Code Biology

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 (including observers) 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.

Over the years within his logic Peirce proposed many analogous formal definitions of the sign as an element of a triadic relation associating it with an object and an interpretant. However, in 1904 he expanded this triad to a system of six relates, while in 1906 he referred in draft letters and manuscripts to the sign as a medium for the communication of a form. Meanwhile, in the final lecture on pragmatism of 1903, he had claimed that the elements of every concept enter logical thought by the gate of perception and exit by the gate of purposeful action, and the article posits this principle as a basic but necessary framework for the process of semiosis. In 1907 he further advanced the principle that signs and their meaning can be recognised by inference only-they are not given as such in perception. This raises the question of how perception accords with the process of semiosis and with the notion that the sign functions as a medium in this process. The paper explores the implications and analytical potential of this relation associating what is deemed a Peircean conception of semiosis with perception and logic.

The consideration of semiotic relations and operations in genetic coding leads to a revision of the accepted understanding of the sign as a kind of substitute associated with some object by social conventions. The new perspective allows us to eliminate the conventional and socially determined characteristics of signs as conditio sine qua non and adopt a broader understanding of sign production as an inherent property of systems that control information processes. An exemplification of such a system is the GC (the genetic code), it encompasses correlation schemes between nucleotides and amino acids. It also includes operations that regulate and interact with the context (environment). The recognition of conventionality as a necessary condition can be reformulated and replaced by interaction schemes. As a first step, we reconsider the representation of the genetic code as a static vocabulary and recognize its dynamic character – in this case a sign as determined association between the signified and the signifier arises every time as a result of an operation performed here and now, as a codepoiesis (or semiopoiesis) in action. At the same time, the nature of semiosis at each stage of the gene expression (DNA - mRNA - tRNA) is changed. These stages can be considered as a transition from hypertext (genome as a set or sequence of texts) to a single text (gene) and sign (tRNA). A full-fledged sign as a triadic relationship (sign vehicle – sense – meaning) is represented by tRNA. Additionally, in association with mRNA, tRNA acts as a second-order signifier for a complex sign: codon of mRNA → {(tRNA anticodon +tRNA) → amino acid}.

Cet article propose une mise à jour de la phytosémiotique en articulant codes, signes et actes de transformation au sein du vivant végétal. À partir de l’héritage d’Uexküll et des apports de la biosémiotique, il montre comment les plantes interprètent des informations et modèlent leur Umwelt par des processus matériels de signification, du niveau cellulaire à l’écologique. En reconsidérant l’auto-organisation comme un phénomène sémiotique, le texte discute la pertinence de notions comme lecture, mémoire et apprentissage appliquées aux végétaux, en dialogue avec les théories de Barbieri (sémiotique minimale) et des approches contemporaines de la sensibilité végétale. L’argument central défend une continuité des interactions sémiotiques et met en évidence le rôle des codes (biochimiques, électriques) dans la production d’actions transformantes, soulignant ainsi la dimension matérielle, située et relationnelle de la signification chez les plantes.

The paper demonstrates that the concept proposed by Alexander Spirov reflects the ongoing paradigm shift and inspires new approaches in biosemiotics and semiotic pragmatics. The shift involves a move from describing coding languages to describing languages that regulate them. This requires considering the agentivity (or quasi-agency) of sign systems, which leads to a scenario where the sign system functions as both its own subject and object, thus reviving Peirce's idea of the sign as a quasi-mind. An analysis of the primary regulatory mechanisms shows that regulatory codes: (a) create specific conditions for coding, (b) govern and control coding processes, and (c) consist of the same elements as coding elements, although are interpreted differently. Their interpretant is not amino acids or proteins but the processes of activation or suppression. Communication and information processes at the biomolecular level allow pragmatics to be understood as semiotic operations associated with intrasystem self-regulation and the system's external interaction with its context (environment). The processes within a system, as described by Alexander Spirov, create contexts and interfaces for interaction between different systems. This implies that a system of signs can act as an agent that communicates or interprets, akin to Peirce's notion of the quasi-mind. This understanding has the potential to significantly reshape the current approaches to pragmatics and semiosis.

The development of artificial intelligence and the new understanding of biomolecular processes for transmitting genetic information have emphasized the necessity to consider semiotic activity, that may operate autonomously from human cognition. In this regard, Charles Peirce's latest conception of semiosis is of particular interest. For Peirce, semiosis is an interpretation that doesn't necessitate an external interpreter. A sign is viewed as a quasimind, and semiotic processes are carried out by these signs, specifically through the quasiminds that are embedded within them: a quasi-utterer and a quasi-interpreter. Semiosis can thus be viewed as an ongoing, personalized interaction of structural semiotic entities (quasiminds). The latest findings in molecular genetics and their implications in biosemiotics shed light on a unique aspect of interpretation: it can occur without an external interpreter owing to its mechanism of self-organization. By studying communication and information processes at the biomolecular level, we can redefine pragmatics as operations intricately linked with systemic self-regulation and interaction with the environment.

