DK: Darwinian evolution initiated as described in Figure 3 favors development of more complicated forms (i.e.,proto-aaRS) able to specifically interact with additional amino acids, thus assigning new codons.
Reply: This is a hypothesis. A claim. Where is the evidence that the evolution of proto-aaRS is possible or even feasible on prebiotic earth? Why would Darwinian evolution produce such complex proteins prebiotically, if there is no function for them, unless they perform their job in a fully developed translation system?
Claim: Based on Figure 2, we suggest two major periods of code development along with aaRS formation.Pre-LUCA I is the first period where only class II proto-aaRS existed with mostly GC-rich RNA andcharge Gly, Ala, Pro, Thr and Ser by protoforms of GlyRS, AlaRS, ThrRS, ProRS and SerRS. Duringpre-LUCA I, there were only short peptides with few motifs and limited functionality, therefore, for some of the essential functions of ribozymes would be selected.
Reply: How do you go from the hypothesized premise, to a logical follow-up, to say: therefore..... ?? This seems to me to be made up conjecture, without basis and evidence in the real world. if your proposal is Darwinian Evolution, there would have to be something to select to have an advantage of survival. I see nothing of the sort here.
Claim: The pre-LUCA II period wasestablished after the fidelity of the RNA-replication peptide was enhanced to incorporate efficientlyA and U bases during the first enzymatic RNA replication.
Reply: Here, again, you write about a hypothesized scenario, which exists in your ideas. Where is the scientific evidence as premise to make up such claims ?
On a side note about aaRS:
Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?
Question: In order to check and repair errors, you need knowledge of the correct, and the wrong state of affairs. How could this knowledge have emerged by non-intelligent mechanisms?
Aminoacyl-tRNA synthetase error minimization by preferential binding of the right amino acids, and selective editing and proofreading of near cognate amino acids
Aminoacyl-tRNA synthetase Pre-transfer editing: Pre-transfer editing has been described in both class I and class II aaRSs and takes place after aa-AMP synthesis but before the aminoacyl moiety is transferred to the tRNA. 9
Aminoacyl-tRNA synthetase Post-transfer editing: Post-transfer editing takes place after the transfer of the amino acid to the tRNA and involves the hydrolysis of the ester bond, in a domain separated from the active site.
Aminoacyl-tRNA synthetase Editing factors: Another important component of the translation quality control machinery is the trans-editing family, free-standing proteins that are not synthetases but are in some cases homologs to the editing domains of such enzymes. The role of these trans-editing factors is to clear the misacylated tRNA before it reaches the ribosome, acting as additional checkpoints to ensure fidelity.
Aminoacyl-tRNA synthetases (aaRSs), selectively hydrolyze ( chemical reaction in which a molecule of water ruptures one or more chemical bonds ) incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. 12
In addition to misactivation of genetically encoded proteinogenic amino acids (GPAs), cells also encounter non-proteinogenic amino acids (NPAs) environmentally or as metabolic by-products, and must discriminate against these substrates to prevent aberrant use in protein synthesis.
Furthermore: How do you explain the Intra-protein signalling channels in Aminoacyl-tRNA synthetase that are essential in translation ???
INTRAPROTEIN communication channels signal from one allosteric binding site where codon recognition takes place, to the other where after recognition, the right amino acid is selected, to be attached afterwards to the tRNA, which transfers it in the next step to the assembly site in the Ribosome, where the condensation reaction takes place, the amino acids is attached and protein polypeptide elongation takes place.
On a sidenote: