria began to steer. One of their chemical sensing systems became linked to their flagella, allowing them to change their direction.

This hypothesis is not the unveiling of absolute truth. Scientists don't have that power. What scientists can do is create hypotheses consistent with previous observations—in this case, observations of the variations in flagella, the components that play other roles in bacteria, and the ways in which evolution combines genes for new functions. Pallen and Matzke's hypothesis may well prove to be flawed, but the only way to find out is to search the genomes of E. coli and other microbes for more clues as to how the flagellum was assembled, to study how intermediate structures work, and perhaps even to genetically engineer some of the intermediate steps that have disappeared. A better hypothesis may emerge along the way. But it is a far superior hypothesis to one built on nothing but appearances and a personal sense of disbelief.

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