Genesis: The Scientific Quest for Life's Origin

by Robert M. Hazen

  The fourth and favored genetics-origin model of Orgel and many followers is based on a nucleic-acid molecule such as RNA—a single-stranded polymer that acts both as a carrier of information and as a catalyst that promotes self-replication. Orgel proposed this model in 1968, long before any experimental evidence supported such a notion. “I must confess to a strong, longstanding bias in favor of [this] explanation,” he remarked recently. “It is, at the very least, the model that can be studied most easily in the laboratory.”

  How to choose? When evaluating various origin-of-life models, scientists aren't restricted to chemical experiments alone. The metabolism-first models of Wächtershäuser, de Duve, and others are equally influenced by top-down studies of molecular phylogeny, which point to deeply embedded, primordial biochemical pathways. The principle of continuity demands an unbroken path from ancient geochemisty to modern biochemistry. Hence, the citric acid cycle that lies at the heart of all modern metabolism becomes a prime target for studies of protometabolism.

  In like fashion, top-down studies of molecular genetics have zeroed in on RNA as the essential core molecule of ancient genetics.

  THE RNA WORLD

  Few events have electrified the origin-of-life community as much as the early 1980s discovery of RNA ribozymes—strands of RNA that not only carry genetic information, but also act as catalysts. Sidney Altman of Yale and Thomas Cech of the University of Colorado independently demonstrated that a particular segment of RNA can accelerate key biochemical reactions. This startling finding, which won Altman and Cech the Nobel Prize in 1989, inspired a new vision of life's origin.

  Modern life relies on two complexly interrelated molecules: DNA, which carries information, and proteins, which perform chemical functions. This interdependence leads to a kind of chicken-and-egg dilemma: Proteins make and maintain DNA, but DNA carries the instructions to make proteins. Which came first? RNA, it turns out, has the potential to do both jobs

  The RNA World theory quickly emerged following the discovery of ribozymes. It champions the central role of genetic material in the dual tasks of catalyst and information transfer. Over the years, “RNA World” has come to mean different things to different people, but three precepts are common to all versions of the theory: (1) Once upon a time, RNA rather than DNA stored genetic information; (2) ancient RNA replication followed the same rules as modern DNA replication by matching pairs of bases: A-U (the pyrimidine uracil, whose DNA equivalent is thymine) and C-G; and (3) ancient RNA played the same catalytic roles as modern protein enzymes. In this scenario, the first life-form was simply a self-replicating strand of RNA, perhaps enclosed in a protective lipid membrane. According to most versions of this hypothesis, modern metabolism emerged later, as a means to make RNA replication more efficient.

  Two factors may have contributed to the speed with which the RNA World idea caught on. For one thing, a generation after the Miller–Urey experiment, there were still few solid clues about how to make the transition from the prebiotic soup to cellular life. The origin-of-life community was poised to try something new, and RNA provided a compelling original angle, rich in experimental possibilities. In addition, evidence of the dual role of RNA, as both catalyst and carrier, proved seductive to the new generation of biologists, who were born and raised in the age of molecular genetics. To many researchers, life and genetics are synonymous, so the RNA World idea resonates deeply.

  The more that biologists learn about RNA, the more remarkably versatile it seems. One big surprise came from the study of ribosomes, lumpy cellular structures that help to assemble proteins. Ribosomes consist of a complex intergrowth of proteins and several RNA strands. Many biologists assumed that the proteins play their usual active role as the enzymes that do the actual assembly work, while RNA merely holds the ribosomes together. However, recent studies prove just the opposite—that RNA mediates the critical step of linking up the protein's constituent amino acids. In essence, RNA does the heavy lifting in protein assembly—a discovery that strongly reinforces RNA's presumed ancient role in biochemistry.

  RNA's probable antiquity is underscored by a growing list of other biochemical studies. For example, RNA nucleotides play key structural roles in a variety of essential biological catalysts called coenzymes. These versatile catalysts promote vital reactions at the very heart of the citric acid cycle (the difficult synthesis of citrate from oxaloacetate, for instance). Coenzymes also mediate the manufacture of lipids and other essential biomolecules. And recently, scientists at Yale discovered “riboswitches”—remarkable segments of RNA that change shape when they bind to specific molecules in the cell. These chemical sensors then regulate the cell's chemistry by turning genes on and off.

