The essay is a critical review of three possible approaches in the theory of knowledge while tracing the biological roots of knowledge: empiricist, rationalist and developmentalist approaches. Piaget's genetic epistemology, a developmentalist approach, is one of the first comprehensive treatments on the question of tracing biological roots of knowledge. This developmental approach is currently opposed, without questioning the biological roots of knowledge, by the more popular rationalist approach, championed by Chomsky. Developmental approaches are generally coherent with cybernetic models, of which (...) the theory of autopoiesis proposed by Maturana and Varela made a significant theoretical move in proposing an intimate connection between metabolism and knowledge. Modular architecture is currently considered more or less an undisputable model for both biology as well as cognitive science. By suggesting that modulation of modules is possible by motor coordination, a proposal is made to account for higher forms of conscious cognition within the four distinguishable layers of the human mind. Towards the end, the problem of life and cognition is discussed in the context of the evolution of complex cognitive systems, suggesting the unique access of phylogeny during the ontogeny of human beings as a very special case, and how the problem cannot be dealt with independent of the evolution of coding systems in nature. (shrink)

It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...) origins of life based on the ribosome and then to account for the refined codes through a process of ambiguity reduction, something more is required. Barbieri has not provided an adequate account of emergence, or the basis for providing such an account. I will argue that Stanley Salthe has clarified to some extent the nature of emergence by conceptualizing it as the interpolation of new enabling constraints. Clearly, codes can be seen as enabling constraints. How this actually happens, though, is still not explained. Stuart Kauffman has grappled with this issue and shown that it radically challenges the assumptions of mainstream science going back to Newton. He has attempted to reintroduce real possibilities or potentialities into his ontology, and argued that radically new developments in nature are associated with realizing adjacent possibles. This is still not adequate. What is also involved, I will suggest, utilizing concepts developed by the French natural philosopher Gilbert Simondon, is ‘transduction’ as part of ‘ontogenesis’ of individuals in a process of ‘individuation’, that is, the emergence of ‘individuals’ from preindividual fields or milieux. (shrink)

This two-part article presents the research program for a theory and empirical analysis of religious evolution. It is assumed that religion isprimarilya co-evolution to societal evolution, which in turn is a co-evolution to mental, organic, and physical evolution. The theory of evolution is triangulated with the systems theory and the semiotically informed theory of communication, so that knowledge can be gained that would not be acquired by only one of the three theories: The differentiation between religion and its environment can (...) be reconstructed based on the theory of evolution. The elements of the theory of evolution can be understood as the formation of systems. The semiotically informed theory of communication clarifies the conditions of the combination of both the systems theory and the theory of evolution as well as its objects. In turn, the combination of the systems theory and the theory of evolution can describe how communication—including religion and science—evolves and is structured. (shrink)

C.H. Waddington’s concepts of ‘chreods’ (canalized paths of development) and ‘homeorhesis’ (the tendency to return to a path), each associated with ‘morphogenetic fields’, were conceived by him as a contribution to complexity theory. Subsequent developments in complexity theory have largely ignored Waddington’s work and efforts to advance it. Waddington explained the development of the concept of chreod as the influence on his work of Alfred North Whitehead’s process philosophy, notably, the concept of concrescence as a self-causing process. Processes were recognized (...) as having their own dynamics, rather than being explicable through their components or external agents. Whitehead recognized the tendency to think only in terms of such ‘substances’ as a bias of European thought, claiming in his own philosophy ‘to approximate more to some strains of Indian, or Chinese, thought, than to western Asiatic, or European, thought.’ Significantly, the theoretical biologist who comes closest to advancing Waddington’s research program, also marginalized, is Mae-Wan Ho. Noting this bias, and embracing Whitehead’s and Waddington’s efforts to free biology from assumptions dominating Western thought to advance an ontology of creative causal processes, I will show how later developments of complexity theory, most importantly, Goodwin’s work on oscillations, temporality and morphogenesis, Vitiello’s dissipative quantum brain dynamics, Salthe’s work on hierarchy theory, biosemiotics inspired by Peirce and von Uexküll, Robert Rosen’s work on anticipatory systems, together with category theory and biomathics, can augment while being augmented by Waddington’s work, while further advancing Mae-Wan Ho’s radical research program with its quest to understand the reality of consciousness. (shrink)

Intersemiotic translation (IT) was defined by Roman Jakobson (The Translation Studies Reader, Routledge, London, p. 114, 2000) as “transmutation of signs”—“an interpretation of verbal signs by means of signs of nonverbal sign systems.” Despite its theoretical relevance, and in spite of the frequency in which it is practiced, the phenomenon remains virtually unexplored in terms of conceptual modeling, especially from a semiotic perspective. Our approach is based on two premises: (i) IT is fundamentally a semiotic operation process (semiosis) and (ii) (...) IT is a deeply iconic-dependent process. We exemplify our approach by means of literature to dance IT and we explore some implications for the development of a general model of IT. (shrink)

