Genesis: The Scientific Quest for Life's Origin

by Robert M. Hazen

  Here's what Spiegelman and co-workers did to make their molecules evolve. They allowed the chemical mix to make copies for just 20 minutes. During that short period, some RNA sequences bound strongly to Q replicase and duplicated rapidly, while others interacted poorly with Q replicase and were inefficiently copied. After 20 minutes, when the solution had become enriched in RNA strands that easily replicate, they transferred a small amount of that liquid into a new beaker with fresh Q replicase and RNA building blocks. Then they ran the experiment for another 20 minutes and transferred a small amount of the second batch of RNA copies into a third beaker with fresh Q replicase.

  Seventy-four times they repeated the process, gradually reducing the time allowed for the reaction to proceed. Each step preferentially selected those RNA strands that were copied most efficiently. By the end of the experiment, the length of the most efficient RNA strands had been shortened to a sixth of the original size, and these evolved RNA sequences were being copied 15 times faster than before. Similar experiments generated strands of RNA that were unusually resistant to high temperature or to the effects of damaging chemicals. Under such severe selection pressure (time, temperature, or some other stress), the Q RNA evolved.

  SELF-REPLICATING RNA

  “Spiegelman monsters,” as these systems came to be known, are not alive. Only by the most overt manipulation (cycling through a succession of beakers, for example) does the Q RNA evolve. But the repetitive selection process developed by Spiegelman's group proved that molecular systems under competitive pressure can be induced to evolve—a result that suggested to many researchers a brave new world of artificially evolved molecules designed to accomplish specific chemical tasks.

  Harvard Medical School biologist Jack Szostak has set his sights even higher. Indeed, Szostak's overriding ambition is nothing less than to design an evolving life-form in his lab. “Our ultimate goal is to create life,” he admits.

  Jack impresses you as someone who is supremely happy in his profession. Unassuming and quiet by nature, he often wears a half-smile, as if he were amused by a private joke. Despite his 50-odd years, his slender build and the bright eyes behind round-framed glasses make him look like a scientific Harry Potter—and he is in fact a bit of a wizard.

  For Jack, RNA is the key. He began his scientific career studying yeast chromosomes—an important mainstream task in molecular biology that sheds light on how DNA operates in humans. Chromosomes are elongated structures that divide and separate during cell division; they carry all of yeast's DNA. Szostak and his student, Andrew Murray, synthesized one from scratch. “Even then,” he recalls, “my guiding principle was that the best way to show that you really understand how something works is to try to build it from pieces and then see if it works as expected.” [Plate 8]

  The study of yeast DNA was a crowded field, and Szostak itched to try his hand at something different. The discovery in the early 1980s of ribozymes—RNA that behaves as a catalyst—was too seductive to pass up, and he soon changed research directions.

  In their first series of ribozyme experiments, Szostak and a group of his students focused on engineering chains of RNA that can copy other RNA molecules. Such an “RNA replicase” represents a first key step in designing a self-replicating chemical system. Success came in 1989, when he and Jennifer Doudna (now a professor at Berkeley) made an RNA molecule that copies short RNA sequences, albeit rather sloppily. Other high-profile papers soon followed, as their ability to manipulate RNA improved. These were spectacular advances, but still a long, long way from a reliable self-replicating RNA strand. They'd have to do better, but how? Jack decided to let molecular evolution work for him.

  Szostak's objective was to evolve an RNA molecule that would attach strongly and selectively to a “target molecule” of distinctive shape. His team tackled RNA evolution by first generating a solution with more than 10 trillion random RNA sequences, each about 120 “letters” long. They poured this RNA-rich solution into a beaker whose glass sides had been coated with the target molecule. After sitting for a few minutes, the vast majority of RNA chains had done nothing, but a few RNA strands, by chance, were able to grab onto the target molecule and thus remained firmly attached to the beaker. When they flushed the RNA solution out of the beaker, those relatively few RNA sequences that bonded to the target molecule remained behind.

