“The only real valuable thing is intuition.—”Einstein

“When I was an undergraduate, two theories were held up for ridicule, to show how farfetched scientific theories can get. One was the theory of continental drift and the other was the symbiotic theory of the origin of the cell.” –William Culberson, professor of Botany at Duke University.

In the summer of 1912, not far from their house in the French Pyrenees, three boys found a cave. They were experienced at exploring; it occupied their free hours, and so they decided to go in. As they did, they came to a small cliff that they climbed until they reached a wide cave gallery. Within the gallery, they found a passage that left the cave like a chimney. The chimney tunnel extended further in its narrowness than they might have hoped. The reasonable response would have been to turn back, yet they pressed deeper. Their shoulders and chests grew so tight that at times it was difficult to breathe. They climbed until they arrived at a place where stalactites blocked their progress. Again, they might have stopped, but they were boys and they could see something on the other side, some further chamber, and so they chipped at one of the pillars and then made their way through. As the anthropologist Lawrence Robbins wrote of what happened next, “they slipped into the unknown, entering a part of the cave that was last seen by humans in he Ice Age.” The tunnel opened into an enormous gallery. The boys were sweaty, exhilarated, and happy to have come through intact. Soon they were speechless, beyond excitement. They could not see well, but in the sweep of their light they found the claw marks of cave bears, bones of large animals, and then footprints that they would later learn were more than 10,000 years old. Then, further down the cave, they saw what was to be their biggest discovery, four, upright clay bison, each the size of a small dog and more than 15,000 years old, pointed as though ready to charge. The boys stood silent. Eventually they hugged, climbed back up through the tunnel, and told the world.

This is how we imagine science. We climb through a hole into a new chamber of the world, laugh, weep, and then the New York Times calls. What the biologist Lynn Margulis would come to believe she had discovered was not unlike a cave full of art. It was a set of signs written within a cell’s walls. She read them and understood. She came out of the cave and announced her finding. Then things departed from the script. No one believed her.

Lynn Margulis was born in a working class neighborhood on the South Side of Chicago where she used to “romp along the connected rooftops and fire escapes of Chicago’s second city of garages.” From an early age, she saw the world from a different, more rarified, perspective. The oldest of four sisters, she grew up tough and responsible. She also grew up, photos and friends combine to attest, beautiful and brilliant. In 1952, at age 14, she went to college at the University of Chicago. It was there that she would find science and, on the stairwell of Eckhart Hall, the boy who would become her first husband. In just a few years, she would begin to pursue science and raise a family. Things from then on would happen quickly. She graduated from the University of Chicago and enrolled in a master’s degree program at the University of Wisconsin where she began her studies while pregnant. She slept through classes as she nourished both ideas and her first son. She was a woman working in what was still a “man’s field.” Her world was filled with hurdles that, without slowing down, she leapt.

Mid‐way through her master’s degree, Margulis looked at amoebas through the microscope for the first time. Margulis had been taught to trust little beyond her own observations, whether those be observations of old, ignored books or, in this case, cells. As she observed these particular cells she was struck by their tiny organs (technically “organelles”). She looked into the amoebas and found important details. Here was the mitochondria, the cell’s powerhouse; in among the other organs of the cell, the nucleus, the cell’s brain; the vacuoles, the cells’ garbage piles. In plant cells, there were chloroplasts, the machinery that harnesses all of the sunlight that we ultimately eat. On the cells’ surface were the beating flagella, the waggling, legs and arms. Under the microscope she found for herself the simple structures responsible for life, the blocks out of which we are all made. Lynn Margulis had not yet discovered anything. She had seen the tunnels and caves of the cell and in them, signs of other chambers, and in them new discoveries. The cells’ organs had been studied for centuries. The shape of these structures and aspects of their function was thought to be relatively well‐known by the time Margulis began to work. Less considered was the origin of these structures, how from something simpler they evolved.

In the early days of cell biology, there were more vague notions than facts. One of those vague notions was that there might be DNA outside of the nucleus in the cytoplasm, the jellylike fluid of the cell in which the organelles float. While Margulis was a master’s student at the University of Wisconsin, she and one of her professors, Hans Ris, had talked about the implications of the DNA in the cytoplasm. No one knew why DNA should be in the cytoplasm nor for sure that it was there at all, and yet the mere possibility was as intriguing as a secret passage in a cave. Margulis and Ris did not yet have enough observations to require explanation, and yet they wondered what those they did have might mean. Margulis’s discussions with Ris were interesting enough that she wanted to study cytoplasmic DNA for her PhD thesis at the University of California, Berkeley. Studying a potentially nonexistent thing for a PhD project is generally frowned upon (note the lack of funding for Bigfoot research). Her advisors objected but she persisted, a persistence for which she found herself soon, she thought, rewarded. A year later, in 1961, Margulis found what she thought to be evidence of DNA in the chloroplasts of Euglena, a green protist. Margulis presented the results the same year at the meetings of the Society of Protozoologists. The findings were still preliminary but merited mention on a list of the presentations from the meetings of “more than routine significance.” The Euglena results were a narrow opening into the story of cells, and so Margulis started to try to move some rocks at the cave entrance in order that she might break trough.

The results of Margulis’s Euglena experiments suggested the presence of DNA in the chloroplasts within cytoplasm, but were not proof positive. Then in 1963, three years after Margulis had begun her PhD thesis, Hans Ris and W. S. Plaut (her former advisor at Wisconsin) discovered DNA in chloroplasts of Chlamydamonas. In a picture in their published paper, the stained DNA appear as three white round patches against the darker background of the cell. Like all round shapes on a dark background, the patches look like planets or stars. The big white spot of the nucleus’s DNA is at the center, and on either side, as though orbiting, are two smaller forms, the chloroplasts each white with the density of DNA. At that time, there was no accepted explanation for why DNA would be in the chloroplast or more generally anywhere outside of the nucleus. Ris and Plaut, however, noted that the DNA in the chloroplast bore some coarse resemblance to the DNA in some bacteria. Ris and Plaut went on to notice other similarities between chloroplasts and bacteria in general and with blue/green algae more specifically. The chloroplast, like blue‐green algae, has a double membrane that surrounds it, a kind of wall within the bigger wall of the cell. Both contain a similarly organized photosynthetic apparatus through which light is converted to food. Both contain ribosomes. The question then became whether such similarities were more than coincidence and if so to what to attribute them. Ris and Plaut had an idea. They argued that perhaps these similarities were no coincidence. Perhaps, as a marginalized Russian scientist (to whom we will return) had suggested sixty years prior, and as Margulis had raised as a possibility at the Protozoology meeting, chloroplasts are blue green algae that were incorporated into another cell and were living in a symbiosis. Plant cells and the cells of other green eukaryotes (such as Euglena and Chlamydamonas) were actually composed, they were arguing, of two species. Ris and Plaut concluded the article by noting that with the demonstration of the similarities between chloroplasts and “free living organisms, endosymbiosis must again be considered seriously as a possible evolutionary step in the origin of complex cells systems,” like plants or even humans.

