A short history of nearly everything (42 page)

Some scientists now think that there could be as much as 100 trillion tons of bacteria living beneath our feet in what are known as subsurface lithoautotrophic microbial ecosystems—SLiME for short. Thomas Gold of Cornell has estimated that if you took all the bacteria out of the Earth’s interior and dumped it on the surface, it would cover the planet to a depth of five feet. If the estimates are correct, there could be more life under the Earth than on top of it.

At depth microbes shrink in size and become extremely sluggish. The liveliest of them may divide no more than once a century, some no more than perhaps once in five hundred years. As theEconomist has put it: “The key to long life, it seems, is not to do too much.” When things are really tough, bacteria are prepared to shut down all systems and wait for better times. In 1997 scientists successfully activated some anthrax spores that had lain dormant for eighty years in a museum display in Trondheim, Norway. Other microorganisms have leapt back to life after being released from a 118-year-old can of meat and a 166-year-old bottle of beer. In 1996, scientists at the Russian Academy of Science claimed to have revived bacteria frozen in Siberian permafrost for three million years. But the record claim for durability so far is one made by Russell Vreeland and colleagues at West Chester University in Pennsylvania in 2000, when they announced that they had resuscitated 250-million-year-old bacteria calledBacillus permians that had been trapped in salt deposits two thousand feet underground in Carlsbad, New Mexico. If so, this microbe is older than the continents.

The report met with some understandable dubiousness. Many biochemists maintained that over such a span the microbe’s components would have become uselessly degraded unless the bacterium roused itself from time to time. However, if the bacterium did stir occasionally there was no plausible internal source of energy that could have lasted so long. The more doubtful scientists suggested that the sample may have been contaminated, if not during its retrieval then perhaps while still buried. In 2001, a team from Tel Aviv University argued thatB. permians were almost identical to a strain of modern bacteria,Bacillus marismortui , found in the Dead Sea. Only two of its genetic sequences differed, and then only slightly.

“Are we to believe,” the Israeli researchers wrote, “that in 250 million yearsB. permians has accumulated the same amount of genetic differences that could be achieved in just 3–7 days in the laboratory?” In reply, Vreeland suggested that “bacteria evolve faster in the lab than they do in the wild.”

Maybe.

It is a remarkable fact that well into the space age, most school textbooks divided the world of the living into just two categories—plant and animal. Microorganisms hardly featured. Amoebas and similar single-celled organisms were treated as proto-animals and algae as proto-plants. Bacteria were usually lumped in with plants, too, even though everyone knew they didn’t belong there. As far back as the late nineteenth century the German naturalist Ernst Haeckel had suggested that bacteria deserved to be placed in a separate kingdom, which he called Monera, but the idea didn’t begin to catch on among biologists until the 1960s and then only among some of them. (I note that my trustyAmerican Heritage desk dictionary from 1969 doesn’t recognize the term.)

Many organisms in the visible world were also poorly served by the traditional division. Fungi, the group that includes mushrooms, molds, mildews, yeasts, and puffballs, were nearly always treated as botanical objects, though in fact almost nothing about them—how they reproduce and respire, how they build themselves—matches anything in the plant world. Structurally they have more in common with animals in that they build their cells from chitin, a material that gives them their distinctive texture. The same substance is used to make the shells of insects and the claws of mammals, though it isn’t nearly so tasty in a stag beetle as in a Portobello mushroom. Above all, unlike all plants, fungi don’t photosynthesize, so they have no chlorophyll and thus are not green. Instead they grow directly on their food source, which can be almost anything. Fungi will eat the sulfur off a concrete wall or the decaying matter between your toes—two things no plant will do. Almost the only plantlike quality they have is that they root.