Biosemiotics is a growing fi eld that investigates semiotic processes in the living realm in an attempt to combine the fi ndings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “ signals, ” “ codes, ”and “ information processing ”in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as biology (...) interpreted as a study of living sign systems — which also means that semiosis or sign process can be seen as the very nature of life itself. In other words, biosemiotics is a field of research investigating semiotic processes (meaning, signification, communication, and habit formation in living systems) and the physicochemical preconditions for sign action and interpretation. -/- (...). (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive (...) tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics. (shrink)

This paper explores the critical conditions of such semiotic realism that is commonly presumed in the so-called Copenhagen interpretation of biosemiotics. The central task is to make basic biosemiotic concepts as clear as possible by applying C.S. Peirce’s pragmaticist methodology to his own concepts, especially to those that have had a strong influence on the Copenhagian biosemiotics. It appears essential to study what kinds of observation the basic semiotic concepts are derived from. Peirce had two different derivations to the concept (...) of sign, both having a strong logical character. Therefore, it is discussed at length what Peirce’s conception of logic consists of and how logical concepts relate to the concepts of other sciences. It is shown that Peirce had two different perspectives toward sign, the ‘transcendental’ one and the objective one, and only the latter one is executable in biosemiotic applications. Although Peirce’ theory of signs seems to appear as twofold (if not even manifold), it is concluded that the ore conception has been stable. The apparent differences are presumably due to the different perspectives of consideration. Severe limitations for the application of Peirce’s semiotic concepts follow from this analysis that should be taken into account in biosemiotics relying on its Copenhagen interpretation. The first one concerns the ‘interpreter’ of a suggested biosemiotic sign — whether it is ‘we’ (as a ‘meta-agent’) or some genuine biosemiotic ‘object-agent’. Only if the latter one is determinable, some real biosemiotic sign-action may occur. The second one concerns the application of the concept of the object of sign — its use is limited so that a sign has an object if and only if it seeks a true conception about it. This conclusion has drastic further consequences. Most of the genuinely biosemiotic sign-processes do not tend toward truth about anything but toward various practical ends. Therefore, the logical concept of sign, e.g. the one of Peirce’s semeiotic, is an insufficient concept for biosemiotics. In order to establish a sufficient one, Peircean theoretical ethics and esthetics are introduced. It is concluded that they involve simpler and more general but still normative concept of sign — the concept of anticipative or constructive representation that does not represent any object at all. Instead, it is a completely future-oriented representation that guides action. Objective ethics provides the suitable concept of representation, but it appeals to objective esthetics that provides a theory of (local) natural self-normativity. The concepts of objective logic form the special species of objective ethics. The conclusion is that biosemiotics should be based on applied objective ethics and esthetics rather than on (Peircean semeiotic) logic and its metaphysical application. Finally, the physiosemiotic over-generalization of the concept of sign is shortly discussed. It is suggested that it would be more appropriate to rename such controversial generalizations than to adhere to semiotic terminology. Here, again, Peirce appears as a healthy role model with his ‘ethics of terminology’. (shrink)

The starting point for this article is the question of the relationship between Darwinism and Christian theology. I suggest that evolutionary theory presents three broad issues of relevance to theology: the phenomena ofcontinuity, naturalism, andcontingency. In order to formulate a theological response to these issues I draw on the semiotics (theory of signs) and cosmology of the American philosopher Charles Sanders Peirce. Peirce developed a triadic theory of signs, underpinned by a threefold system of metaphysical categories. I propose a semiotic (...) model of the Trinity based on Peirce's semiotics and categories. According to this model the sign‐processes (such as the genetic “code”) that are fundamental to life may be understood as vestiges of the Trinity in creation. I use the semiotic model to develop a theology of nature that addresses the issues raised by evolutionary theory. The semiotic model amounts to a proposal for a new metaphysical framework within which to understand the relationship between God and creation and between theology and science. (shrink)