The paper formulates the concept of linguistic Umwelten out of Uexküll’s definition of Umwelt in terms of a closed unity of perceptual and agentive worlds. Linguistic Umwelten must be plural because language cannot explain the unparalleled cumulative or historical aspect of human culture, if language is abstractly construed as a faculty that is distinct from the traditions in which it manifests. Relying on authors like Peirce, Tullio De Mauro, and Marcello Barbieri, I argue that each human being dwells in a minimum of two Umwelten, namely the world of perceptual objects and at least a world of words. Employing Giorgio Prodi’s insights and the idea of distributed languaging, I translate Saussure’s circuit de la parole in terms of a Funktionskreis connecting the speaker’s effector organ with the hearer’s perception organ: individual organisms A and B, namely the speaker and the hearer, are organically entangled during their conversation and a linguistic Umwelt emerges as a pairing of A’s effectual world with B’s receptive world as much as a pairing of B’s effectual world with A’s receptive world. To show the explanatory potential of the new concept of linguistic Umwelten, I use it to account for polysemiosis (the fact that human communication always employs at least two semiotic systems). Eventually, I derive the concept of personal Umwelt from the previously introduced notions of the world of perceptual objects and the linguistic Umwelt: the personal Umwelt is the individual perceptual world as affected by the intersubjective linguistic Umwelt.

This article demonstrates that the concept proposed by Alexander Spirov reflects the ongoing paradigm shift and inspires new approaches in biosemiotics and semiotic pragmatics.
The shift involves a move from describing coding languages to describing languages that regulate them. This requires considering the agentivity (or quasi-subjectivity) of sign systems,
which leads to a scenario where the sign system functions as both its subject and object, thus
reviving Peirce's idea of the sign as a quasi-mind. An analysis of the primary regulatory
mechanisms shows that regulatory codes: (a) create specific conditions for coding, (b) govern
and control coding processes, and (c) consist of the same elements as coding elements, although are interpreted differently. Their interpretant is not amino acids or proteins but the
processes of activation or suppression. Communication and information processes at the biomolecular level allow pragmatics to be understood as semiotic operations associated with intra-system self-regulation and the system's external interaction with its context (environment). The processes within a system, as described by Alexander Spirov, create contexts and
interfaces for interaction between different systems. This implies that a system of signs can  act as an agent that communicates or interprets, akin to Peirce's notion of the quasi-mind. This understanding has the potential to significantly reshape the current approaches to pragmatics and semiosis.
Keywords: genetic information, pragmatics, biosemiotics, regulatory codes, Charles Peirce
Показано, что предложенная А.В. Спировым концепция есть следствие и свидетельство происходящей смены парадигм и может послужить импульсом для новых
направлений в биосемиотике и для семиотической прагматики в целом. Происходит
сдвиг акцента с описания языков кодирования на описание языков управления языками
кодирования, и это приводит к необходимости рассмотрения агентивности (или квазисубъектности) знаковых систем. В результате сама знаковая система выступает
как сама-по-себе субъект и объект, что воскрешает идею Ч. Пирса о знаке как квазиразуме. Анализ базовых регуляторных механизмов выявляет, что регуляторные коды a)
создают особые условия для кодирования; б) управляют процессами кодирования;
в) состоят из тех же элементов, что и кодирующие элементы, но читаются отличным образом: их интерпретантой будут не аминокислоты или белки, а операции активации или опрессии. Коммуникация и информационные процессы на биомолекулярном уровне позволяют понимать прагматику как семиотические операции, связанные
с внутрисистемной саморегуляцией и внешнесистемным взаимодействием с контекстом (средой). Описанные А.В. Спировым процессы развертывания внутрисистемной
информации оказываются также и генерацией контекстов и интерфейсов межсистемного взаимодействия. В этом смысле знаковая система может функционировать
как говорящий или интерпретирующий агент, или пирсовский квазиразум. Подобный
подход может радикально изменить представления о прагматике и семиозисе.
Ключевые слова: генетическая информация, прагматика, биосемиотика, рег

The submitted thesis deals with the topic of organic memory, its definition and function, as well as its conceptions from various historical points of view. I use the term “organic memory” in respect to some authors who have previously dealt with this subject (Elsasser 1987, Otis 1994, Barbieri 2003) and also as a term by which to represent a kind of memory distinct from neuronal/cerebral memory.

