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naraburns  nihil supernum  1yr ago (text post)   30433 thread views

Culture War Roundup for the week of November 21, 2022

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So I don't believe that number at all

That's your right of course but in the final accounting I'd take his word over yours.

you could totally imagine a "replicator" that barely works in specific contexts slowly evolving or something.

Why couldn't ribozymes evolve into dna-protein interactions? That seems very plausible.

Then where is the evidence for that wondrous mechanism? Or for it being workable, even if inefficient?

I like the turn of phrase once used by Land in his «Hell-baked» (on an adjacent topic): «machinery extant, or even rigorously imaginable». We can imagine pretty wild stuff, even perpetual motion engines or FTL travel, but it is not clear if your imagination is rigorous by the standards of current biomolecular knowledge. Often things that have been totally unworkable only become obviously unworkable and wild in retrospect; but that doesn't mean we should confuse the degree of our uncertainty about mechanisms and the probability of those things being workable. We do not know the bounds yet. We know the fundamental laws, though.

The entire chapter 11 of the book is devoted to walking through assumptions people can make for the world of plausible common ancestors of the DNA-based life that are substantially much simpler than LUCA or distributed-LUCA, and inherent inconsistencies of those models. In chapter 12 lies the reasoning for why we end up empty-handed when looking for very simple replicators and why the transition ought to have been that sharp. It begins with what sorts of replication can work at all, and the conditions for very basic protein motifs already ubiquitous in the inferred LUCA genome, such as the P-loop. Then it addresses the most simple model of all, RNA world:

Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication (the Eigen threshold): If the product of the error (mutation) rate and the information capacity (genome size) is below the Eigen threshold, there will be stable inheritance and hence evolution; however, if it is above the threshold, the mutational meltdown and extinction become inevitable (Eigen, 1971). The Eigen threshold lies somewhere between 1 and 10 mutations per round of replication (Tejero, et al., 2011); regardless of the exact value, staying above the threshold fidelity is required for sustainable replication and so is a prerequisite for the start of biological evolution (see Figure 12-1A). Indeed, the very origin of the first organisms presents at least an appearance of a paradox because 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 (Penny, 2005).

The crucial question in the study of the origin of life is how the Darwin-Eigen cycle started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses with the replication fidelity of only about 10–3 and viroids that replicate with the lowest fidelity among the known replicons (about 10–2; Gago, et al., 2009), replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required.

…Indeed, comparative-genomic reconstructions of the gene repertoire of LUCA(S) point to a complex translation system that includes at least 18 of the 20 aminoacyl-tRNA synthetases (aaRS), several translation factors, at least 40 ribosomal proteins, and several enzymes involved in rRNA and tRNA modification. It appears that the core of the translation system was already fully shaped in LUCA(S) (Anantharaman, et al., 2002).

…So an inevitable (even if perhaps counterintuitive) conclusion from the comparative analysis of ancient paralogous relationship between protein components of the translation system is that, with the interesting exception of the core ribosomal proteins, all proteins that play essential roles in modern translation are products of a long and complex evolution of diverse protein domains. Here comes the Catch-22: For all this protein evolution to occur, an accurate and efficient translation system is required. This primordial translation system might not need to be quite as good as the modern version, but it seems a safe bet that is must have been within an order of magnitude from the modern one in terms of fidelity and translation rates to make protein evolution possible.

The unique property of RNA that makes it a credible—indeed, apparently, the best—candidate for the central role in the primordial replicating system is its ability to combine informational and catalytic functions. Thus, it was extremely tempting to propose that the first replicator systems— the first life forms—consisted solely of RNA molecules that functioned both as information carriers (genomes and genes) and as catalysts of diverse reactions, including, in particular, their own replication and pre- cursor synthesis. This bold speculation has been spectacularly boosted by the discovery and subsequent study of ribozymes (RNA enzymes) […] All this progress notwithstanding, the ribozyme polymerases that are currently avail- able are a far cry from processive, sufficiently accurate (in terms of the Eigen threshold) replicases, capable of catalyzing the replication of exogenous templates and themselves. Enzymes with such proper- ties appear to be a conditio sine qua non for the evolution of the hypothetical RNA World. Besides, even the available ribozymes with the limited RNA polymerase capacity are rather complex molecules that consist of some 200 nucleotides and could be nontrivial to evolve in the prebiotic setting.

An estimate based on the functional tolerance of well-characterized ribozymes to mutations suggests that, at a fidelity of 10–3 errors per nucleotide per replicase cycle (roughly, the fidelity of the RNA-dependent RNA polymerases of modern viruses), an RNA “organism” with about 100 “genes” the size of a tRNA (80 nucleotides) would be sustainable. Such a level of fidelity would require only an order of magnitude improvement over the most accurate ribozyme polymerases obtained by in vitro selection. This might be an approximate upper bound of complexity on ensembles of co-evolving “selfish cooperators” that would have been the “organisms” of the RNA World. Even under the best-case scenario, the RNA World hardly has the potential to evolve beyond very simple “organisms.” To attain greater complexity, invention of translation and the Protein Breakthrough (the relegation of most catalytic activities to proteins) were required. […] The main general point about the evolution of translation is that selection for protein synthesis could not have been the underlying cause behind the origin of the translation system. To evolve this com- plex system via the Darwinian route, numerous steps are required, but proteins appear only at the last steps; until that point, an evolving organ- ism “does not know” how good proteins could be. As discussed in Chapter 9, many situations exist in which evolution seems to exhibit some foresight capability; however, these cases are effectively based on extrapolation, whereas, in the case of translation, there is nothing to extrapolate from. […] Thus, the only conceivable route for the emergence of translation seems to be exaptation: Intermediate stages in the evolution of the translation system must have been selected for functions other than protein synthesis. [no exaptation model makes good sense.]

natural flow reactors etc.

Only after a great deal of this review he gets to that lower bound of initial complexity.

I admit that the likelihood of him being wrong is a hell of a lot more than 1 to -1000th, but there is good reason to state that figure without caveats as the best estimate for the likelihood of abiogenesis in a single Hubble volume, given all we know.

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