In 1963, with exciting discoveries seemingly close at hand, Margulis left, with her husband and son, for her husband’s new job in Massachusetts. She had not yet finished her PhD and was working with a difficult PhD advisor who “graduated almost no one.” She did not file her PhD for another two years and, in the meantime and afterward, was working a part time job at Brandeis University to pay the bills. She and her husband would soon divorce and she would find herself taking care of her two sons largely on her own while working a short‐term job. These were not good circumstances for developing theory, but Margulis was captivated by her work. She wanted badly to continue working on the ideas of endosymbiosis. She would soon propose a new vision of the entire history of life, through the lens of endosymbiosis. The term endosymbiosis (endo for inside) referred to the presence of one symbiotic partner (here the chloroplast) inside the other cell itself, living in a symbiotic relationship. At that time, the living world was divided into four kingdoms. Three of the kingdoms, the animals, the plants, and the protists were eukaryotes. Eukaryotes possess a nucleus and organelles (tiny organs) cloaked in membranes. Of the three eukaryote kingdoms, the plants differed in containing an addition organelle—chloroplasts for harnessing light. The fourth kingdom, and the only kingdom of prokaryotes, was that of the bacteria. The bacteria lacked a nucleus, organelles (such as the mitochondria and chloroplasts) with membranes, and true cilia and flagella. The bacteria were, in general, far simpler cells and so, as is often the case with simpler organisms, believed

to be primitive, perhaps not unlike the first cells. An evolutionary story that united these four kingdoms had to explain both their differences and their similarities. If one assumed the Monera were the primitive ancestors, one then needed to ttained a nucleus, mitochondrian and flagella and cilia. For plants, there was then the additional question of the origin of the chloroplast. There were few obvious intermediate life forms, few steps preserved in the fossil record. To many, the problem seemed intractable. Margulis was moving toward a theory that would explain not just the DNA in chloroplasts, but the relationships among the four kingdoms of life. She had worked for her thesis on the autonomy of chloroplasts in Euglena, but that work had offered her a window into a broader theory. It was a theory based on simple Leeuwenhoek‐like observations coupled with reading the work of earlier, relatively ignored scientists with similar ideas. As she worked at Brandeis, her ideas began to crystallize. They would lead her to a conclusion that seemed, to her, almost inevitable. She began to believe not only that the chloroplasts in plant cells were bacteria, but also that the mitochondria in all eukaryote cells were bacteria, and then even that the cilia and flagella (and later also the centrioles that hold the chromosomes in place during cell division), were ancient bacteria. All of these parts of eukaryotic cells, Margulis was to argue, arose through symbioses, events in which one cell engulfed another and then the two cells, one inside, one surrounding, took advantage of each others’ respective life skills. Margulis was casting the entire history of the evolution of eukaryotic life in the context of symbiosis. Our lives, the lives of all animals and plants, were thus fused lives, chimera composed of multiple species. As Margulis would later put it, “any living being larger than a bacterium is a superorganism,” a collective that evolved through the bodily fusion of two or more earlier cells. It was a revolutionary set of ideas. We were, she argued, inhabited by multitudes without which we would die, without which we did not exist at all. Margulis began to think of humans and all other animals as neither animal nor bacteria but instead something in between. There are incentives to positing outrageous theories as a graduate student, or shortly thereafter—fame, name recognition, controversy. Those incentives balance a huge body of disincentives. In young scientists, big truths and practicality do battle. They must. Practicality would suggest that for a young scientist with children and little job security, a revolutionary theory is a) likely to be wrong, b) unlikely to be believed even if it is right and c) likely to get you ostracized by your peers, denied tenure and a job as wait staff.

Margulis would call these events symbiogenesis, where the genesis refers to the origin of a new species or kind of life through the merger of two or more existing species.With those odds, one has to love a young scientist who decides to go forth with a crazy theory, even if it is wrong. Even wrong ideas, in youth, can be beautiful. Lynn Margulis’s idea was beautiful and maybe even right and so she went forth. She published her first paper on what would soon be called the Serial Endosymbiosis Theory (SET) in 1967. The paper, entitled “Origin of Mitosing Cells” was a pared down version of what was soon to develop into a much broader argument. It would be followed by a slightly bolder paper entitled, “Evolutionary Criteria in Thallophytes: A Radical Alternative,” in which Margulis laid out her theory in more detail. To many, it would seem that the radical alternative was not the theory but rather Margulis. In 1969, divorced from her first husband, while still working on what amounted to a part‐time job at Brandeis University in Massachusetts and pregnant with her daughter Jennifer, Lynn Margulis was at home for long periods. In her telling, this home stay offered the advantage of many hours of uninterrupted thoughts. Those thoughts in turn led to a more expanded version of her ideas on mitochondria and chloroplasts, and ultimately ideas about life itself. The more Margulis looked, the more it seemed that the world was decomposing into parts, each with a separate history. Her body and her daughter’s body were not single things; they were separate but linked in a kind of symbiosis. Each of their bodies on its own was also a kind of community or maybe even a commune, lives with disparate interests and separate histories, commingling for years to achieve their separate goals. Well into her pregnancy, it seemed as if at the heart of life there were symbioses. For two centuries, male biologists had emphasized the role of struggle, competition, and war in evolution. Lynn Margulis was offering a very different view. The ideas flowed. She wrote an entire book and then more. There were hundreds and hundreds of pages of thoughts. When she entered college, Lynn had wanted to be a writer of fiction. Here she found herself instead writing a story of life so new that many thought it was fiction. She wrote quickly to meet a deadline a publisher had given her. She paid for drawings for the book herself. She eventually pared back the manuscript, culled it into a reasonable‐length book and, half‐sure of greatness in these ideas, sent the book to New York, to the academic press with whom, during the process of writing at nights, she obtained a contract but no advance. She was alternately thrilled and worried. For whole days, worry would win out. Then she would write some more and think again that she was right, that she had for the first time in history seen clearly the history of life. The publisher did not write back, not for months. Finally, there was word, a rejection letter. It offered no explanation and was unsigned. Lynn would later learn that other scientists’ critiques of the manuscript had been so harsh that the publisher cancelled the project. The critiques had been so harsh that the publisher had initially not even bothered to let her know. Her first paper on endosymbiosis, finally published in 1967, had also been rejected, in that case twenty times en route to publication. She may have known by then that hers was to be a battle uphill, but what she could not have yet known was that it was a very long hill. Lynn’s daughter was born. Her own symbioses became more complex. Her two sons were getting older. Her ex‐husband, was contributing almost nothing to childcare. This was not a time to pursue wild ideas. It was a time for stable projects that would produce publishable work and grant funds. It was a time to convince her new department head at Boston University, where she was by then employed, that she deserved her job. But this was not Lynn Margulis’s way. It never would be. She worked even harder on the manuscript, refined her ideas and stayed up later and later to rewrite and reconsider. She had plenty of time to water down her new theory. Instead, she again made it bolder.