The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits. (i) It makes a bridge to neurobiological models of the brain that have also adopted an evolutionary dynamics point of view, thus opening a new horizon for studying how human brains achieve the remarkably complex competence for language. And (ii) it suggests a new foundation for studying cultural language change as an evolutionary dynamics process. The paper sketches this novel perspective, provides references to empirical data and computational experiments, an...

This paper proposes, from a semiotic perspective on cognition and working towards a cognitive perspective on semiosis, an analysis of the inter-semiotic translation processes (Torop, 2002) surrounding the maguey and other cacti, ancestral plants that now decorate public spaces in Mexico City. The analysis involves three semiotics, Peircean semiotics, bio-semiotics, and cultural semiotics, and draws from other disciplines, such as Biology, Anthropology, and Sociology, in order to construct a dialogue on a transdisciplinary continuum. The maguey and other cactus plants are resources that have a variety of uses in different spaces. In rural spaces, they are used for their fibers (as thread in gunny sacks, floor mats, and such), for their leaves (as roof tiles, as support beams, and in fences), for their spines (as nails and sewing needles), and their juice is drunk fresh (known as aguamiel or neutli), fermented (a ritual beverage known as pulque or octli), or distilled (to produce mescal, tequila, or bacanora). In urban spaces, cacti are used as an element of identity in the Mexico City coat of arms, as decorative plants, and as plant/objects for everyday usescoat-hooks, trash receptacles, and as refuge for street vendors (underemployment). Cacti are also used with religious significance, at the feet of the Virgin of Guadalupe, who protects passers-by. Cacti are plants that grow naturally in Mexican rural spacesideal environments and habitats for thembut which are planted and cared for by human hands in urban spaces creating a socio-cultural landscape. This transition from rural to urban spaces is what we consider to be the inter-semiotic translation from rural to urban, from natural to cultural, from biological to socio-cultural (artistic, literary, cinematic, and pictorial). We arrive at the interesting conclusion that in Mexico, these plants hold importance today (in the 21 st century) because they are inscribed in a biological/natural/ruralhuman/cultural/urban responsive and cyclical process, with all the biological, sociological, anthropological and economic meaning that is produced in that cycle.

For a long time it has been assumed that the rules of the genetic code were determined by chemistryeither by stereochemical affinities or by metabolic reactionsbut the experimental evidence has revealed a totally different reality; it has been shown that any codon can be associated to any amino acid, and this means that there is no deterministic link between them. The genetic code, in other words, is based on arbitrary, or conventional, rules and this raises a formidable problem: how can arbitrary rules exist in Nature? We know that such rules exist in culture, but there is an abyssal difference between biology and culture, because the cultural codes are shortlived, whereas the biological codes are the most conserved entities in evolution. Biological codes, in other words are fundamentally different from cultural codes and we do need a model that makes us understand how they came into being. In this paper it is shown that the origin of biological codes takes place in five phases (beginning, evolution, optimization, major transition and conservation) and this suggests a general model for their development. According to this model, a biological code evolves in a system as a means of solving a local problem, but then it becomes the tool of a much larger change in macroevolution. This is the great potential of the biological codes: their ability to bring into existence absolute novelties that change the whole course of the history of life. Different major transitions were based on different codes, but we can also recognize some common features in all of them. This indicates that coding is a universal mechanism that Nature has employed many times in the course of evolution to solve a wide variety of different problems. 1.1. Beginning The first rules of a code appear in a system as a means of performing a particular function, and their arbitrariness implies that the first version of a code is necessarily ambiguous.

The discovery of the double helix suggested in no uncertain terms that the sequence of nucleotides is the information carried by a gene (Watson and Crick 1953). A few years later, the study of protein synthesis revealed that the sequence of nucleotides in genes determines the sequence of amino acids in proteins, with a process that amounts to a transfer of linear information from genes to proteins. In both types of molecules, therefore, biological information was identified with, and defined by, the specific sequence of their subunits. This idea was immediately accepted into the Modern Synthesis because it provided the molecular basis of both heredity and natural selection. Heredity became the transmission of information from one generation to the next, the short-term result of molecular copying. The long-term repetition of copying, on the other hand, is inevitably accompanied by errors, and in a world of limited resources not all copies can survive and a selection is bound to take place. That is how natural selection came into being. It is the long-term result of molecular copying, and can exist only in a world of informational molecules. Information has become in this way the key concept of modern biology, but also the object of a fierce controversy. The reason is that information, heredity and natural selection simply do not exist in the world of chemistry, and this creates a contrast with the idea that "life is chemistry". This view was proposed for the first time by Jan Baptist van Helmont (1648), and has been re-proposed countless times ever since. One of the most recent formulations has been given by Günther Wächtershäuser (1997) in these terms "If we could ever trace the historic process backwards far enough in time, we would wind up with an origin of life in purely chemical processes". Wächtershäuser claimed that "information is a teleological concept", and that science does not really need it: "On the level of nucleic acid sequences it is quite convenient to use the information metaphor… and apply teleological notions such as 'function' or 'information'… but in the course of the process of retrodiction the

