One of my favorite places to visit in Southern California is the Venice Beach Boardwalk. On most days, this tourist hotspot is filled with all sorts of people: locals riding skateboards; tourists strolling the boardwalk or riding rented bikes along the path near the beach; street evangelists; artists selling their creations under easy-ups; and homeless people, some just hanging out and others asking for money.
And, of course, there are the Venice Beach street performers, singing songs and playing their instruments, dancing, executing acrobatic routines, even eating fire. Perhaps my favorite street performer is “the Venice Beach Glass Man” who jumps from a chair onto a pile of broken glass in his bare feet.
The Glass Man has a well-scripted routine. I know because I have seen him perform many times. Throughout his act, he works the crowd, adding to a pile of broken glass shards at the base of a chair, while the crowd chants “Hooba, hooba!” at his urging. The tension mounts as he gets up and down from the chair before he finally jumps onto the glass pieces. Of course, after he jumps, he works the crowd one more time, hoping to get a good payday for his efforts.
Recently, a research team from the Foundation for Applied Molecular Evolution (FAME), led by origin-of-life researcher Steve Benner, hoped to get their own payday from pieces of glass when they demonstrated that ribonucleotides (the building blocks of RNA) could be assembled into RNA polymers (around 90 to 300 subunits in size) by glass catalysts.1 They argue that glasses would have been present on early Earth, formed when large impactors struck the planet’s surface, melting mafic (basaltic and diabasic) materials that then experienced rapid (quenched) cooling upon exposure to air or water. These crystalline silicates would have been, in effect, glasses.
The research team maintains that their findings add fresh support for the RNA world hypothesis, making it that much more reasonable to think that life arose on Earth via chemical evolution. According to their model, RNA molecules would have assembled on early Earth when ocean water replete with ribonucleotides washed over pieces of glass located on volcanic islands.
But a careful assessment of their work shatters this illusion. The work by the FAME researchers is highly contrived, raising questions about its geochemical relevance.
The RNA World Hypothesis Many origin-of-life investigators think that RNA pre-dated both DNA and proteins as the premier replicator and information-harboring molecule. Accordingly, RNA operated as a self-replicator that catalyzed its own synthesis. The RNA world hypothesis posits that, over time, numerous RNA molecules displaying diverse catalytic activities emerged. At this point in life’s history, biochemistry would have centered exclusively around RNA. With time, proteins (and eventually DNA) joined RNA in the cell’s arsenal. During the transition to the contemporary DNA-protein world, RNA’s original function became partitioned between proteins and DNA, and RNA assumed its current intermediary role in the central dogma of molecular biology. RNA ancestral molecules presumably disappeared without leaving a trace of their primordial existence, save for the current roles played by messenger, transfer, ribosomal, and micro RNAs.
Validating the RNA World Hypothesis To substantiate the RNA world hypothesis, researchers need to:
Discover reasonable prebiotic chemical routes that would have generated RNA’s building blocks (nucleobases, ribose, and phosphate) under the conditions of early Earth.
Identify reasonable prebiotic routes that would have assembled these building blocks into ribonucleotides.
Find reasonable prebiotic routes that would have assembled RNA from its building blocks into molecular chains long enough to form ribozymes.
RNA Assembly on Glass In an attempt to satisfy the third criterion, the FAME scientists explored the role that glasses may have played during chemical evolution. These investigators exposed solutions of ribonucleotides dissolved in pure water to different types of powdered glasses. These glasses, composed of pure silicon oxides, were made in the lab and included andesite, basalt, diabase, and nephelinite.
Gel electrophoresis (a technique used to separate DNA fragments) of the reaction products revealed both low and high molecular weight materials. The high molecular weight products were digestible by an enzyme that specifically degrades RNA. This sensitivity indicates that the high molecular weight products are RNA molecules with at least some of the molecular species formed with 3’ to 5’ linkages (which are the bonds that naturally occur in RNA to join ribonucleotides together in a molecular chain). The researchers estimated the size of the high molecular weight products to be between 90 and 300 nucleotides in length.
Kinetic analysis of the reaction indicated that the glasses were, indeed, functioning as true catalysts. The researchers also learned that the type of glass influenced the extent of the reaction, with diabase performing the best. They ranked the effectiveness of the glass catalysts as diabase > basalt >> (much greater than) nephelinite > andesite >> quartz (control).
The research team thinks that this work provides insight as to how RNA may have emerged on early Earth, helping to solidify the case for the RNA world hypothesis. At first blush, it would seem they are right. If glasses were abundant on early Earth and ribonucleotides were present at high enough levels, then RNA could have formed via glass catalysts.
Is the Glass-Catalyzed Polymerization of RNA Geochemically Relevant? Unquestionably, the FAME researchers demonstrated that—in principle—glasses on early Earth could catalyze the formation of RNA molecules of sufficient length to form functional ribozymes from ribonucleotides. But for this work to be enlisted in support of the RNA world hypothesis, this reaction must have been productive under primordial conditions, which can differ substantially from the conditions researchers use in the laboratory. To put it differently, the reaction must be geochemically relevant.
The necessity of prebiotic reactions displaying geochemical relevance exposes one of the chief problems with work in prebiotic chemistry: unwarranted researcher involvement.
Ideally, humans would not intervene at all in any prebiotic study. But this goal isn’t always possible. Researchers involve themselves in the experimental design out of necessity, but also to ensure that the study results are reproducible and interpretable. If researchers don’t set up the experimental apparatus, adjust the starting conditions, add the appropriate reactants, and analyze the product, then by definition the experiment would never happen. Utilizing carefully controlled conditions and chemically pure reagents is necessary for reproducibility and to make sense of the results. In fact, this level of control is essential for proof-of-principle and mechanistic prebiotic studies—and perfectly acceptable.
