The Tangled Tree

by David Quammen

  Never. I didn’t explain to her, but the reason was simple: Woese died, in late 2012, an old man taken down hard and fast by pancreatic cancer, just before I picked up the trail.

  “To everybody, he was Carl,” she said. “He was not a boss.”

  Bonen showed me a photograph, a memento from her personal files: the youngish Carl Woese in his lab, bathed by yellow-green light, jaw set firmly, gazing up at a pattern of dark spots. Short brown hair, striped sport shirt, handsome and jaunty enough to have stood onstage amid the Beach Boys. Almost apologetically, she said: “That’s the only good picture I have.” This was all different from what I had expected. My mental image was of the later man: the shy, crotchety, and august Dr. Carl Woese.

  He was shy, yes, Bonen said. But “august,” no, that was wrong, not a word she would ever . . . and here again her voice fell away. Then she added: “I only knew him in a short period of time.”

  15

  Ken Luehrsen, soon after Linda Bonen’s short period, had a different sort of experience in the Woese lab. He was an undergraduate at Illinois when he first encountered Woese as one of the instructors for a seminar in developmental biology, well outside Woese’s field of expertise. The logic behind this mismatch, according to Luehrsen, was that “other professors just liked to hear Carl’s take on things so they might incorporate some of his ideas into their own research.” Woese was notoriously brilliant, full of ideas, but jealous of his expended effort. “Undoubtedly, Carl found an opportunity to get a teaching credit where he didn’t have to do too much work.” In a seminar, students would be assigned to make presentations explicating this journal paper or that one, and Woese could easily moderate the discussion. He hated classroom teaching of the more arduous sort—preparing and delivering lectures, God forbid—because “he felt it took him away from his real love: understanding the origin and evolution of life.”

  After the seminar acquaintance, Luehrsen went to this formidable figure and asked to do an honors project under his guidance. Woese not only accepted him but also, to Luehrsen’s surprise, “he plopped me down in his office,” a very small room containing two desks, both covered with chaotic stacks of papers, and said (either seriously or as a tease) that it was so he “could keep an eye on me.” Luehrsen was befuddled. Should he really be there? Should he scram whenever the phone rang and give Woese his privacy? His discomfort eased when he saw that Woese himself spent little time in that office and most of his time in the lab, “reading 16S rRNA fingerprints at his light board.”

  After Woese’s death, Ken Luehrsen wrote a short memoir describing the man’s work, his temperament, and their interactions so long ago, for publication with other Woese tributes in a scientific journal. He brought it all to mind again when I tracked him down in San Carlos, California, on the edge of Silicon Valley, where he was now a senior scientist and biotech inventor in the late afternoon of his career, consulting for a small company lodged behind glass doors in an office park. By that time, he held many patents in biotechnology, for methodologies to create antibodies and other molecular products, and lived comfortably in an old counterculture enclave across the peninsula, a place known as Half Moon Bay, from which he could commute to the action. He worked when he felt like it. At this firm, he was the grizzled elder, surrounded by smart young colleagues seated in carrels, for whom “Woese” was at most a dimly recognizable name, like “Darwin” or “Fibonacci.” Tall and thin, with a goatee, relaxed and a little sardonic, Luehrsen suggested we escape downtown for sushi—after which we talked for most of the afternoon.

  “I may have been a junior at the time,” he said about his first acquaintance with Woese. “I didn’t know anything.” Despite Luehrsen’s ignorance, the great man invested some effort in him; a private tutorial was less abhorrent to Woese than lecturing at banks of indifferent faces. “He explained to me what he was doing. I maybe understood a quarter of it.” But the youngster paid close attention and caught on fast. “I think he saw somebody who was interested, and I was a pretty hard worker.”

