A Brief History of Creation

by Bill Mesler

  By the spring of 1976, Woese’s team had accumulated complete 16S rRNA sequences from a large variety of bacteria. He and his team then turned their attention to a unique set of microbes known as methanogens. Unusual microbes to the extreme, methanogens had been named for their strange ability to produce methane as a by-product of metabolizing carbon dioxide and molecular hydrogen for energy. Because of their observable, physical characteristics, scientists had long assumed that methanogens were a form of bacteria, but Woese’s genetic data established that they were not bacteria at all. He realized that he and his colleagues had upset the foundation of biological taxonomy. Instead of two ancient lineages—eukaryotes and prokaryotes—there were three, all of which had branched off separately soon after the beginning of life.

  Woese called his new family the “archaebacteria” but later shortened the name to simply “archaea,” meaning “the ancient ones.” He then began redrawing the tree of life. In Woese’s tree, everything that would have made up Darwin’s tree could be grouped into a mere twig at the end of a single branch. By the time Woese was finished, the tree looked more like a complex, asymmetric snowflake with three distinct branches going in different directions from the base. He called these three main divergences “domains.” The discovery came to be known in microbiology circles as the “Woesian revolution.”

  In 1977, Woese, Fox, and NASA jointly announced the discovery of the archaea in a press release that coincided with the publication of a scientific paper in the Proceedings of the National Academy of Sciences. The discovery was greeted with skepticism, incredulity, and, at times, anger. It didn’t help that Woese had already developed a reputation with some scientists as an odd recluse who was working on an impossible question. Some saw his data as too fragmented to redraw the map of evolutionary relationships. A few thought he was a little crazy. One of the most influential evolutionary biologists of the twentieth century, the German-American biologist Ernst Mayr, became Woese’s most ardent critic, telling the New York Times that Woese’s work was sheer nonsense. Woese’s preferred form of defense against critics was to send repeated letters to the editor, which did little to help his cause. When the first major scientific conference was held to discuss his theories, he was not even invited. He might not have attended even if he had been.

  Woese holds a model of RNA in 1961.

  By the mid-1980s, Woese’s views had nevertheless gained some acceptance. In 1992, he was awarded microbiology’s most prestigious award, the Leeuwenhoek Medal of the Royal Netherlands Academy of Arts and Sciences, conferred once every ten years. In 1996, Woese, his fellow University of Illinois professor Gary Olsen, and their teams published the first complete genome structure of an archaean, Methanococcus jannaschii. In an article in Science, they concluded that the archaea are more closely related to humans than to bacteria. “The archaea are related to us, to the eukaryotes,” Woese said in an interview shortly after the discovery. “They are descendants of the microorganisms that gave rise to the eukaryotic cell billions of years ago.”

  Woese’s work on Methanococcus jannaschii turned the tide of scientific opinion heavily in his favor. The new taxonomy was adopted by most scientists. Reflecting on his dramatic vindication, Science dubbed Woese “Microbiology’s Scarred Revolutionary.” The moniker stuck with him for the rest of his life.

  The Tree of Life according to Chambers (top left), Woese (top right), and Darwin (bottom).

  THE WOESIAN REVOLUTION had a profound impact on the study of the origin of life. Before Woese, the question of origin was approached mainly from the bottom up. Scientists like Stanley Miller and Sidney Fox had searched for the earliest chemical processes that led, step by step, to the creation of the first living organism, by starting with the earliest steps that must have been necessary for life to appear.

  Woese strengthened the case for approaching the question from the opposite direction. The history of life could be traced backward using the evolutionary evidence that still existed in the genes of modern organisms, each of which had evolved from a common ancestor. Tracing the genetic records of different species made it possible to obtain a picture of the earliest ancestor. The characteristics shared by the clusters of microorganisms that made up the bottom of the tree were likely traits they held in common with LUCA. And those traits could show not only what LUCA looked like, but what the world that LUCA was adapted to live in looked like. It was still a hazy picture, but it was far less hazy than it had been before.