  The inevitable conclusion: RNA is a very ancient molecule that seems to “do it all.”

  CAVEATS

  Today, every origin-of-life meeting features sessions dedicated to RNA World studies. A thousand articles amplify the idea, and hundreds of researchers have pursued variations on the theme. There can be little doubt that the emergence of RNA represents a crucial step in life's origin. However, decades of frustrating chemical experiments have demonstrated that the RNA World could not possibly have emerged fully formed from the primordial soup. There must have been some critical transition stage that bridged the prebiotic milieu and the RNA World.

  I am persuaded by those who argue that a self-replicating metabolic system must have emerged first, followed by some form of genetic molecule that was both structurally simpler and chemically more stable than RNA. Only much later did the mechanisms of RNA genetics and ribozymes come into play. Here are some reasons:

  1. Metabolism, which in its earliest stages uses rather simple molecules in the C–O–H (and maybe S) chemical system, seems vastly easier to jump-start than genetics. By contrast, the RNA World scenario relies on exact sequences of chemically complex nucleotides in the C–O–H–N–P system. Accordingly, modern cells synthesize nucleic acids through metabolism, but RNA synthesis is several steps removed from the core metabolic cycle, the citric acid cycle. This layering of a simple core metabolism surrounded by successively more complex layers of synthesis suggests that metabolism came first and other chemical pathways were added later.

  2. Many of the presumed protometabolic molecules are synthesized with relative ease in experiments that mimic prebiotic environments, à la Miller–Urey. RNA nucleotides, by contrast, have never been synthesized from scratch, in spite of decades of focused effort.

  3. Even if a prebiotic synthetic pathway to nucleotides could be found, a plausible mechanism to link those individual nucleotides end-to-end into an RNA strand has not been demonstrated. So it's not obvious how catalytic RNA sequences would have formed spontaneously in any prebiotic environment.

  Sometimes you have to place your bets and put your cards on the table. I view the RNA World as a critical, but relatively late, transitional stage that occurred when life was well established on Earth—well after the emergence of a stable, evolving metabolic world, and before the modern DNA-protein world. Biologists seem reasonably confident that the last stages of this evolution—the transition from the RNA World to a DNA-protein genetic system—can be understood. Top-down studies of modern life-forms and the genetic code provide abundant clues about that process.

  The greater mystery lies in the seemingly intractable gap between primitive metabolism and RNA. Before we can contemplate the RNA World, therefore, we have to address the pre-RNA World. By what chemical process did the first information-bearing system emerge?

  17

  The Pre-RNA World

  I've been waiting all my life for an idea like this.

  Simon Nicholas Platts, 2004

  What preceded the RNA World? We understand a lot about the possible earliest stages of life's emergence—how to make the prebiotic soup with all sorts of interesting molecules and how to assemble those molecules into a variety of larger useful structures. At the other end of the story, we have a good handle on how s
trands of RNA might function as evolving, self-replicating systems (as we'll see in the next chapter). But there's that maddening gap between the primordial soup and the RNA World. Stanley Miller sums up the problem: “Identifying the first genetic material will provide the key to understanding the origin of life. RNA is an unlikely candidate.”

  To be sure, there have been numerous creative attempts to close this gap. Several researchers have approached the problem by proposing simpler types of precursor genetic polymers that might have arisen before RNA. In a tour de force research program, the Swiss chemist Albert Eschenmoser explored the stabilities of more than a dozen variants of RNA with modified sugar-phosphate backbones. He systematically replaced the 5-carbon sugar ribose with various other 4-, 5- and 6-carbon sugars and discovered seven new kinds of stable nucleic-acid-like structures. Most significant was the discovery by Eschenmoser and colleagues of a nucleic acid with the 4-carbon sugar threose (the molecule was dubbed TNA). Unlike ribose, which must be synthesized through a rather cumbersome sequence of chemical steps, threose can be assembled directly from a pair of 2-carbon molecules. This difference makes TNA a much more likely molecule than RNA to arise spontaneously from the prebiotic soup.

