The Tangled Tree

by David Quammen

  “Big Tree is the major statement from my lab. The work is my conception. And I have put far more hours directly into that work than anyone else, including yourself. By all these criteria, I should be first author.”

  Woese recognized that Fox would soon be up for tenure; that Fox faced a struggle, also, to win grants for his own lab. Since “you feel your funding is at stake,” Woese added grudgingly, “I will allow this to be the overriding consideration, and so will defer to your wishes on authorship. But know that I do so with ambivalence. It would certainly not be proper if this became known as your work or that I needed you to analyze my data for me. That must not happen.”

  Back at the point when Woese had proposed taking first authorship himself, Fox told me, “I put my foot down, and resisted that. And that’s when he terminated our . . .” Another pause, for care in phrasing: “. . . basically terminated our collaboration at that time.”

  Woese signaled the termination in his August 27 letter. He was dissatisfied with their method of data analysis, he explained—the method Fox had devised, generating a similarity coefficient. Woese hoped to find a better approach and apply it to some of the more peculiar bacteria. “I frankly wanted to do all of this with yourself, but your recalcitrance has made that impossible, so I now proceed alone.” In fact, he was proceeding with two other colleagues and, just as Fox was jealous of his authorship, they would be of theirs, Woese claimed. So he was taking Fox’s name off that other paper.

  “These matters are a bit sticky,” he ended the letter, “but if we are open about them they will be only differences of scientific opinion.” It was a nice analgesic platitude meant to dull, slightly, the sting of the slap. His relations with George Fox, once the scrawny postdoc, smart enough to learn from him, smart enough to challenge him, were never the same. Their names would appear together on just a few further papers, in the early 1980s, as the two men came to closure on work done in the 1970s. But they didn’t talk science anymore—not in the fresh, daring, mutually energized way that they had.

  Meanwhile the Big Tree paper went to press. It was published by Science, in the issue of July 25, 1980, with its title corrected for spelling: “The Phylogeny of Prokaryotes.” Instead of comparing just four strains of archaea and nine other creatures, it drew upon molecular sequences from more than 170 different organisms. First among its assertions was that the special molecule, 16S rRNA, could be and had been very useful in discerning evolutionary relationships. Its second main point was that, notwithstanding the title, “prokaryote” is a meaningless category. There are no prokaryotes. There are only bacteria, archaea, and eukaryotes. This was reflected, ever more clearly, in the new data. Its third point, somewhat unexpected and stated indirectly, was that Lynn Margulis had been right about endosymbiosis. The eukaryotic cell “is now recognized to be a genetic chimera,” a compound creature, resulting from ancient convergence events among several lineages, including the bacteria that became mitochondria and chloroplasts. Beyond these three points, the paper focused on classification of groups within the first two of its three kingdoms, the Bacteria and the Archaea. And, of course, it offered, in graphic form, a big tree.

  This one resembled a grand candelabra, with stems for thirty candles. Five of those stems represented groups of archaea, three led to all the eukaryotes (a vast kingdom, in our perceptions, but tangential to the paper’s focus), and the rest stood for groups of bacteria. The particulars of relatedness among those five archaeal and twenty-two bacterial stems held high interest for microbiologists at the time, but I don’t ask you to share that interest. It’s microbe arcana. Never mind. The more intriguing aspect of the Big Tree is how Woese and Fox chose to root their three kingdoms: ambiguously. The three major limbs don’t rise from a single trunk. Each one emerges separately from a rounded base—like a great mound of dirt—bearing the somewhat mysterious label “Common Ancestral State.”

  “Here’s one of the things that’s important to me,” Fox said across his cheese and my pepperoni. I had brought out my annotated, underlined copy of the 1980 paper. “See that tree?”

  “Yeah,” I said. The article was folded open to page 459. “Yeah, that is the Big Tree, right?”

  “That is the Big Tree. And you’ll notice the root.”

  The “Big Tree” of Fox, Woese, and colleagues, 1980.

  Yep. “Common ancestral state,” I read. “Not a single ancestor, but an ‘ancestral state.’ Right?”