This is the second article in a series of review articles addressing biosemiotic terminology. The biosemiotic glossary project is designed to integrate views of members within the biosemiotic community based on a standard survey and related publications. The methodology section describes the format of the survey conducted July–August 2014 in preparation of the current review and targeted on Jakob von Uexküll’s term ‘Umwelt’. Next, we summarize denotation, synonyms and antonyms, with special emphasis on the denotation of this term in current (...) biosemiotic usage. The survey findings include ratings of eight citations defining or making use of the term Umwelt. We provide a summary of respondents’ own definitions and suggested term usage. Further sections address etymology, relevant contexts of use, and related terms in English and other languages. A section on the notion’s Uexküllian meaning and later biosemiotic meaning is followed by attempt at synthesis and conclusion. We conclude that the Umwelt is a centerpiece phenomenon, a phenomenon that other phenomena in the living realm are organized around. To sum up Uexküll’s view, we can characterize an Umwelt as the subjective world of an organism, enveloping a perceptual world and an effector world, which is always part of the organism itself and a key component of nature, which is held together by functional cycles connecting different Umwelten. In order to pay respect to Uexküll’s work, we must move from notion to model, from mention of Uexküll’s Umwelt term to actual application of it. (shrink)

Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular end it was expressed by Howard Pattee’s analysis of the genetic code, whereas at the human end it took the form of Thomas (...) Sebeok’s investigation into the biological roots of culture. Other proposals appeared in the years that followed and gave origin to different theoretical frameworks, or different schools, of biosemiotics. They are: (1) the physical biosemiotics of Howard Pattee and its extension in Darwinian biosemiotics by Howard Pattee and by Terrence Deacon, (2) the zoosemiotics proposed by Thomas Sebeok and its extension in sign biosemiotics developed by Thomas Sebeok and by Jesper Hoffmeyer, (3) the code biosemiotics of Marcello Barbieri and (4) the hermeneutic biosemiotics of Anton Markoš. The differences that exist between the schools are a consequence of their different models of semiosis, but that is only the tip of the iceberg. In reality they go much deeper and concern the very nature of the new discipline. Is biosemiotics only a new way of looking at the known facts of biology or does it predict new facts? Does biosemiotics consist of testable hypotheses? Does it add anything to the history of life and to our understanding of evolution? These are the major issues of the young discipline, and the purpose of the present paper is to illustrate them by describing the origin and the historical development of its main schools. (shrink)

Thomas Sebeok and Noam Chomsky are the acknowledged founding fathers of two research fields which are known respectively as Biosemiotics and Biolinguistics and which have been developed in parallel during the past 50 years. Both fields claim that language has biological roots and must be studied as a natural phenomenon, thus bringing to an end the old divide between nature and culture. In addition to this common goal, there are many other important similarities between them. Their definitions of language, for (...) example, have much in common, despite the use of different terminologies. They both regard language as a faculty, or a modelling system, that appeared rapidly in the history of life and probably evolved as an exaptation from previous animal systems. Both accept that the fundamental characteristic of language is recursion, the ability to generate an unlimited number of structures from a finite set of elements (the property of ‘discrete infinity’). Both accept that human beings are born with a predisposition to acquire language in a few years and without apparent efforts (the innate component of language). In addition to similarities, however, there are also substantial differences between the two fields, and it is an historical fact that Sebeok and Chomsky made no attempt at resolving them. Biosemiotics and Biolinguistics have become two separate disciplines, and yet in the case of language they are studying the same phenomenon, so it should be possible to bring them together. Here it is shown that this is indeed the case. A convergence of the two fields does require a few basic readjustments in each of them, but leads to a unified framework that keeps the best of both disciplines and is in agreement with the experimental evidence. What is particularly important is that such a framework suggests immediately a new approach to the origin of language. More precisely, it suggests that the brain wiring processes that take place in all phases of human ontogenesis (embryonic, foetal, infant and child development) are based on organic codes, and it is the step-by-step appearance of these brain-wiring codes, in a condition that is referred to as cerebra bifida, that holds the key to the origin of language. (shrink)

This paper examines the biosemiotic approach to the study of life processes by fashioning a series of questions that any worthwhile semiotic study of life should ask. These questions can be understood simultaneously as: (1) questions that distinguish a semiotic biology from a non-semiotic (i.e., reductionist–physicalist) one; (2) questions that any student in biosemiotics should ask when doing a case study; and (3) still currently unanswered questions of biosemiotics. In addition, some examples of previously undertaken biosemiotic case studies are examined (...) so as to suggest a broad picture of how such a biosemiotic approach to biology might be done. (shrink)

The “histone code” conjecture of gene regulation is our point of departure for analyzing the interplay between the (quasi)digital script in nucleic acids and proteins on the one hand and the body on the other, between the recorded and organic memory. We argue that the cell’s ability to encode its states into strings of “characters” dramatically enhances the capacity of encoding its experience (organic memory). Finally, we present our concept of interaction between the natural (bodily) world, and the transcendental realm (...) of the digital codes. (shrink)

