The origin of the genetic code and origin of ideas.

Inouye et al. (2020) use the observation that Ser is coded in the genetic code by two blocks of codons that differ on more than one base to understand some aspects of the origin of the genetic code organization. I argue instead that this observation per se cannot be used to understand any aspect of the origin of the genetic code, unless it is accompanied by other assumptions concerning in the specific case: (i) the ancestrality of some amino acids, (ii) the hypothesis that the first mRNA to be translated was poly-G, which can be translated into poly-Gly, and (iii) an evolutionary mechanism for the genetic code origin based on the duplication of tRNAs. However, both the tRNA duplication mechanism and the existence of poly-G as the first mRNA to be translated are not corroborated as mechanisms through which the genetic code would have been structured. For example, the origin of the actual mRNA should have been preceded by the evolution of a proto-mRNA which evidently already coded for more than one amino acid. Therefore, when it evolved from proto-mRNA, the mRNA should already have coded for more than one amino acid. In other words, poly-G as mRNA would most likely never have existed because the first mRNAs already had to code for more than one amino acid. On the contrary, all these assumptions would have been operational if the observations of Inouye et al. (2020) had been discussed within the coevolution theory of the origin of the genetic code, which they do not.

An RNA Ring was Not the Progenitor of the tRNA Molecule.

I analyzed the model that suggests that an RNA ring might have been the progenitor of the tRNA molecule (Demongeot and Moreira in J Theor Biol 249:314-324, 2007; Demongeot and Seligmann in J Mol Evol 1-23, 2019a; Demongeot and Norris in Life 9(2):51, 2019). In particular, I analyze three ways in which this precursor, especially in its RNA hairpin form, could have evolved into the complete tRNA molecule. These three modalities are based on multiple duplication events, and therefore, appear to be less parsimonious than that which assumes that this molecule originated through one duplication of a single hairpin structure. The conclusion is, therefore, that the latter model appears to be preferable with respect to that of the RNA ring, also because there are many independent observations and some of a historical nature that would corroborate it in an extraordinary way.

Common ancestry of eukaryotes and Asgardarchaeota: Three, two or more cellular domains of life?

There is much evidence that eukaryotes have many traits in common with archaea and in phylogenetic analyses they are closely linked. In particular, it has been suggested that Asgardarchaeota would be part of the same clade of eukaryotes. If so - and being the difference between Asgardarchaeota and eukaryotes very large - then all this would imply that their common ancestor was a progenote, i.e. a protocell in which the relationship between genotype and phenotype was still evolving. This, in turn, would imply that true cells would appear on the tree of life only later, that is to say, only when the ancestor of Asgardarchaeota and the one of eukaryotes appeared. However, this way of seeing would define these ancestors as primary fundamental cells, namely, as cellular domains of life because it would be in this evolutionary stage that true cells would appear for the first time. Finally, the Asgardarchaeota-eukaryote transition is discussed, that is, some aspects of eukaryogenesis and the taxonomic rank of eukaryotes are analyzed.

A comparison between two models for understanding the origin of the tRNA molecule.

I respond to criticisms raised by Kim et al. (2018) to my model concerning the origin of the tRNA molecule. In particular, their model would hypothesize the tRNA originated due to the ligation of three hairpin structures followed by two deletions, while my model predicts that this molecule derived from the assembly of only two hairpin-like structures. Thus, using the Ockham razor, the latter model would be chosen because it required fewer hypotheses. Furthermore, the predictions on homology between the different regions of the tRNA molecule as predicted by my model would be statistically more significant than those predicted by their model. Moreover, it would be above all the existence of molecular fossils - i.e. the split tRNA genes - to corroborate the model of the assembly of only two hairpins. These fossils would be completely absent from the Kim et al. (2018) model.

A qualitative criterion for identifying the root of the tree of life.

I suggest -as a criterion for identifying the root of the tree of life - that the group of organisms with the greatest molecular variability in phylogenetic deep characters represents the root of this tree. Indeed, it is expected that in the circumstance of the origin of a given trait several biochemical pathways would have contemporary evolved, for example. The presumed very strong selective pressure acting for the first time on the appearance of the function of that phylogenetically deep trait would have caused its multiple appearance exactly because these traits were originating for the first time. As a result, several pathways would have evolved simultaneously to solve that impelling function. In addition, the evolutionary stage of the progenote would seem that favours per se the formation of these multiple traits - that is to say, performing equivalent or similar function - because it would represent the evolutionary stage in which the origins of all cellular structures occurred. Therefore, it is in this particular evolutionary circumstance that it was - by definition - in the condition that allowed the emergence, for example, of several alternative biochemical pathways to solve the same evolutionary task. Consequently, I here discussed the possibility that the superphylum of DPANN archaea and that of CPR bacteria - especially if considered as a single group of organisms - are/is considered the root of the tree of life, exactly because they would seem to exhibit relatively higher molecular variability in phylogenetically deep characters when compared with other phyla of archaea and bacteria.