The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost 4 billion years later, at the end of life's history. Today it is widely assumed that these are the only codes that exist in Nature, and if this were true we would have to conclude that codes are extraordinary exceptions because they appeared only at the beginning and at the end of evolution. In reality, various other organic codes (codes between organic molecules) have been discovered in the past few decades. In 1975, the American biochemist Gordon Tomkins published a paper entitled The Metabolic Code. Biological symbolism and the origin of intercellular communication (Tomkins 1975). That was the very first announcement of a new organic code after the discovery of the genetic code, but tragically Tomkins died that very year and his new world of organic symbolism remained unexplored. Some 10 years later, Edward Trifonov started a lifelong campaign in favour of the idea that genomes carry several overlapping codes simultaneously, not just the classic triplet code, and gave them the collective name of sequence codes (Trifonov 1987, 1989, 1999). Finally, at the end of the 1990s and in the early 2000s, a whole set of new organic codes came to light. Among them: the adhesive code (

Biosemiotics asserts the idea that semiosis is fundamental to life, and that all living creatures are therefore semiotic systems. The idea itself is strongly supported by the evidence of the genetic code-but thus far it has made little impact in the scientific world, and is largely regarded as the basis for a philosophy of meaning, rather than a basis for a science of meaning. This is regrettable, but perhaps understandable from the scientists' point of view. Scientists know that the cell is the necessary unit of all life. I will argue here, then, that Biosemiotics can become a science only if it can prove that the cell is, in fact, a semiotic system-i.e., that semiosis exists at the cellular level. To do this, we first need to define what is semiosis, so that we can be explicit about what exactly constitutes a semiotic system. So far, we have had two main answers to this question. One is the model proposed by Saussure, who defined a semiotic system as a duality of ' signifier and signified'. The other is the model of Peirce, who pointed out that interpretation is an essential component of semiosis and defined a semiotic system as a triad of ' sign, object and interpretant'. After the discovery of the genetic code, each of these two models have been applied to biology and have given rise to two distinct schools of biosemiotics. One is the school of Marcel Florkin (1974), which is based on the model of Saussure, and the other is the school of Thomas Sebeok (1972, 2001), which is based on the model of Peirce. Unfortunately, neither of them can be applied to the cell, and that is why most biologists continue to be skeptical about biosemiotics. There is however a third model of semiosis that is actually applicable to the cell. It is based on the theory that the cell is a trinity of genotype, phenotype and ribotype (Barbieri 1981, 1985, 2003). Here, the ribotype is the ribonucleoprotein system of the cell and represents its ' codemaker' , i.e., the seat of the genetic code. This model assumes that semiosis is defined by coding, not by interpretation, and is therefore referred to as the code model of semiosis. This paper is dedicated to illustrating this third model and, above all, to showing that the cell is a true semiotic system.

Modern biology has not yet come to terms with the presence of many organic codes in Nature, despite the fact that we can prove their existence. As a result, it has not yet accepted the idea that the great events of macroevolution were associated with the origin of new organic codes, despite the fact that this is the most parsimonious and logical explanation of those events. This is probably due to the fact that the existence of organic codes in all fundamental processes of life, and in all major transitions in the history of life, has enormous theoretical implications. It requires nothing less than a new theoretical framework, and that kind of change is inevitably slow. There are too many facts to reconsider, too many bits of history to weave together in a new mosaic. But this is what science is about, and the purpose of the present paper is to show that it can be done. More precisely, it is shown that the whole natural history of the brain can be revisited in the light of the organic codes. What is described here is only a bird's-eye view of brain macroevolution, but it is hoped that the extraordinary potential of the organic codes can nevertheless come through. The paper contains also another message. The organic codes prove that life is based on semiosis, and are in fact the components of organic semiosis, the first and the most diffused form of semiosis on Earth, but not the only one. It will be shown that the evolution of the brain was accompanied by the development of two new types of sign processes. More precisely, it gave origin first to interpretive semiosis, mostly in vertebrates, and then to cultural semiosis, in our species.