The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how the stands-for relation is (...) realized is named the symbol-matter problem. (4) A necessary physical condition is that all informational vehicles are material boundary conditions or constraints acting on the lawful dynamics of local systems. It is useful to define a dependency hierarchy of information types: (1) syntactic information (i.e., communication theory), (2) heritable information acquired by variation and natural selection, (3) non-heritable learned or creative information, and (4) measured physical information in the context of natural laws. High information storage capacity is most reliably implemented by discrete linear sequences of non-dynamic vehicles, while the execution of information for control and construction is a non-holonomic dynamic process. The first epistemic cut occurs in self-replication. The first interpretation of base sequence information is by protein folding; the last interpretation of base sequence information is by natural selection. Evolution has evolved senses and nervous systems that acquire non-heritable information, and only very recently after billions of years, the competence for human language. Genetic and human languages are the only known complete general purpose languages. They have fundamental properties in common, but are entirely different in their acquisition, storage and interpretation. (shrink)

According to David Chalmers, the hard problem of consciousness consists of explaining how and why qualitative experience arises from physical states. Moreover, Chalmers argues that materialist and reductive explanations of mentality are incapable of addressing the hard problem. In this chapter, I suggest that Chalmers’ hard problem can be usefully distinguished into a ‘how question’ and ‘why question,’ and I argue that evolutionary biology has the resources to address the question of why qualitative experience arises from brain states. From this (...) perspective, I discuss the different kinds of evolutionary explanations (e.g., adaptationist, exaptationist, spandrel) that can explain the origins of the qualitative aspects of various conscious states. This argument is intended to clarify which parts of Chalmers’ hard problem are amenable to scientific analysis. (shrink)

A common method of making a theory more understandable is to compare it to another theory that has been better developed. Radical interpretation is a theory that attempts to explain how communication has meaning. Radical interpretation is treated as another time-dependent theory and compared to the time-dependent theory of biological evolution. The main reason for doing this is to find the nature of the time dependence; producing analogs between the two theories is a necessary prerequisite to this and brings up (...) many problems. When the nature of the time dependence is better known it might allow the underlying mechanism to be uncovered. Several similarities and differences are uncovered, and there appear to be more differences than similarities. (shrink)

It is here proposed an analysis of symbolic and sub-symbolic models for studying cognitive processes, centered on emergence and logical openness notions. The Theory of logical openness connects the Physics of system/environment relationships to the system informational structure. In this theory, cognitive models can be ordered according to a hierarchy of complexity depending on their logical openness degree, and their descriptive limits are correlated to Gödel-Turing Theorems on formal systems. The symbolic models with low logical openness describe cognition by means (...) of semantics which fix the system/environment relationship, while the sub-symbolic ones with high logical openness tends to seize its evolutive dynamics. An observer is defined as a system with high logical openness. In conclusion, the characteristic processes of intrinsic emergence typical of “bio-logic” - emerging of new codes-require an alternative model to Turing- computation, the natural or bio-morphic computation, whose essential features we are going here to outline. (shrink)

A common method of improving how well understood a theory is, is by comparing it to another theory which has been better developed. Radical interpretation is a theory which attempts to explain how communication has meaning. Radical interpretation is treated as another time dependent theory and compared to the time dependent theory of biological evolution. Several similarities and differences are uncovered. Biological evolution can be gradual or punctuated. Whether radical interpretation is gradual or punctuated depends on how the question is (...) framed: on the coarse-grained time scale it proceeds gradually, but on the fine-grained time scale it proceeds by punctuated equilibria. Biological evolution proceeds by natural selection, the counterpart to this is the increase in both correspondence and coherence. Exaption, mutations, and spandrels have counterparts metaphor, speech errors, and puns respectively. Homologous and analogs have direct counterparts in specific words. The most important differences originate from the existence of a unit of inheritance occurring in biological evolution - there is no such unit in language. (shrink)

The concept of biological information, and information in general, usually presupposes a purely quantitative view of reality. Even though actualist quantification has an important place in the description of the world, a nominalistic stance that tries to simplify reality in purely actualist terms inevitably runs into inconsistencies; these inconsistencies have been pointed out by the critical assessments of the notion of biological information. Rather than calling for an abandonment of the informational terminology, we try to rethink information as a part (...) of an event, the description of which cannot be exhausted by a physicalist, mechanistic, temporally static view of reality. Reconceptualizing the notion of biological information in terms of a process of interpretation rather than as an informational object allows us to transcend the limitations imposed by an analysis of reality that depends on a fixed, finite structure of outcome. Thus, we argue that measuring biological information is intrinsically problematic. (shrink)