  One of the problems, though, was the unique manner in which the oldest life-forms had shared their genetic information. This unusual way of sharing genes would lead Woese to make one of his most daring and controversial assertions, that the first life was not an organism at all, but rather a community of organisms that freely swapped information in a collective genetic pool through a process called “horizontal gene transfer.” It was an idea that sprang from Woese’s attempts at unlocking the genetic code.

  Woese was fascinated by the code’s resistance to change over billions of years, and through millions of distinct evolutionary branches. With a few very minor exceptions, every modern blue whale, redwood tree, human, and microbe speaks an identical genetic language—remarkable, considering that human languages, over remarkably short timescales, tend to drift into dialects. The genetic code has barely changed at all for billions of years. The reason for its durability remained an enigma as scientists first began to confront the problem in the 1960s.

  Woese saw a clue in a discovery that had been made in 1951 by a Seattle physician named Victor Freeman. Freeman discovered that genes from a virus that infects a disease-causing strain of the bacterium Corynebacterium diphtheriae could be used to transform a harmless bacterial strain into a virulent one. This finding explained why people infected with diphtheria sometimes don’t get sick immediately but often succumb to symptoms later. Perhaps more important, Freeman’s observations of Corynebacterium diphtheriae documented one of the first known examples of horizontal gene transfer, the swapping of genes between distinct organisms. Eventually, many—perhaps even most—microorganisms would be found to use horizontal gene transfer. Woese hypothesized that this mode of genetic exchange explained why the genetic code had not changed in billions of years. Organisms needed a stable, uniform language with which they could genetically “speak” to each other. If their genetic code changed, the beneficial trait of being able to swap genetic information with other organisms would be lost.

  The discovery of horizontal gene transfer also solved an evolutionary problem. Darwin’s concept of natural selection works best in complex modern organisms that reproduce sexually. Parents have children whose genes are a mixture of the genes of both parents, as well as various accumulated mutations. But most microorganisms produce asexually.* With only one real parent, the offspring are essentially clones, and variation arises only from the mutations caused by environmental insults such as radiation or copying errors. The effects of such mutations are usually unnoticeable, often bad, and sometimes lethal. Every so often, though, they are positive. On rare occasions, they even provide an adaptive advantage for an organism. But relying solely on the accumulation of mutations is a very slow way for evolution to proceed.

  The traditional picture painted by biology was one of complex organisms—the higher eukaryotes—rocketing along the evolutionary ladder by sexual reproduction, while lowly prokaryotes were left to plod along with whatever mutations were provided by random chance. Horizontal gene transfer provided an explanation for the rapid evolution of the earliest microorganisms.† By swapping information freely, similar to the way Corynebacterium diphtheriae does, early microbes would have been able to speed their own evolution by drawing upon a much larger gene pool. Woese called horizontal gene transfer “the tide that lifts all boats.”

  Eventually, biologists would come to understand that genes are swapped between very distantly related species of bacteria, and that genes can even be scavenged from dead bacteria. When organisms die, their
genetic material can linger in the environment for significant periods before decaying. Microorganisms are capable of actually ingesting this discarded DNA and incorporating it into their own genomes. Bits of genetic information are quite literally everywhere in the environment, the Earth being like a giant library from which microbes can borrow.

  Woese’s last observation about horizontal gene transfer was that it not only complicated the early part of the tree of life but upended it all together. With primitive organisms sharing information so freely, the root of the tree of life was really more like a web, connected not by traditional straight-line patterns of descent but by crisscrossing connections established by horizontal gene transfer. Woese’s revisions to the structure of the base of the tree undermined Darwin’s idea of a single common ancestor from which all modern organisms spring. In Woese’s view, tracing the tree back to a single ancestor was impossible. The deepest we can see back into that line is a roiling mess of indiscrete organisms evolving in an interdependent fashion.