In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the daughter cells. This intriguing phenomenon is achieved by a variety of processes that have been collectively termed epigenetics: the stable and inheritable changes in gene expression patterns. This article reviews the extremely rich and exquisitely multi-scale physical mechanisms that govern the biological processes behind the initiation, spreading and inheritance of epigenetic states. These include not only the changes in the molecular properties associated with the chemical modifications of DNA and histone proteins, such as methylation and acetylation, but also less conventional changes, typically in the the physics that governs the three-dimensional organization of the genome in cell nuclei. Strikingly, to achieve stability and heritability of epigenetic states, cells take advantage of many different physical principles, such as the universal behavior of polymers and copolymers, the general features of dynamical systems, and the electrostatic and mechanical properties related to chemical modifications of DNA and histones. By putting the complex biological literature under this new light, the emerging picture is that a limited set of general physical rules play a key role in initiating, shaping and transmitting this crucial "epigenetic landscape". This new perspective not only allows to rationalize the normal cellular functions, but also helps to understand the emergence of pathological states, in which the epigenetic landscape becomes dysfunctional.

1 Anna Aragno 2 Marcello Barbieri 3 Gérard Battail 4 Leonardo Bich 5 Marcos Buckeridge 6 Han-liang Chang 7 Joachim De Beule 8 Peter Dittrich 9 Wanderley dos Santos 10 Isabel Ferreira 11 Elena Fimmel 12 Simone Giannerini 13 Mario Giampietro 14 Louis Goldberg 15 Diego Gonzalez 16 Dennis Görlich 17 Markus Gumbel 18 Jannie Hofmeyr 19 Jean-Luc Jestin 20 Stefan Kühn 21 João Carlos Major 22 David Monacchi 23 Sonja Prohaska 24 Hervé Seligmann 25 Candice Shelby 26 Peter Stadler 27 Liz Stillwaggon Swan 28 Lutz Strüngmann 29 Morten Tønnessen 30 Peter Wills 31 Andrew Winters

Tels les poissons qui vivent dans l'eau mais ne la connaissent pas, nous sommes pétris de sens, et nous ne savons pas ce que c'est, ou du moins, pas suffisamment pour pouvoir en donner une définition claire et consensuelle. Le discours du linguiste Oswald Ducrot est, à cet égard, sans équivoque : « Quelqu'un qui pourrait dire ce qu'est le sens donnerait aussitôt la clef qui résout tous les problèmes philosophiques. Tout ce que je veux et peux faire, c'est indiquer comment, en tant que linguiste, on rencontre-je ne dirais pas cette notion de sens, car cela supposerait qu'on la connaisse, et qu'il s'agisse d'une notion. Ce qu'on rencontre, c'est la nécessité d'employer, dans le travail de description des mots comme « sens » ou « signification », sans trop savoir ce qu'ils veulent dire, sans savoir même s'ils veulent dire quelque chose. » (Ducrot, 2000, p. 97) De fait, le sens a été le « grand absent » de la linguistique et, aux dernières nouvelles, il le reste. Cela, en dépit des efforts de nombreux chercheurs qui, à l'instar de Ducrot, tentent encore de donner une caractérisation de cette « face cachée du signe » en restant dans l'intralinguistique. On peut comprendre qu'il soit difficile pour certains de renoncer à une forme d'autorité sur le territoire du sens après les espoirs soulevés par la perspective computosymbolique 2 mais, précisément, ces derniers ne peuvent plus être entretenus. Les constats sont, là encore, parfaitement clairs : le modèle du code se révèle insuffisant. 1 Cet article constitue la version largement revue et corrigée d'un chapitre original intitulé « Lo schema come istanza del senso » publié en italien dans Braga Illa F. (a cura): A proposito di rappresentazioni. Alla ricerca del senso perduto. Bologna, Edizioni Pendragon, 2006, pp. 171-199. Je remercie l'éditeur d'avoir donné son autorisation à cette reproduction « majorante ». 2 L'association de racines latine et grecque est généralement hétérodoxe. Mais en l'occurrence, cette dissonance apparaît opportune car elle souligne le fait que, décidément, le computo-symbolique, ne fonctionne pas, au moins pour ce qui nous occupe.

Stratégie, risque, incertitude et complexité Selon l'acception héritée de l'art militaire, la stratégie se caractérise par la planification et le calcul. Elle vise à rassurer le décideur en réduisant l'incertitude quant à l'issue de ses décisions. Elle

This commentary explores biological models of analogical (iconic) and associative (indexical) learning in support of Illusion 1 and Illusion 4 in D. Noble's target article. The intent is to support Noble's theses of emergent higher level functionality from lower level stochastic dynamics and his etiological claim that "there is no privileged level of causation" through a biosemiotic lens. Upon these arguments, a case for creative agency via higher-dimensional constraints will also be made in support of Noble's claim that organismic behavior is actively directed by an agent.

