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Biochemists: RNA world has run its course. Huh?


RNA World is the theory that the earliest life forms used RNA to perform functions now carried out by DNA because RNA was more likely to somehow fall into place. From Jordana Cepelewicz at Quanta:

… Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely. In Wills’ view, RNA might have been able to catalyze its own formation, making it “chemically reflexive,” but it lacked what he called “computational reflexivity.”

“A system that uses information the way organisms use genetic information — to synthesize their own components — must contain reflexive information,” Wills said. He defined reflexive information as information that, “when decoded by the system, makes the components that perform exactly that particular decoding.” The RNA of the RNA world hypothesis, he added, is just chemistry because it has no means of controlling its chemistry. “The RNA world doesn’t tell you anything about genetics,” he said.

Nature had to find a different route, a better shortcut to the genetic code. Carter and Wills think they’ve uncovered that shortcut. It depends on a tight feedback loop — one that would not have developed from RNA alone but instead from a peptide-RNA complex. … More.

Rob Sheldon, our physics color commentator and author of Genesis: The Long Ascent, comments,

Isn’t it amazing how many evolution “solutions” illuminate a problem that was never mentioned previously? The article dishes on RNA-world only because the authors have another “ribosome-world” theory that solves the problem of functional information.

You also notice how these “worlds” are getting ever more complicated? The “first thing” that existed is now billions of times more complicated than coacervates. At what point is it simpler to believe that working cells just “appeared” out of nothing? I mean if you’re going to invoke a miracle, you might as well make sure it is big enough to not need any supporting characters.

Not to worry. This bus makes regular stops at RNA World.

See also: Welcome to “RNA world,” the five-star hotel of origin-of-life theories (Now check out.)

Mung @4: Exactly! Eric Anderson
Otangelo Grassy Very informative comment. Thanks. Dionisio
THE RNA WORLD, AND THE ORIGINS OF LIFE http://reasonandscience.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life The RNA world hypothesis, to be true, has to overcome major hurdles: 1. Availability of the 20 different amino acids on a prebiotic earth. So far, only 12 of the canonical ones have been synthesized in the laboratory 2. The twenty canonical ones would have to be selected amongst hundreds 3. The homochirality problem is unsolved. This is an “intractable problem” for chemical evolution 4. RNA has been called a “prebiotic chemist's nightmare” because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a “water problem”. Finally, some bonds in RNA appear to be “impossible” to form under any conditions considered plausible for early Earth. In chemistry, when free energy is applied to organic matter without Darwinian evolution, the matter devolves to become more and more “asphaltic”, as the atoms in the mixture are rearranged to give ever more molecular species. In the resulting “asphaltization”, what was life comes to display fewer and fewer characteristics of life. 6. Systems of interconnected software and hardware like in the cell are irreducibly complex and interdependent. There is no reason for information processing machinery to exist without the software and vice versa. 7. A certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded 8. RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes 9. In order a molecule to be a self-replicator, it has to be a homopolymer, of which the backbone must have the same repetitive units; they must be identical. On the prebiotic world, the generation of a homopolymer was however impossible. 10. Not one self-replicating RNA has emerged to date from quadrillions (10^24) of artificially synthesized, random RNA sequences. 11. Over time, organic molecules break apart as fast as they form 12. How could and would random events attach a phosphate group to the right position of a ribose molecule to provide the necessary chemical activity? And how would non-guided random events be able to attach the nucleic bases to the ribose? The coupling of a ribose with a nucleotide is the first step to form RNA, and even those engrossed in prebiotic research have difficulty envisioning that process, especially for purines and pyrimidines.” 13. L. E. Orgel: The myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA's catalytic potential. 14. Macromolecules do not spontaneously combine to form macromolecules 15. The transition from RNA to DNA is an unsolved problem. 16. To go from a self-replicating RNA molecule to a self-replicating cell is like to go from a house building block to a fully build house. 17. If two amino acids are located within the peptidyl transferase center, they will easily form a peptide bond. But as soon as you do that in the absence of the ribosome, the ends of the amino acids come together, forming a cyclic structure. Polymers cannot form. But if the ends are kept apart, by a theoretical primitive ribosome, a chain of peptide bonds could grow into a polymer. 30 Proponents of the RNA world hypothesis commonly argue that it has been proven that RNA's could self-replicate. Let's suppose that were true, that is as if self-replication could produce a hard drive. To go from a hard drive ( which by itself requires complex information to be assembled, in case of biology, DNA, not RNA since it's too unstable, ) that does not explain the origin of the information to make all life essential parts in the cell. It is as to go just from a hard drive storage device to a self replicating factory with the ability of self replication of the entire factory once ready, to respond to changing environmental demands and regulate its metabolic pathways, regulate and coordinate all cellular processes, such as molecule and building block biosynthesis according to the cells demands, depending on growth, and other factors. The ability of uptake of nutrients, to be structured, internally compartmentalized and organized, being able to check replication errors and minimize them, and react to stimuli, and changing environments. That's is, the ability to adapt to the environment is a must right from the beginning. If just ONE single protein or enzyme - of many - is missing, no life. If topoisomerase II or helicase are missing - no replication - no perpetuation of life. Why would a prebiotic soup or hydrothermal vents produce these proteins - if by their own there is no use for them? Paul Davies The Algorithmic Origins of Life Despite the conceptual elegance of the RNA world, the hypothesis faces problems, primarily due to the immense challenge of synthesizing RNA nucleotides under plausible prebiotic conditions and the susceptibility of RNA oligomers to degradation via hydrolysis 21 Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital-first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. Otangelo Grasso
I like how they make it look like the RNA is a nice linear strand. By what miraculous means is it prevented from folding up on itself into a knotted strand that then has to be untangled in order to be copied? Mung
gpuccio, You've made a very interesting observation: Their breakthrough conclusions are amazingly clever and far ahead of the rest of the academic crowd. :) Nobody could have thought of that until now. :) Dionisio
"Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely." What an insight! Who would ever have said such a thing? :) But, of course, there must be a "solution": "coevolution of RNA and peptides" Coevolution! Of course, of course... gpuccio
"...With little help from researchers RNA can replicate, evolve and interact with the environment..." Why didn't they say so many years ago when they came up with this dumb idea that dumb luck equals researchers or better? I think whoever collected Nobel Prizes or other for these ideas, should return all of them to dumb luck, who, or which, deserves it fully... BTW: Nobody seems to mention where the energy for the RNA world miracle came from? Was it dumb luck too or the sun? Can't remember any of this nonsense... J-Mac

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