  At first, only the tiniest fraction of the random RNA sequences attached to the target, but Szostak's team collected those precocious strands and made trillions of approximate copies—similar sequences but with lots of random mutations thrown in. Then they repeated the experiment and picked out a second generation of RNA sequences that did the job better than those from the first. Again and again, they cycled the RNA, each time copying the best sequences and thus improving the speed and accuracy with which the RNA latched onto the glass-bound target molecules. After several dozen cycles, the surviving RNA strands had evolved to the point where they were perfectly adapted to the assigned task. This elegant evolutionary process has now been extended to the design of numerous new RNA sequences with a wide range of specialized functions, from locking onto viruses to splicing DNA.

  With their new procedures, Jack Szostak and his colleagues have turned their attention to self-replicating RNA. In 2001, David Bartel, a former Szostak graduate student now at MIT and the Whitehead Institute, managed to produce an impressive RNA sequence that can grab onto a shorter piece of RNA up to 14 letters long and copy it. Optimistic researchers are convinced that it's only a matter of time before self-replicating RNA strands more than a hundred letters long will be commonplace. If so, then synthetic life may not be far behind.

  SYNTHETIC LIFE

  Self-replicating RNA is not alive, but it's getting closer. It's a big molecule that carries genetic information, catalyzes its own reproduction, and mutates and evolves to boot. But no plausible geochemical environment could feed such an unbound molecule, nor would it have survived long under most natural chemical conditions.

  One key to survival is protection, and that's where a lipid membrane comes in. Building on David Deamer's discoveries, Szostak protégés Martin Hanczyc and Shelley Fujikawa have experimented with ways that membranes might have encapsulated RNA strands. Among their findings: Lipid vesicles that are squeezed through tiny pores stretch out, divide, and start to grow larger—a process that mimics cell division. What's more, the process is greatly accelerated by the addition of fine-grained clay minerals, some of which end up inside the vesicles. Recall that Jim Ferris at RPI demonstrated that clays can attract and help to assemble RNA strands. So, in the spirit of Pier Luigi Luisi's Lipid World, it might be possible to make cell-like structures that spontaneously incorporate RNA-bound clay particles.

  This behavior of lipids and RNA has led Szostak and his students to propose a remarkable scenario for the first life-form to evolve by natural selection. Imagine a lipid vesicle that contains self-replicating RNA. Previous authorities have suggested that RNA must have played many roles in such a protocell (roles that DNA and proteins play today)—manufacturing new membrane molecules, controlling cell shape and size, copying itself, and more.

  Szostak's team realized that RNA could drive cell growth by the much simpler process of internal pressure. RNA pushes out on the membrane, which in turn presses on neighboring protocells. They speculated that this contact would promote the transfer of lipids from cells with less internal pressure (hence, less RNA) to those with more. Thus the competition for space would lead to a natural-selection process. Protocells with more RNA would be more successful.

  To test their ideas, they first prepared one set of vesicles filled with a solution of the sugar sucrose and another set filled with pure water. When mixed together and confined, the sucrose-ladened vesicles grew larger by drawing lipids from their sugarless neighbors. Repeating the experiment with RNA strands yielded the same results. Vesicles swollen with RNA grew, as the adjacent empty vesicles shrank.

  Previous workers had assumed that
RNA would have to learn how to accomplish several tasks—lipid synthesis, self-replication, metabolic functions, and more—before a protocell could evolve by natural selection. Szostak's latest results suggest a much simpler scenario, in which the only essential task for protocell competition is RNA self-replication. “If we can get self-replicating RNAs,” Szostak suggests, “then we can put them into these simple membrane compartments and hope to actually see this competitive process of growth.” The more RNA a vesicle captures and copies, the more successfully it will compete with its neighbors—a sort of molecular the-rich-get-richer scheme. In such a world, the most efficient RNA replicators would enjoy a tremendous advantage. With the emergence of competition, Darwinian evolution could take center stage.

