Genesis: The Scientific Quest for Life's Origin

by Robert M. Hazen

  SHARING

  Nick Platts' model crystallized in a flash, but was it reasonable? Did it make sense? He decided the best strategy was to bounce the idea off other people.

  (A) Nick Platts' PAH World hypothesis rests on the ability of polycyclic molecules to self-organize into stacks. (B) Once stacked, the PAHs would tend to attract small flat molecules (notably the bases of DNA and RNA) to the edges. (C) A molecular backbone forms to link the bases into a long chain. (D) The RNA-like chain of bases separates from the PAHs and folds into a molecule that carries information. (E) Complex assemblages of these chains have the potential to catalyze reactions. These drawings are adapted from Nick Platts' unpublished manuscript.

  I must have been about tenth on his list. Nick appeared at my office door on the afternoon of Thursday, May 27th. “You got a few minutes?” he asked, taking a seat. I nodded, hoping for a progress report on the stalled thesis experiments. “I've found something extraordinary,” he began. “I think I've discovered how life began.”

  And so he described his hypothesis—the self-assembly of functionalized PAHs, the selection of flat molecules along the edges, the fortuitous spacing of the bases. He sat on the edge of his chair, leaning toward me and gesticulating as he spoke. Nick was clearly exhausted from almost two days without sleep; his voice took on a manic intensity. “This is a once-in-a-lifetime moment! I've never been part of anything this big!”

  I was a bit taken aback by what sounded like a wildly speculative idea. It seemed at first like another distraction, just weeks before his scheduled doctoral defense.

  “I told Dave Deamer and he loves the idea.” Nick rattled off the names of half a dozen other origin-of-life experts he'd already contacted. “No one can think of an objection.” Then, paradoxically, “We've got to keep this secret. Someone else will be sure to steal the idea, so don't tell anyone.”

  “Can you propose any experimental tests?” I asked him. A safe, neutral question, while I considered how else to respond.

  He deflected the question. “There's lots we can do, but we have to get this out fast. I've been drafting a manuscript. I'd like you to be a coauthor. Where do you think we should submit it?”

  A manuscript? Coauthorship? Nick had just raised the stakes. I was uncomfortable with being an author unless I could contribute something original to the paper, but I was happy to discuss publication strategy. I thought the ideal forum for a short, high-impact outline would be a 700-word “Brief Communication” in Nature or a similarly concise “Brevia” in Science. Proceedings of the National Academy of Sciences was another option, but PNAS articles are generally longer, and Nick had no data yet with which to flesh out his hypothesis. He agreed to adopt the short Nature format, while I promised to read his paper and comment quickly.

  The next day, Nick e-mailed me a 700-word draft for “Edge-derivatised and stacked polycyclic aromatic hydrocarbons (PAHs) as essential scaffolding at the origin of life.” I could tell from the title that the paper was going to need some work. Even so, as I read the text I warmed to the elegant theory.

  The hallmark of any useful scientific hypothesis is that it makes unambiguous predictions. Nick's hypothesis made testable predictions by the bundle. First, functionalized PAHs must self-assemble into stacks. The stacked PAHs, furthermore, must be of similar size and shape. PAH edges must attract a variety of molecules, but there must be a preferential selection for flat, baselike molecules. And the bases must also be aligned vertically. If only we could confirm at least one of these predictions.

  George Cody provided the chemical evidence that made me a believer. Coal, George's specialty, is loaded with PAHs. It turns out that there's already an extensive scientific literature on the ability of functionalized PAHs to self-organize into stacks—a process known as discotic organization. A quarter-century of publications had already elaborated on Nick Platts' prediction. Neither Nick nor I had ever heard the word “discotic” until Cody mentioned it, drawing on seminars he'd heard on the subject while working at Exxon. I returned to Nick's manuscript with a red pen and renewed intensity. My principal contribution was to come up with a catchier title, “The PAH World.”