The universal ancestor, the deeper nodes of the tree of life, and the fundamental types of primary cells (cellular domains).

I have analyzed the deep nodes of the topology of the tree of life as supported by Castelle and Banfield (2018). My arguments imply that the last universal common ancestor (LUCA) and the ancestors of bacteria and archaea were of progenotes. Furthermore by this topology, the bacterial candidate phyla radiation (CPR) and the superphylum of archaea known as DPANN would have derived directly from these pre-cellular ancestors. Such proto-cell ancestors would have given rise to four new fundamental types of primary cells-four cellular domains of life, because ordinarily such progenote ancestors would not be classified as cells.

A Non-neutral Origin for Error Minimization in the Origin of the Genetic Code.

Massey (J Mol Evol 67:510-516, 2008; J Theor Biol 408:237-242, 2016; Nat Comput. https://doi.org/10.1007/s11047-017-9669-3, 2018) claims that the error minimization of the genetic code is derived by means of a neutral process and was not due to the action of natural selection. Here, I argue that this neutralist hypothesis of the origin of error minimization is not based directly on any neutral process but it could be only indirectly. On the contrary, it has been natural selection that has acted during the origin of the genetic code determining the property that similar amino acids are coded by similar codons within the genetic code table.

On Earth, there would be a number of fundamental kinds of primary cells - cellular domains - greater than or equal to four.

In the studies regarding the deep nodes of the tree of life, there is an assumption that might be false. Usually, it is assumed that these nodes - that is to say, those for example regarding the ancestors of bacteria and archaea - are believed to be completely evolved cells and not protocells. In other words, in these studies, it is rarely stressed that, on the contrary, these nodes might correspond to evolutionary stages of premature cells, namely, progenotes. This observation has extremely relevant consequences. Indeed, if the nodes, for example, of the ancestors of bacteria and archaea would correspond to progenotic evolutionary stages, then this should imply that the number of fundamental kinds of primary cells (cellular domains), present on Earth, would be at least four and not two or three as it is currently believed. As a matter of fact, if these two nodes would correspond to two progenotes then, evidently, the fully evolved cells (genotes) - to which we should refer to be able to establish how many fundamental kinds of primary cells are present on Earth - would characterize less deep nodes of these two. Thus, since there is a strong evidence that the ancestors of archaea and bacteria have been of progenotes, these reasonings would assume a particular importance. For instance, it is maintained that one of these fundamental primary cells might be represented by the typical cell of superphylum of the DPANN. In other words, the DPANN superphylum might be a so far non-recognized cellular domain of life.

The genetic code is not an optimal code in a model taking into account both the biosynthetic relationships between amino acids and their physicochemical properties.

We have considered a model for the origin of the genetic code that takes into account the two factors that have determined its evolution: the biosynthetic relationships between amino acids and their physicochemical properties. The model evaluates the biosynthetic relationships between amino acids considering of constraints based on the biosynthetic families of amino acids. These biosynthetic constraints are able to define six subsets of codes - that we have analyzed - in which the evolution of the genetic code might have passed. At the same time, the physicochemical properties of amino acids have been described by means of two scales of polarity, considered solely or combined with the molecular volume of amino acids. Furthermore, we have considered three cost functions. The results maintain the hypothesis that the genetic code organization is not optimal even in these subsets containing a very limited number of elements. That is to say, the genetic code is not a local or absolute minimum. For instance, only a few amino acid exchanges would have rendered the genetic code more optimized or even they would have transformed it into a completely optimized code. This would imply that the evolution of the genetic code, not considering these possibilities, has evolved through different pathways from the one that was oriented to a high optimization. Moreover, the combination of polarity and the molecular volume of amino acids results to have been more significant than when the only polarity is considered, in conditioning the evolution of the genetic code contrary to that reported in the literature. However, this is not such to produce an organization of the genetic code optimized if referred to these two properties. Nevertheless, these two properties being crucial in defining the structure of proteins, they would have affected the origin of the genetic code by means of the selective pressure directed to improve the ancestral enzymatic catalysis. As a whole these observations contradict the predictions of the physicochemical theories of the origin of the genetic code because the non-optimization of the genetic code organization - even in subsets of codes with a very low element number - would deny the absolute importance of the physicochemical properties of amino acids in its structuration, which, on the contrary, is expected from these theories. Conversely, these same observations would be in perfect agreement with the coevolution theory of the origin of the genetic code because they would explain both the not fundamental role of the physicochemical properties in organizing the genetic code and the importance of these properties in the evolution of coded catalysis - that is to say, of the genetic code - both predicted by this last theory.

Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory.

Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code". And, given that in the genetic code table are mirrored both the biosynthetic relationships between amino acids and their physico-chemical properties, all this would be a test that would falsify the physico-chemical theories of the origin of the genetic code. That is to say, if the physico-chemical properties of amino acids had a fundamental role in organizing the genetic code, then we would not have duly revealed the presence - in the genetic code - of the biosynthetic relationships between amino acids, and on the contrary this has been observed. Therefore, this falsifies the physico-chemical theories of genetic code origin. Whereas, the coevolution theory of the origin of the genetic code would be corroborated by this analysis, because it would be able to give a description of evolution of the genetic code more coherent with the indisputable empirical observations that link both the biosynthetic relationships of amino acids and their physico-chemical properties to the evolutionary organization of the genetic code.

The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal significance is measurable. These two codes codify roughly for the two ARS classes, in particular, the CAG code for the class II while the UNN/NUN code for the class I. Furthermore, the subclasses of ARSs show a statistical significance of their distribution in the genetic code table. Nevertheless, the more sensible explanation for these observations would be the following. The observation that would link the two classes of ARSs to the CAG and UNN/NUN codes, and the statistical significance of the distribution of the subclasses of ARSs in the genetic code table, would be only a secondary effect due to the highly significant distribution of the polarity of amino acids and their biosynthetic relationships in the genetic code. That is to say, the polarity of amino acids and their biosynthetic relationships would have conditioned the evolution of ARSs so that their presence in the genetic code would have been detectable. Even if the ARSs would not have-on their own-influenced directly the evolutionary organization of the genetic code. In other words, the role that ARSs had in the origin of the genetic code would have been entirely marginal. This conclusion would be in perfect accord with the predictions of the coevolution theory. Conversely, this conclusion would be in contrast-at least partially-with the physicochemical theories of the origin of the genetic code because they would foresee an absolutely more active role of ARSs in the origin of the organization of the genetic code.

An Autotrophic Origin for the Coded Amino Acids is Concordant with the Coevolution Theory of the Genetic Code.

The coevolution theory of the origin of the genetic code maintains that the biosynthetic relationships between amino acids co-evolved with the genetic code organization. In other words, the metabolism of amino acids co-evolved with the organization of the genetic code because the biosynthetic pathways of amino acids occurred on tRNA-like molecules. Thus, a heterotrophic origin of amino acids-also only of those involved in the early phase of the structuring of the genetic code-would seem to contradict the main postulate of the coevolution theory. As a matter of fact, this origin not being linked to the metabolism of amino acids in any way-being taken from a physical setting-would seem to remove the possibility that this metabolism had instead heavily contributed to the structuring of the genetic code. Therefore, I have analyzed the structure of the genetic code and mechanisms that brought to its structuring for understanding if the coevolution theory is compatible with autotrophic or heterotrophic conditions. One of the arguments was that an autotrophic origin of amino acids would have the advantage to be able to directly link their metabolism to the structure of the genetic code if-as hypothesized by the coevolution theory-the biosyntheses of amino acids occurred on tRNA-like molecules. Simultaneously, a heterotrophic origin would not have been able to link the metabolism of amino acids to the structure of the genetic code for the absence of a precise determinism of allocation of amino acids, that is to say of a clear mechanism-linked to tRNA-like molecules, for example-that would have determined the specific pattern observed in the genetic code of the biosynthetic relationships between amino acids. The conclusion is that an autotrophic origin of coded amino acids would seem to be the condition under which the genetic code originated.

The lack of foundation in the mechanism on which are based the physico-chemical theories for the origin of the genetic code is counterposed to the credible and natural mechanism suggested by the coevolution theory.

