The Tangled Tree: A Radical New History of Life. David Quammen

and van Niel offered that fresh analysis along with the prokaryote category in a new paper, published in 1962, titled “The Concept of a Bacterium.” By their lights, the “abiding intellectual scandal of bacteriology” was that no such concept had ever been clearly delineated. What was a bacterium? Um, hard to say.

      They tried to correct that by placing bacteria and blue-green algae together as prokaryotes, and setting them in contrast to the alternative category, eukaryote, which encompasses all other forms of cellular life. The chief distinguishing features of a prokaryote, according to Stanier and van Niel, were: (1) no cell nucleus, (2) cell division by simple fission, rather than the elaborate process of chromosome pairing known as mitosis, and (3) a cell wall strengthened by a certain sort of latticework molecule with a fancy name, peptidoglycan. I know, it looks like the moniker of a flying reptile from the Jurassic. Forget about it for now, and when peptidoglycan comes back as an important clue toward understanding the deepest structure of the tree of life, and the twig on the branch on the limb from which we humans have sprouted, I’ll remind you.

      The dichotomy between prokaryotes and eukaryotes, creatures without cell nuclei and those with, relatively simple beings and relatively complex, became a fundamental organizing principle of biology. Stanier and his two coauthors of a textbook would later say that it “probably represents the greatest single evolutionary discontinuity to be found in the present-day living world.” It was also a salubrious reminder to humans of our inescapable linkage to other creatures, including some very humble ones. We are, at the most basic level of classification, eukaryotes. So are amoebae. So are yeasts. So are jellyfish, sea cucumbers, the little parasites that cause malaria, and rhododendrons. To an average person, the gap between an amoeba and a bacterium may seem narrow (partly because most of us have never, or at least not since high school biology, looked through a microscope at either), but the prokaryote-eukaryote distinction reveals it as oceanic. You could think of the living world—and, beginning from Stanier and van Niel’s 1962 paper, biologists did think of the living world—as divided into proks and euks.

      Besides putting that idea into play, “The Concept of a Bacterium” is notable for having signaled surrender, by Stanier and van Niel, in the battle of bacterial taxonomy. About this they were candid, confessional, and brusque. Ever since Leeuwenhoek, microbiologists had been seeking the best way to classify bacteria. Ever since Darwin, they had been arguing about how one bacterium was related to another. Enough was enough. “Any good biologist finds it intellectually distressing to devote his life to the study of a group that cannot be readily and satisfactorily defined.” C. B. van Niel himself had devoted forty years. He and Stanier now alluded to the “elaborate taxonomic proposal” they had published back in 1941, “which neither of us cares any longer to defend.” Never mind that. They admitted having “become sceptical about the value” of any such formal systems, or the effort spent to develop them, although they still affirmed the importance of figuring out just what the devil bacteria are.

      This skepticism, this taxonomist’s despair, had been wiggling up inside van Niel for a long time. Two decades earlier, even as he was signing onto that first elaborate proposal, he had confessed his gloom to Stanier in a letter: “Many, many years ago I often went around with a sense of futility of all our (my) efforts. It made me sick to go around in the laboratory (this was in Delft) and talk and think about names and relations of microorganisms.” Was any of it real? Was there any value to putting bacteria into labeled boxes? “During those periods I would go home after a day at the lab, and wish that I might be employed somewhere as a high-school teacher.” Not that he would enjoy such teaching, he realized, but at least “it would give me some assurances that what I was doing was considered worth-while.” Nowadays we might see that as a signal of bipolar disorder, but it’s just as likely that van Niel simply viewed bacterial taxonomy with great clarity.

      Under their revised spellings, prokaryote and eukaryote, those two became enshrined for a generation as the most fundamental categories of life. Eukaryotes had cell nuclei. Prokaryotes did not. That dichotomy seemed to represent, as Stanier and his coauthors had written, the greatest single evolutionary divide in the living world. There were two basic kinds of creature, the proks and the euks, and there was nothing between.

      What makes this worth knowing is that Carl Woese proved it wrong.

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      As of early 1976, with Ken Luehrsen and others still helping, Woese had done his unique form of catalog analysis on samples from roughly thirty species, using differences in ribosomal RNA molecules to measure their relatedness. Most were prokaryotes, but he also looked at a few eukaryotes (which carried that slightly different molecule in their ribosomes, 18S rRNA instead of 16S), including yeast, for purposes of gross comparison. He could tell a prok from a euk just by inspecting the spots on a sheet of film. And he was eager to see those “unusual bacteria,” the methanogens, about which Ralph Wolfe had alerted him.

      The tricky thing about methanogens was that, since oxygen poisoned them, they were hard to grow in a laboratory. But Wolfe’s lab team included an ingenious doctoral student, Bill Balch, who had solved that problem by devising a way to culture methanogens in pressurized aluminum tubes with black rubber stoppers, and using syringes to move things in and out. Balch gave the methanogens an atmosphere of hydrogen and carbon dioxide instead of oxygen, plus a liquid growth medium, and they thrived. Woese sent his own postdoc, a rangy young man named George Fox, trained in chemical engineering, to work with Balch on growing some of these methanogens and tagging them with radioactive phosphorus. Fox, Ken Luehrsen, and other members of the Woese lab then combined their efforts on the rest of the process: extracting the radioactive RNA, purifying it to get concentrations of 16S and 5S molecules, chopping those molecules into pieces, running the electrophoresis to separate the fragments, and printing the spots onto films. Their first methanogen carried a formal name so long (Methanobacterium thermoautotrophicum) that even Woese himself dismissed that as “a fourteen-syllable monstrosity” and preferred using a shorter label, denoting the particular laboratory strain: delta H. Examining its primary fingerprint on his light board, Woese noticed something odd.

      He was practiced enough by now at reading such fingerprints that he could immediately recognize a certain pair of small fragments, common to all bacteria, that “screamed out” their membership in the prokaryotes. He looked for them on the primary film from delta H. They were missing. Intrigued but patient, he waited for the secondary fingerprint, with the fragments pulled sideways to reveal more detail. He got that from his technician several days later. On June 11, 1976, he taped the primary film up on his light board again, with the secondary now in front of him on the light table, and began trying to interpret what he saw. He intended, as usual in this stage of the process, to use the secondary film as a guide for inferring the base sequences of the fragments in the primary pattern. Apart from his board and his table, the room was dark. His face, we can imagine, reflected an eerie glow. Quickly he noticed more oddities.

      The two missing fragments were still missing, but it wasn’t just that. Woese turned to a different part of the pattern, expecting to see another familiar fragment—a “signature” sequence in all prokaryotes. Not there. Instead, he found a strange fragment, a longish sequence that shouldn’t have been present at all. “What was going on?” he later recalled wondering. This methanogen rRNA just “was not feeling” prokaryotic. And the more fragments he sequenced, the less prokaryotic it felt. By this time, he knew the sequences of ribosomal RNA in bacteria so intimately that his “feel” for the molecule was a