Theoretical origin of life; based on calculus and chance (Introduction)

by David Turell , Friday, March 15, 2019, 19:00 (2080 days ago) @ David Turell

The working of the genome is analyzed and 'discovery' and magical self-organization of a mass of unexplained suddenly appearing proteins on a rocky planet is proposed to start life:

https://www.biorxiv.org/content/biorxiv/early/2017/05/22/140657.full.pdf

"Concluding remarks
" The direct evolution of a coupled world of genetic information and encoded functional proteins in real-¬‐world molecular biology is far more plausible than any scenario in which there was an initial RNA World of ribozymes sophisticated enough to operate a genetic code. The preservation of encoded information processing during the historically necessary transition of any such system to the ancestral aaRS enzymes of molecular biology appears to be impossible, rendering the notion of an RNA Coding World scientifically superfluous. While this conclusion is grounded in an understanding of exactly how the dynamical architecture of molecular biology can solve the computational chicken-¬‐egg paradox of code evolution, it leaves a host of problems concerning the evolution of the complex apparatus of translation unresolved. On the other hand, recognition of the role of reflexivity in driving the intrinsic self-¬‐organisation of molecular biological coding has stimulated a deeper enquiry into the relationships between structural determinants of the aaRS coding apparatus (Carter and Wills, 2017). The formal requirement for reflexive information that encodes assignment catalysts according to the rules of the code they execute is grounded in a more elementary, physical reflexivity. Instantiation of the computational requirement of reflexivity in the dynamic processes of real-¬‐world molecular interactions demanded of nature that it fall upon, or we might say “discover”, a self-¬‐amplifying set of nanoscopic “rules” for the construction of the pattern that we recognize as “coding relationships” between the sequences of two types of macromolecular polymers. However, nature is innately oblivious to such abstractions: the matching of amino acids to codons is achieved by folded aaRS structures that are, at least according to quantum mechanical demands, “accidentally” produced through the computationally controlled placement of amino acids with different physical properties in specific positions of variants of two basic protein folds, labeled “Class I” and “Class II”. Even this simplest of distinctions had to be a discovery of itself, a “bootblock” that could be built upon and elaborated into the improbably refined system of the universal genetic code through the hierarchical nesting of variant codon-¬‐amino acid pairings. This evolution was continuously driven by newly distinguishable structural elements of folded proteins being able to distinguish more accurately between amino acids and corresponding tRNA sequence motifs, at each point precisely instantiating a “difference that makes a difference”, which Bateson (1972) defined as the elementary unit of naturally functional information. Although the basic steps taken by nature cannot yet be outlined, we are nonetheless approaching the point where aaRS phylogenetics studies can take us closer to that goal. Furthermore, we can now understand how the self-¬‐organised state of coding can be approached “from below”, rather than thinking of it as existing on the verge of a catastrophic fall over a cliff of errors: an incremental improvement in the accuracy of translation will produce replicase molecules that are more faithfully produced from the gene encoding them, probably leading to an incremental improvement in information copying, in turn providing for the selection of narrower genetic quasispecies, an incrementally better encoding of the protein functionalities on which the system relies, including accurate translation. The vicious circle can wind up rapidly from below as a self-¬‐amplifying process, rather than winding down the cliff from above, the push-¬‐pull tension stably maintaining the system near a tipping point, where, all else being equal, informational replication and translation remain impedance matched--that is,until the system falls into a new vortex of possibilities.”

Comment: Yes, a new vortex of possibilities. Under this bright cloud of smoke-screen verbiage all depends upon chance and magical self-organization from suddenly appearing proteins. Read skeptically.

Note this admission from the abstract:

" The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide·RNA world."