  It was 1974 when Luehrsen joined the Woese lab as an undergraduate assistant, paired with a graduate student and assigned the unenviable job of extracting radioactive rRNA from bacterial cultures. They would dump ten millicuries (a large dose) of P-32 into this culture or that and, after overnight incubation to let the bacteria suck it up, spin the mixture in a centrifuge to gather the hot bacteria into a little pellet. After dissolving the pellet in a buffer, they would squash that brew through the laboratory version of a French press, not too unlike the one you might use for coffee. This served to rip open the bacterial cells and set their innards adrift. Luehrsen and his partner would then pull out the ribosomal RNA by chemical extraction, after which the different fractions—the 16S molecules versus the others, including that shorter one, known as 5S—were separated using Mitch Sogin’s home-built cylinders of acrylamide gel. In addition to acrylamide (today recognized as a probable carcinogen), they were working with phenol, chloroform, ethanol, and the radioactive phosphorus. “What a mess that often was! The Geiger counter was always screaming,” Luehrsen wrote in his memoir.

  One of the bacteria he cultured and squashed was Clostridium perfringens, the microbe responsible for gas gangrene, an ugly form of necrosis that takes hold in muscle tissue made vulnerable by wounds, especially the sort that lay open among injured soldiers on battlefields. When he realized this, Luehrsen complained, but Woese “just chuckled and said not to worry” in the absence of an open wound. He had been to medical school for “two years and two days,” Woese said, and he could assure Luehrsen that Clostridium perfringens was unlikely to give him gangrene. Luehrsen took the episode as a lesson—not a lesson to trust Woese but to rely on his own perspicacity more—and never probed the matter of why Woese had quit medical school two days into his third-year rotation in pediatrics.

  After graduating from Illinois in 1975, Ken Luehrsen stayed to work toward a PhD under Woese’s supervision, just as Woese shifted the lab’s focus, slightly but critically, in a way that would lead toward his most startling discovery. So far, they had targeted their molecular analyses on common bacteria and a few other single-celled organisms such as yeast—easy to obtain, easy to grow in the lab. But that was just a preliminary effort as they refined their methods. “One of the things he wanted to do was to look at unusual bacteria,” Luehrsen told me. Woese hoped this might give a view “deep into evolution,” where he could see “deep divergences” between one big branch of life and another. So he struck up a collaboration with a colleague in the Microbiology Department, Ralph Wolfe, one of the world’s leading experts in culturing a group known as the methanogens.

  Methanogens: their name derives from an odd aspect of their biochemistry, producing methane as a byproduct while metabolizing hydrogen and carbon dioxide in environments lacking oxygen. To say it more plainly, these bugs generate swamp gas in muddy wetlands, from which it bubbles up, and similar gas in the bellies of cows, whence it emerges by belch and fart. Certain methanogens also thrive beneath the Greenland ice cap, deep in the oceans, and in other extreme environments, such as hot desert soils. Despite these shared metabolic traits, Ralph Wolfe advised Woese, there was an odd discontinuity among the assemblage of methanogens—discontinuity in terms of their shapes. Some were cocci (spherical), some were bacilli (rod shaped). Since the cocci and the bacilli were considered two distinct kinds of bacteria, microbiologists had been puzzled about how to classify the methanogens—together by metabolism or separately by shape. That conundrum captured Woese’s interest.

  Having told me this much, and more, Ken Luehrsen finished our conversation and sent me away with some gifts. One was a black-and-white print of a photo he took in the mid-1970s, a snapshot, showing Woese at his light board, engrossed before a pattern of dark spots, with a handful of felt-tip pens for color coding what he saw, a pencil for data registry behind his right ear. Luehrsen’s other gift was a single yellowing sheet—not a copy, the original—from his own noteboo
k of the time. It was a catalog of fragments from an organism, more of those telling blurts of the four coding letters, neatly recorded in two columns. UCUCG. CAAG. GGGAAU, and dozens more. At the top, also hand lettered, an abbreviation indicated the name of the organism as it was known at the time: Methanobacterium ruminantium. Later, I realized that, notwithstanding the name, this was no bacterium. Luehrsen had given me the genetic rap sheet on a separate form of life.

  Annotating RNA fragments on a “fingerprint” film.

  16

  How do you classify the methanogens? Where do they fit on the tree of life? To what other little bugs are they most closely related? Those questions, which Woese and his colleagues were asking themselves in the mid-1970s, fell within the scope of an important discipline with a dry name: bacterial taxonomy. That’s the enterprise of sorting bacteria into nested groups: species, genera, families, etcetera. You name something Methanobacterium ruminantium, and then where do you put it?

  This may sound like an exercise in arcana, a marginal activity of risible triviality beside which stamp collecting looks like an adventure sport. Bacteria are tiny, relatively simple, invisible. But if being invisible made things unimportant, gravity and microwaves would be unimportant too. It’s useful to recall that most life-forms on Earth are microbial, that they determine the conditions of existence for the rest of us, and that even the human body contains at least as many microbial cells (those tiny passengers that live in your gut, on your skin, in the follicles of your eyelashes, and elsewhere) as human cells. Your environment is highly microbial too. Your food. The air you breathe. Microbes run the world, and a very large portion of those microbes are bacteria. Some of them serve as helpful partners of humanity. Some are benign. Some are rapacious, ready to poison your blood, fill your lungs, kill you. So it’s no small matter, telling one bacterium from another.

  Scientists once believed it might be possible to do this from visual evidence obtained through a microscope. They even presumed that the concept of species, as understood for animals and plants and fungi, could be applied to bacteria. These were useful simplifications in their era—like the simplifications of Newtonian physics, before correction by Einstein—but that era was a long time ago.

  The early hero in the field was a man named Ferdinand Julius Cohn, a botanist and microbiologist at the University of Breslau (now Wrocław, Poland) during the late nineteenth century. Cohn is an appealing figure, and only partly because his important contributions have been overshadowed by those of better-remembered contemporaries whose accomplishments were more practical and dramatic: Louis Pasteur, Robert Koch, Joseph Lister. They worked on disease, agriculture, and wine. Cohn worked mainly on describing and classifying microscopic organisms. No one makes Hollywood movies about bacterial taxonomists.

  Cohn wasn’t the first researcher to classify bacteria, making distinctions between kinds, trying to place the whole group in its proper position on the tree of life. But his effort was more hardheaded and percipient than the others, and he did much to bring bacteriology out of a fog of confusions that had lingered for more than a century, ever since startled observers such as Leeuwenhoek had noticed these little creatures through simple microscopes. Several insights and adjustments of method helped him make progress. Microscopy improved, with better lenses and precision instruments in which they were mounted. Cohn’s lab started culturing bacteria on solid media such as slices of cooked potato, not in liquid nutrient, the old way. That allowed Cohn to choose, cultivate, and consider different strains separately. Also, he recognized that physiological and behavioral characteristics as well as structural ones could be useful for distinguishing bacterial species: How do they grow in different media? How do they move? By this time, too, Cohn had embraced Darwin’s theory of evolution, and so it made sense to him that bacterial strains might change and adapt over time. This was incremental change, very different from the sort of utter transformation—one bacterial form suddenly morphing into another—that some scientists imagined to occur. Cohn didn’t buy transformation. He saw bacteria as fundamentally stable in their identities. Finally, he published his system, dividing them into four tribes: spherical, rod shaped, filamentous, and spiral, each of which got an imposing Latinate name. Within the tribes, he drew finer distinctions, separating them into genera and species.

  Not everyone in the field accepted Cohn’s classification of bacterial species or his conviction about their stable identities, and the idea of shape-shifting bacteria lingered for more than a decade. The longer judgment of science historians was good to him, as a man and a scientist, noting his “reserve” against self-promotion, his modesty, his eloquent lecturing, and his success in “disentangling almost everything that was correct and important out of a mass of confused statements on what at that time was a most difficult subject to study.” Besides arguing for the reality of bacterial species and sketching a way to classify them, Cohn did much, along with Pasteur, to kill the resilient delusion that new life-forms arise by spontaneous generation. They don’t, he showed. When bacteria seem to appear out of nowhere, it’s because they have arrived from somewhere: contamination, floating through the air, reawakening spores. Cohn’s work was “entirely modern in its character and expression,” according to an authoritative chronicler of the field, writing in 1938, “and its perusal makes one feel like passing from ancient history to modern times.” But what looked modern in 1938, of course, doesn’t look modern now.