  By Tuesday, June 1st, Nick had received comments from more than a dozen scientists from around the world and the draft manuscript was taking final form. He called a meeting of Carnegie coauthors—nine of us in all—at the Lab's library. We sat around a massive mission oak table and worked through the paper one last time. Should we talk about the common mineral graphite, which also has flat carbon rings? Had we included the most appropriate references? Should we propose specific experiments? Our biggest concern was Nick's figure, which needed to make the essentials of the model as clear as possible, and he agreed to redo it. He submitted the PAH World paper to Nature on Thursday, June 3rd, just nine days after his epiphany.

  OPINIONS

  Nick had no time to relax. Whether or not Nature accepted the paper, he wanted us to stake a claim. We began e-mailing the manuscript, designated “in review,” to a dozen astrobiologists and origins experts to request their comments. We focused on leading RNA World proponents—Jerry Joyce, Leslie Orgel, Jack Szostak—figuring they would have the most to gain from the novel idea.

  Responses came quickly and with varying degrees of enthusiasm. A few scientists who were good friends of the Lab were warmly congratulatory, but most respondents remained cautious, and almost everyone cited the need for experimental evidence. Jack Szostak responded in less than an hour with some skepticism, adding “I think it's worth pursuing experimentally—it would certainly be cool if an effect could be demonstrated.” The next day Leslie Orgel chimed in, “An experimental demonstration of your scheme might be interesting, but I wouldn't advise publishing without showing that it works well.”

  “I thought it was interesting and certainly appealing,” echoed Jerry Joyce. “However, it would help tremendously if there were some experimental support.”

  Andy Knoll joined the chorus: “For now it is fascinating speculation, but the ideas seem amenable to what you guys do best—careful experimentation.”

  Evidently the editors at Nature agreed. We received the form rejection letter a week later. “Thank you for submitting your contribution, … which we are unable to consider for publication.” Boilerplate didn't make their decision any easier to swallow. “Because of severe space constraints … we are unable to return individual explanations to authors….”

  EXPERIMENTS

  Experimental evidence seemed the obvious key to securing support for the PAH World hypothesis. Unfortunately, experiments take time, and that was one commodity of which Nick Platts had precious little at this stage in his graduate work.

  In such circumstances, it's best to think boldly. Nick envisioned a single sequence of experiments that might validate every facet of his theory. His plan: First obtain a sample of a modest-sized PAH, one with a dozen or so interlocking rings. He settled on the elegant, symmetrical hexabenzocoronene (HBC), with its starlike pattern of 13 rings. Put the HBC into a flask with some water, functionalize the molecules by irradiation with an ultraviolet lamp, then measure the system for discotic organization. That much we were pretty confident would work, based on a survey of the discotics literature. Then add base molecules, such as adenine and guanine (the A and G of the RNA alphabet to the system and see if the PAHs bond to them. Finally—and we all knew that this would be a long shot—add a molecule that might serve as a backbone, such as formaldehyde, and see if the bases would link together into a long sequence reminiscent of a genetic polymer.

  The experimental protocols looked good on paper, but there were problems from the start. Pure PAHs (as opposed to random sooty mixtures) turn out to be almost impossible to find commercially, and when you do, they're impossibly expensive. Nick located one European supplier who would sell us tiny amounts of HBC for a thousand dollars—the equivalent of more than a million dollars for ten grams! That clearly wasn't going to work.

  Nick contacted other l
abs in Europe and Japan, hoping for a complimentary supply, but tracking one down might take weeks or months. Meanwhile, he manufactured some PAHs of his own by burning acetylene in air and catching the sooty residues in one of my more expensive glass beakers. Gradually, the soot, which is a mixture of hundreds of different PAHs ranging in size from a few rings to hundreds, piled up.

  I offered to try another angle: purifying PAHs from soot by TLC—the thin-layer chromatography technique I had learned in Dave Deamer's lab (see Chapter 11). Nick agreed, and we ordered a supply of trichlorobenzene, one of the solvents of choice when working with PAHs.