Lynn Margulis came to the conclusion that key organs of eukaryote cells (mitochondria, chloroplasts, and flagella, cilia and centrioles) were ancient bacteria, engulfed by another cell, based on several pieces of evidence. As already mentioned, it had recently been discovered that mitochondria and chloroplasts had DNA (most of “our” DNA is in our cells’ nuclei). Other biologists had suggested mitochondria and chloroplasts “looked like” bacteria. Margulis found such similarities compelling. The evidence for cilia and flagella was more preliminary. Cilia, flagella, and centrioles are all composed of an array of fibers called microtubules, arranged in a pattern very similar to fiber inside a certain kind of bacteria, spirochetes. Finally, symbiotic microbes living in relationships such as this, were very common elsewhere, in the cells of insects, in amoeba, and green ciliates, etc… To Margulis, the grand theory was thus simple; the history of life’s most important events was a series of mergers.

Yet this was not the traditional story, the Darwinian story, of competition and evolution by slow, accumulated, change. The story, she would argue, began with a low‐oxygen world. In that world, the first photosynthetic bacteria produced oxygen. With time, other bacteria evolved to use oxygen in respiration. A single cell, already possessing a nucleus but not yet the machinery (a mitochondrian) for using oxygen, then engulfed one of those respiring bacteria, which would become the mitochondrian.lxxiv The two species were more successful together than apart, and so the relationship continued. One individual of that new, combined species then engulfed a photosynthetic bacteria, a cyanobacteria, and became capable not only of respiration but also of photosynthesis. From that second event would descend, ultimately, the plants. Somewhere along the line, another bacterium, perhaps a coil‐shaped spirochete, had also been engulfed, which formed the cilia and flagella and perhaps even the centrioles52 within eukaryotic cells. It was this last event that helped shape the functioning of the nucleus, of cell division and even of cell mobiThese steps were the major events in the evolution of life. All the rest was icing. In each case, the bacteria that had been consumed began to lose some of those features now unnecessary inside its host. The host, in turn, did the same. It began to rely on the cell it had incompletely consumed to turn food energy into usable energy. Soon, without its guest the host could not survive, and without its host neither could the guest. From those three original events, every protist, plant and animal and more generally every eukaryote would descend. It was, as Margulis saw it, our defining series of moments. It took a large body of accumulated evidence for Margulis to finalize her ideas of serial endosymbiosis. Yet, as often seems the case with big discoveries, other researchers had come to similar ideas with less evidence. They had been speculating even more wildly with even fewer facts. The stories of these scientists, had Margulis cared to look, were often not very promising models for hat she would continue to face.

In the late 1800s, lichens had been hypothesized to be not one, but multiple organisms. They were speculated (as we now know to be the case) to be a symbiosis between an algae and a fungus. The theory was controversial, but also exciting. If lichens were really the combined result of multiple interacting species, perhaps such arrangements were common in nature. It would not take long for a few wild scientists (there are always a few) to suggest as much. The Russian scientist Konstantin S. Merezhkovsky argued in 1909 that the pale green chloroplasts in plant cells evolved from bacteria ingested by plant ancestors.lxxv To Merezhkovsky, if lichens were composed of multiple creatures, then why not trees? The green of forests was not plant matter at all, Merezhovsky would contend, but instead the ancient cyanobacteria held up by trees in every leaf, like so many guests standing in the windows of a house, candles in their hands. These were the torches that lit life. Bacteria, hitching a ride and providing some sugar in return. To the bacteria in plant cells we might owe everything, he speculated. Merezhovksy’s idea, expressed as a footnote to his broader work, had initially spurred Ris and then through Ris, Margulis’s thinking on chloroplasts. In Russia, Merezhkovsky was largely alone in his theorylxxvi. Similar ideas had emerged elsewhere, however. Ivan Wallin was born in 1883 was born in Stanton, Ohio, to Swedish parents. He would make his way to a professorship position at the University of Colorado, Boulder where, among other things, he taught anatomy. There, in the name of education, he stood students before a cadaver and asked them questions. When they were wrong, he whacked them (the students, not the cadaver) in the chest. The students, right or wrong, whacked or not, then helped Wallin build his cabin, not far from Boulder. In the cabin, Wallin took the students’ money in poker and drank. Wallin did much of his research in a shed behind the University of Colorado, Boulder’s classrooms or in the cabin his students built. It was in these makeshift facilities that, in looking into cells, he discovered ‐‐ he thought ‐‐ that mitochondria were still bacteria capable of life on their own. He went so far as to claim that he could grow mitochondria outside of the cell in which they were found (a claim which Margulis would also, at least initially, offer). Wallin, like Merezhkovsky, put forth ideas very similar to those that Margulis would later advocate. The ideas were less refined, but Wallin and Merezhkovsky were working in earlier times, when our understanding of the workings of cells was also less refined. No one believed Wallin. He was criticized so harshly that he eventually quit research at the age of 40. Many thousands of miles away Merezhkovsky was also marginalized and then forgotten. In thinking about the likes of Wallin, Merezhovksy, and later Margulis, Richard Klein and Arthur Cronquist, two scientists at the New York Botanical Garden, would call the idea that chloroplasts were symbionts, a bad penny that “has been circulating for a long time.lxxvii”Clearly, the implication was that Margulis ought to drop the dirty, hand‐me‐down. Instead, Margulis, with the insights of new research on the workings of cells and the structure of DNA, would build on Wallin and Merezhovsky. If she were right, her role could be to construct a broader theory and gain acceptance for it, much in the way that Galileo brought Copernicus’s revolution to the world. Galileo had nearly lost his head. Margulis bent hers down and harged. She was, as she would later say in an interview, “not afraid of anything.