  Other scientists took a different chemical tack. In 1991, the Danish chemist Peter Nielsen and colleagues synthesized a novel genetic molecule—a “peptide nucleic acid” (PNA), which features RNA-like bases bound to a backbone of amino acid molecules. The reliance on readily available amino acids, rather than problematic sugar phosphates for the polymer backbone, appealed to many members of the origins community. The discovery of PNA also underscored the chemical richness of plausible genetic molecules.

  These immensely creative efforts expand the repertoire of prebiotic possibilities. They also hold the promise of providing new kinds of synthetic genetic molecules that can interact with modern cells yet not interfere with cellular function—a potential boon to medical research. Nevertheless, no one has managed to achieve a plausible prebiotic synthesis of these alternative nucleotides, much less a viable genetic polymer. The door is wide open for new ideas.

  THE PAH WORLD

  ***WARNING: The following section presents an intriguing hypothesis, but one that is highly speculative and as yet untested. Such novel ideas fuel origins research, though most are eventually cast aside—the victims of faulty chemical reasoning or failed experimental predictions. Whatever the outcome, this story epitomizes the exhilarating process of scientific exploration.***

  In May of 2004, Simon Nicholas (“Nick”) Platts was in trouble. After almost five years of fruitless graduate work, and approaching his fortieth birthday, he was about to be deported to his native Australia with no degree and no job. [Plate 6]

  Nick's life had defied the traditional arrow-straight science career path that most of us knew: college, graduate school, postdoc, and tenure track. A gifted chemist and enthusiastic educator, he went from a master's degree in chemistry to teaching at Melbourne Grammar School. Only at the advanced age of 35 did he resolve to return to university, get a doctorate, and do some research. Life's chemical origin was one topic that really excited him, so he applied to Rensselaer Polytechnic Institute in Troy, New York, to work with Jim Ferris.

  His new RPI colleagues found Nick to be outgoing and supportive, always ready to help others with their research, and eager to teach undergraduate chemistry, but progress on his thesis project suffered. After three years in Troy, he moved to Washington, D.C., and the Carnegie Institution as a NASA-sponsored predoctoral fellow, a position that would allow him to acquire his doctorate from RPI, but do the research in a new setting with fewer distractions. He had two years left to complete a thesis.

  Nick was full of ideas. Early in 2003, he came to me with plans for an elegant experiment on the possible influence of Earth's magnetic field on the origin of biological homochirality. Could I provide some lab space?

  “OK, but for how long?” I asked. My lab is small and space is at a premium.

  “Once it's set up, the experiment should take only a couple of weeks,” he assured me, so I offered him the necessary space for a few months.

  “No worries!” his Aussie reply.

  Nick started with a flurry of activity, marking out a good fraction of my lab bench with masking tape, cordoning off a sink that might otherwise splash onto the lab's delicate apparatus, assembling an elaborate optical table, and filling cabinets with hardware, but his progress soon slowed. Crucial supplies were on back order, funds were needed for a special laser, other difficulties followed. More than a year later, the sequestered lab space, still piled high with equipment, was gathering dust. When pressed about his plans, Nick was vague and evasive. Many of us feared that he would be forced to leave the Geophysical Lab empty-handed at the end of June 2004. A sense of shared responsibility weighed heavily on George Cody, Marilyn Fogel, and me.

  EUREKA!

  Nick Platts' life changed dramatically for the better on Tuesday, May 25, 2004. That's when the central idea for his PAH World scenario crystallized. Max Bernstein, a colleague of Lou Allamandola at NASA Ames, had planted the seeds for the concept at an RPI seminar in November 2001. Bernstein's talk had emphasized the occurrence of polycyclic aromatic hydrocarbons in deep space, and it got Nick thinking about PAH chemistry. A September 2003 conference in Trieste in celebration of the 50th anniversary of Stanley Miller's breakthrough experiment inspired more progress. “On the return flight,” Nick remembers, “I scribbled the idea on the back of a United Airlines ticket.”

