A general model on the origin of biological codes

For a long time it has been assumed that the rules of the genetic code were determined by chemistry either by stereochemical affinities or by metabolic reactions but the experimental evidence has revealed a totally different reality; it has been shown that any codon can be associated to any amino acid, and this means that there is no deterministic link between them. The genetic code, in other words, is based on arbitrary, or conventional, rules and this raises a formidable problem: how can arbitrary rules exist in Nature? We know that such rules exist in culture, but there is an abyssal difference between biology and culture, because the cultural codes are short-lived, whereas the biological codes are the most conserved entities in evolution. Biological codes, in other words are fundamentally different from cultural codes and we do need a model that makes us understand how they came into being. In this paper it is shown that the origin of biological codes takes place in five phases (beginning, evolution, optimization, major transition and conservation) and this suggests a general model for their development. According to this model, a biological code evolves in a system as a means of solving a local problem, but then it becomes the tool of a much larger change in macroevolution. This is the great potential of the biological codes: their ability to bring into existence absolute novelties that change the whole course of the history of life. Different major transitions were based on different codes, but we can also recognize some common features in all of them. This indicates that coding is a universal mechanism that Nature has employed many times in the course of evolution to solve a wide variety of different problems.