The scenes that Lynn envisioned in our early history, of fusing cells, were not unlike the meeting of continents. The continents fused to create something novel, a supercontinent (akin to her superorganism). In the model of the continents, there was also a model of discovery that might have seemed similar to Lynn, had she noticed. In the 1950s, 500 years after Anton Kirchner had initially suggested that the continents moved about like plates, Alfred Wegener reframed the same hypothesis. Wegener had more evidence than did his predecessor. He could match up the places where coal was found and suggest that those were the areas of ancient forests. He could match up related species on opposite sides of the sea. He could compare the rocks of Morocco and their ancient kin in Connecticut. He saw patterns that seemed to imply that pieces of the Earth’s crust that were long considered joined had once been separate, just as pieces of our cells might have once lived free. As late as 1970 (the year Margulis was made Associate Professor at the University of Boston), not all reasonable scientists believed in plate tectonics. There were patterns, but no sense of what shoved the continents together or pushed them apart. Scientists would believe the theory only when Wegener’s advocacy combined with a more mechanistic theory of the underlying process. When deep‐sea rifts were discovered, the process became apparent. Where continents were pushed together, mountains formed or the crust melted. Where they pulled apart, the Earth was hot with the splitting of rock. Earlier scientists had suggested that mitochondria and chloroplasts were endosymbionts. Margulis believed that she had elaborated the mechanisms by which those endosymbioses evolved. But what Lynn Margulis ultimately needed, if she was to be believed by more than a few other scientists, were more details of the process of how endosymbiosis arose. She needed the cellular equivalent of magma, evidence of the collision. She needed concrete evidence because what she was proposing was more revolutionary than the idea that the continents, long fixed, moved. She was proposing that our bodies were made of multiple bodies, that something as deep as our identity was divided along ancient lines. Margulis’s book on her new theory was finally published in 1971. It was greeted by unceremoniouscriticism, even hate mail. One of the more supportive reviewers wrote, “Readers will find this book sprawling, stimulating, irritating and challenging but they will have difficulty ignoring it.” Her ideas were too bold and widely ranging. She garnered a few supporters, but, it seemed, precious few. She went ahead on the strength of her convictions. Evolution was meant to be frugal and consistent. Her hypotheses were complex and idiosyncratic. They were not testable. Her critics would argue against her ideas, in forum after forum, but she, like her book, could not be ignored.

Slowly, she would gather something of a following, nothing universal and unanimous, but enough to keep her going. By 1970, a review article by Peter Raven,53 then at Stanford University, suggested that her Serial Endosymbiosis Theory was widely believed and that the critics were louder than their numbers. Despite whatever support Margulis had, the fights continued and so did Margulis. Margulis was, with her ideas, stubborn. Richard Dawkins, one of the living granddaddies of evolution, has framed Lynn’s stubbornness negatively. “She would not change her mind,” even, he would go on to imply, when the evidence was overwhelming (Dawkins in saying this was, of course, quick to highlight his own willingness to listen). Others saw her stubbornness as a necessary reality, what one must have when one is right and everyone else disagrees. Scientists are supposed to listen. They are supposed to constantly consider and reconsider their ideas. They are supposed to respond to criticism. Yet criticism will come regardless of whether one is right or wrong. Lynn Margulis had to listen well enough to be bent by the tide when she was wrong, but not so limply that she would bend even when she was right. Scientists before her had advocated the symbiotic origin of mitochondria and chloroplasts. They had both bent to the tide. She would not.

continue reading in Every Living Thing

In part because of my grandfather I have always felt a responsibility to answer questions people ask about science. This year, I decided I would make this responsibility more conscious. I would try to focus much of my writing on answering questions that came up in my daily life, questions that I am responsible for because I am a scientist. It was a sort of New Year’s resolution. My other resolution was to write shorter articles.

1— Sitting around enjoying a glass of wine with my family and our friends Ari Lit and Michelle Trautwein, Ari asked, Hey dude, why do we drink alcohol? Do monkeys drink alcohol? This led me to think about the big story of alcohol and, in as much, to write a whole series about our complex relationship with the yeasts that, as waste, produce our favorite drinks. It ended up becoming a forty thousand word online series, about alcohol, civilization and yeast. So much for the resolution to write short articles. Also, I forgot to check on the monkeys.

2— My favorite questions tend to come from kids and earnest parents. This year at my daughter’s school, every third student and then every other students and then, jeez, almost every student seemed to have lice. Parents asked me, “what should we do about lice?” This was a follow-up to an article I had written years prior in response to a similar query. I was able to tell the story of how the louse problem (or success, depending on your perspective) came to be, over the last million years. But I failed to really answer what a parent should do if their kid gets lice. It turns out parents whose kids have lice don’t want to hear about ancient hominids and their lice. Go figure.

Continue reading at Scientific American

When a true genius appears in this world, you may know him by this sign, that the dunces are all in confederacy against him. – Jonathan Swift

(excerpted–and updated–from Every Living Thing in honor of Carl Woese who died on 12/30/2012. Thank you Carl Woese. Thank you  for rearranging the evolutionary tree, that we might see, even if we just as quickly forget, our place in things.)