Tels les poissons qui vivent dans l'eau mais ne la connaissent pas, nous sommes pétris de sens, et nous ne savons pas ce que c'est, ou du moins, pas suffisamment pour pouvoir en donner une définition claire et consensuelle. Le discours du linguiste Oswald Ducrot est, à cet égard, sans équivoque : « Quelqu'un qui pourrait dire ce qu'est le sens donnerait aussitôt la clef qui résout tous les problèmes philosophiques. Tout ce que je veux et peux faire, c'est indiquer comment, en tant que linguiste, on rencontre-je ne dirais pas cette notion de sens, car cela supposerait qu'on la connaisse, et qu'il s'agisse d'une notion. Ce qu'on rencontre, c'est la nécessité d'employer, dans le travail de description des mots comme « sens » ou « signification », sans trop savoir ce qu'ils veulent dire, sans savoir même s'ils veulent dire quelque chose. » (Ducrot, 2000, p. 97) De fait, le sens a été le « grand absent » de la linguistique et, aux dernières nouvelles, il le reste. Cela, en dépit des efforts de nombreux chercheurs qui, à l'instar de Ducrot, tentent encore de donner une caractérisation de cette « face cachée du signe » en restant dans l'intralinguistique. On peut comprendre qu'il soit difficile pour certains de renoncer à une forme d'autorité sur le territoire du sens après les espoirs soulevés par la perspective computosymbolique 2 mais, précisément, ces derniers ne peuvent plus être entretenus. Les constats sont, là encore, parfaitement clairs : le modèle du code se révèle insuffisant. 1 Cet article constitue la version largement revue et corrigée d'un chapitre original intitulé « Lo schema come istanza del senso » publié en italien dans Braga Illa F. (a cura): A proposito di rappresentazioni. Alla ricerca del senso perduto. Bologna, Edizioni Pendragon, 2006, pp. 171-199. Je remercie l'éditeur d'avoir donné son autorisation à cette reproduction « majorante ». 2 L'association de racines latine et grecque est généralement hétérodoxe. Mais en l'occurrence, cette dissonance apparaît opportune car elle souligne le fait que, décidément, le computo-symbolique, ne fonctionne pas, au moins pour ce qui nous occupe.

Kull, Kalevi 2023. Necessary conditions for semiosis: A study of vegetative subjectivity, or phytosemiotics. In: Coca, Juan R.; Rodríguez, Claudio J. (eds.), Approaches to Biosemiotics. Valladolid: Ediciones Universidad Valladolid, 59–74.

We provide a critical analysis of minimal conditions for the semiotic triad, to be identifiable in organisms. Semiosis is the process of meaning-making, which means that it creates relations unusual for physical and chemical descriptions. Since the semiosic relations emerge in complex organic systems of certain kind, we require a list of necessary and sufficient conditions for identification of the features of semiosis (triadicity, irreducibility, umwelt, double description, codes, arbitrariness, learning, relation-process duality, etc.), we suggest a core structure for minimal model of semiosis which is necessary for the relation of difference. We also review some earlier work on the topic.

At the heart of evolutionary theory lays the notion of replication. Unfortunately, this notion is far less exact than the weight of its importance. In this paper, it is argued that replication always involves coding. Furthermore, when a theory of evolution is built on replication based on coding, a unifying and coherent picture arises that sheds new light on some of the controversies and open questions in contemporary biology, such as what are the roles of phylogeny and ontogeny in evolution, and how to characterize and explain the increase of biological complexity.

Relational biology relies heavily on the enriched understanding of causal entailment that Robert Rosen's formalisation of Aristotle's four causes has made possible, although to date efficient causes and the rehabilitation of final cause have been its main focus. Formal cause has been paid rather scant attention, but, as this paper demonstrates, is crucial to our understanding of many types of processes, not necessarily biological. The graph-theoretic relational diagram of a mapping has played a key role in relational biology, and the first part of the paper is devoted to developing an explicit representation of formal cause in the diagram and how it acts in combination with efficient cause to form a mapping. I then use these representations to show how Von Neumann's universal constructor can be cast into a relational diagram in a way that avoids the logical paradox that Rosen detected in his own representation of the constructor in terms of sets and mappings. One aspect that was absent from both Von Neumann's and Rosen's treatments was the necessity of a code to translate the description (the formal cause) of the automaton to be constructed into the construction process itself. A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

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.

