RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems

Arguments against the stereochemical theory of the origin of the genetic code

I support the hypothesis that stereochemical theory is unnatural because it is based on artificial and not simple mechanisms as required for a good theory. Indeed, for stereochemical theory the origin of the genetic code requires, in the first place, a primary interaction, for example, between a codon and an amino acid on a proto-tRNA. But this interaction is a necessary but not sufficient condition, because the evolution of the mRNA molecule, which would really define the genetic code, is still necessary for the complete origin of the genetic code. In other words, the need for two molecules, tRNA and mRNA, to define the genetic code, with their at least partial independence would testify to an artificial mechanism typical of stereochemical theory because it would not guarantee that amino acid-codon (or -anticodon) assignments realized in the first phase of the origin of the genetic code, would necessarily be maintained also in the second phase of its completion. Furthermore, the genetic code encodes for amino acids but amino acids are not the truly functional aspect, they are only intermediaries, of their final products, proteins, which are the only true entities actually coded by genes. Therefore, it would not be immediately clear from the point of view of stereochemical theory, to say why it is the amino acids and not the proteins that are involved in the primary stereochemical interactions that would have led to the origin of the genetic code. Hence, at least some of the stereochemical theory models would be not very credible, not being able to say much about the coding of proteins by genes. Finally, I inspected the genetic code table following the logic that more closely similar amino acids should - according to stereochemical theory - be coded by highly similar codons, finding that only a few pairs of amino acids actually satisfy this logic, further discretizing the stereochemical theory.

The Origin of Genetic Code and Translation in the Framework of Current Concepts on the Origin of Life

The origin of genetic code and translation system is probably the central and most difficult problem in the investigations on the origin of life and one of the most complex problems in the evolutionary biology in general. There are multiple hypotheses on the emergence and development of existing genetic systems that propose the mechanisms for the origin and early evolution of genetic code, as well as for the emergence of replication and translation. Here, we discuss the most well-known of these hypotheses, although none of them provides a description of the early evolution of genetic systems without gaps and assumptions. The RNA world hypothesis is a currently prevailing scientific idea on the early evolution of biological and pre-biological structures, the main advantage of which is the assumption that RNAs as the first living systems were self-sufficient, i.e., capable of functioning as both catalysts and templates. However, this hypothesis has also significant limitations. In particular, no ribozymes with processive polymerase activity have been yet discovered or synthesized. Taking into account the mutual need of proteins and nucleic acids in each other in the current world, many authors propose the early evolution scenarios based on the co-evolution of these two classes of organic molecules. They postulate that the emergence of translation was necessary for the replication of nucleic acids, in contrast to the RNA world hypothesis, according to which the emergence of translation was preceded by the era of self-replicating RNAs. Although such scenarios are less parsimonious from the evolutionary point of view, since they require simultaneous emergence and evolution of two classes of organic molecules, as well as the emergence of synchronized replication and translation, their major advantage is that they explain the development of processive and much more accurate protein-dependent replication.

Are molecular alphabets universal enabling factors for the evolution of complex life?

Terrestrial biosystems depend on macromolecules, and this feature is often considered as a likely universal aspect of life. While opinions differ regarding the importance of small-molecule systems in abiogenesis, escalating biological functional demands are linked with increasing complexity in key molecules participating in biosystem operations, and many such requirements cannot be efficiently mediated by relatively small compounds. It has long been recognized that known life is associated with the evolution of two distinct molecular alphabets (nucleic acid and protein), specific sequence combinations of which serve as informational and functional polymers. In contrast, much less detailed focus has been directed towards the potential universal need for molecular alphabets in constituting complex chemically-based life, and the implications of such a requirement. To analyze this, emphasis here is placed on the generalizable replicative and functional characteristics of molecular alphabets and their concatenates. A primary replicative alphabet based on the simplest possible molecular complementarity can potentially enable evolutionary processes to occur, including the encoding of secondarily functional alphabets. Very large uniquely specified ('non-alphabetic') molecules cannot feasibly underlie systems capable of the replicative and evolutionary properties which characterize complex biosystems. Transitions in the molecular evolution of alphabets can be related to progressive bridging of barriers which enable higher levels of biosystem organization. It is thus highly probable that molecular alphabets are an obligatory requirement for complex chemically-based life anywhere in the universe. In turn, reference to molecular alphabets should be usefully applied in current definitions of life.