We address issues of description of the origin and evolution of the genetic code from a semiotics standpoint. Developing the concept of codepoiesis introduced by Barbieri, a new idea of semio-poiesis is proposed. Semio-poiesis, a recursive auto-referential processing of semiotic system, becomes a form of organization of the bio-world when and while notions of meaning and aiming are introduced into it. The description of the genetic code as a semiotic system allows us to apply the method of internal reconstruction to (...) it: on the basis of heterogeneity and irregularity of the current state, to explicate possible previous states and various ways of forming mechanisms of coding and textualization. The revealed patterns are consistent with hypotheses about the origin and evolution of the genetic code. (shrink)

Umerez’s analysis made me aware of the fundamental differences in the culture of physics and molecular biology and the culture of semiotics from which the new field of biosemiotics arose. These cultures also view histories differently. Considering the evolutionary span and the many hierarchical levels of organization that their models must cover, models at different levels will require different observables and different meanings for common words, like symbol, interpretation, and language. These models as well as their histories should be viewed (...) as complementary rather than competitive. The relation of genetic language and human language is the central issue. They are separated by 4 billion years and require entirely different models. Nevertheless, these languages have in common a unique unlimited expressive power that allows open-ended evolution and creative thought. Understanding the nature of this expressive power and how it arises remains a basic unsolved problem of biosemiotics. (shrink)

The article deals with the notion of the genetic code and its metaphorical understanding as a “language”. In the traditional view of the language metaphor of the genetic code, combinations of nucleotides are signs of amino acids. Similarly, words combined from letters represent certain meanings. The language metaphor of the genetic code, 171–200, 2011) assumes that the nucleotides stay in the analogy to letters, triples to words and genes to sentences. We propose an application of mathematical linguistic methods on the (...) notion of the genetic code. We provide quantitative analysis of mRNA strings and natural language texts. This analysis is sensitive to the detection of the code units hierarchy. We also take into consideration a representative quantitative analysis of DNA, RNA and proteins. Our analysis of mRNA confirms an assumption that the design of the genetic code cannot analogize DNA bases and letters. The notion of the letter is much more appropriate if analogized with triplets or amino acids, 187–191, 2017). (shrink)

We discuss the role of linguistic metaphors as a cognitive frame for the understanding of genetic information processing. The essential similarity between language and genetic information processing has been recognized since the very beginning, and many prominent scholars have noted the possibility of considering genes and genomes as texts or languages. Most of the core terms in molecular biology are based on linguistic metaphors. The processing of genetic information is understood as some operations on text – writing, reading and editing (...) and their specification (encoding/decoding, proofreading, transcription, translation, reading frame). The concept of gene reading can be traced from the archaic idea of the equation of Life and Nature with the Book. Thus, the genetics itself can be metaphorically represented as some operations on text (deciphering, understanding, code-breaking, transcribing, editing, etc.), which are performed by scientists. At the same time linguistic metaphors portrayed gene entities also as having the ability of reading. In the case of such “bio-reading” some essential features similar to the processes of human reading can be revealed: this is an ability to identify the biochemical sequences based on their function in an abstract system and distinguish between type and its contextual tokens of the same type. Metaphors seem to be an effective instrument for representation, as they make possible a two-dimensional description: biochemical by its experimental empirical results and textual based on the cognitive models of comprehension. In addition to their heuristic value, linguistic metaphors are based on the essential characteristics of genetic information derived from its dual nature: biochemical by its substance, textual (or quasi-textual) by its formal organization. It can be concluded that linguistic metaphors denoting biochemical objects and processes seem to be a method of description and explanation of these heterogeneous properties. (shrink)

We discuss the role of linguistic metaphors as a cognitive frame for the understanding of genetic information processing. The essential similarity between language and genetic information processing has been recognized since the very beginning, and many prominent scholars have noted the possibility of considering genes and genomes as texts or languages. Most of the core terms in molecular biology are based on linguistic metaphors. The processing of genetic information is understood as some operations on text – writing, reading and editing (...) and their specification (encoding/decoding, proofreading, transcription, translation, reading frame). The concept of gene reading can be traced from the archaic idea of the equation of Life and Nature with the Book. Thus, the genetics itself can be metaphorically represented as some operations on text (deciphering, understanding, code-breaking, transcribing, editing, etc.), which are performed by scientists. At the same time linguistic metaphors portrayed gene entities also as having the ability of reading. In the case of such “bio-reading” some essential features similar to the processes of human reading can be revealed: this is an ability to identify the biochemical sequences based on their function in an abstract system and distinguish between type and its contextual tokens of the same type. Metaphors seem to be an effective instrument for representation, as they make possible a two-dimensional description: biochemical by its experimental empirical results and textual based on the cognitive models of comprehension. In addition to their heuristic value, linguistic metaphors are based on the essential characteristics of genetic information derived from its dual nature: biochemical by its substance, textual (or quasi-textual) by its formal organization. It can be concluded that linguistic metaphors denoting biochemical objects and processes seem to be a method of description and explanation of these heterogeneous properties. (shrink)

In the field of biosemiotics in our time, Ferdinand de Saussure's theory of semiology has been dismissed for its glottocentric, anthropocentric, and dyadic characteristics and as such unsuitable for the said field. Such accusation is symptomatic of an extremely narrow view of Saussure, which ignores the efforts he made in tackling problems concerning the unification of biology and semiotics . A broader view of Saussure, emerging from the newly-discovered orangery manuscripts along with his thought-provoking course lectures, reveals that his epistemology (...) is actually grounded in evolutionary differences and the concept of uniformitarianism. In order to demonstrate the value of his ideas, this paper proceeds through five sections. To begin with, the understandings and misunderstandings of key terms are summarized while seeking to reconcile arbitrary and relatively arbitrary modes of consciousness within the network of differences that Saussure proposes in his manuscripts. My study points out how such a network blurs disciplinary or systematic boundaries between language and non-verbal systems and how it might serve as a framework for appreciating true analogies between natural sciences and the science of language. The paradox of analogy, torn between the synchronic and diachronic schemes of time, is discussed. This unravels several strings that have made the functioning of analogy into such a delicate point in Saussure's theory of evolution. The concept of état de langue is made comprehensive in relation to appropriations of Darwinian model and Neo-Darwinian ideas. Saussure's model of evolution explicates the phenomenon of symbiogenesis, which is non-linear, non-adaptive, non-restrictive as regards localities, yet claims certain truths about nature and culture. Finally, my study draws attention to the implications of conceptualizing non-linear evolution within and across systems. There are indeed disparities between Saussure's epistemology and that of biosemiotics: nineteenth-century confused epistemology reoccurred within biosemiotics in its early phase. (shrink)