One day in Illinois, Carl Woese decided that he would like to understand how all of the organisms around him, the birds, trees, bugs, humans and most importantly, the microbes, were related. He had no good reason to believe he could do such a thing and little hope of much support in the endeavor. It was, at the time, impossible. As R. Y. Stanier said in 1970, speculation about evolutionary history was, “a relatively harmless habit, like eating peanuts, unless it assumes the form of an obsession; then it becomes a vice.lxxx” To many, such evolutionary “speculation” was both unwarranted and intellectually dangerous, but, as would soon become clear, not to Carl Woese.

Carl Woese did not want to speculate. He would instead try to invent a method of seeing evolutionary history, a kind of microscope through which to visualize relationships among species. Carl Woese thought that with this new method he might delve into the history of life and understand  the broadest patterns of evolutionary change. Mark Twain said that a man with a new idea is a crank until he succeeds. Twain does not need to state the related assertion, that a man with a new idea who never succeeds is forever a crank.

Carl Woese was serious about science from an early age. For him “there was no other way to cope with (his) world.” For Woese, even as a young boy, there seemed to be “two worlds, that of nature and that of people. The first was vast, wonderful, inscrutable, frightening, exciting, enticing, always moving, but nevertheless with an immutable consistency—it was a never failing touchstone of truth. The world of people was the opposite; inconsistent, ever arbitrary, full of contradiction, anthropomorphizing, untrustworthy—almost devoid of truth.lxxxi54” Woese was called to a quiet life of science and inquiry. He chose microbiology, but could have been an astronomer or a physicist. What was important was the search for truths.

Like Linnaeus, Leeuwenhoek and many others, Carl Woese started his career at the periphery of his scientific field. Trained as a physicist for his undergraduate degree at Amherst College and then as a biophysicist for his doctorate at Yale University, he studied the physics of the cell, the bump and grind of microscopic machinery. He worked at General Electric and then the Pasteur Institute before being hired as a Professor at the University of Illinois in 1964. At Illinois, he studied ribosomal RNA. Watson and Crick had decoded the language of DNA, but Woese was interested in translation, the process in the ribosome by which a specific RNA is converted into protein and hence function. Woese perceived that at that moment, with DNA deciphered, it “was the time to start thinking about the evolution of the cell55 and its macromolecular componentry.lxxxii” It was time to start thinking about the deep evolution of life. Woese felt that “a slight diversion” was in order from his main research, in order to address these questions. That diversion occupied his days.

To make an evolutionary tree of all life, including microbial life, one would need to study an attribute of that life that changed slowly and hence allow the differences between very old lineages to be compared. The building blocks that make up the ribosome, your ribosome, my ribosome, every ribosome, seemed to Woese like a good candidate. The ribosome is composed of protein and then also, and this is the key, a special kind of RNA, ribosomal RNA (rRNA). The rRNA in the ribosome interacts with the messenger RNA to convert it to protein. In every living cell, rRNA performs nearly exactly the same task. rRNA aids in the translation of rRNA to protein, and Woese hoped to translate the history of life as recorded in rRNA.

Ribosomal RNA is a foundation upon which evolution’s building stands. Change it a little and the building begins to creak. Change it a lot, and it will fall. In the same way that all wheels are round and those that are not function poorly, there is but one good way to be an rRNA molecule, one good way to keep the machinery of life rolling. And so, unlike many genes, the genes of ribosomal RNA cannot change much, through time or species, over millions or even billions of years. As DNA is copied by cells’ tiny chemical monks, the DNA that codes for ribosomal RNA must be copied near perfectly, and so too the rRNA itself. Consequently, the differences in the ribosomal ll. Your ribosomal RNAs are like mine. Mine are like a squirrel’s. A squirrel’s ribosomal RNAs are very similar to a tree’s. The monks in cells make mistakes in copying the genes for ribosomal RNA, but they make few. Such mistakes accumulate very slowly through time.

Woese’s idea of understanding the evolution of a group of organisms based on some feature of their physical structure (such as their RNA structure) was not novel. Other biologists were doing similar work with proteins. The longer two proteins were separated in evolutionary time, the more different they would be. Such  work rested on the work that had been done for centuries–nearly since Linnaeus–comparing external features of plants and animals. If the sex organs are more different, Linnaeus almost but didn’t say, two species had been diverging for more time. By looking at differences and similarities, it was becoming clear, one might assemble life’s  evolutionary tree, or at least parts of the tree.

When most biologists imagined an evolutionary tree, however, they thought about big species—tigers and tiger lilies. Woese imagined that microbes could be mapped onto a tree, put on their right branch. He wanted to “move the evolutionary discussion away from animals and plants and onto the molecular level, where it belonged in the 20th century.lxxxiii” and he thought it could be done with rRNA in which he saw grand possibilities. Differences in rRNA, Woese posited, meant evolutionary differences in time. The more different two species were in their rRNA, the longer they had been separate. Leave two monks in two different dimly lit rooms to copy a text. Let them make each subsequent copy based on the copy before it. With time, the mistakes they make will accumulate. The two sets of copies will diverge. If one knew the rate at which the monks made mistakes, he could look at the final products, the newest copies, and by comparing their differences estimate how long the two monks had been separately working.

Woese wanted to know, when different types of organisms diverged, how long different lineages had been separated in their proverbial rooms copying the text. He also wanted to know what that first text looked like, to look into the recesses of time and find the first life. He began to compare the ribosomal RNA of different species in order to construct a microbial evolutionary tree. Woese began optimistically, believing that “only technological problems seemed to stand in (the) way: growing the various organisms and doing so in a low phosphate, radioactive medium; tweaking the … method to fit needs; finding needed help; and so on.” Those technological challenges would be formidable. He was, as a side project, initiating an entirely new field of inquiry using a method no one else had used (and that no one else would use for years). If he were right, his method would, like the microscope or the telescope, make visible what had long been unseen. It as far wmore likely that he would be wrong. These are also the basic components of DNA, except Uracil is replaced by Thymine. The differences between you and a microbe are nearly entirely due simply to the arrangement of those nucleotides. Each three letter stretch of DNA codes for a particular amino acid, such that if one knows where to start reading on a stretch of DNA, one can read out the amino acids that will be produced. 58 An rRNA with the code AGCUAAACG would be fragmented into two pieces, AG and then CUAAACG. If the rRNA was then split at its Adenines it would be divided into more pieces, A and G from the AG and then CUA, A, A, and then CG from the remaining section. And so on.