  Every year, Jack Szostak moves closer to his goal of creating a self-replicating, encapsulated, evolving chemical system in the lab. If and when he or his successors accomplish this, it will be a historic achievement. Synthetic life will also trigger a new flood of ethical questions about the potential dangers of scientific research, as well as philosophical questions about the meaning of life. But will synthetic life tell us how life emerged on Earth?

  A synthetic RNA organism will certainly give credibility to the RNA World hypothesis that a strand of RNA (or some precursor genetic molecule) formed the basis of the first evolving, self-replicating chemical system. But laboratory-created life will not have emerged spontaneously from chemical reactions among the simple molecular building blocks of the prebiotic Earth. Researchers still stack the deck by supplying a steady source of RNA nucleotides and vesicle-forming lipids. And so, for the time being, deep mysteries remain.

  19

  Three Scenarios for the Origin of Life

  Anyone who tells you that he or she knows how life started on the sere Earth some 3.45 billion years ago is a fool or a knave.

  Stuart Kauffman, At Home in the Universe, 1995

  What do we know for certain? Scientists have learned that abundant organic molecules must have been synthesized, and must have accumulated, in a host of prebiotic environments. They have also demonstrated many processes by which biomolecular systems—including lipid membranes and genetic polymers—might have formed on mineral surfaces. As molecular complexity increased, it seems plausible that simple metabolic cycles of self-replicating molecules emerged, as did self-replicating genetic molecules.

  So we've learned a lot, but what we know about the origin of life is dwarfed by what we don't know. It's as if we were trying to assemble a giant jigsaw puzzle. A few pieces clump together here and there, but most of the pieces are missing and we don't even have the box to see what the complete picture is supposed to look like.

  The greatest mystery of life's origin lies in the unknown transition from a more-or-less static geochemical world with lots of interesting organic molecules to an evolving biochemical world in which collections of molecules self-replicate, compete, and thereby evolve. How that transition occurred seems to boil down to a choice among three possible scenarios.

  1. Life began with metabolism, and genetic molecules were incorporated later: Following Günter Wächtershäuser's hypothesis, life began autotrophically. Life's first building blocks were the simplest of molecules, while minerals provided chemical energy. In this scenario, a self-replicating chemical cycle akin to the reverse citric acid cycle became established on a mineral surface (perhaps coated with a protective lipid layer). All subsequent chemical complexities, including genetic mechanisms and encapsulation into a cell-like structure, emerged through natural selection, as variants of the cycle competed for resources and the system became more efficient and more complex. In this version, life first emerged as an evolving chemical coating on rocks.

  The true test of this origin scenario rests on chemical synthesis experiments. Starting with simple molecules and common minerals subjected to plausible prebiotic conditions, researchers must discover a way to jump-start a self-replicating cycle of molecules that mimics the core citric acid metabolism of modern life-forms. We're close, and several of the essential steps have been accomplished. A key missing experiment is the synthesis of 4-carbon oxaloacetate from 3-carbon pyruvate, perhaps using sulfur analogs in an environment rich in hydrogen sulfide. If that step can be demonstrated, and a self-sustaining cycle of reactions maintained, then metabolism-first will be the model to beat.

  2. Life began with self-replicating genetic molecules, and metabolism was incorporated later: According to the RNA World hypothesis, life began heterotrophically and relied on an abundance of molecules already present in the environment. Organic molecules in the prebiotic soup, perhaps aided by clays or PAHs or some other template, self-organized into information-rich polymers. Eventually, one of these polymers (possibly surrounded by a lipid membrane) acquired the ability to self-replicate. All subsequent chemical complexities, including metabolic cycles, arose through natural selection, as variants of the genetic polymer became more efficient at self-replication. In this version, life first emerged as an evolving polymer with a functional genetic sequence.