I analyze the mechanism on which are based the majority of theories that put to the center of the origin of the genetic code the physico-chemical properties of amino acids. As this mechanism is based on excessive mutational steps, I conclude that it could not have been operative or if operative it would not have allowed a full realization of predictions of these theories, because this mechanism contained, evidently, a high indeterminacy. I make that disapproving the four-column theory of the origin of the genetic code (Higgs, 2009) and reply to the criticism that was directed towards the coevolution theory of the origin of the genetic code. In this context, I suggest a new hypothesis that clarifies the mechanism by which the domains of codons of the precursor amino acids would have evolved, as predicted by the coevolution theory. This mechanism would have used particular elongation factors that would have constrained the evolution of all amino acids belonging to a given biosynthetic family to the progenitor pre-tRNA, that for first recognized, the first codons that evolved in a certain codon domain of a determined precursor amino acid. This happened because the elongation factors recognized two characteristics of the progenitor pre-tRNAs of precursor amino acids, which prevented the elongation factors from recognizing the pre-tRNAs belonging to biosynthetic families of different precursor amino acids. Finally, I analyze by means of Fisher's exact test, the distribution, within the genetic code, of the biosynthetic classes of amino acids and the ones of polarity values of amino acids. This analysis would seem to support the biosynthetic classes of amino acids over the ones of polarity values, as the main factor that led to the structuring of the genetic code, with the physico-chemical properties of amino acids playing only a subsidiary role in this evolution. As a whole, the full analysis brings to the conclusion that the coevolution theory of the origin of the genetic code would be a theory highly corroborated.

A Model for the Origin of the First mRNAs.

I present a model for the evolution of the genetic code that seems to predict, in a totally natural way, the origin of the first mRNAs. In particular, the model--bestowing to peptidated-RNAs the major catalytic role in the phase that triggered the genetic code origin--suggests that interactions between peptidated-RNAs led to the synthesis of these ancestral catalysts. Within every group of these interactions, a pre-mRNA molecule evolved that was able to direct all interactions between peptidated-RNAs of that particular group. This represented an improvement in the coding of these interactions compared to the interaction groups that did not evolve these pre-mRNAs. This would represent a natural and intrinsic tendency. Therefore, these molecules of pre-mRNAs were positively selected because they improved the synthesis of the catalysts through this first form of coding of interactions among peptidated-RNAs. Thus, according to the model were the pairings--involving a base number greater than three (ennuplet code)-between peptidated-RNAs and pre-mRNAs that would represent the first form of the genetic code. The evolution of this ennuplet code to the triplet code might have been simply triggered by the natural tendency to make the reading module-that is the interactions between peptidated-RNAs and pre-mRNAs--of the different ennuplets to the triplet uniform, because in this way the heterogeneity existing in interactions between the aminoacylated or peptidated-RNAs and pre-mRNAs was eliminated. That is to say, there might have been the natural tendency toward the triplets because these would have made these interactions more efficient, given that the ennuplets were at least more cumbersome and therefore less economic and with an inferior adaptive value; and also because the triplets would represent the simpler choice among that available given that the doublets would have codified too few meanings and quartets instead too many. Therefore, the genetic code would result from a very long era of interactions among peptidated-RNAs under the continuous and fundamental selective pressure for improving catalysts' syntheses and thus catalysis. The model is strongly corroborated by the explanation that the tmRNA molecule (transfer-messenger RNA) would seem to be the very molecule of pre-mRNAs that the model predicts. In other words, the tmRNA would be the molecular fossil of the evolutionary stages that led to the appearance of the first mRNAs.

The non-biological meaning of the term "prokaryote" and its implications.

The meaning of the term prokaryote is critically analyzed. The conclusion reached is that this term does not have a real biological sense, above all because we are not able to link to this term a specific biological characteristic, i.e. the hypothetical evolutionary stage of the prokaryote would seem to have been unable to result in a completed cell, which could possibly be due to the recapitulation of the fundamental characteristics that might have been common to bacteria and archaea. This would define a biological immaturity of this evolutionary stage because otherwise we would have found traits already clearly defined at this level of cellular evolution. Therefore, the lack of well-defined traits characterising the prokaryote would seem to imply an evolutionary stage still in rapid evolution, i.e. with a tempo and a mode of evolution typical of a progenote. This in turn would seem to imply that the last universal common ancestor (LUCA) has been a progenote at least when the domains of life are only two-the bacterial and archaeal domains-because, in this case, the LUCA's node should coincide with that of prokaryote on the tree of life. Instead, if the root of the tree of life would be placed in the bacterial domain or in the archaeal one, we might again, very likely, have a LUCA with a character of progenote being, under these conditions, the LUCA a prokaryote-like organism.

On how many fundamental kinds of cells are present on Earth: looking for phylogenetic traits that would allow the identification of the primary lines of descent.