At the outset, several things separated Woese’s work from everybody else’s. First, the rRNA analyses took far, far, more time than the existing protein analyses and required unique skills, such that only Woese could do them. Second, no one, including Woese’s peers and department head, knew why on Earth he would do them.lxxxiv Further, the questions Woese wanted to get at, the evolutionary tree of microbial life or even of life more generally were viewed, as Woese’s colleagues were to make clear, as unanswerable. Woese’s colleagues wondered what he was trying to do. He needed to focus on work that would yield something. He seemed obsessed, even bothered. His willingness to participate in the niceties of daily society was dissolving. Biologists can, in focusing on a narrow piece of the world, focus so intensely that everything else seems irrelevant. The talk at the coffee pot is ridiculous banter, informal greetings a waste of time. Departmental meetings, advising students, emptying one’s garbage all become things left to someone else, someone not so involved. This is the kind of intensity that biologists and scientists, more generally, both fear and love. Scientists obsessed like this, if right, can be vindicated royally. Imagine, they might say, how much less he would have done had he brushed his hair more often. But scientists obsessed like this on a research question that does not lead to discovery are running very quickly into oblivion, very quickly into drink, spirituality, madness or all of the above.

Woese toiled. There is no other word for it. Ribosomal RNA like all RNA is made up of a simple alphabet of nucleotides, Adenines, Guanines, Cytosines and Uracils57. Woese had to decode tiny sections of rRNA at a time. He had to do it through a method that ultimately converted the rRNA code into black smudges on photo paper. He would fragment segments of rRNA at each Guanine nucleotide.58 Each of the resulting fragments was then fragmented again at each of the other types of nucleotides, systematically, monotonously. Woese could then photograph the distribution resulting fragments and, like a code breaker, work backward, letter by letter, to what t have been. As he split the rRNA into its bits, there was a sense of discovery every day in the lab. The photographs of the dissected bits of rRNA were beautiful, like abstract paintings, each one different and each one representative of some part of the evolutionary tree. Yet the tedium was overwhelming, something like trying to read a copy of Shakespeare left on the moon using a telescope. The beauty of the text, the book of life, could be missed in the difficulty of the process at hand. Woese’s lab and office piled thick with photo sheets for RNA comparisons. His shelves were soon covered with yellow Kodak boxes to hold the film. Light boxes were brought in from who knows where and each one always had a film on it. His chairs were taken over and then his desk and then the floor. This went on for weeks, months and then years, without an answer, without a revolution, without a natural order. It just went on. He went home some days saying to himself, “Woese, you have destroyed your mind again today.lxxxv” He spent every day in front of the film sheets, brooding over patterns. After ten years of toil, he had catalogued just sixty bacterial species, sixty of the hundreds of thousands of species thought to exist.59 He was forty seven. He had written essentially no papers on his results. He had told few about what he was doing. He had taught no one his methods. He was the only one in the world who could decode rRNA and in doing so, he hoped, reveal life’s story. Like Leeuwenhoek with his microscope, he was alone.

It was then that one of Woese’s colleagues threw him a rope, albeit one that neither appreciated the importance of at that moment. Woese’s colleague Ralph Wolfe wondered if Woese would work with him on a separate project. Wolfe thought, contrary to the public opinion, that Woese was making exciting progress, that the two of them together might make more progress on one particular group of organisms. Wolfe was the much better known of the two scientists and might have felt himself something of a mentor. Wolfe asked Woese if he would “run the rRNA” of a group of methane producing bacteria he was working on, a group of life forms found in sewer sludge and related environments. Woese had, several years earlier, talked with Wolfe about looking at some of these methanogens.lxxxvi Wolfe had not yet been able to grow them in the lab, a necessity for the quantity of material Woese needed, but by the beginning of 1976, he could.lxxxvii Wolfe could by then “grow a kilogram of methanogens” in bottles pressurized with CO2.lxxxviii These methanogens, Wolfe told Woese, were united by their chemistry (they all produce methane as a byproduct of their metabolism) and unique enzymes and seemed very different from other bacteria.60 No one knew quite what kind of bacteria they were related to. One possibility was that the methanogens were not really related to each other at all, but had simply evolved convergent traits to deal with their particular lifestyle (For many of the initial samples, that lifestyle was living in sewage. One of the first species sequenced was Methanobacterium ruminatum, named for the cow guts it calls home.). The other possibility was that they were a unique evolutionary group. It was a perfect challenge for Woese.

By the time that Wolfe offered Woese his specimens (first a species with the Linnaean name of Methanobacterium thermoautotrophicum, which, if you read Latin, says it all and then some), Woese had already constructed, species by species, a tree of life. It was his private tree based, at that time, on tens of microbial species. He had shown few others, or maybe he had shown no one at all. It was there, in his office, in yellow Kodak boxes, arranged in a way clear only to him. Woese would turn on his record player, put on an old jazz record and marvel at what he had revealed. He was close to seeing the history of early life. He began, again letter by letter, to analyze Wolfe’s samples. He looked at the negatives in an upright light box, with the lights in the room off. He would look at the signs of the nucleotides, his own face by lit by the light passing through the photos of rRNA nucleotides. He arranged the negatives and organized them and then translated. Almost immediately, what he saw was surprising. After the first step, the “signatures were remarkably distinct” from those of any bacteria he had yet looked at. Each of the first nucleotide signatures he was accustomed to seeing in all bacteria, was missing. When he did the more detailed work, to actually decode, nucleotide by nucleotide, the sequence of the RNA, the results continued to be surprising. Now he saw some RNA sequences that he associated with bacteria, but others were missing. It was as if the RNA were from something that was half bacteria, half eukaryote. As Woese would later say in an interview, “by this point one stops wondering what they have done wrong and begins to ask what this all means.” He had an idea, but before he said anything he repeated the whole process from scratch, a second, and then a third, and then even more times.lxxxix The results were the same. The samples were not, Woese thought, bacteria, nor were they eukaryotes,xc but instead something else entirely, some new form of life. Now here was the kind of discovery Woese had worked for all those years. Woese has never been prone to outbursts, but if he ever did yell with joy and dance in his office of rRNA and jazz, these were the days. Woese rushed to find his postdoctoral fellow, George Fox, to “share (his) out‐of‐biology experience” with someone. Fox was skeptical so Woese ran to tell Wolfe, saying, as Wolfe remembers, “Wolfe, these methanogens are not bacteria.” Wolfe told Woese they had to be. “Of course they are bacteria ; they look like bacteria, he would later remember saying, “Now, calm down; come out of orbit.xci”

