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We present a scenario for the origin of biological coding. In this context,coding is a semiotic relationship between chemical information stored in onelocation that links to chemical information stored in a separate location.Coding originated by the cooperative interaction of two, originally separatecollectively autocatalytic sets, one for nucleic acids and one for peptides.When these two sets interacted, a series of RNA-folding-directed processes ledto their joint cooperativity. The amino acyl adenylate, today amino acid-AMP,was the first covalent association made by these two collectively autocatalyticsets and solidified their interdependence. This molecule is a palimpsest ofthis era, and is a relic of the original semiotic, and thus coding,relationship between RNA and proteins. More defined coding was driven byselection pressure to eliminate waste in the collective autocatalytic sets.Eventually a 1:1 relationship between single amino acids and short RNA pieces(e.g., three nucleotides) was established, leading to what is today known asthe genetic code. Transfer RNA aminoacylating enzymes, or aaRSs, aroseconcomitantly with the advent of specific coding. The two classes of aaRSenzymes are remnants of the duality of complementary information in two nucleicacid strands, as originally postulated by Rodin and Ohno. Every stage in theevolution of coding was driven by the downward selection on the components of asystem to satisfy the Kantian whole. Coding was ultimately forced because therewere at least two chemically distinct classes of polymers needed for open-endedevolution; systems with only one polymer cannot exhibit this characteristic.Coding is thus synonymous with life as we know it, and can be thought of as aphase transition in the history of the universe.

Mixed Anhydrides at the Intersection Between Peptide and RNA Autocatalytic Sets: Evolution of Biological Coding