  Even the devoutly empirical Ferdinand Cohn made mistakes. For one: after all his research, he still believed, as many of his colleagues did, that bacteria belong to the kingdom of plants. So his tree of life, by later standards, was badly wrong. For another: the premise of radical transformation, one bacterial form to another, turns out to be vastly more complicated than he could imagine.

  17

  Chaos” was the name of the group into which Linnaeus, the great systematizer, in the 1774 edition of his Systema Naturae, had lumped Leeuwenhoek’s bacteria and other little creatures. That was a durable judgment. Even well into the twentieth century, decades after Ferdinand Cohn, experts were still arguing about whether bacterial taxonomy was a meaningful enterprise or hopelessly chaotic.

  Beginning in 1923, the standard source for identifying bacteria was a thick compendium, Bergey’s Manual of Determinative Bacteriology, edited by the bacteriologist David Hendricks Bergey. But as microbiology progressed, it became clear that the Bergey’s system was vague, inconsistent, and, on some fundamentals, inaccurate. It didn’t offer a tree of bacterial life. It was only a glorified field guide. Still, other researchers who critiqued Bergey’s Manual, and then tried to improve on it, found the critiquing much easier than the improving. The task of bacterial classification was just so difficult. There was almost no fossil record of bacterial ancestors. There weren’t enough differences of external shape and internal anatomy, even as seen through powerful microscopes, to support fine distinctions. Physiological characters could also be misleading, if they reflected parallel adaptations rather than shared ancestry. What did that leave for a classifier to use? (Hint: Carl Woese would offer an answer, but not until 1977.) This conundrum came to a head in 1962, when two of the world’s leading microbiologists, C. B. van Niel and Roger Stanier, essentially threw up their hands in despair.

  Van Niel was a Dutchman, educated in Delft, who in 1928 decamped to California, where he taught at a marine biological station that was part of Stanford University. His particular interests were bacterial physiology and taxonomy. Roger Stanier was a younger Canadian who became van Niel’s student, then his special protégé, then his collaborator. In 1941, when Stanier was still just twenty-five years old, he and van Niel coauthored an influential paper on bacterial classification.

  That paper stood as definitive for a generation—until both authors renounced it. Stanier himself later admitted some embarrassment about it, all the more so because he had arm-twisted van Niel to sign on as coauthor—student and teacher together, although the wo
rk was mainly Stanier’s. What the paper contained, besides a pointed critique of Bergey’s Manual, was a shiny new proposal for classifying bacteria—not just a checklist or a field guide but a “natural” system reflecting their evolutionary relationships. That system divided the familiar bacteria into four major groups (as Ferdinand Cohn had done) and placed them in a kingdom of simple creatures along with just one other group: the blue-green algae.

  Algae? Yes, the blue-green algae, as they were then called, had long been an ambiguous group, because they seemed to straddle the line between bacteria and plants. (This was partly what allowed Cohn to believe that all bacteria were plants—the blurry lines around blue-green algae.) Algae was a catchall term for a loose assemblage of creatures that photosynthesize, including these tiny blue-green creatures, but that didn’t mean all algae shared a single common ancestor. Did they? Stanier and van Niel said no. By their new definition of things, blue-green algae were more similar to bacteria than to other algae, and these two groups should be lumped together in a kingdom of their own, apart from everything else. Eventually they labeled such cells procaryotic—meaning “before kernel,” as I’ve mentioned—and set them in contrast to eucaryotic cells, comprising all else. (Their spellings were later corrected, from more accurate transliteration of the Greek roots, to prokaryotic and eukaryotic.) The kernel in question was a cell nucleus. Just as a bacterium doesn’t have one, neither do the creatures that were then known as blue-green algae (and are now classified as cyanobacteria). Advances in microscopy since the end of World War II, including electron microscopy, had given microbiologists a better view of those distinctions and others, making possible a fresh analysis of what a bacterium is—and what it isn’t. Stanier 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.