The next step was to examine other methanogens and other species that were morphologically similar to the methanogens. By the end of the year, the team, led by Woese, had decoded the gene sequences of the RNA of five other methanogens. More were in the works, but the result was getting more and more clear. The methanogens were very different. Once “a second methanogen was characterized and showed itself to be related to the first, there was no doubt” that they had found a new form of life, Woese would later say. This form of life had been different from the others, bacteria and Eukaryotes, a very long time. Understanding how these methanogens related to other kinds of life was, it seemed to Woese, a big discovery. Woese later wrote of the moment, “Darwin had long ago said that there would come a day when there would be very fairly true genealogical trees of each great kingdom of nature. Perhaps that day was at hand!”

Woese would immediately write two papers about his new finds. One paper was written sed on the new kind of microbe.61 The other paper, however, written with George Fox, Wolfe’s postdoc, was the one that would prove more controversial xcii. The first place that anyone saw the results of the paper with Fox was in the newspapers. Woese was 49. He had worked without recognition for decades, but that was to change this day. The news media saw an advance copy of the edition of the Proceedings of the National Academy of Sciences in which the Woese and Fox article was to appear. The media found the result tantalizing. The New York Times ran the headline, “Scientists Discover a Form of Life That Predates Higher Organisms,” on page 1, November 2, 1977. The first lines of the article summed up the outrageousness of what the scientific article was about to claim, that scientists had described a “third kingdom of living material composed of ancestral cells that abhor oxygen, digest carbon dioxide and produce methane.” Woese was thrilled with the popular attention for the find, but his mood would change. Woese had discovered, or he so argued, an entirely new domain of life. The monks in these single cells, however faithful to the ancient text, had long, long, been separate from those of all others. Woese and Fox went on to argue that there are three major divisions of life: one is bacteria, one is the lump of flesh and plant that includes all eukaryotes. The third is Archaea,62 the group that Woese, Wolfe and their labs had just discovered, essentially, in specimen jars in their office In Woese’s scheme, not only are humans a tiny branch on the tree of life, but so are mammals, so are vertebrates, so are all other animals. Most of life, from an evolutionary perspective, is microbial‐everything else a minor branch, a fit of evolutionary whimsy. This is what Woese has gone on to contend to this date. To the extent that he changed his opinion, it was only to become even bolder in his statements, to argue, through new results, that he could see even further back in time.

Woese did not think personality was part of science, that scientists themselves are an important part of how science should be recorded. As a consequence, we have few direct views into what Woese would think in those years in which he was buried, religiously, in his office, working. Those views  we do have, though, tell miles. The day the announcement of Woese and Wolfe’s finding came out in the newspaper, November 3rd, 1977, Woese was thrilled. He thought the revolution had begun. He asked a woman at a fast food restaurant if she knew who he was. She looked at him, thought for a while and struggled for the answer. He prompted her by mentioning his discovery. She then realized, oh yeah, “You’re Bob’s dad.xciii” He was, of course, but Woese had thought deeply, without whimsy or humour, that his discovery would be big enough that the woman at the checkout line in fast‐food counter would know who he was. He was wrong. It was, in many other ways, not Woese’s day. What followed was angry; hate mail, promises of academic oblivion. Both Woese and the relative innocent in this enterprise, Wolfe, would be attacked. Ralph Wolfe recalled that: “One Nobel Prize winner, Salvador Luria, called me and said, ‘Ralph, you’re going to ruin your career. You’ve got to disassociate yourself from this nonsense!xciv’ Wolfe “wanted to crawl under something and hide.xcv” He did not disassociate himself (though he did take a vacation) but nearly everyone else did. The criticism of Woese was never very public. It was, the “talk of corridors.” Woese was “itching for (his critics) to come after (him) in print. But none of them would!” So Woese kept working, knowing that many of his colleagues quietly doubted him. Woese thought the “matter would resolve scientifically.” There were reasons to be skeptical. The question Woese proposed to address, the relatedness of the deepest lineages of life, was still seen as too deep in the early time to answer. If Leeuwenhoek looked up God’s dress, Woese was trying something bolder, more inappropriate. He was trying to do so with a new ribosomal RNA method that no one else was using. No one else was familiar with it. No one else had confidence in it. In short, Woese had proposed to have answered an unanswerable question with an unlikely and unknown method. Even for those who knew his method, it seemed, well, insufficient. Woese had proposed a new domain of life and a reordering of life’s tree to put man, all animals and plants, as minor players circling a microbial Earth. He had, late at night, with charcoal on the cave walls of science, sketched a tree. At its base was a microbe, perhaps something like an Archaean. From that microbe would descend three great lineages, the Archaea, the Bacteria and the Eukaryotes. Within the eukaryote branch, the most recent of the tree, were all the fungi, all the plants, all the protists and all the animals. All vertebrates were a twig 135 branch on the small, recent, branch of the animals. We were in this big tree, not worth drawing, too mall a twig to make it into the big story, which was, in nearly its entirety, about microbes. Woese went back to science, back to work on Archaea, for thirty years. He had made an extraordinary claim and despite everything, he still believed in his work. He went back to his light table and went through sequences one by one. He added other microbial lineages to his analyses. He studied, along with a growing number of other scientists, other unique features of the Archaea. They had different lipids (fats). They had different metabolisms. If people thought him a bit of a crank before, this would not help things. He buried himself in his discovery. Since Leeuwenhoek, there were the microscopic things and the big things. The big things were the more important, the main story, and then the microbes, the back‐story. Woese was trying to turn the back‐story into the plot.

Woese was like Leeuwenhoek. He could see something others had not seen. He could see it because of his method. Like Leeuwenhoek, he was confident. What remained to be seen was, if, like e was right.