Even less comfortably susceptible to categorization was the peculiar group of organisms formally called myxomycetes but more commonly known as slime molds. The name no doubt has much to do with their obscurity. An appellation that sounded a little more dynamic—“ambulant self-activating protoplasm,” say—and less like the stuff you find when you reach deep into a clogged drain would almost certainly have earned these extraordinary entities a more immediate share of the attention they deserve, for slime molds are, make no mistake, among the most interesting organisms in nature. When times are good, they exist as one-celled individuals, much like amoebas. But when conditions grow tough, they crawl to a central gathering place and become, almost miraculously, a slug. The slug is not a thing of beauty and it doesn’t go terribly far—usually just from the bottom of a pile of leaf litter to the top, where it is in a slightly more exposed position—but for millions of years this may well have been the niftiest trick in the universe.

And it doesn’t stop there. Having hauled itself up to a more favorable locale, the slime mold transforms itself yet again, taking on the form of a plant. By some curious orderly process the cells reconfigure, like the members of a tiny marching band, to make a stalk atop of which forms a bulb known as a fruiting body. Inside the fruiting body are millions of spores that, at the appropriate moment, are released to the wind to blow away and become single-celled organisms that can start the process again.

For years slime molds were claimed as protozoa by zoologists and as fungi by mycologists, though most people could see they didn’t really belong anywhere. When genetic testing arrived, people in lab coats were surprised to find that slime molds were so distinctive and peculiar that they weren’t directly related to anything else in nature, and sometimes not even to each other.

In 1969, in an attempt to bring some order to the growing inadequacies of classification, an ecologist from Cornell University named R. H. Whittaker unveiled in the journalSciencea proposal to divide life into five principal branches—kingdoms, as they are known—called Animalia, Plantae, Fungi, Protista, and Monera. Protista, was a modification of an earlier term,Protoctista , which had been suggested a century earlier by a Scottish biologist named John Hogg, and was meant to describe any organisms that were neither plant nor animal.

Though Whittaker’s new scheme was a great improvement, Protista remained ill defined. Some taxonomists reserved it for large unicellular organisms—the eukaryotes—but others treated it as the kind of odd sock drawer of biology, putting into it anything that didn’t fit anywhere else. It included (depending on which text you consulted) slime molds, amoebas, and even seaweed, among much else. By one calculation it contained as many as 200,000 different species of organism all told. That’s a lot of odd socks.

Ironically, just as Whittaker’s five-kingdom classification was beginning to find its way into textbooks, a retiring academic at the University of Illinois was groping his way toward a discovery that would challenge everything. His name was Carl Woese (rhymes with rose), and since the mid-1960s—or about as early as it was possible to do so—he had been quietly studying genetic sequences in bacteria. In the early days, this was an exceedingly painstaking process. Work on a single bacterium could easily consume a year. At that time, according to Woese, only about 500 species of bacteria were known, which is fewer than the number of species you have in your mouth. Today the number is about ten times that, though that is still far short of the 26,900 species of algae, 70,000 of fungi, and 30,800 of amoebas and related organisms whose biographies fill the annals of biology.

It isn’t simple indifference that keeps the total low. Bacteria can be exasperatingly difficult to isolate and study. Only about 1 percent will grow in culture. Considering how wildly adaptable they are in nature, it is an odd fact that the one place they seem not to wish to live is a petri dish. Plop them on a bed of agar and pamper them as you will, and most will just lie there, declining every inducement to bloom. Any bacterium that thrives in a lab is by definition exceptional, and yet these were, almost exclusively, the organisms studied by microbiologists. It was, said Woese, “like learning about animals from visiting zoos.”

Genes, however, allowed Woese to approach microorganisms from another angle. As he worked, Woese realized that there were more fundamental divisions in the microbial world than anyone suspected. A lot of little organisms that looked like bacteria and behaved like bacteria were actually something else altogether—something that had branched off from bacteria a long time ago. Woese called these organisms archaebacteria, later shortened to archaea.

It has be said that the attributes that distinguish archaea from bacteria are not the sort that would quicken the pulse of any but a biologist. They are mostly differences in their lipids and an absence of something called peptidoglycan. But in practice they make a world of difference. Archaeans are more different from bacteria than you and I are from a crab or spider. Singlehandedly Woese had discovered an unsuspected division of life, so fundamental that it stood above the level of kingdom at the apogee of the Universal Tree of Life, as it is rather reverentially known.