Meaning is a central concept of (bio)semiotics. At the same time, it is also a word of everyday language. Here, on the example of the world information, we discuss the “reduction-inflation model” of evolution of a common word into a scientific concept, to return subsequently into everyday circulation with new connotations. Such may be, in the near future, also the fate of the word meaning if, flexed through objectified semantics, will become considered an objective concept usable in semiotics. We argue (...) that reducing meaning to a technical term essentially synonymous to code and stripped of most of the original semantic field is not a necessary prerequisite for a meaningful application of the concept in semiotics and in biology. (shrink)

Evolution and life phenomena can be understood as results of history, i.e., as outcomes of cohabitation and collective memory of populations of autonomous entities across many generations and vast extent of time. Hence, evolution of distinct lineages of life can be considered as isomorphic with that of cultures. I argue here that cultures and culture-like systems – human culture, natural languages, and life forms – always draw from history, memory, experience, internal dynamics, etc., transforming themselves creatively into new patterns, never (...) foreseen before. This is possible thanks to the fact that all forms of life are descendants of life. Ontogeny and speciation in various lineages draw from continuous re-interpretation of conservative genetic/generic “texts”, as well as from changes of the interpretative process itself. The result is continuous appearances of new lineages-cultures and/or communities-cultures, in a semiotic process of re-interpretation and inventing new ways of living. The topic is developed here on the backgrounds of ideas presented by R. A. Rappaport in “Ritual and religion in the making of humanity” and J. Flegr in “Frozen evolution”. (shrink)

In the case of living beings – the very concept of “level” of organization becomes obscure: it suggests a value-based assessment, assigning notions like “lower” and “higher” with rather vague criteria for constructing the ladder of perfection, complexity, importance, etc. We prefer therefore the term “domain”, entities ranking equal. Domains may represent natural entities as well as purely human constructs developed in order to gain understanding of some facets of living things; living, evolved beings as well as those abstract constructs, (...) such as genotype and ‘niche’ which have been developed in the search for better understanding of such living things. Delimitation of such domains is sometimes a question of the dexterity of the researcher, and sometimes draws from the tradition in a given field. Such domains are not completely translatable to each other. Rather, they interact by a process that we call here reciprocal formation. Life is unique among multi-domain systems. In contrast to purely physical systems, life is a semiotic system driven by the historical experience of lineages, interpreted and re-interpreted by the incessant turnover of both individuals and their communities. This paper provides cases of domain interrelations, and addresses two questions: How do new qualities of inter-domain interaction emerge historically? How do new domains emerge in evolution. Two approaches, physical and biosemiotic, are discussed as we seek to get a better understanding of the overarching tasks. (shrink)

We discuss the difference between formal and natural languages, and argue that should the language metaphor have any foundation, it’s analogy with natural languages that should be taken into account. We discuss how such operation like reading, writing, sign, interpretation, etc., can be applied in the realm of the living and what can be gained, by such an approach, in order to understand the phenomenon of life.

The emergence of novelty in the realm of the living remains, despite the long tradition of evolutionary biology, unwelcome, calling for explanation by old, established knowledge. The prevailing neodarwinian evolutionary paradigm approaches living beings as passive outcomes of external (and extraneous, hence “blind”) formative forces. Many teachings opposing Darwinism also take the existence of eternal, immutable and external laws as a necessary prerequisite. Ironically enough, authors who oppose Darwinian theory, and admit that living beings possess a “self”, often accentuate internal, (...) ideal and eternal harmony,which is incompatible with historical changes; moreover such harmony is again imposed by external, atemporal “laws”. I describe here a third approach embodied by the names of two unrelated scholars, Stuart Kauffman (biology, physics) and Juri Lotman (semiotics, culturology). Their approach suggests thatthe evolution of organisms, minds, cultures — is a continuous negotiation (semiosis) of ‘laws’, driving to ever broader spaces of freedom and constantly larger autonomy of existence. (shrink)

En este artículo defendemos la necesidad de reformular los conceptos de constreñimiento del desarrollo y variación considerando trabajos empíricos y teóricos recientes, principalmente sobre genes Hox, estado filotípico y morfogénesis. Argumentamos que la noción de variación isotrópica e ilimitada asociada con las teorías darwinianas y neodarwinianas deben ser reconsideradas a la luz de los aportes recientes de la biología del desarrollo. En esta visión, la variación estaría constreñida y sesgada. Esta reforma del concepto de variación coincide con la reformulación del (...) de constreñimiento, los cuales serían entendidos como un factor causal positivo en la evolución, en contraposición a como suelen ser entendidos en biología. (shrink)

