Microcosm (21 page)

The Dover trial was a creationist disaster. The Dover School Board members who had brought
Of Pandas and People
into the school were defeated by a slate of opponents to the policy even before the trial was over. Other intelligent design–friendly board of education members have lost their seats in Kansas and Ohio. Judge Jones’s decision was so thorough that it will probably set a precedent for any future cases on the teaching of creationism in whatever guise it takes.

Remarkably, though, creationists still love
E. coli.
Access Research Network, another organization that promotes intelligent design, has plastered its flagellum on T-shirts, aprons, beer steins, baseball jerseys, coffee mugs, calendars, greeting cards, calendars, tote bags, and throw pillows. All these creationist items can be purchased on a Web site. The site declares: “The output of this mechanism is used to drive a set of constant torque proton-powered reversible rotary motors which transfer their energy through a microscopic drive train and propel helical flagella from 30,000 to 100,000 rpm. This highly integrated system allows the bacterium to migrate at the rate of approximately ten body lengths per second. Would you please find out who filed the patent on this thing?”

The message you’ll actually get on your flagellum apron will be far simpler. Above the picture of the flagellum it reads, “Intelligent Design Theory.” And below: “If it looks designed, maybe it is.”

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.

NETWORKS UNDER CONSTRUCTION

In order to build a flagellum,
E. coli
does not simply churn out all the proteins in a blind rush. It controls the construction with a sophisticated network of genes. Only when it detects signs of stress does it switch on the flagella-building genes, and it uses a noise filter to avoid false alarms. It turns the genes on step by step as it gradually builds up the flagellum, then it turns them off. And like the flagellum,
E. coli’
s control networks have an ancient history of their own.

In 2006, M. Madan Babu, a biologist at the University of Cambridge, and his colleagues published a major investigation of how
E. coli’
s circuitry evolved. They began by searching for
E. coli’
s genetic switches—the proteins that grab on to DNA and turn on, turn off, or otherwise influence other genes. They ended up with more than 250 of them. They then combed through the scientific literature to figure out which genes these switches controlled. All told, Babu and his colleagues mapped a dense web of 1,295 links joining 755 genes.

The map Babu’s team drew looks a lot like the hierarchy of a government or a corporation. A few powerful genes sit at the top, each directly controlling several other genes. Those middle-manager genes control many other genes in turn, which may control still others. This organization allows
E. coli
to cope with changes in its environment with swift, massive changes to its biology. Babu’s map also let him survey
E. coli’
s network down to its smallest circuits.

Once Babu had finished his map of
E. coli’
s network, he could reconstruct its history. He compared it with the networks in 175 other species of microbes. Babu discovered a network core shared by all of them, made up of 62 genetic switches controlling 376 genes, for a total of 492 links. This core, Babu concluded, existed in the common ancestor of all living things.

This core network offers some hints of what that common ancestor was like. It already had sensors, which allowed it to detect different kinds of sugar and monitor its own energy levels. It could detect oxygen, not to breathe it—since the atmosphere was nearly oxygen free—but probably to protect itself from its own toxic oxygen-bearing waste. This ancestral microbe was already using genetic switches to control iron-scavenging genes, to create the building blocks for proteins and DNA. It was, in other words, a fairly supple little bug.

From that common ancestor every living thing today evolved. Along the way its network evolved as well. The lineage that led to
E. coli
gained new circuits to sense and feed on new sugars, for example. Experiments on living
E. coli
have helped shed light on how mutations and natural selection rewired its network. One of the simplest means by which
E. coli’
s network can be rewired is the accidental duplication of a chunk of DNA. In some cases, the duplication may create two copies of the same switch. If the gene for one of those switches mutates, it may begin to control a different gene. In other cases, extra copies of genes created by duplications are controlled by the switch that turned on the original gene.

The ancestors of
E. coli
rewired their networks as they adapted to new ways of life. Sometimes only minor tinkering with a circuit would produce an important adaptation—adding an extra switch to a gene, for example, or taking one away. One of these tinkered circuits allows
E. coli
to sense a drop in oxygen and switch its metabolism over to oxygen-free pathways. It is almost identical, gene for gene, to an oxygen-sensing circuit in
Haemophilus influenzae,
a species of bacterium that infects the bloodstream. In
H. influenzae
one switch turns on two genes, which then activate all the other genes required to shift the microbe to an oxygen-free metabolism. It’s a fast circuit, which suits
H. influenzae
well since it lives in the blood and experiences rapid drops in oxygen as it moves from arteries to veins.

E. coli,
on the other hand, does not make snap decisions about oxygen. Living in the relatively stable environment of the gut, it does not experience the sudden, long-term drops in oxygen that
H. influenzae
does. A slight fluctuation might be a false alarm, which would cause
E. coli
to invest a lot of energy making new enzymes that would be of no use. And that fact of life is reflected in
E. coli’
s oxygen circuit. It is identical with
H. influenzae’
s circuit but for one extra gene, called NarL: