This article presents an update on known and unknown biological codes. While the genetic code has been recognized as a code for decades, most other codes were hidden in the shadow of this hallmark discovery. It was the dawn of the new millennium when the histone language and code were proclaimed in the years 2000 and 2001, respectively, marking the start of an explosion in the number of published codes across all biological disciplines since then. Actually, there are hundreds to (...) thousands of biological codes, but only a fraction—although still a substantial number—have been explicitly described as such. A first assessment of those codes allows for a simple categorization into structural and regulatory codes, at the same time maintaining Marcello Barbieri´s initial differentiation of organic versus neural codes. The article reviews prominent codes and showcases restriction-modification and toxin-antitoxin systems as code systems that have gone unrecognized until today. This article should read as a motivation for all those who want to discover ever more new codes—from literature or in the field. (shrink)

A promising recent approach for understanding complex phenomena is recognition of anticipatory behavior of living organisms and social organizations. The anticipatory, predictive action permits learning, novelty seeking, rich experiential existence. I argue that the established frameworks of anticipation, adaptation or learning imply overly passive roles of anticipatory agents, and that a fictionalist standpoint reflects the core of anticipatory behavior better than representational or future references. Cognizing beings enact not just their models of the world, but own make-believe existential agendas as (...) well. Anticipators embody plausible scripts of living, and effectively assume neo-Kantian or pragmatist perspectives of cognition and action. It is instructive to see that anticipatory behavior is not without mundane or loathsome deficiencies. Appreciation of ferally fictionalist anticipation suggests an equivalence of semiosis and anticipation. (shrink)

The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or (...) conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics. (shrink)

Biosemiotics argues that “sign” and “meaning” are two essential concepts for the explanation of life. Peircean biosemiotics, founded by Tomas Sebeok from Peirce’s semiotics and Jacob von Uexkül’s studies on animal communication, today makes up the mainstream of this discipline. Marcello Barbieri has developed an alternative account of meaning in biology based on the concept of code. Barbieri rejects Peircean biosemiotics on the grounds that this discipline opens the door to nonscientific approaches to biology through its use of the concept (...) of “interpretation.” In this article, it is noted that Barbieri does not adequately distinguish among Peirce’s semiotics, Peircean biosemiotics, and “interpretation-based” biosemiotics. Two key arguments of Barbieri are criticized: his limited view of science and his rejection of “interpretation-based” biosemiotics. My argument is based on tools taken from a different approach: Robert Rosen’s relational biology. Instead of “signs” and “meanings,” the study begins in this case from the “components” and “functions” of the organism. Rosen pursues a new definition of a law of nature, introduces the anticipatory nature of organisms, and defines the living being as a system closed to efficient cause. It is shown that Code Biosemiotics and Peircean biosemiotics can share a common field of study. Additionally, some proposals are suggested to carry out a reading of Rosen’s biology as a biosemiotic theory. (shrink)

Post-translational histone modifications and their biological effects have been described as a ‘histone code’. Independently, Barbieri used the term ‘organic code’ to describe biological codes in addition to the genetic code. He also provided the defining criteria for an organic code, but to date the histone code has not been tested against these criteria. This paper therefore investigates whether the histone code is a bona fide organic code. After introducing the use of the term ‘code’ in biology, the criteria a (...) putative organic code such as the histone code must conform to in order to be recognised as an organic code are described. Our current knowledge of histones and their major post-translational modifications, and the specific protein binding domains that recognise and translate these into specific biological effects, is then reviewed in detail. The histone modification system is then placed in the context of an organic code and it is concluded that it fulfils all the requirements of an organic code. The marks produced on histones by processes such as acetylation and methylation act as organic signs that are translated into unique biological effects, their biological meanings. These translations are accomplished by effector proteins that consist of a binding domain that recognises a specific histone mark and a regulatory domain that mediates the biological effect. Crucially, these domains can be experimentally interchanged between different effector proteins, thus altering the rules that specify the relationships between sign and meaning. The effector proteins therefore fulfil the role of adaptor molecules. (shrink)

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the (...) most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics. (shrink)

The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used to obtain the nucleotide sequences; In the first one, chunks of equal length are considered. In the second approach, the whole RNA genome is divided into parts by adenine or the most frequent nucleotide as a “space”. Rank–frequency distributions are studied in both cases. (...) The defined nucleotide sequences are signs comparable to a certain extent to syllables or words as seen from the nature of their rank–frequency distributions. Within the first approach, the Pólya and the negative hypergeometric distribution yield the best fit. For the distributions obtained within the second approach, we have calculated a set of parameters, including entropy, mean sequence length, and its dispersion. The calculated parameters became the basis for the classification of viruses. We observed that proximity of viruses on planes spanned on various pairs of parameters corresponds to related species. In certain cases, such a proximity is observed for unrelated species as well calling thus for the expansion of the set of parameters used in the classification. We also observed that the fifth most frequent nucleotide sequences obtained within the second approach are of different nature in case of human coronaviruses. We expect that our findings will be useful as a supplementary tool in the classification of diseases caused by RNA viruses with respect to severity and contagiousness. (shrink)

This paper analyses Bohr’s complementarity framework and applies it to biosemiotic studies by illustrating its application to three existing models of living systems: mechanistic biology, Barbieri’s version of biosemiotics in terms of his code biology and Markoš’s phenomenological version of hermeneutic biosemiotics. The contribution summarizes both Bohr’s philosophy of science crowned by his idea of complementarity and his conception of the phenomenon of the living. Bohr’s approach to the biological questions evolved – among other things – from the consequences of (...) an epistemological lesson of quantum theory and in light of complementarity of observer as a priori living creature and ex post scientific explanation of the living. In a manifestation of the phenomenon of the living, each model of living system and its description makes accessible – from its own presuppositions, contexts and concepts – some features which are not accessible from the others. Nevertheless, for a general understanding of that phenomenon, incompatible sophisticated approaches are equally necessary. Bohr’s epistemology of complementarity turns out to be a heuristic and methodical framework for testing the extent to which biosemiotics can become one of the special sciences or its potential as a cross-disciplinary branch of study. (shrink)

In the ‘Barbieri’s Concept of Mechanisms’ section on page 12 of above mentioned article.

The fossil record shows that the stromatolites built by cyanobacteria 2 and 3 billion years ago are virtually identical to those built by their modern descendants, which is just a part of much evidence revealing that bacteria have barely changed in billions of years. They appeared very early in the history of life and have conserved their complexity ever since. The eukaryotes, however, did the opposite. They repeatedly increased the complexity of their cells and eventually broke the cellular barrier and (...) gave origin to all living creatures that we see around us. This gives us one of the major problems in evolution: why have the prokaryotes maintained the same complexity throughout the history of life while the eukaryotes have become increasingly more complex? Here it is shown that a solution does exist, but it is based on experimental data that so far have largely been ignored. It is based on the discovery that, in addition to the genetic code, many other organic codes exist in living systems. The potential to generate organic codes was already present in the common ancestor but was not transmitted indefinitely to all its descendants. After the genetic code and the signal transduction codes that gave origin to the first cells, the prokaryotes evolved no other organic code, whereas the ancestors of the eukaryotes continued to explore the coding space and gave origin to splicing codes, histone code, cytoskeleton codes, tubulin code, compartment codes, and sequence codes. This experimental fact suggests that the prokaryotes did not increase their complexity because they did not evolve new organic codes, whereas the eukaryotes became increasingly more complex because they maintained the potential to bring new codes into existence. (shrink)

There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids. The error-minimization theory maintains that in primitive systems the apparatus of protein synthesis was extremely prone to errors, and postulates that the genetic code evolved in order to minimize the deleterious effects of the (...) translation errors. This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity and eventually removed it altogether. This proposal is distinct from the stereochemical and the coevolution theories because they do not contemplate any ambiguity in the genetic code, and it is distinct from the error-minimization theory because ambiguity-reduction is fundamentally different from error-minimization. The concept of ambiguity-reduction has been repeatedly mentioned in the scientific literature, but so far it has remained only an abstract possibility because no model has been proposed for its mechanism. Such a model is described in the present article and may be the first step in a new approach to the study of the evolution of the genetic code. (shrink)

This essay employs Charles Peirce’s triadic semiotics in order to develop a biosemiotic theory of life that is capable of illuminating the function of information in living systems. Specifically, I argue that the relationship between biological information structures , selecting environments, and the adapted bodily processes of living organisms is aptly modelled by the irreducibly triadic relationship between Peirce’s sign, object, and interpretant, respectively. In each instance of information-based semiosis, the information structure is a complex informational sign that represents the (...) informational object ; and the bodily, behavioral, mental, or intellectual processes that are organized by the informational sign to more or less accurately interpret the present environment constitute a complex informational interpretant—a living, interpreting organism. The essay begins by discussing the precise sense in which this biosemiotic theory is based upon Charles Peirce’s semiotic theory. Next, the theory is developed at length in relation to genetic information structures. Finally, I present a brief outline of how the theory applies to neural and linguistic information structures. The essay concludes with a reflection upon the anti-reductionist implications of the theory. (shrink)

This article argues that many, if not most, behavior descriptions and sequencing are in essence an interpretation of signs, and are evaluated as sequences of signs by researchers. Thus, narrative analysis, as developed by Barthes and others, seems best suited to be used in behavioral/biosemiotic studies rather than mathematical modeling, and is very similar to some classic ethology methods. As our brain interprets behaviors as signs and attributes meaning to them, narrative analysis seems more suitable than mathematical modeling to describe (...) and study behavior. Mathematical models are, on many occasions, extremely reductionist and simplifying because of computational and/or numerical representation limitations that lead to errors and straitjacketing interpretations of reality. Since actual animals are not as optimal in real life as our mathematical models, here it is proposed that we should consider logical/verbal models and semantic interpretations as equally or even better suited for behavioral analysis, and refrain from enforcing mathematical modeling as the only way to study and understand biological problems, especially those of a behavioral and biosemiotic nature. (shrink)

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)

Barbieri introduced and developed the concept of organic codes. The most basic of them is the genetic code, a set of correspondence rules between otherwise unrelated sequences: strings of nucleotides on the one hand, polypeptidic chains on the other hand. Barbieri noticed that it implies ‘coding by convention’ as arbitrary as the semantic relations a language establishes between words and outer objects. Moreover, the major transitions in life evolution originated in new organic codes similarly involving conventional rules. Independently, dealing with (...) heredity as communication over time and relying on information theory, we asserted that the conservation of genomes over the ages demands that error-correcting codes make them resilient to casual errors. Moreover, the better conservation of very old parts of the genome demands that they result from combining successively established nested codes such that the older an information, the more numerous component codes protect it. Barbieri’s concept of organic code and that of genomic error-correcting code may seem unrelated. We show however that organic codes actually entail error-correcting properties. Error-correcting, in general, results from constraints being imposed on a set of sequences. Mathematical equalities are conveniently used in communication engineering for expressing constraints but error correction only needs that constraints exist. Biological sequences are similarly endowed with error-correcting ability by physical-chemical or linguistic constraints, thus defining ‘soft codes’. These constraints are moreover presumably efficient for correcting errors. Insofar as biological sequences are subjected to constraints, organic codes necessarily involve soft codes, and their successive onset results in the nested structure we hypothesized. Organic codes are generated and maintained by means of molecular ‘semantic feedback loops’. Each of these loops involves genes which code for proteins, the enzymatic action of which controls a function needed for the protein assembly. Taken together, thus, they control the assembly of their own structure as instructed by the genome and, once closed, these loops ensure their own conservation. However, the semantic feedback loops do not prevent the genome lengthening. It increases both the redundancy of the genome and the information quantity it bears, thus improving the genome reliability and the specificity of the enzymes, which enables further evolution. (shrink)

In biosemiotics, some oppose the study of sign relations to empirical work on bio-mechanisms. Urging consilience between these views, we show the value of Alain Berthoz’s concept of simplexity. Its heuristic power is to present molecules, cells, organisms and communities as using tricks to self-fabricate by agglomerating ‘simplex’ bio-mechanisms. Their properties enable living systems to self-sustain, adapt and, at best, to thrive. But simplexity also empowers agents to engage with their surroundings in novel ways. Life thus not only generates know-how (...) but also social organisation. With languaging, people can act and inhibit: they can also simplexify. As a result, we can see a fruit as ripe, feel when things are awry or behave in ways likely to be judged to be apt. While all living beings make situated use of the historical and the local, humans also bind these with the use of both practices and artifacts. As a result, brains come to emulate what occurs in-between persons and their surroundings. In pursuing the basis for our powers, we focus on inhibition. This simplex trick enables a plant to use dormancy, a bird to learn, and a person to mesh languaging with other aspects of action/perception. Indeed, inhibition enriches human style phenomenology as impersonal resources are used to expand our epistemic horizons. Experience links a self-fabricating body, ancient bio-mechanisms, community-based concerns and epigenetically derived know-how. (shrink)

The possible evolutionary significance of epigenetic memory and codes is a key problem for extended evolutionary synthesis and biosemiotics. In this paper, some less known original works are reviewed which highlight theoretical parallels between current evolutionary epigenetics, on the one hand, and its predecessors in the eco-physiology of higher nervous activity, on the other. Recently, these areas have begun to converge, with first evidence now indicating the possibility of transgenerational epigenetic inheritance of conditional associations in the mammalian nervous system, and (...) related findings in other taxa. This can serve as an interesting example of evolutionary code-making, where the molecular mechanisms underlying arbitrary associations between stimuli involve lasting changes in gene expression that may be transmitted epigenetically across generations, and which in some cases could be further assimilated into the genome over subsequent evolution. Although preliminary, such epigenetic scenarios would also offer an interesting, if so far overlooked parallel to earlier research carried out by one of I.P. Pavlov’s leading students, acad. P.K. Anokhin, and his colleagues, but also by eminent eco-physiologists of the time, several of whom offered arguments for the possibility of unconditional reflexes representing evolutionarily later, specialized, and reduced forms of associative reflexes, from which they may be derived. Although discarded under the growing dominance of modern synthesis, these early epigenetic investigations may deserve renewed attention in the modern context, and if further confirmed, could open essentially new perspectives on the morphofunctional evolution of the nervous system. (shrink)

The article reconciles contentious issues between code biology and biosemiotics. The framework of semantic biology and molecular meaning woven around organic codes by Marcello Barbieri defied classical informational conceptualizations of meaning in the biological realm while the discourse on meaning and agency and their respective (in)dependency on interpretation continues. Whereas the role of codes in agency is often secondary to other aspects, I present here a more consistent picture– integrating codes and artifacts to smoothly transcend from the world of mechanistic (...) molecular meaning to organismic agency. Interpretation is presented as a call-to-action based on intraindividual states, and sense-making as call-to-change based on interindividual communication. (shrink)

This article deals with the question of how self-organization in living organisms is realized. Self-organization may be observed in open systems that are out of equilibrium. Many disequilibria-conversion phenomena exist where free energy conversion occurs by spontaneously formed engines. However, how is self-organization realized in living entities? Living cells turn out to be self-organizing disequilibria-converting systems of a special kind. Disequilibrium conversion is realized in a typical way, through employing information specifying protein complexes acting as nano engines. The genetic code (...) enables processing of information—derived from coding DNA—to produce these molecular machines. Hence, information is at the core of living systems. Two promising approaches to explaining living cells containing sequences carrying information are mentioned. Also discussed is the question of whether a second concept of self-organization—namely, the Kantian concept—applies. (shrink)

In this article two questions are discussed with regard to semiosis in protein biosynthesis for nano engines. (1) What kind of semiosis is involved in the construction of these proteins? and (2) How can we explain the semiotic process observed? With regard to the first issue we draw attention to comparisons between semiosis in protein biosynthesis and human natural language. The notion of normativity appears to be of great importance for both. A comparison also demonstrates differences. Nevertheless, because of the (...) normative symbolic information processing in it, we suggest to employ the term symbolic reference (employed in linguistics as a distinguishing feature of human language) to indicate the semiotic processes in protein biosynthesis. With regard to explaining semiosis in protein synthesis we compare different approaches. We conclude that a Kantian approach should be preferred. In such an approach strengths of the mechanistic and organicist approaches can be combined, and the observed symbolic information processing acknowledged. (shrink)

Peirce is the father of semiotics. However, his theory was developed long before the developments in information theory. The codification procedures studied by the latter turn out to be crucial also for biology. At the root of both information and semiosis there are equivalence classes. In the case of biological systems, we speak of functional equivalence classes. Equivalence classes represent the grid that organism impose on biochemical processes and signals of the external or internal environment. The whole feedback circuit that (...) is built in this way allows information control. Symbolic systems represent another kind of dealing-with-information as far as they deal with the matching of our concepts with the world. (shrink)