This paper presents evidence for a psychological coding process that meets the criteria that define such processes in organic nature and culture. The recognition of these previously unknown encoding sequences is derived from the recent formulation of an adaptive mental module of the mind—the emotion processing mind—that has evolved to cope with traumatic events and the unique, language derived, explicit human awareness of personal mortality. The emergent awareness of death has served as a selection factor for the evolution of a (...) two-system, emotion-processing mind, with conscious and unconscious components, an arrangement that allows for the invocation of conscious denial, which in turn has fostered the use of encoding when faced with death-related traumas. The paper offers several ways in which evolved mental adaptations have features that are shared with those that are biological. Many aspects of these mental adaptive efforts are comparable to attempts at defense that are carried out by the immune system. In addition, the adaptive approach has been the foundation for the discovery of laws of communication, and thus of the mind, that are on a parallel with those found through mathematical models drawn from Newtonian physics. (shrink)

This paper develops the ideas of the Swiss zoologist Adolf Portmann or, more precisely, his concept of organic self-representation, wherein Portmann considered the outer surface of living organisms as a specific organ that serves in a self-representational role. This idea is taken as a starting point from which to elaborate Portman’s ideas, so as to make them compatible with the theoretical framework of biosemiotics. Today, despite the many theories that help us understand aposematism, camouflage, deception and other phenomena related to (...) the category of mimicry, there still is a need for a general theory of self-representation that would re-synthesize evolutionary, morphogenetic and semiotic aspects of the surface of organisms. Here, Adolf Portmann’s concept of self-representation is considered as an important step towards the biosemiotics of animal form. (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)

Throughout the history of molecular biology, the primary meaning of biological information has been taken from the image of a word-based linguistic code. I want to argue that the metaphor of such a code does not begin to capture either the variety or the richness of the processes by which nucleotide sequences inform biological processes. Current research demonstrates that nucleotide sequences inform not only development but also heredity and evolution, and they do so in all sorts of ways. Even though (...) they do not exhaust the varieties of biological information employed in these processes, I claim that the power of DNA sequences to inform these processes is richer and perhaps far greater than the conventional understanding of genetic information permits, indeed richer than what any of our images of simple linguistic codes or of senders and receivers permits. Rather than a tape in a Turing machine or a message or signal sent through the generations, DNA is first and foremost a physicochemical structure with a range of potential uses by the physicochemical arsenal of biological cells that is so large as to expose the poverty of our most familiar metaphors. Recognition of this fact leads us to conclude that DNA is both more and less than we thought—more because it carries both symbolic and non-symbolic information and less because accepting that fact undermines its radical distinction from other biological molecules. (shrink)

Both biosemiotics and evolutionary epistemology are concerned with how knowledge evolves. (Applied) Evolutionary Epistemology thereby focuses on identifying the units, levels, and mechanisms or processes that underlie the evolutionary development of knowing and knowledge, while biosemiotics places emphasis on the study of how signs underlie the development of meaning. We compare the two schools of thought and analyze how in delineating their research program, biosemiotics runs into several problems that are overcome by evolutionary epistemologists. For one, by emphasizing signs, biosemiotics (...) needs to delineate a semiotic threshold, which is a problem not encountered by evolutionary epistemologists. Instead, the latter recognizes that all organisms are knowers that evolve knowledge, which they recognize to extend toward phenomena produced by organisms such as behavior, cognition, language, culture, science, and technology. Secondly, biosemiotics attempts at continuing adaptationist notions on how organisms relate to their environment, while especially Applied Evolutionary Epistemology comes to redefine the nature of the organism–environment relationship in such a way that it recognizes the spatiotemporal boundedness of existence, which in turn makes adaptationist accounts obsolete. (shrink)

This edited volume provides a biosemiotic analysis of the ecological relationship between food and medicine. Drawing on the origins of semiotics in medicine, this collection proposes innovative ways of considering aliments and treatments. Considering the ever-evolving character of our understanding of meaning-making in biology, and considering the keen popular interest in issues relating to food and medicines - fueled by an increasing body of interdisciplinary knowledge - the contributions here provide diverse insights and arguments into the larger ecology of organisms’ (...) engagement with and transformation through taking in matter. Bodies interpret molecules, enzymes, and alkaloids they intentionally and unintentionally come in contact with according to their pre-existing receptors. But their receptors are also changed by the experience. Once the body has identified a particular substance, it responds by initiating semiotic sequences and negotiations that fulfill vital functions for the organism at macro-, meso-, and micro-scales. -/- Human abilities to distill and extract the living world into highly refined foods and medicines, however, have created substances far more potent than their counterparts in our historical evolution. Many of these substances also lack certain accompanying proteins, enzymes, and alkaloids that otherwise aid digestion or protect against side-effects in active extracted chemicals. Human biology has yet to catch up with human inventions such as supernormal foods and medicines that may flood receptors, overwhelming the body’s normal satiation mechanisms. This volume discusses how biosemioticians can come to terms with these networks of meaning, providing a valuable and provocative compendium for semioticians, medical researchers and practitioners, sociologists, cultural theorists, bioethicists and scholars investigating the interdisciplinary questions stemming from food and medicine. (shrink)