Coding characteristics have been discovered not only in protein synthesis, but also in various other natural processes, thus showing that the genetic code is not an isolated case in the organic world. Other examples are the sequence codes, the adhesion code, the signal transduction codes, the splicing codes, the sugar code, the histone code, and probably more. These discoveries however have not had a significant impact because of the widespread belief that organic codes are not real but metaphorical entities. They are supposed to lack arbitrariness and codemakers, the two qualifying features of real codes. Here it is shown that the arbitrariness issue can be solved on an experimental basis, while the codemaker issue is dependent on our theoretical description of the cell and can only be solved by a new concept. In order to appreciate the reality of the organic codes, in short, it is necessary to have not only a more critical evaluation of the experimental data but also a new theory ...

For a long time it has been assumed that the rules of the genetic code were determined by chemistryeither by stereochemical affinities or by metabolic reactionsbut the experimental evidence has revealed a totally different reality; it has been shown that any codon can be associated to any amino acid, and this means that there is no deterministic link between them. The genetic code, in other words, is based on arbitrary, or conventional, rules and this raises a formidable problem: how can arbitrary rules exist in Nature? We know that such rules exist in culture, but there is an abyssal difference between biology and culture, because the cultural codes are shortlived, whereas the biological codes are the most conserved entities in evolution. Biological codes, in other words are fundamentally different from cultural codes and we do need a model that makes us understand how they came into being. In this paper it is shown that the origin of biological codes takes place in five phases (beginning, evolution, optimization, major transition and conservation) and this suggests a general model for their development. According to this model, a biological code evolves in a system as a means of solving a local problem, but then it becomes the tool of a much larger change in macroevolution. This is the great potential of the biological codes: their ability to bring into existence absolute novelties that change the whole course of the history of life. Different major transitions were based on different codes, but we can also recognize some common features in all of them. This indicates that coding is a universal mechanism that Nature has employed many times in the course of evolution to solve a wide variety of different problems. 1.1. Beginning The first rules of a code appear in a system as a means of performing a particular function, and their arbitrariness implies that the first version of a code is necessarily ambiguous.

Abstract: Biosemiotics asserts the idea that semiosis is fundamental to life, and that all living creatures are therefore semiotic systems. The idea itself is strongly supported by the evidence of the genetic code — but thus far it has made little impact in the scientific world, and is largely regarded as the basis for a philosophy of meaning, rather than a basis for a science of meaning. This is regrettable, but perhaps understandable from the scientists ’ point of view. Scientists know that the cell is the necessary unit of all life. I will argue here, then, that Biosemiotics can become a science only if it can prove that the cell is, in fact, a semiotic system — i.e., that semiosis exists at the cellular level. To do this, we first need to define what is semiosis, so that we can be explicit about what exactly constitutes a semiotic system. So far, we have had two main answers to this question. One is the model proposed by Saussure, who defined a semiotic system as a duality of ‘s...

The genesis of time is explained in the spirit of constructivism combined with the
activity approach to cognition. The cardinal temporal categories of present, past, and future are discussed in terms of action-thoughts understood as elementary units of activity whose structure is determined by linguistic semiosis. Husserl’s tripartite model of the phenomenology of time (prime perception, retention, protention) is applied to the analysis of the subject’s experience of his actions. It is demonstrated that, while our lived present is composed of the actually performed actions, our past and future are constructed by reflexive action-thoughts in the cognitive domain of language. It is emphasized that the construction of a temporal sequence that unites what is and what already or still is not, is possible only in linguistic semiosis. The analogy with Husserl’s tripartite structure of the time-consciousness flow helps elucidate the triad ‘present-past-future’ as an instance of the epistemological trap of language: ‘past’ and ‘future’ are mental constructs that belong to the present just as any other act of thinking.

This paper provides a general framework for understanding targeted search. It begins by defining the search matrix, which makes explicit the sources of information that can affect search progress. The search matrix enables a search to be represented as a probability measure on the original search space. This representation facilitates tracking the information cost incurred by successful search (success being defined as finding the target). To categorize such costs, various information and efficiency measures are defined, notably, active information. Conservation of information characterizes these costs and is precisely formulated via two theorems, one restricted (proved in previous work of ours), the other general (proved for the first time here). The restricted version assumes a uniform probability search baseline, the general, an arbitrary probability search baseline. When a search with probability q of success displaces a baseline search with probability p of success where q > p, conservation of information states that raising the probability of successful search by a factor of q/p(>1) incurs an information cost of at least log(q/p). Conservation of information shows that information, like money, obeys strict accounting principles.

