Codepoietic biological evolution: From the origin of life to eukaryogenesis

Evolution is an intrinsic property of autopoietic systems performing natural computation, which is based on an internal formal self-description representing the arrangement of digital and analog coding structures. Autopoietic systems are capable of assigning new values to previously unproven (ambiguous) statements, which occurs, in particular, in conditions beyond the limits of adaptability. This process, defined by Marcello Barbieri as codepoiesis, occurs through the introduction of new codes or the rearrangement of existing ones, increasing the computing power of biological systems. Formally, it corresponds to Gödel numbering, representing a non-conventional algorithm that takes a sentence from a formal system and turns it into a numerical metacode, uniquely encoding each sentence in a given formal system. Ribotype, as a set of RNA molecules, serves as a codemaking component that logically preceded the information-storage (genotype) and metabolic (phenotype) components and determined the codepoietic process throughout biological evolution. In the early stages of evolution, alternative realizations of codepoiesis occurred in the appearance of distinct domains of Bacteria and Archaea. Both bacteria and archaea utilize horizontal gene transfer in evolution; in bacteria, it is constrained by DNA sequence divergence and repair mechanisms, while in archaea, it is more internally driven via the use of unique mechanisms like cell fusion, lower stringency for homology in recombination, and specialized, aggregate-based DNA repair. The interaction between bacteria and archaea in evolution led to different types of symbiotic relations and finally resulted in the appearance of eukaryotic cells, which triggered further complexification and the emergence of multicellularity. It is concluded that the codepoietic process represented the basic driving mechanism of biological evolution from the appearance of the first living organisms to the development of complex behaviour and consciousness.