Pragmatic turn in biology: From biological molecules to genetic content operators

Abstract

Erwin Schrödinger‘s question “What is life?” received the answer for decades of “physics + chemistry”. The concepts of Alain Turing and John von Neumann introduced a third term: “information”. This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings “sequence space”. Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract ”sequence space” concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

Keywords: Life; Information; Quasi-species; Incompleteness theorem; Genetic content operators

Core tip: Meaning in natural languages/codes and communication is context dependent. In contrast, artificial formalizable (algorithm based) languages employ a “universal“ syntax in order to determine meaning independent of the contextual circumstances. It is empirically evident that no natural language speaks itself as no natural code codes itself. It always requires living agents that share a competence to generate and interpret these natural codes. Therefore I suppose that changes in the genetic code, which are of evolutionary relevance, are rather the result of fine-tuned processes by a large network of mobile genetic elements, persistent viruses, its defectives and other genetic parasites that alter DNA sequences. In this respect DNA remains as ecosphere habitat for social interacting RNA inhabitants. This represents a pragmatic turn in biology from syntax centered molecular biology to pragmatics centered agents interactions.