***

Vindication for big speculative ideas comes slowly. It must trickle in on the back of new results. It comes, paper after paper, until at some undefined point, what was once heretical has become the status quo. Copernicus published, posthumously or nearly so, his treatise suggesting that the Earth and other planets circle the sun. It would take generations for this idea to become fully accepted. A few believed easily, but one of those, Galileo, went on trial for that belief and another, Bruno, was burned at the stake. Yet, it was not long before average citizens looked up and imagined the sun as stationary, the Earth as moving, to the extent that they looked up at all. If you now open an introductory college biology book, you will, more likely than not, find that Carl Woese is mentioned alongside the idea that there are three main divisions of life, the Archaea, the Bacteria and the Eukaryotes. We now accept as near law Woese’s new divisions of life. It is now presented in introductory biology class by tired professors who flash the information up on the board early in the morning, read through it, as they gaze into groups of somnambulant students, less worried about their place relative to the Archaea than about what they will do that evening, who the girl with the long hair is in front of them, or why their professor has now worn the same shirt three lectures in a row. But don’t be confused. Woese’s result was both right and revolutionary. It’s just that we quickly grow used to revolutions once they happen; the idea that the Earth circles the sun is now, on most days, unremarkable, so too Woese’s revolutionary change, one that altered  our place in the living world, permanently.

(story continued in Every Living Thing)

Image provided courtesy of of University of Illinois Archives. 

Brother of the blowfly… no one gets to heaven without going through you first. –Yusef Komunyakaa

Sixteen years ago, my wife and I, along with our friend Audrey were standing outside a guesthouse near the towns of Boabeng and Fiema in Ghana when Kojo, a young boy, approached on a bicycle. His whole shadow rose and fell with each turn of the crooked front wheel. Behind him were miles of fields and the dust-dry trees of forest. He stopped in front of me and opened his hand to reveal a small crumpled note. I unfolded it and read, “My friends, two of my children have died, i.e. the black and white colobus monkeys. Please come, quickly!” The note was signed, “the chief, Nana”

In the conjoined town of Boabeng and Fiema, two species of monkey are considered by many to be living gods—fuzzy masters of the universe. As with any god, the relationships people form to the monkeys are individual. Some treat them with absolute reverence. Others scold them like misbehaving but well-loved children. Then there are the evangelical Christians in the town next door. They sneak into the forest and kill the monkeys both to discourage the worship of false gods and to eat said false gods. Apparently, sacred monkeys taste like chicken.

On this particular day, a taxi had hit and killed two monkeys as they tried to cross the red-dirt road into town. In addition to evangelicals, cars are one of several features of modern West African life with which these sacred monkeys can come into conflict, others being agriculture, logging, and hunger. In Boabeng and Fiema when monkeys die they are buried in simpler versions of the ceremonies reserved for humans. It was one of these funerals to which we had just been invited.

Continue reading at Scientific American

Once the diversity of the microbial world is catalogued… it will make astronomy look like a pitiful science. – Julian Davies

For Neil Armstrong, the giant step for mankind was taken on the moon. For Jeff Leach, it might just be in the colon, at least if he can find the money.

Jeff Leach called me not so long ago to ask me about my colon. Well, that isn’t totally right. He called to tell me about other peoples. Is that worse?

In the colon live trillions of bacteria (though such estimates are guesses as wild as those about the numbers of stars), a universe of planet-sized cells just above the sphincter. These bacteria are important, but uncharted. The most poorly known feature of these beasts is how they vary from one person to the next and why. Your metabolism, immune health, propensity to diabetes and ability to digest seaweed have all, recently, been suggested to depend upon the microbes on or inside you, but on what does the composition of those microbes themselves depend?

This is a version of the belly button mystery I discussed last week—the mystery of what determines just which microbes you have and depend on (or fight). Leach wants to understand what determines the wild life of your colon.

Most readers of Scientific American are aware that their bodies are covered inside and outside with microbes on which his or her life, odor, and much else depend—their cloak of cells. But this consensus is new. In the 1960s Lynn Margulis posited that the mitochondria in our cells and chloroplasts in plant cells were relictual bacteria, evidence of ancient symbioses. She also argued that symbiosis were everywhere, a dominant feature of evolution. She was right on all counts, the founding mother of the microbiome. She was also ignored. Not long after, Carl Woese went into his lab proposing to look at the nucleotides of bacteria to create evolutionary trees of microbes. He was laughed at, but went on to found modern evolutionary biology. Then, in the 1980s, while using LSD and driving around with his girlfriend Kary Mullis had the idea to use the enzymes in an Archaean (a group of microbes that Woese put on a totally unique branch of the tree of life) to amplify DNA and, in essence, produce much more of it for analysis. Together these accomplishments set the stage for the modern field of microbial ecology and evolution. For all of this work, Margulis, Woese and Mullis were regarded as crazy (They were not then, though each of them would ultimately turn to forms of wildness with time. Perhaps when you are once right and no one listens, you can come to believe that every time that no one listens you are right).

Leach wants to take the insights of Margulis and the tools of Woese and Mullis and go big. He is a go big or go home kind of guy. He has the “let’s go kick some butt,” demeanor of a high school wrestling coach one win shy of the state championship. His perspective is that he can only really understand what is going on by seeing samples of feces (from toilet paper wipes) from thousands and thousands of samples. With those samples, Leach wants to study the variation among people in terms of their gut microbes (or at least the ones that end up in feces). With so many samples he might be able to understand the effect of subtle differences among individuals. Are vegan’s microbiomes different from those of vegetarians? Or what effect does having a dog have on your microbiome? Or do probiotics have any effect on the micrbiome at all (they affect rat and mouse microbiomes, but alas rats and mice aren’t the ones buying the stuff)? This sort of ambitiousness is possible only because Leach has teh good fortune to be able to work after the earlier, harder, times. Leach wants to see with the tools he has inherited. Galileo had a telescope. Anton Von Leeuwenhoek had a single-lens microscope. Leach has bundled up pieces of used Charmin, that and modern genetics.

Leach thinks that there are healthy microbial communities and sick ones, that most of us tend to have somewhat to very sick ones and if we understand the variation we might understand how to eat, live, and farm (microbes) in such a way as to favor the healthy ones. He wants to study whole families, including cats, dogs and all the rest. This is an exciting idea, but it, like hundreds of other exciting ideas about gut microbes, still needs to be tested. The field is in its stumbling infancy. The field needs the data; Leach needs the data.

Continue reading at Scientific American