  Nick had other concerns besides experiments. He was still determined to publish his idea, so he prepared a new version of the short paper and submitted it to Science on Thursday, July 15th.

  Lots of people at Carnegie had been aware of the PAH World buzz and wanted to hear from Nick first hand. He presented an informal talk to the Carnegie campus on Friday afternoon July 2nd and again for a NASA Astrobiology Institute video seminar on Monday, July 12th. Each talk provided an opportunity to hone his arguments and to field a new round of questions and comments from origins experts across the spectrum.

  His thesis defense also loomed large. Scrambling to write up an expanded description of his hypothesis and assemble whatever support he could from the published literature, Nick cobbled together a doctoral dissertation and headed back up to Troy for a July 20th defense. We all wondered whether he could pull it off. As it turned out, his thesis committee, chaired by chemistry professor Gerry Korenowski, was more than a little impressed by Nick's elegant vision. In five years of graduate work he had demonstrated his depth of chemical understanding and intuition. The PAH World hypothesis established beyond doubt that he had earned the right to be called “Doctor Platts.” They granted Nick an extra week to polish up his prose, and on July 27th he successfully defended what has to be one of the most unusual chemistry theses in RPI's history.

  MOVING ON

  Having his doctorate in hand was a tremendous relief, but Nick's problems weren't over. His visa was about to run out unless he could find a science job in the United States. Could I help?

  Nick's inspiration centered on the behavior of self-organizing amphiphilic molecules. The logical person to call was Dave Deamer, who received some support from our NASA Astrobiology Institute grant to study molecular self-organization. Dave had also published some intriguing speculations about the energetic role of functionalized PAHs, which might have gathered light to power a sort of primitive photosynthesis. I sent Dave a long e-mail describing Nick's unusual circumstances and his special gifts. Dave, always kind and gracious, responded almost immediately. Yes, he thought he would have a research slot opening up in the fall. When could Nick start?

  Nick is in Santa Cruz now, attempting the experiments that may support or refute his ingenious model. It's too soon to tell if the PAH World hypothesis will pan out, but whatever the outcome of Nick Platts' work, we'll know more than we did before. PAHs, or PNA, or some other information-rich, self-replicating genetic system must have emerged on the path to the RNA World. That first genetic molecule must have been much more resilient than RNA, though it was undoubtedly significantly less efficient as a replicator. At some point, as self-replicating genetic molecules became more competitive, RNA took over. The era of Darwinian evolution had begun.

  18

  The Emergence of Competition

  It is evident that once a self-replicating, mutating molecular aggregate arose, Darwinian natural selection became possible and the origin of life can be dated from this event. Unfortunately, it is this event about which we know the least.

  Carl Sagan, 1961

  Life's most poignant hallmark is inescapable, inexorable change. Each of us is born, grows old, and dies. Each species arises from prior species, fills its own niche for a time, and eventually becomes extinct. In such a sweeping, undirected evolutionary drama, the human species might be seen as but one small, insignificant player. Little wonder that Darwin's theory of evolution by natural selection has met with so much hostility.

  The process of evolution by natural selection rests on two incontrovertible facts. First, every population is genetically diverse, possessing a range of traits. Second, many more individuals are born than can hope to survive. Consequently, over time those individuals with more advantageous traits are more likely to survive and pass on their genetic characteristics to the next generation. This selection process drives evolution.

  Even today, almost a century and a half after the publication of The Origin of Species, a vocal minority of Americans views the theory of evolution as a dangerous and subversive doctrine that substitutes materialism for faith. Efforts to expunge Darwin from textbooks and to augment curricula with thinly veiled religious beliefs in the guise of “scientific creationism” or “intelligent design” continue unabated in many states.

  But natural selection is not a sinister development in life's emergence. On the contrary, evolution is the natural and necessary sorting-out process that led to the origin of life.

  MOLECULAR SELECTION AND EVOLUTION

  Imagine yourself back to the primitive Earth more than 4 billion years ago, to a time before life had emerged. Oceans and shorelines must have held a bewildering, chaotic diversity of organic molecules from many sources. Somehow that confused chemical mess had to be sorted out. Two connected processes—molecular selection and molecular evolution—winnowed and modified the prebiotic mélange.