  Right, he said. This mound represented a world of precellular life; a world of primeval twitching almost four billion years ago; a world of naked molecules (maybe RNA in particular) that had acquired the capacity to replicate themselves; a world before living things could be sorted into species, let alone into kingdoms. “We refused to decide the triumvirate,” he said. Sprouting three limbs independently from the mound was a way of saying: Who knows how the three kingdoms are ultimately related? Who knows which came first, or how they diverged, or which is most closely akin to which other? Not us! It was an act of candid agnosticism, the best that could be done at the time.

  “Okay. Now the secret thing,” Fox said. For a moment, he looked sly, insofar as a sixty-nine-year-old molecular evolutionist seated over a Coke and a plain pizza can look sly. “The secret thing to realize is . . . I don’t believe in trees. And Carl didn’t either.”

  “Okay,” I echoed, wondering what would come next.

  “Because that’s not the way evolution works.”

  47

  The way evolution works was still being discovered and contested. Charles Darwin had been deeply percipient in recognizing the mechanism of natural selection, and he had persuasively described its workings in The Origin; but he didn’t explain everything about how lineages change and diverge, and he wasn’t right about everything that he did explain. Darwin knew nothing about the mechanisms of inheritance, for instance, and very little about the lives of microbes. Ivan Wallin and Lynn Margulis, among others who did study microbes, argued that symbiotic combining of one life-form with another had done more, in generating evolutionary novelty, than the incremental variations, the random mutations, that supposedly fueled natural selection. By the time Fox and Woese and their colleagues published Big Tree, there were other new ideas and new questions too. Some of them focused on that mysterious mound, at the base of the Fox-and-Woese tree, labeled “Common ancestral state.” What did the words mean? What was in there?

  George Fox got his associate professorship at Houston in 1982 and continued working on early evolution, but not with Carl Woese. As for Woese, he found new collaborators and proceeded with his own long-term project of discerning the course of deep evolutionary events, the shape of the tree of life, from the evidence coded in ribosomal RNA. His laboratory methods changed during the 1980s, as new technologies for molecular sequencing made that part of the work less arduous, less toxic, more precise, and much faster, but his interests and goals remained constant. By the mid-1980s, he was drawing trees based on complete sequences of ribosomal RNA, not just catalogs of short fragments.

  Molecular sequencing, even then, wasn’t the only approach to discerning a deep tree of life. Some researchers still embraced the idea of using morphology—comparison of shapes—rather than comparison of linear sequences of RNA or DNA. Among them was James Lake, at the University of California, Los Angeles (UCLA), who studied ribosome structure by way of electron microscopy. Lake was another of those scientists who gravitated to biology after training in physics. He had gotten interested in ribosome shapes back in the late 1960s during a postdoc fellowship at the Harvard Medical School, when he discovered that he could detect the three-dimensional structure of a ribosome from electron micrographs. That led to his recognition that ribosome shapes seem to differ consistently, between one group of microbes and another, and then to the notion that comparing such differences might be a valid way of defining phylogenetic units—maybe even kingdoms. In 1984 he and several colleagues published their analysis of ribosome shapes as seen in r
epresentative bacteria, archaea, and eukaryotes.

  Some of those ribosomes looked like rubber duckies. Some looked like a fist with its thumb out to hitchhike. Some looked a bit more like popcorn. Lake’s team carefully measured and quantified the differences. They found four basic shapes that, by their argument, served to characterize four fundamentally distinct kinds of life. This method split away the sulfur-dependent microbes that live in hot, acidic environments from the rest of Woese’s archaea. Lake named that sulfur-breathing group the Eocyta (its members would be “eocytes”) and declared it an independent kingdom. So now again, if you bought this, there were four kingdoms of life. Furthermore, by Lake’s analysis, his eocytes seemed more closely related to eukaryotes, such as us, than to what remained of the archaea. Woese wasn’t happy.