In 1976, he startled the world—or at least the little bit of it that was paying attention—by redrawing the tree of life to incorporate not five main divisions, but twenty-three. These he grouped under three new principal categories—Bacteria, Archaea, and Eukarya (sometimes spelled Eucarya)—which he called domains.

Woese’s new divisions did not take the biological world by storm. Some dismissed them as much too heavily weighted toward the microbial. Many just ignored them. Woese, according to Frances Ashcroft, “felt bitterly disappointed.” But slowly his new scheme began to catch on among microbiologists. Botanists and zoologists were much slower to admire its virtues. It’s not hard to see why. On Woese’s model, the worlds of botany and zoology are relegated to a few twigs on the outermost branch of the Eukaryan limb. Everything else belongs to unicellular beings.

“These folks were brought up to classify in terms of gross morphological similarities and differences,” Woese told an interviewer in 1996. “The idea of doing so in terms of molecular sequence is a bit hard for many of them to swallow.” In short, if they couldn’t see a difference with their own eyes, they didn’t like it. And so they persisted with the traditional five-kingdom division—an arrangement that Woese called “not very useful” in his milder moments and “positively misleading” much of the rest of the time. “Biology, like physics before it,” Woese wrote, “has moved to a level where the objects of interest and their interactions often cannot be perceived through direct observation.”

In 1998 the great and ancient Harvard zoologist Ernst Mayr (who then was in his ninety-fourth year and at the time of my writing is nearing one hundred and still going strong) stirred the pot further by declaring that there should be just two prime divisions of life—“empires” he called them. In a paper published in theProceedings of the National Academy of Sciences , Mayr said that Woese’s findings were interesting but ultimately misguided, noting that “Woese was not trained as a biologist and quite naturally does not have an extensive familiarity with the principles of classification,” which is perhaps as close as one distinguished scientist can come to saying of another that he doesn’t know what he is talking about.

The specifics of Mayr’s criticisms are too technical to need extensive airing here—they involve issues of meiotic sexuality, Hennigian cladification, and controversial interpretations of the genome ofMethanobacterium thermoautrophicum , among rather a lot else—but essentially he argues that Woese’s arrangement unbalances the tree of life. The bacterial realm, Mayr notes, consists of no more than a few thousand species while the archaean has a mere 175 named specimens, with perhaps a few thousand more to be found—“but hardly more than that.” By contrast, the eukaryotic realm—that is, the complicated organisms with nucleated cells, like us—numbers already in the millions. For the sake of “the principle of balance,” Mayr argues for combining the simple bacterial organisms in a single category, Prokaryota, while placing the more complex and “highly evolved” remainder in the empire Eukaryota, which would stand alongside as an equal. Put another way, he argues for keeping things much as they were before. This division between simple cells and complex cells “is where the great break is in the living world.”

The distinction between halophilic archaeans and methanosarcina or between flavobacteria and gram-positive bacteria clearly will never be a matter of moment for most of us, but it is worth remembering that each is as different from its neighbors as animals are from plants. If Woese’s new arrangement teaches us anything it is that life really is various and that most of that variety is small, unicellular, and unfamiliar. It is a natural human impulse to think of evolution as a long chain of improvements, of a never-ending advance toward largeness and complexity—in a word, toward us. We flatter ourselves. Most of the real diversity in evolution has been small-scale. We large things are just flukes—an interesting side branch. Of the twenty-three main divisions of life, only three—plants, animals, and fungi—are large enough to be seen by the human eye, and even they contain species that are microscopic. Indeed, according to Woese, if you totaled up all the biomass of the planet—every living thing, plants included—microbes would account for at least 80 percent of all there is, perhaps more. The world belongs to the very small—and it has for a very long time.

So why, you are bound to ask at some point in your life, do microbes so often want to hurt us? What possible satisfaction could there be to a microbe in having us grow feverish or chilled, or disfigured with sores, or above all expire? A dead host, after all, is hardly going to provide long-term hospitality.