« on: 27/05/2020 21:31:24 »
In the 1950's, it was discovered, by pure science observations; no bias, that proteins fold with exact folds. Like repeatable science experiments, protein fold the same way each time no matter who does the observing. Although this observation has been duplicated in the lab and is common knowledge for over 60 years, there is still no statistical explanation. The main theory cannot even explain this yet is remains.
This is no mystery if one assumes first that evolution selects for proteins that fold rapidly. At a deeper level chemistry is based on quasicrystalline projections from 12-D space. This is the data space of the 24-D code space of the extended binary Golay code space. Its structure group is the uniquely privileged group of finite simple groups. Why quasicrystals can form is another mystery solved by these facts.
However, I have found seams that can make things easier. Imagine an applied approach that only needs water to explain the parallel universe of the organics. Now we do it the other way around and water into the diversity of organics. But we could use one simple molecule; H2O, to simulate any organic in water since water will forma unique shell around any organic or organic surface. Modeling becomes an order of magnitude easier,
On the contrary modeling is easier if you do it in terms of the main phases involved. That way you are dealing with primary interactions rather than secondary interactions of water in nonaqueous phases. The three main biochemically active liquid phases of early life are water, toluene, and ASF (ammonium sulfate in formamide). The last two are residual liquids after deep freezing. All the solvents, of course, have multiple solutes.
I have been working on describing in detail the first generation ribosome, which includes a Halloysite nanotube. The precursor to the larger unit of the modern ribosome was bound to the end of this nanotube. This mechanism traveled down the protochromosomes that had a cylindrical core protein passing through 12 bp (base pair) stem loops of RNA, These were translated either into GSGSGS type sequences by the 1 bit code ( G=guanosine -> glycine=G, C=cytodine -> serine=S) or into tetrapeptides by the 3 bp code. The insertion of an extra S giving an SSGSS seqence within a poly-GS sequence triggered the formation of the LVPR tetrapeptide (L=leucine, V=valine, P=proline, R=arginine). These sequences are found in modern protein linkers. Hexa-LVPR peptides with a poly-GS linker running the length of the protochromosome was such a more highly stabilizing core protein for the 3bp code that the intermediate 2 bp code was never filled. (P kinks the polypeptide promoting a circular conformation; R binds to phosphate in RNA.)
LV was subsequently changed to IV (I=isoleucine, which increased the attraction to toluene.) Upon decomposition of the organism IV sequences were protected from racemization. (Presumably they had been intercolated into Halloysite nanotubes serving as a storage area.) Thus there are CC meteorites with enantiomeric excesses only in I and V. The PR sequences led to PR rich histones, the modern protein spools upon which DNA is wound. The protochromosomes had variable RNA binding energies. This was affected by molecules similar to metatetramethylferrocenium formate. The formate would bind to ribose and the positive end of arginine, reducing the binding energy to RNA. The larger part of this molecule was in the hydrophobic part of the core protein. The ribose/formate complex led to enantiomeric excesses of sugar acids in some CC meteorites.
As you can see the structure of this first generation ribosome is strongly validated by modern data. This last universal common ancestor was a eukaryote that has so far not left distinctive fossil evidence. I will expand on my reply at 24/05/2020 22:29:56, in which I mistakenly referred to the Mozambique rift (opposite side of a crustal plate). The late protoeukaryotic refuge was at the Iapetus rift, whose modern crustal location is around Iceland. Since then the area has been deeply covered in basalt so no fossils can be found. After beginning in the early Cryogenian this rift completely separated the earlier terrains of modern Scandinavia and North America just before the beginning of the Cambrian radiation of higher eukayotes.