The phylogenetic analyses as far as the identification of the number of domains of life is concerned have not reached a clear conclusion. In the attempt to improve this circumstance, I introduce the concept that the amino acids codified in the genetic code might be of markers with outstanding phylogenetic power. In particular, I hypothesise the existence of a biosphere populated, for instance, by three groups of organisms having different genetic codes because codifying at least a different amino acid. Evidently, these amino acids would mark the proteins that are present in the three groups of organisms in an unambiguous way. Therefore, in essence, this mark would not be other than the one that we usually try to make in the phylogenetic analyses in which we transform the protein sequences in phylogenetic trees, for the purpose to identify, for example, the domains of life. Indeed, this mark would allow to classify proteins without performing phylogenetic analyses because proteins belonging to a group of organisms would be recognisable as marked in a natural way by at least a different amino acid among the diverse groups of organisms. This conceptualisation answers the question of how many fundamental kinds of cells have evolved from the Last Universal Common Ancestor (LUCA), as the genetic code has unique proprieties that make the codified amino acids excellent phylogenetic markers. The presence of the formyl-methionine only in proteins of bacteria would mark them and would identify these as domain of life. On the other hand, the presence of pyrrolysine in the genetic code of the euryarchaeota would identify them such as another fundamental kind of cell evolved from the LUCA. Overall, the phylogenetic distribution of formyl-methionine and pyrrolysine would identify at least two domains of life--Bacteria and Archaea--but their number might be actually four; that is to say, Bacteria, Euryarchaeota, archeobacteria that are not euryarchaeota and Eukarya. The usually accepted domains of life represented by Bacteria, Archaea and Eukarya are not compatible with the phylogenetic distribution of these two amino acids and therefore this last classification might be mistaken.

The split genes of Nanoarchaeum equitans have not originated in its lineage and have been merged in another Nanoarchaeota: a reply to Podar et al.

I reply to the suggestion of Podar et al. (2013) that the split genes of Nanoarchaeun equitans are a derived character, showing that their analysis is mistaken. In particular, I show that the split genes both proteins and tRNAs have not been split in N. equitans and have been on the contrary merged in the nanoarchaeon sequenced recently by Podar et al. (2013). This implies that the main argument of Podar et al. (2013) that there should be: "a unique propensity for splitting in the Nanoarchaeota that is most dramatically manifested in the Nanoarchaeum equitans lineage" is false. On the other hand, the analysis seems to favor the hypothesis that the split genes are an ancestral character. This would strengthen to greater extent a model for the origin of the tRNA molecule.

The genetic code did not originate from an mRNA codifying polyglycine because the proto-mRNAs already codified for an amino acid number greater than one.

I reply to Bernhart and Patrick (2014) that claim that the first amino acid to be codified in the genetic code was glycine, and that from mRNAs codifying for polyglycine originated all other codons of the genetic code. Indeed, given that the origin of protein synthesis should have preceded the one of the genetic code, then proto-mRNAs codifying for polimeric catalysts of the world in which originated the protein synthesis, should have been the more direct ancestors of mRNAs that originated in the world in which evolved the true genetic code. Therefore, it is clear that there would have been at least a partial evolutionary continuity between these proto-mRNAs and mRNAs. This evolutionary continuity has as logical consequence that cannot have existed of mRNAs codifying for only an amino acid because these mRNAs would descend from proto-mRNAs that already codified for more than one amino acid. Therefore, these mRNAs would not have reshaped their codifying capability to a single amino acid, without loss in the meaning of their coding, and this could not have occurred being counter selected. I also reply to other imprecisions made by Bernhart and Patrick (2014).

RNA editing and modifications of RNAs might have favoured the evolution of the triplet genetic code from an ennuplet code.

Here we suggest that the origin of the genetic code, that is to say, the birth of first mRNAs has been triggered by means of a widespread modification of all RNAs (proto-mRNAs and proto-tRNAs), as today observed in the RNA editing and in post-transcriptional modifications of RNAs, which are considered as fossils of this evolutionary stage of the genetic code origin. We consider also that other mechanisms, such as the trans-translation and ribosome frameshifting, could have favoured the transition from an ennuplet code to a triplet code. Therefore, according to our hypothesis all these mechanisms would be reflexive of this period of the evolutionary history of the genetic code.

Theories of the origin of the genetic code: Strong corroboration for the coevolution theory.

I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons and that of amino acids. Instead, the intervention of natural selection in organizing the genetic code would appear to be highly compatible with the main mechanism of structuring the genetic code as supported by the coevolution theory. This would make the coevolution theory the only plausible explanation for the origin of the genetic code.