Authors: Carl Zimmer
As with most scientific debates in biology, the tree-versus-web debate is not an all-or-nothing battle. The web champions, such as Doolittle, don’t deny that organisms are related to one another by common descent. They just think that searching for one true tree of life by comparing genes is a futile quest. The tree champions do not deny that horizontal gene transfer happens or that it is biologically important. They simply argue that the right genes can reveal the true relationships among all living things on Earth.
As scientists have begun to compare the entire genomes of many species for the first time, a number of them have decided that the tree of life still stands. Howard Ochman came to this conclusion on the basis of a survey he and his colleagues made of
E. coli
and a dozen other species of bacteria. The scientists found a number of genes that showed signs of having moved by horizontal transfer. But most of those genes had moved relatively recently—only after each species in their study had branched off from the others.
Horizontal gene transfer is common, the scientists found, but the genes usually don’t survive very long in their hosts. Many of them become disabled by mutations, turning into pseudogenes. Eventually, other mutations slice the genes out of their genomes completely, and the bacteria suffers no ill effects from the loss. A few genes ferried into the ancestors of
E. coli
and other bacteria did manage to establish themselves and can still be found in many living species today. But in order to avoid oblivion, they seem to have abandoned their wandering ways. Once a virus inserted them into a host genome, they did not leave it again. Ochman and his colleagues concluded that even though genes regularly move between the branches of life, the branches remain distinct.
THE ROAD TO
ESCHERICHIA
The newest versions of the tree of life look nothing like Haeckel’s Christmas tree. Scientists can now compare thousands of species at once, and the only way to draw all of their branches is to arrange them like the spokes on a wheel. At the center of the wheel is the last common ancestor of all life on Earth today. From the center you can move outward, steering from branch to branch to follow the evolution of a particular lineage. To get to our own species, you first travel up to the common ancestor of archaea and eukaryotes. From there you bear right onto the eukaryote branch. Our ancestors remained single-celled protozoans until about 700 million years ago. They parted ways with the branches that would give rise to multicellular plants and fungi. Eventually the path takes you to the animal kingdom. Bear right again and you follow our ancestors as they become vertebrates. The ancestors of other vertebrates branch off along the way: zebrafish, chickens, mice, chimpanzees. Finally the line ends with
Homo sapiens.
But enough about you. A different route travels from the common ancestor to
E. coli.
The journey is just as long and no less interesting.
The last common ancestor of all living things was probably much simpler than
E. coli.
While each species today carries some unique genes, it also shares genes found in all other species. These universal genes probably are the legacy of the last common ancestor. A simple search for universal genes brings up a pretty short list, about 200 genes long. The common ancestor probably had a bigger genome, because many genes have been lost over the history of life. Christos Ouzounis and his colleagues at the European Bioinformatics Institute in Cambridge estimate that its full genome contained somewhere between 1,000 and 1,500 genes. Even if Ouzounis is right, however, the last common ancestor of all living things had only a third or a quarter of the genes that a typical strain of
E. coli
has today.
That last common ancestor did not have early Earth all to itself. It shared the planet with an uncountable number of other microbes. Over time the other branches on the tree of life became extinct while our own survived. The world on which these early microbes lived was profoundly different from our own. Four billion years ago, Earth was regularly devastated by gigantic asteroids and miniature planets. Some of the impacts may have boiled off the oceans. As the water slowly fell back to Earth and grew into seas again, life may have found refuge in cracks in the ocean floor. It may be no coincidence that on the tree of life some of the deepest branches belong to heat-loving species that live in undersea hydrothermal vents.
Once Earth became more habitable, the descendants of the common ancestor fanned out. They spread across the seafloor, growing into lush microbial mats and reefs. Continents swelled up, and early organisms moved ashore, forming crusts and varnishes. Along the way they evolved new ways to feed and grow. Some bacteria and archaea consumed carbon dioxide and used iron or other chemicals from deep-sea vents as a source of energy. They built up a supply of organic carbon that other microbes began to feed on.
E. coli
may descend from those ancient scroungers. Its ancestors certainly could not have been living inside humans 3 billion years ago, or inside any other animal for that matter. Some of
E. coli’
s closest living relatives (a group collectively known as gamma-proteobacteria) offer some clues to what
E. coli’
s ancestors might have been doing then. Some eat oil that oozes from cracks in the seafloor. Others live on the sides of undersea volcanoes, where they glue themselves to passing bits of proteins.
E. coli
may have acquired its metabolism from such carbon-scrounging ancestors.
E. coli’
s complex social life—forming biofilms, waging wars with colicins, and so on—may have also had its origins in free-living ancestors in the ocean. Aquatic microbes today have intensely social lives, living mainly in biofilms rather than floating alone as individuals.
About 2.5 billion years ago, the ancestors of
E. coli
were rocked by a planetwide catastrophe: oxygen began to build up in the atmosphere. To us oxygen is essential to life, but on the early Earth it was poison. Initially the planet’s atmosphere was a smoggy mix of molecules, including heat-trapping methane produced by bacteria and archaea. Free oxygen was rare, in part because the molecules rapidly reacted with iron and other elements to form new molecules. Life changed the planet’s chemistry when some bacteria evolved the ability to capture sunlight. They gave off oxygen as waste, and after 200 million years it began to build up in the atmosphere. Unless an organism can protect itself, oxygen can be lethal. Thanks to its atomic structure, oxygen is eager to attack other molecules, wresting away atoms to bond with. The new oxygen-bearing molecules can roam through a cell, wrecking DNA and other molecules they encounter.