  This scenario, with its appealing reliance on the multiple ancient roles of RNA, lacks only the crucial support of an experiment that demonstrates the plausible prebiotic synthesis of a genetic polymer—RNA or its precursor. If an experiment successfully demonstrates the facile synthesis of such a polymer from prebiotic building blocks, then the biggest gap in our understanding of life's origin will have been filled. In that case, many experts will conclude that the problem of life's chemical origin has been solved.

  3. Life began as a cooperative chemical phenomenon arising between metabolism and genetics: A third scenario rests on the possibility that neither protometabolic cycles (which lack the means of faithful self-replication) nor protogenetic molecules (which are not very stable and lack a reliable source of chemical energy) could have progressed far by themselves. If, however, a crudely self-replicating genetic molecule became attached to a crudely functioning surface-bound metabolic coating, then a kind of cooperative chemistry might have kicked in. The genetic molecule might have used chemical energy produced by metabolites to make copies of itself, while protecting itself by binding to the surface. Any subsequent variations of the genetic molecules that fortuitously offered protection for themselves or for the metabolites, or improved the chemical efficiency of the system, would have been preserved preferentially. Gradually, both the genetic and metabolic components would have become more efficient and more interdependent.

  Such a “dual origins” model might at first seem to introduce a needless complication (not to mention sounding like a wishy-washy compromise). Nevertheless, exactly this kind of symbiotic coupling of metabolism and genetics is now thought to have occurred early in the history of cellular life. Crucial features of our own cells suggest an ancient cooperative merging of early, more primitive cells. If experiments establish easy synthetic pathways to both a simple metabolic cycle and to an RNA-like genetic polymer, then such a symbiosis may provide the most attractive origin scenario of all.

  We don't yet know the answer, but we're poised to find out. Each day, new experiments expose more of the truth and winnow the possibilities. Each day, we get closer to understanding. And whatever the correct scenario, of one thing we can be sure: Ultimately, competition began to drive the emergence of ever more elaborate chemical cycles by the process of natural selection. Inexorably, life emerged, never to relinquish its foothold on Earth.

  Epilogue

  The Journey Ahead

  Once to every man and nation comes the moment to decide, In the strife of truth with falsehood, for the good or evil side; Some great cause, some new decision, offering each the bloom or blight, And the choice goes by forever 'twixt that darkness and that light.

  James Russell Lowell, 1845

  The theory of emergence points to a gradual, inexorable evolution of the cosmos, from atoms to galaxies to planets to life. Each emergent step arises from the interactions of numerous agents and yields an outcome much g
reater than the sum of its parts. Each emergent step increases the degree of order and complexity, and each step follows logically, sequentially from its predecessor.

  We recognize this majestic progression only in hindsight. Emergent phenomena remain elusive—exceedingly difficult to predict from observations of earlier stages. Given hydrogen atoms, a tremendous conceptual leap is required to predict the brilliance of stars or the variety of planets. Given planets, no theoretician alive could predict the emergence of cellular life in all its diversity—nor, given cellular life, could anyone foresee the emergence of consciousness and self-awareness. The inherent novelty and layered complexity of emergent phenomena all but preclude prediction.

  We are left, then, to ponder the possible existence of higher orders of emergence—stages of complexity that our brains can no more comprehend than a single neuron can comprehend the collective state of consciousness. Does the universe hold levels of emergence beyond individual consciousness, beyond the collective accomplishments of human societies? Might the cooperative awareness of billions of humans ultimately give rise to new collective phenomena as yet unimagined? If higher stages of emergence await our discovery, then science and theology may someday converge into a more unified vision of the cosmos and our place in it.

  As we search beyond the cookbook “how” of life to questions of meaning and value, the concept of emergence holds a powerful message. Each of our lives is shaped by the same two competing powers of creation and destruction that have held sway throughout the history of the cosmos: emergence and entropy. The second law of thermodynamics states that entropy—the disorder of the universe—must increase. Yet in discrete, precious pockets of matter—on planets, in oceans, within our own conscious brains—astonishing levels of emergent complexity arise spontaneously.