  Molecular selection, by which a few molecules earned starring roles in life's origin, proceeded on many fronts. Some molecules were inherently unstable or unusually reactive and so they quickly disappeared from the scene. Other molecules proved to be soluble in the oceans and so were removed from contention. Still other molecular species sequestered themselves by bonding strongly to surfaces of chemically unhelpful minerals or clumped together into gooey masses of little use for the emergence of life.

  Earth's many cycles amplified these emergent selection processes. Tidal pool cycles of wetting and evaporation concentrated molecules, while the Sun's ultraviolet radiation fragmented the least stable molecular species. Pulses of hydrothermal seawater delivered new supplies of chemicals to deep-ocean vents, where differential adsorption and detachment of molecules on reactive mineral surfaces concentrated a select subset of molecular species. Day and night, hot and cold, sun and rain, high tide and low—these and other periodic phenomena refined the chemical mix.

  In every geochemical environment, each kind of organic molecule had its reliable sources and its inevitable sinks. For a time, perhaps for hundreds of millions of years, a kind of molecular equilibrium persisted, as the new supply of each molecular species was balanced by its loss. Such an equilibrium assemblage features nonstop reactions among molecules, to be sure, but the system does not necessarily evolve.

  At some point, by processes as yet poorly understood, a self-replicating cycle of molecules emerged, thereby changing the character of molecular selection. Even a relatively unstable collection of molecules could persist in significant concentrations if it made copies of itself. Molecules within that first self-replicating collection would have thrived at the expenses of other molecular species.

  Theorists imagine a more interesting possibility—an ancient environment in which two or more self-replicating cycles of molecules competed for atoms and energy. Such competition inevitably arose as new molecular species offered alternative chemical pathways, or perhaps as changes in environment triggered slight variations in a cycle. Dueling molecular networks would have vied for resources, mimicking life's unceasing struggle for survival. In such a competitive environment, increasingly efficient cycles emerged and flourished at the expense of less efficient variants, slowly shifting the molecular balance. Molecular evolution had begun on Earth.

  The dynamic, competitive tussle of molecular evolution differs fundamentally from the more passive process of molecular selection. Competition among self-replicati
ng cycles drives evolutionary change, fostering efficiency and introducing novelty. That's why many origin experts draw the arbitrary line that separates living from nonliving systems at the emergence of a self-replicating chemical cycle that began to evolve by this powerful process of natural selection.

  Replication of a cycle, in and of itself, is not enough to claim life. The cycle must also possess a sufficient degree of variability so that when it competes for resources, more efficient variants win out. Over time the system changes, becoming more adept at gathering atoms and energy. Under these conditions, the emergence of increasing molecular complexity is inevitable, as new chemical pathways overlay the old. So it is that life has continued to evolve over the past 4 billion years of Earth history.

  EVOLUTION IN THE LAB

  A theory, no matter how plausible, requires experimental testing, but how can one test molecular evolution in a laboratory? That challenge seems almost beyond imagining, yet that is exactly what a few teams of biochemists have done.

  Laboratory studies of molecular evolution began in the 1960s at the University of Illinois, where Professor Sol Spiegelman and his colleagues investigated a tiny virus called Q (pronounced “que-beta”) that attacks the common bacterium E. coli. Q is nothing more than a protein shell surrounding a small loop of RNA. Its entire existence is devoted to infecting E. coli cells and inducing those cells to make more copies of the Q virus. To do that, one of Q's proteins, Q replicase, has to make copies of Q RNA.

  This close relationship between Q replicase and Q RNA suggests a promising experiment. If you put some Q replicase and a Q RNA strand into a test tube along with lots of small RNA building blocks, you'll wind up with countless new Q RNA strands. One caveat: Q replicase makes lots of mistakes, so each new RNA strand is likely to vary slightly from the original.