  In his view, as he told Lake by letter, “all your proposal does is muddy the waters.” They had been on genial terms, these two men, following an invitation by Lake and a visit to UCLA by Woese the previous year, but now that geniality ended. Woese’s camp, including German colleagues such as Wolfram Zillig who shared his fondness for the archaea, sharply criticized Lake’s methodology and conclusions; Lake criticized theirs in return. Woese told him directly: “Your apparent need to have there be a new kingdom detracts from your presentation of a solid contribution.” Jan Sapp called this “the battle of the kingdom keepers,” waged not just through personal letters but also from the podium at scientific meetings and on the news and letters pages of Nature. Zillig dismissed the whole episode as a “ridiculous intermezzo” and told Woese: “I must admit that I have greatly underestimated the stupidity of the scientific community and/or the persuasive power of Lake.” The ferocity of the intermezzo, as documented by Sapp, left me surprised by the mildness of James Lake himself when I met him thirty years later at UCLA.

  He was a tall man, slightly bent by the years if not the battles, with pale-blue eyes and thick gray hair, wearing a lavender cardigan and chinos, gently solicitous and hospitable as he led me to his office. It was Friday afternoon, and his manner and looks suggested a retired Presbyterian minister just after a round of golf. We talked across his desk, piled high with scientific papers, above which on a shelf sat a two-color plaster model of a ribosome, roughly the size of a human heart. He spoke of his soured relationship with Woese, and Woese’s response to Lake’s eocyte theory of four kingdoms, as though still baffled by the depth and rancor of negativity.

  “Either you’re with him or you’re not with him,” Lake said. At first, Lake had been with Woese on the integrity of Archaea as a kingdom. When that changed, when Lake’s research led toward an alternate view, “I told him the reasons, and there was a sort of intransigence there.” It was as though a switch had been flipped, terminating their cordiality, making Lake not just an intellectual competitor but also a perpetrator of falsehood and confusion. At that point, as Lake recalled, “It became, ‘Pull out all the stops and try to ruin this theory.’ ” By the consensus of other expert voices, Woese won that battle of the kingdoms, if not the war.

  In 1987 Woese published a thick review paper, himself as sole author, surveying the field of bacterial evolution and, beyond that, the whole enterprise of phylogenetics. He began with a historical recap of ideas in microbial classification, as it was done formerly on the evidence of morphology via microscopy, and amid that discussion, he inserted a full-page reprint of Haeckel’s tree of all organisms, with its rooting in the Moneres and its three limbs. It was classic and it was orderly, Woese granted, but it was wrong. In contrast to all such earlier efforts, from Linnaeus with his two kingdoms of life, to Haeckel with his three kingdoms, to Whittaker and Margulis with their five kingdoms, to Lake with his four kingdoms, Woese touted his own method (phylogeny by sequences of ribosomal RNA) and his own three kingdoms. “The cell is basically an historical document,” he wrote, “and gaining the capacity to read it (by the sequencing of genes) cannot but drastically alter the way we look at all of biology.” The ribosomal RNAs were the best and most reliable texts within cells, ancient and revealing, because they occur in all living organisms, they contain much information, and that information has changed slowly over the vast reaches of time. They contain evidence for distinguishing one kingdom from another as those kingdoms diverged, so long ago, in the period of early life. Having made that argument, he offered another tree.

  The most notable aspect of this one was that it had no trunk. It had no roots. The three limbs emerged from a point at the center of the page, like a starburst pattern from a lone fireworks rocket exploding against a dark sky. That rootlessness was another way of saying what Woese and Fox had suggested with the mystery mound in Big Tree: Events here, unknown. Not even 16S rRNA can tell us. But he put a label to that zone of ignorance. He gave a name to the kind of creature that had existed there, existed then, just before the Big Bang of life led to the Big Tree: progenote. Somewhere at the nexus of his three major limbs—but unmarked on his figure—resided the progenote.

  The progenote was a theoretical construct, as he explained. It was a hypothetical entity that came before—that had to have come before—the more knowable evolutionary history of cells. It was something more simple and less organized than a cell. “The certainty that progenotes existed at some early stage in evolution,” he wrote, “follows from the nature of the translation apparatus”—that is, from the universal utility of ribosomes, turning code into proteins to make life possible. This progenote thing wasn’t a brand-new idea in 1987. Woese had coined the name and sketched the concept a decade earlier, in another paper with George Fox during that interesting year, 1977. Now he elaborated. A progenote was an organic unit capable of self-replication, but its genome probably consisted of RNA, not DNA. Its mechanism for translating that genome to produce proteins was rickety and imprecise—very prone to mistakes. Its proteins, therefore, were small and inefficient. It was still in the process of inventing—evolving, by trial and error—the ribosome. “Like the radio, the automobile, and similar devices, translation had to evolve through stages, from a much more rudimentary mechanism to the present precisely functioning one.” What evidence did Woese have for the existence and nature of the progenote? Logic. Supposition. Informed guesswork. There were no data from the progenote era. There were no fossils, and there was no 16S rRNA. He was simply pondering the topic—what came just before life as we know it?—more carefully and yet more daringly than anyone else.