Most bodies in this world do not have brains and the minority of animal species that do have brained bodies are descendents from species with more distributed or decentralized nervous systems. Thus, bodies were here first, and only relatively late in evolution did the bodies of a few species grow supplementary organs, brains, sophisticated enough to support a psychological life. Psychological life therefore from the beginning was embedded in and served as a tool for corporeal life. This paper discusses the (...) semiotically controlled dynamics of bodily existence that has allowed the evolution of these seemingly ‘unnatural’ mental and even linguistic kinds of species. It is shown how the skin, on the one hand, makes us belong in the world, and on the other hand, is part of the huge landscape of membranes across which the semiotic self incessantly must be reconstituted. The discussion moves on to the intracellular world of signal transduction through which the activity of single cells are put to service for bodily needs. The paper further considers the mechanisms behind homeostasis and the semiotics of the psycho-neuro-endocrine integration in the body. The concept of semiotic emergence is introduced and a holistic marker hypothesis for why some animals may have an experiential life is suggested. (shrink)

This paper argues that the Extended Synthesis, ecological information, and biosemiotics are complementary approaches whose engagement will help us explain the organism-environment interaction at the cognitive level. The Extended Synthesis, through niche construction theory, can explain the organism-environment interaction at an evolutionary level because niche construction is a process guided by information. We believe that the best account that defines information at this level is the one offered by biosemiotics and, within all kinds of biosemiotic information available, we believe that (...) ecological information is the best candidate for making sense of the organism-environment relation at the cognitive level. This entanglement of biosemiotics, ecological information and the Extended Synthesis is promising for understanding the multidimensional character of the organism-environment reciprocity as well as the relation between evolution, cognition, and meaning. (shrink)

This paper reviews and extends ideas of eukaryotization by endosymbiosis. These ideas are put within an historical context of processes that may have led up to eukaryotization and those that seem to have resulted from this process. Our starting point for considering the emergence and development of life as an organized system of chemical reactions should in the first place be in accordance with thermodynamic principles and hence should, as far as possible, be derived from these principles. One trend to (...) be observed is the ever-increasing complexity resulting in several layers of compartmentalization of the reaction system, either spatial (of which the eukaryotic cell is an example), or functional (as in the gradually deepening distinction between metabolic, enzymatic and information-storing functions within the cell). One of the causes of this complexification of living systems will have been the changes in environmental conditions, particularly the geochemical impoverishment of the biosphere during geological history, partly brought about by living systems themselves, and partly by the trend towards increasing efficiency and specificity of the reactions that occur. (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)

What should be the ontology of the world such that life and cognition are possible? In this essay, I undertake to outline an alternative ontological foundation which makes biological and cognitive phenomena possible. The foundation is built by defining a model, which is presented in the form of a description of a hypothetical but a logically possible world with a defined ontological base. Biology rests today on quite a few not so well connected foundations: molecular biology based on the genetic (...) dogma; evolutionary biology based on neo-Darwinian model; ecology based on systems view; developmental biology by morphogenetic models; connectionist models for neurophysiology and cognitive biology; pervasive teleonomic explanations for the goal-directed behavior across the discipline; etc. Can there be an underlying connecting theme or a model which could make these seemingly disparate domains interconnected? I shall atempt to answer this question. By following the semantic view of scientific theories, I tend to believe that the models employed by the present physical sciences are not rich enough to capture biological (and some of the non-biological) systems. A richer theory that could capture biological reality could also capture physical and chemical phenomena as limiting cases, but not vice versa. (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 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)

Biosemiotics—a discipline in the process of becoming established as a new research enterprise—faces a double task. On the one hand it must carry out the theoretical and experimental investigation of an enormous range of semiotic phenomena relating organisms to their internal components and to other organisms (e.g., signal transduction, replication, codes, etc.). On the other hand, it must achieve a philosophical re-conceptualization and generalization of theoretical biology in light of the essential role played by semiotic notions in biological explanation and (...) modeling. This paper attempts to contribute to the second task by tracing some aspects of the historical evolution of explanatory models in biology. In so doing, a parallel can be drawn between the present status of biosemiotics and that of physics during the early decades of the last century. By following the career of the concept instrument (organon) in Aristotelian science, we revisit historical stages of the antithetical (but often complementary) roles of mechanical and teleological forms of explanation. The impact of the introduction of the organic codes in biology is seen to be somewhat analogous to that of the introduction of the quantum of action in physics. Faced with intractable empirical facts, physicists combined experimental results and bold philosophical speculation to create quantum physics—a wider, deeper framework that accommodates the new facts through a wholesale reformulation of the classical ideas. Essential to this development was the articulation of the epistemic functions of instruments, which was absent from classical physics. Similarly, the consideration of the role of instruments in biology may lead to a synthesis of Aristotelian and Kantian intuitions within a wider framework capable of joining now separate perspectives, such as Jablonka’s four-fold view of inheritance information, Barbieri’s theory of artifactual copymakers and codemakers, and recently developed models of causation based on the idea of manipulative interventions. (shrink)