For the first billion and a half years of life, the planet had been mercifully free of the oxygen menace. And then, 2.5 billion years ago, oxygen levels rose tenfold. The oxygen revolution may have driven many species extinct, while others found refuge in places where oxygen levels remained low—deep inside mudflats, for example, or at the bottom of the ocean. But some species, including the ancestors of
E. coli,
adapted. They acquired genes that protected them from oxygen’s toxic effects. Once shielded, their metabolism evolved to take advantage of oxygen, using it to get energy out of their food far more efficiently than before. Today
E. coli
can still switch back and forth between its ancient oxygen-free metabolism and its newer network, depending on how much oxygen it senses in its environment.
The other major revolution that
E. coli’
s ancestors experienced was delivered by our own ancestors. Early eukaryotes, biologists suspect, were the predators of the early Earth. They were much like amoebas today, which prowl through soil and water in search of prey they can engulf. Bacteria that could defend themselves against these predators were favored by natural selection. Today bacteria have an impressive range of defenses against amoebas and other eukaryote predators. They can produce toxins that they can inject with microscopic needles into the amoebas. Their mucus-covered biofilms are difficult for predators to penetrate. Even when ingested, bacteria can avoid destruction.
In some cases, bacteria may have turned the tables on their predators. Amoebas today get sick with bacterial infections caused by species that have evolved the ability to infect and thrive inside hosts. Some bacteria are more polite lodgers, providing single-celled protozoans with life-giving biochemistry. Early eukaryotes acquired oxygen-breathing bacteria this way, and those bacteria are still part of our own cells today. Algae acquired photosynthesizing bacteria, and among their descendants are the plants that make the land green. Thanks to these bacterial partners, the continents could begin to support a massive ecosystem, with forests and grasslands and swamps becoming home to animals of all sorts, from insects to mammals.
These animals, the descendants of the predatory eukaryotes that harassed bacteria billions of years earlier, now became a new ecosystem for bacteria to invade. Thousands of species of microbes, including the ancestors of
E. coli,
adapted to the food-rich realm of the animal gut. They brought with them their abilities to break down organic carbon, communicate with one another, and cooperate. They had come a long way from the common ancestor of all living things. But as they took up residence inside humans and other animals, they had in their own way brought some branches of the tree of life together again.
E. COLI
GOES TO COURT
The federal courthouse in Harrisburg, Pennsylvania, is a nondescript box of dark glass. Its judges deal mostly in humdrum conflicts over funeral-parlor regulations, liquor-store licenses, airport parking lots. But in 2005 a surge of people—reporters, photographers, and onlookers—hit the courthouse like a rogue wave. One case had drawn them all:
Kitzmiller v. Dover Area School District.
Eleven parents from the small town of Dover had taken their local board of education to court. They charged that the board was introducing religion into science classes. The world’s attention was fixed on the case because it represented the first time the courts would consider creationism in its latest incarnation, known as intelligent design. The trial opened on September 26, 2005. Projectors had been brought into the court, and the lawyers and expert witness used them to display images on a large screen. Again and again the same image appeared: the flagellum of
E. coli.
Over the past twenty-five years
E. coli’
s flagellum has become an icon to creationists, a molecular weapon they try to wield against the evils of Darwin and his followers. For decades they have touted it in lectures and books as a clear-cut example of the handiwork of a divine designer. But it was not until the Dover case that they had the opportunity to present the flagellum to the world.
The strategy failed miserably. At the end of the trial, Judge John E. Jones ruled against the school board, in part because its case for the flagellum’s intelligent design was so weak. In fact, flagella are a fine example of how evolution works and a clear demonstration of why creationism fails as science.
Creationism—the belief that life’s diversity originated from specific acts of divine creation—first emerged in American history during the early years of the twentieth century. But it was never a single body of ideas. Some creationists argued that the world was a few thousand years old, while others accepted the geologic evidence of its great age. Some claimed evolution must be wrong because it did not accord with the Bible. Others tried to attack the evidence for evolution. They claimed that living species were so distinct from one another that they could not have evolved from a common ancestor. They pointed out the absence of transitional fossils, such as ones that might link whales to land mammals, and claimed that such gaps were proof that intermediate forms could not possibly have existed. When paleontologists discovered fossils of some of those transitional forms—such as whales with legs—the creationists simply retreated to another gap.
While creationists failed in the scientific arena, they had more luck in public high schools. In the 1920s, state legislatures began banning the teaching of evolution, and many of those laws stayed on the books for more than thirty years. It was not until 1968 that the U.S. Supreme Court ruled that banning the teaching of evolution amounted to imposing religion on students. If creationists could not keep evolution out of classrooms, they would try to get creationism in alongside it. They began to claim that creationism is sound science that deserves to be taught. These self-styled “creation scientists” founded organizations with august names, such as the Institute for Creation Research. They began working on a textbook about creation science that they wanted introduced into schools. And they looked around the natural world for things they could claim as scientific evidence of creation.
Biology had changed dramatically since the birth of creationism. Molecular biologists were plunging into the exquisite complexity of cells, discovering clusters of proteins working together like the parts of machines. Creation scientists mined the new research for structures they claimed were the result of creation, not evolution. One of the things they chose was
E. coli’
s flagellum.
In 1981, Richard Bliss, chairman of the Education Department of the Institute for Creation Research, came to West Arkansas Junior College to give a talk about creation science. He told his audience that in the creation model of life, “we would predict that we’d see a fantastic amount of orderliness, and there is, folks. There’s orderliness on a macro level and on a micro level. The further we get down into the molecular level the more we see this orderliness jump out and scream out at us.” As an example of this order, Bliss showed his audience a picture of
E. coli.
Bliss described its flagellum, detailing the many proteins that make it up and how they work together to make it spin. “I like to call it a Mazda engine,” Bliss said. He hoped that students could be taught the “creation model” of
E. coli’
s flagellum along with the “evolution model” and make up their own minds. “It’s just exciting science and exciting education,” he said.