  Woese’s unrooted tree, 1987, and the “progenote.” Redrawn and modified, from Woese (1987), by Patricia J. Wynne.

  Whatever did occur during that phase of Earth’s history, its most consequential result was a single lineage, some manner of creature, that became the universal ancestor of all three kingdoms of life. For this certitude, we do have evidence: the universality of the genetic code itself, a system that uses the same coding—these bases specify those amino acids—in bacteria, in archaea, and in eukaryotes. The genetic code is the ultimate shared character, uniting all forms of life within one ancestry. And that ancestry had its origin among progenotes.

  “The progenote is today the end of an evolutionary trail,” Woese wrote, “that starts with fact, progresses through inference, and fades into fancy.” The end of a trail tracing backward in time, he meant. “However, in science endings tend to be beginnings.” The flow of genomic data would soon become a deluge, he predicted correctly. The root of the universal tree of life would be identified. We were beginning, he promised, to understand the beginning.

  48

  Back in early 1980, around the time Woese and Fox finished their work on Big Tree, Woese wrote to his friend Otto Kandler in Munich. The letter’s main purpose was to request help on a subject keenly interesting to them both: those unusual cell walls of archaea, Kandler’s specialty. Woese needed electron micrographs, and some help with chemical structure, on which to base illustrations for an article he planned to write for Scientific American. Pivoting from that thought, he told Kandler: “Someday you and I must wr
ite a scientific article together. Our knowledge and approaches complement one another.” What do you say, he asked, about teaming up to make a formal proposal that the archaea should be a full kingdom? He and Kandler and others had been talking that way, treating archaea as a kingdom, but informally, without trying to muster formal taxonomic consensus. “It’s a sort of wild thought.”

  The wild thought seemed less wild with passing years and intervening events. In 1984 Woese received a MacArthur Fellowship for his efforts in phylogenetic analysis and his discovery of the archaea, and in 1988 he was elected to the National Academy of Sciences. Despite the MacArthur honor, and because the Academy had elected him relatively late (at age sixty, whereas Lynn Margulis had been welcomed at age forty-five), he still thought of himself as a neglected outsider. That gave him some latitude to continue being ambitious, bold, and ornery. And he wanted to revisit the status of his beloved archaea. It wasn’t just to get them recognized as a kingdom. He also chafed at the fact that, for a dozen years, by his own doing, they had been burdened with a misleading name.

  Now I’ll clarify something that I’ve left streamlined for simplicity: the original name that Woese and Fox gave these creatures back in 1977, archaebacteria, had endured. Woese himself, his American and German colleagues, and everyone else in the field called them that throughout the period I’ve been describing. The big international meeting in Munich, after which Woese and Kandler and Ralph Wolfe celebrated with champagne in the Bavarian Alps, was billed as “The First Workshop on Archaebacteria.” But that name increasingly rankled Woese, because it undermined the group’s uniqueness, suggesting they were just another branch of bacteria.

  In 1989 he sent an email to Wolfram Zillig, his other close German colleague, addressing the problem. “As time goes by it becomes more and more obvious,” Woese wrote, “that I made a major mistake in naming the archaes.” They weren’t bacteria, of course. They weren’t quasibacteria or ancient precursors of bacteria. Bacteria weren’t even their nearest kin. Some evidence had emerged by that time, in fact, indicating that archaea are more closely related to eukaryotes—more closely related to us—than to bacteria. Woese repeated to Zillig the idea he had earlier suggested to Kandler: Let’s write a paper, a group of us big dogs in the field, proposing the archaeans formally as a kingdom and giving them a new name.