  PROBABLY THE MOST striking thing about the microorganisms that populated the base of Woese’s new tree of life is that many are extremophiles, microorganisms capable of thriving in environments that would be deadly to most modern life. Sometimes popularly known as “superbugs,” varieties of extremophiles have been found living at temperatures far below freezing. Some species of a type called acidophiles live off gases dissolved in raw sewage and excrete acid powerful enough to destroy modern sewer systems.

  Many of the extremophiles at the base of Woese’s tree were hyper­thermophiles. Capable of living in intensely hot aquatic environments, hyperthermophiles were first identified in 1965 by the American microbiologist Thomas Brock, who found them living in hot springs in Wyoming’s Yellowstone National Park. Since then, seventy separate species have been identified, some in hotter-than-boiling deep-sea hydrothermal vents.‡

  For decades, discoveries in geology had been hammering away at the Oparin-Haldane “primordial soup” model of the ancient Earth. Geologists had developed increasingly sophisticated methods of deducing what the early atmosphere was composed of by studying basalts, the rocks left behind by volcanic eruptions. While Oparin envisioned an ancient atmosphere filled with ammonia and methane, it seemed more and more likely that the atmosphere was filled instead with nitrogen and carbon dioxide. By the late 1970s, much of Oparin’s model appeared suspect, as did the underlying mechanisms that Miller’s experiment had suggested. To many, a new model was sorely needed.

  Many scientists saw the presence of extremophiles at the base of Woese’s tree as clues they could use in reimagining the earliest life-form. These were presumably the closest descendants of LUCA, so it stood to reason that their ability to thrive in extreme environments had implications for the kind of environment LUCA arose in. This speculation led to some radical theories. The most resilient of these came from an unexpected source, a Munich patent attorney named Günter Wächtershäuser, who saw metal sulfide mineral surfaces as ideal places for life’s earliest chemistry to get started.

  Wächtershäuser was a friend of Carl Woese with whom Woese had shared his growing doubts about Oparin’s primordial-soup model. An organic chemist before he had turned to the practice of law, Wächtershäuser put his mind to the origin-of-life problem. At the home of their mutual friend, the philosopher Karl Popper, he shared with Woese his novel concept that life began in deep-sea hydrothermal vents, the first of which had been discovered by the research submarine Alvin off the coast of the Galápagos in 1977. Woese was intrigued, and he encouraged Wächtershäuser to work out his model in more detail. Wächtershäuser imagined a series of chemical steps beginning on mineral deposits near hydrothermal vents in the depths of the ocean, where they would have been protected from the hostile environment above. His belief that life began on iron sulfide mineral surfaces gave his model its name: the “iron-sulfur world.”

  Wächtershäuser’s theory gained a strong foothold among adherents of “metabolism first” scenarios, those who saw the evolution of genetic material as something that had happened relatively late in the development of life. He also drew on another implication derived from Woese’s redrawn tree of life. Most of the organisms at the base were autotrophs, with unique metabolisms that function by consuming inorganic substances like carbon dioxide and hydrogen sulfide. An autotrophic origin would sidestep the need for abundant organic molecules that the first cells could “feed on,” which had been a central tenet of Oparin’s model. Finally, Wächtershäuser believed that the most primitive life lacked a cell membrane. This last contention was perhaps the most dubious for more established origin-of-life scientists, most of whom believed some type of chemical barrier was necessary to allow the first living systems to grow more complex.

  Other scientists, notably geochemist Mike Russell, would build on Wächtershäuser’s theory to try to account for the perceived need for a protective cell-like container. Russell and his colleague Allan Hall, both experts in iron sulfide deposits, liked the idea of mineral-rich hydrothermal environments that Wächtershäuser had proposed, but they speculated on the existence of a gentler kind of hydrothermal vent, a great deal cooler than any of those previously observed. The hypothesis received a huge boost in 2000 with the Argo’s discovery of the Lost City, which turned out to be just the kind of hydrothermal field Russell had envisioned. Russell and Hall also came up with a model for the development of a primitive stand-in for a cell membrane. When the alkaline water from these types of hydrothermal vents mixes with the more acidic ocean water, it forms bubbles made of sulfides and other mineral types. These bubbles could have served as primitive membrane-like compartments.