However, when it comes to the geochemical relevance of prebiotic reactions, the highly controlled conditions of the laboratory become a liability. Here researcher intervention becomes potentially unwarranted. It goes without saying that the conditions of early Earth were uncontrolled and chemically and physically complex. Chemically pristine and physically controlled conditions didn’t exist. And, of course, origin-of-life researchers weren’t present to oversee the processes and guide them to their desired ends. Yet, it is rare for prebiotic simulation studies to take the actual conditions of early Earth fully into account in the experimental design. This complication means that many prebiotic studies designed to simulate primordial processes seldom accomplish anything of the sort due to excessive researcher intervention.
Steve Benner acknowledges this problem. When commenting on this study, he states, “One community [of origin-of-life researchers] re-visits classical questions [in prebiotic chemistry] with complex chemical schemes that require difficult chemistry performed by skilled chemists . . . Their beautiful craftwork appears in brand name journals such as Nature and Science. However, precisely because of the complexity of this chemistry, it cannot possibly account for how life actually originated on Earth.”2
Benner and his team argue that it’s the simplicity of the process they discovered that gives it geochemical relevance.
Hidden Complexity Yet the simplicity of a physical or chemical process doesn’t necessarily ensure its geochemical relevance. Moreover, upon closer inspection, it becomes apparent that the RNA assembly by glass catalysts is quite complex. The experimental design masks the complexity of this process. The FAME researchers have, in effect, smuggled complexity into their experiments.
For example, they simply assume that ribonucleotides would be present on early Earth. Yet the prebiotic reaction schemes proposed and explored by origin-of-life researchers for the synthesis of ribonucleotides are characteristically complex and have, at best, questionable geochemical relevance.
Likewise, the researchers take it as a given that the ribonucleotides that would have taken part in the glass-mediated RNA polymerization reactions would have been homochiral. Yet, no process, whether astronomical, physical, or chemical is known to exist with the capabilities of generating homochiral ribonucleotides on early Earth.3 To be fair, origin-of-life researchers have discovered mechanisms that can generate limited chiral enrichment of amino acids and ribonucleotides. But the degree of enrichment is typically small and often would have required highly contrived and unrealistic scenarios on early Earth.
Geochemical Relevance Other aspects of the glass-catalyzed RNA assembly reactions performed by the FAME investigators raise further questions about this study’s relevance to early Earth conditions. For example:
The researchers used powdered glasses as catalysts. Yet on early Earth, the glasses would have existed as large pieces not as powders. Powdering the glasses dramatically increases their surface areas, which improves their performance as catalysts. (All chemical processes take place at surfaces. The more surface area, the faster the reaction.) Yet this act introduced an artificiality into the experimental design that favors the chemistry performed in the laboratory and undermines its relevance to primordial conditions.
The researchers discovered that some of the glasses performed poorly as catalysts. Once they learned about this difference, they used only the high-performing glasses in their experimental design. It is quite possible that the glasses that formed on early Earth were comprised of those types that perform poorly as catalysts.
The FAME researchers used distilled water as the reaction solvent, instead of water with a high concentration and a diversity of salts, which would have been characteristic of primordial aqueous environments. Other researchers who have studied the use of clays as catalytic agents for the assembly of RNAs from ribonucleotides have learned that these reactions require distilled water as the solvent. The addition of salts to the solvent interferes with the RNA polymerization reactions. Could the same be true for RNA assembly using glasses? To the best of my knowledge the FAME team didn’t investigate the effects of dissolved salt concentrations on the glass-catalyzed RNA assembly process. If they did, they chose not to report their results. Given that ions from salts would interact with the chemically active groups at glass surfaces, I think it’s quite possible that RNA assembly with glasses may require distilled water. If so, this reaction has questionable relevance to the setting of early Earth.
The researchers also carried out this study under chemically pristine conditions. They failed to include materials that would have been present on early Earth—perhaps at higher levels than ribonucleotides—that would have interfered with the RNA polymerization reaction. To put it differently, the researchers ignored the homopolymer problem.4
Before analyzing the reaction mixture, the researchers treated the glasses with urea. This compound disrupts hydrogen bond interactions and would have helped dislodge the RNA molecules adsorbed to the glass surface. Adsorption of biomolecules to glass surfaces is a notorious problem that bedevils biochemists. Biochemists must treat glassware before they use it to hold solutions of biomolecules. These treatments involve coating the glassware surfaces to keep the biomolecules dissolved in solution from adsorbing onto the glassware surfaces. Once adsorbed, it is usually rather tricky, if not impossible, to get the biomolecules to desorb. Under primordial conditions, there wouldn’t be chemists around to wash the glasses with urea. Without this step, any RNA molecules formed by the glass catalyzed reaction would have become permanently adsorbed onto the surface of the glass catalyst, frustrating subsequent steps in chemical evolution.
There is more that could be said. Still, the results of the FAME scientists’ work adds to the richness of possible prebiotic reactions and processes that could have conceivably contributed to chemical evolution. But when considering the geochemical relevance of this work, significant questions remain. In reality, origin-of-life researchers are no closer to understanding how life emerged through chemical evolution than they were in the 1950s when investigations into abiogenesis were first codified into a formal scientific discipline.
And for some people, this recognition renders materialistic models for the origin of life to be little more than a pile of broken shards.
Craig A. Jerome et al., “Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses,” Astrobiology 22 (June 2022): 629–636, doi:10.1089/ast.2022.0027.
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