  The germ of an idea gradually developed “on the mental back burner,” but May 25th was the Eureka moment. “It was 5:51 p.m.,” Nick recalls. “That's when I did the drawings. That's when I realized how big this was.” Contrary to popular myth, there aren't many such moments in science.

  Nick's new idea follows in the tradition of other models of pre-RNA genetic polymers, but with an original chemical twist. PAHs would have been abundant among the plethora of prebiotic molecules. (We met them back in Chapters 3 and 5 as significant components of carbonaceous meteorites and, by extension, the cosmic debris that formed our planet.) Each of these flat sturdy molecules consists of fused 6-member rings of carbon atoms with hydrogen atoms around the edge. PAHs are relatively insoluble in ocean water, but under the influence of solar ultraviolet radiation they can be chemically modified, or “functionalized”; hydrogen atoms can be stripped off, and new molecular fragments can take their place. If the PAH edges become decorated with OH, for example, then their solubility in ocean water increases significantly.

  By any calculation, PAHs and their functionalized variants were a significant repository for organic carbon on the primitive Earth. I suspect that some origins chemists thought it a shame to lock up so many potentially useful carbon atoms in the relatively inert, biologically useless PAHs.

  But what if PAHs played a key role in the ancient ocean? What Nick realized was that a functionalized PAH with OH around the edges is an amphiphile—a molecule that both loves and hates water, similar to Dave Deamer's lipids (see Chapter 11). The flat surfaces of the carbon rings repel water (they're hydrophobic), but the OH-bearing edges of the PAHs attract water (they're hydrophilic). So what happens when lots of functionalized PAHs are placed in seawater? How might the hydrophobic parts stay away from water, while the hydrophilic parts remain in contact with the wet surroundings? The simple answer is to assemble a pile of PAHs like a stack of plates in the cupboard. The flat hydrophobic parts shield each other from water, while the edges form the water-bathed outside of the stack. The PAHs self-organize.

  Platts predicted that, once stacked, the system would preferentially bind small flat molecules, like the DNA bases, to the PAH edges and thus concentrate them from the surrounding prebiotic soup. These baselike molecules would attach and break free in a constant game of molecular musical chairs. Gradually, however, a selection process would take place. Because the PAHs are loosely stacked, adjacent flat PAH molecules would slide back and forth and r
otate next to each other, like your hands do when you rub them together on a cold day. This mechanical action would tend to break off any edge-bound molecule that isn't, itself, as flat as a PAH. Consequently, the small, flat, ring-shaped base molecules (the A, C, G, and U of RNA, for example) would bind preferentially around the edges of the stack. What's more, these RNA bases are also amphiphilic, so they might have a tendency to line up more or less on top of each other, forming a kind of ministack. Remarkably, the spacing between the PAH layers (and hence the vertical separation between bases) is 0.34 billionths of a meter—exactly the same spacing as found between the bases of DNA and RNA.

  The result of all this self-organization, according to Nick's PAH World hypothesis, would be a stack of PAHs decorated along the side by an array of small flat molecules, including bases—an arrangement that looks for all the world like the information-rich genetic sequence of DNA or RNA.

  Once bases are effectively stacked, Platts suspects, other small molecules would start to form a backbone linking the bases together into a true information-rich molecule, though those key chemical steps remain fuzzy. Then a change in the ocean water's acidity, as might be experienced by moving from a deep hydrothermal environment to a more shallow zone, might allow the sequence of bases to break free as a true pre-RNA genetic molecule that could fold back on itself to match up base pairs. Eventually, complex assemblies of these polymers might act as catalysts for self-replication and growth.

  Nick's proposal lacked any experimental support. Nevertheless, the PAH World hypothesis seemed to provide a geochemically plausible, self-consistent, conceptually simple, and seamless chemical path from the dilute soup to an RNA-like genetic sequence.