With the publication of this inaugural issue of the internationally peer-reviewed journal Biosemiotics, our still-developing young interdiscipline marks yet another milestone in its journey towards adulthood. For this occasion, the editors of Biosemiotics have asked me to provide for those readers who may be newcomers to our field a very brief overview of the history of biosemiotics, contextualizing it within and against the larger currents of philosophical and scientific thinking from which it has emerged. To explain the origins of this (...) most twenty-first century endeavour effectively, however, will require tracing—at least to the level of a thumbnail sketch—how the ‘sign’ concept appeared, was lost, and now must be painstakingly rediscovered and refined in science. To relate this long history, this article will appear in Biosemiotics in three instalments, examining, respectively: (1) The History of the Sign Concept in Pre-Modernist Science, (2) The History of the Sign Concept in Modernist Science, and (3) The Biosemiotic Attempt to Develop a More Useful Sign Concept for Contemporary Science. In this instalment, we begin our introductory ‘stroll through the woods of sciences and signs’ by following the development of the sign concept within the context of scientific inquiry, in necessarily broad outline, from the beginnings of such inquiry in sixth century BCE, through its long development in the Middle Ages, and up unto the onset of modernity. For only within this larger historical context can our contemporary attempt to develop a naturalistic understanding of sign relations be understood. (shrink)

Despite an impressive number of investigations and indirect evidence, the mechanisms that link patterns and processes across the landscape remain a debated point. A new definition of landscape as a semiotic interface between resources and organisms opens up a new perspective to a better understanding of such mechanisms. If the landscape is considered a source of signals converted by animal cognition into signs, it follows that spatial configurations, extension, shape and contagion are not only landscape patterns but categories of identifiable (...) signals. The eco-field hypothesis, by which cognitive templates are used to identify spatial configurations as carriers of meaning according to an active function, are combined with the sign theory to create an eco-semiotic model of landscape representation. Signs from landscape change in efficacy according to mechanisms of degradation, and metric sign categories have to be considered. An interdisciplinary coalescence is expected by using the theoretical approach in different fields of conservation and resource management and planning. (shrink)

Capturing information means for every organism acquiring knowledge about the living and not living objects that exist in its surroundings. In this way, the “historical” concept of Umwelt, as a subjective surrounding has been recently integrated in the theory of landscape ecology where a landscape is not only a geographical entity but also a cognitive medium. The landscape may be considered a semiotic context used by the organisms to locate resources heterogeneously distributed in space and time. In particular, inside a (...) landscape there are different eco-fields defined as spatial arrangements of objects carrier of meaning that organisms utilize to track resources. Along this epistemic path the sonic component of the landscape is an important carrier of information commonly used by the majority of animal species to managing many vital functions. In particular birds, which are animals with a complex system of acoustic communication, seem to organize acoustic centers for public information. These sonic patterns (soundtopes) are characterized by a great variability in space and time and function like a special eco-field that allows species to share information about the status of resources and the dynamics of populations. The availability of such public information avoids a deeper and more expensive exploration of the environment to assess its quality. (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)

Acoustic codes assure the intra and interspecific communication of vocal animals. They are composed by a sequence of nominal entities and by magnitude modulation confirming in such a way contemporarily a behavioural and ecological nature. The acoustic codes find evidence in the acoustic niche hypothesis by which species in order to reduce interspecific competition occupy a restricted portion of the available frequencies modulating very precise acoustic cues . Their evolution, like other aspect of biology, is under control of the environmental (...) conditions assuming the more favourable configurations. These nominal entities respond also to the amount of energy by which are emitted allowing to the eavesdropping individuals to range the distance at which a potential competitor is broadcasting a signal. Environmental alterations, especially if of anthropogenic origin, can produce severe consequence of the acoustic codes that in turn may affect the prey–predator balance and the complexity of communities. In fact acoustic codes under an environmental constraint like human noise intrusion can be modified in order to reduce a masking effect, demonstrating their phenological plasticity. The new ecological discipline of soundscape ecology offers the possibility to investigate the nature and the evolution of the acoustic codes in different environmental conditions. (shrink)