Trois différentes histoires de chercheurs ayant fondé la discipline, trois sièges, trois lignes de recherche pour un secteur scientifique unique. La philosophie du langage compte aujourd'hui une centaine de membres académiques 1 ainsi qu'un nombre presque égal de membres de la Société de Philosophie du Langage 2 , auxquels il faut ajouter-mis à part les cas d'inscription contemporaine à plusieurs sociétés-les membres de l'Association Italienne de Sémiotique 3 et une partie de ceux de la Société Italienne de Philosophie Analytique 4. De plus, la distribution des membres de la classe SSD M-FIL/05 5 dans les 80 universités italiennes environ n'est pas harmonieuse : on en compte 12 à l'Université de Bologne et aucun dans des centres universitaires comme Pavie, Florence, Pise. D'autre part, procéder par métonymie (en remontant des effets aux causes) voire même par synecdoque (en focalisant notre attention du tout aux parties) nous aide à respecter l'histoire et à ne pas nous perdre dans les détails ou sur une période trop vaste, d'autant plus que l'histoire est récente et que la communauté scientifique reconnaît en son sein, dans une large mesure, la coprésence de plusieurs « âmes ». Même s'il ne s'agit pas d'une condition suffisante pour l'institutionnalisation d'une discipline et encore moins d'une condition nécessaire de façon déterminante, les fondateurs d'une discipline de recherche (eux justement, et non les autres) se révèlent cependant a posteriori « fondamentaux » pour la construction d'un savoir devenu une discipline. C'est du moins la thèse que je tenterai maintenant de prouver, en partant donc des ressources humaines, de celles présentes aux origines et de celles qui ont permis les origines. Etant donné, en effet, que les débuts d'une discipline sont-souvent-un mélange de « génie et de modération », il est nécessaire qu'aux qualités exceptionnelles des fondateurs soient associés également d'autres talents-qu'il s'agisse de leurs propres talents ou le plus souvent de ceux d'autres personnes-capacités d'organisation, flair institutionnel, détermination politico-culturelle. Dans le cas des origines de la philosophie du langage (PDL), en Italie, comment les choses se sont-elles passées ? J'ai posé la question directement à Tullio de Mauro (Rome La Sapienza 6) à Andrea Bonomi (Milan, Università Statale) et à Umberto Eco (Bologne). Il s'agit de trois histoires bien différentes. 1 Pour être précis 113 membres, donc 33 professeurs des universités, 32 maîtres de conférences, 45 chercheurs à durée indéterminée et trois à durée déterminée, au 26 mai 2010. 2 Fondée à Rome en 1994: http://www.sofilin.unical.it/, site en cours de construction. Les membres de la Société ne sont pas tous encadrés d'un point de vue universitaire. 3 Fondée à Bologne en 1972, durant les travaux du XI e Congrès International des linguistes : www.associazionesemiotica.it/. 4 Fondée en 1992 : SIFA, http://sifa.unige.it/. 5 Jusqu'en 1997 M07E; depuis novembre 2009 incorporée dans le macro-secteur 11/D4, Esthétique et Philosophie des langages.

Histone ubiquitylation has emerged as an important chromatin modification with roles in transcription and trans-histone methylation. In the past several years, there has been dramatic progress in the identification of factors that control ubiquitin attachment to the core histones H2A and H2B. Recent advances in this area will be reviewed, and outstanding questions relating to the cellular functions of these modified histones will be discussed.

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that the information of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the 'chemical paradigm', the idea that 'life is chemistry', or, more precisely, that 'life is an extremely complex form of chemistry'. The other is the 'information paradigm', the view that chemistry is not enough, that 'life is chemistry p...

The notion of species-speci fi c modelling allows us to construct taxonomies of mental models, based on the concept of qualia , such as posing 'invariant requests to neural processes', supporting networks of which are subject to selective pressures. The selection is based on their respective capacity to differently adapt to behaviour patterns, which neural networks control. For extremely premature births, thanks to foetalization, in Homo sapiens sapiens , speci fi c neural groups are offered for selection in early critical periods of development and in a social environment. As a consequence, far beyond any other primate, new cognitive devices are developed, which lead to a high level of abstract thinking. Therefore, the reproposition of the culturalhistorical psychology is important. Foetalization and education are the two pillars that give rise to the human being's ability to accumulate a perceivable and collective knowledge, which is precluded to other animal cultures. These are the roots both of consciousness and of the speci fi c mechanisms that give rise to transmissibility and variability and adaptability of the human cultures. The key to this evolutionary quantum leap is the advent of a new class of replicators: memes, de fi ned as informational patterns of a signic nature with a metaphorical, relational organization; memes are the basic framework in the structure of personality both in individuals and in social groups.

In the 'Barbieri's Concept of Mechanisms' section on page 12 of above mentioned article the text erroneously reads 'Rosen, quoting Alberts et al. ( ), highlights…'. The correct text should read 'Barbieri, quoting Alberts et al. ( ), highlights…'. The original article has been corrected.