  Still, many in the field remained unconvinced. Even Russell’s gentler vent was a difficult environment for life to have emerged in. Years after Wächtershäuser first conceived of the iron-sulfur world, only tantalizing glimmers of experimental support had emerged. A large number of scientists believed the key was a molecule that Carl Woese had mused about as far back as 1967. In his first and only book, The Genetic Code, he had suggested the possibility that RNA played a much more important, versatile, and ancient role in the cell than many had believed.

  * There are rare exceptions among higher organisms. Some plants and a few species of insects, fish, lizards, and birds occasionally reproduce through “parthenogenesis,” Greek for “virgin birth.” Parthenogenesis has even been induced in laboratory settings in the eggs of several mammals, including humans, though the offspring are always unhealthy or nonviable.

  † Horizontal gene transfer also seems to be a major reason why bacteria are able to adapt so quickly to antibiotics.

  ‡ Because of the high pressures found in deep-sea environments, water there boils at well over 100°C.

  A CELL IS BORN

  An honest man, armed with all the knowledge available to us now, could only state that . . . the origin of life appears at the moment to be almost a miracle. . . . But this should not be taken to imply . . . that it could not have started on the earth by a perfectly reasonable sequence of fairly ordinary chemical reactions. The plain fact is that the time available was too long, the many microenvironments on the earth’s surface too diverse, the various chemical possibilities too numerous and our own knowledge and imagination too feeble to allow us to be able to unravel exactly how it might or might not have happened such a long time ago, especially as we have no experimental evidence from that era.

  —FRANCIS CRICK, Life Itself, 1981

  IN 1986, AN ARTICLE by the Nobel Prize–winning physicist and biochemist Walter Gilbert appeared in the influential “News and Views” section of the journal Nature. Eight years earlier in the same section, Gilbert had hypothesized the existence of sections of genes called introns that were spliced from their RNA carriers during the process of gene translation to proteins, solving a long-standing problem in biology. This time he was suggesting a solution to an even more important mystery, one that had plagued origin-of-life scientists for decades: the c
hicken-or-egg dilemma of replication or metabolism.

  At some point in the half-billion years or so of evolution that took place before LUCA, an even more primitive organism must have existed, what scientists sometimes call FLO, or the “first living organism.” Such an organism would have been little more than a simple chemical entity, possibly consisting of a single component of the complicated machinery that makes up all modern cells. But which component? At the time scientists like Stanley Miller and Sidney Fox first pursued the question, the answer had seemed rather straightforward: it had to be protein, since proteins were then still thought by many to be both the principal agents of metabolism and the carriers of genetic information. The work of Crick, Watson, and others in elaborating DNA’s role in the cell shifted the focus of many to the principal agent of genetics, which might by itself have been capable of initiating the long chain of evolution. DNA was mere information, though, incapable of accomplishing much on its own. Yet the idea that the first protocell contained DNA and protein seemed too complex. One or the other had to have come first.

  In his 1986 Nature article, Gilbert argued that the solution was that neither had come first. Instead, Gilbert returned to an idea first floated by Carl Woese in 1967. In his book The Genetic Code, Woese had speculated that RNA, the intermediary between DNA and proteins, might have once done the jobs of both. This speculation was followed by a pair of papers published simultaneously in 1968 by Francis Crick and Leslie Orgel, both of which postulated that life was initially based on RNA. Orgel’s paper, “Evolution of the Genetic Apparatus,” would eventually come to be recognized as one of the most elaborate early representations of the idea, although it initially gained very little traction. By 1986, however, scientists had achieved a much deeper understanding of RNA. Gilbert was able to revive the idea because of a groundbreaking discovery independently made during the previous few years by a pair of microbiologists named Thomas Cech and Sidney Altman.