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

Abstract

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. AbstractErwin 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. Witzany G. Pragmatic turn in biology the new paradigm that information is physically embodied in DNA sequences of four different types [1] . In contrast to the years before 1953, the question of "information" now became central: the components of DNA are simple chemicals, but the biological complexity that can be generated by the information of different sequences is revolutionary. The fundamental concept that integrated this new biological "information" with matter and energy was enshrined in the universal Turing machine and von Neumann's self-reproducing machines [2][3][4] . Consequently it follows that biology is physics with computation [5] . This was the core paradigm of molecular biology for almost the n...

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

“…to use codes in the context (pragmatics) of real-life world experience and -history (Witzany 2014(Witzany , 2015a. Applied to the virosphere, we outlined this in detail as a reply to outdated opinions concerning the role of virus within the tree of life (Villarreal and Witzany 2010).…”

Crucial steps to life: From chemical reactions to code using agents

“…From the pragmatic action theoretical perspective the variety of RNA agents that share the competence to act on nucleic acid sequences by several techniques (de novo generation, ligation/degradation, insertion/deletion, silencing, amplification, epigenetic markings, etc.) is coherent with the general assumption that no natural code codes itself but needs some competent agents that act on this code (Witzany, 2011(Witzany, , 2012(Witzany, , 2014bWitzany and Baluska, 2012;Salmena et al, 2011). Now we can ask how these agents evolve, how they interact, co-operate or compete, or even both, at different times, depending on the varying real life context.…”

“…Mathematical analyses of network formation cannot explain the rule-based real-life interactions of social groups that share genetic identities within historically grown ecospheres (Witzany, 2005(Witzany, , 2014b.…”

Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives

“…If we take reproduction only from the physico-chemical perspective, we have to realize that a clonal reproduction can occur only in an identical copy production of the former product, if there is some change in this “error replication” was the term for decades. Nevertheless, as demonstrated by the biocommunication theory—the generation of novelty by agents competent in editing biological codes—this is not an appropriate description 61 . Similar to the generation of poems in a natural language by humans in this reductionistic light would be an error prone reproduction of former available sign sequences into new ones—a rather curious conclusion.…”