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Switch to: References
Citations of:
The organic codes: an introduction to semantic biology
New York: Cambridge University Press (2002)
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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 (...) |
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According to Denis Noble, one of the greatest illusions of the Modern Synthesis is embodied in the Central Dogma, a principle first formulated by Francis Crick in 1958. The principle holds that DNA makes protein, not the other way around. For Noble, the Dogma has contributed to the illusion that genes alone are responsible for the development and evolution of an organism’s phenotype. Though I am largely sympathetic to Noble’s critique, I argue that there may be alternative grounds for accepting (...) |
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Morphology and its relevance for systematics is a promising field for the application of biosemiotic principles in scientific practice. Genital coupling in spiders involves very complex interactions between the male and female genital structures. As exemplified by two spider species,Nephila clavipesandNephila pilipes ssp. fenestrata, from a biosemiotic point of view the microstructures of the male bulb’s embolus and the corresponding female epigynal and vulval parts form the morphological zone of an intraspecific communication and sign-interpreting process that is one of the (...) |
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The concept of protosemiosis or semiosis at the lower levels of the living goes back to Giorgio Prodi, Thomas A. Sebeok and others. More recently, a typology of proto-signs was introduced by Sharov and Vehkavaara. Kull uses the term of vegetative semiosis, defined by iconicity, when referring to plants and lower organism semiosis. The criteria for the typology of proto-signs by Sharov and Vehkavaara are mostly based on two important presuppositions: agency and a lack of representation in low-level semiosis. We (...) |
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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 (...) |
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The aim of this contribution is to investigate certain selected parts of the extended evolutionary synthesis which all have a common denominator, namely evolution by meaning attribution. We start by arguing that living organisms can manipulate and interpret their genetic script via epigenetic modifications in a semiotic manner, that is, by meaning attribution. Genes do not build living beings to be transmitted to future generations. Genes have been shaped by evolution as a memory medium that is transmitted from one generation (...) |
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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 (...) |
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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) (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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Today there are two major theoretical frameworks in biology. One is the ‘chemical paradigm’, the idea that life is an extremely complex form of chemistry. The other is the ‘information paradigm’, the view that life is not just ‘chemistry’ but ‘chemistry-plus-information’. This implies the existence of a fundamental difference between information and chemistry, a conclusion that is strongly supported by the fact that information and information-based-processes like heredity and natural selection simply do not exist in the world of chemistry. Against (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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The fossil record shows that the stromatolites built by cyanobacteria 2 and 3 billion years ago are virtually identical to those built by their modern descendants, which is just a part of much evidence revealing that bacteria have barely changed in billions of years. They appeared very early in the history of life and have conserved their complexity ever since. The eukaryotes, however, did the opposite. They repeatedly increased the complexity of their cells and eventually broke the cellular barrier and (...) |
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The New World of the Organic CodesThe 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 (...) |
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The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different types of signs and has led to the distinction between iconic, indexical and symbolic semiosis. In all these cases, however, semiosis has been defined by the (...) |
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Though the formal coherence and empirical utility of Marcello Barbieri’s concept of organic code have been starting to become established, a general conception of how the semantics of organic codes is related to the pragmatics of their use is still missing. Barbieri took a first step towards such a conception by distinguishing three types of semiosis in living systems: manufacturing, signalling, and interpretive semiosis. This paper integrates Barbieri’s distinction into Roman Jakobson’s systematization of possible functions of messages in order to (...) |
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This article focuses on the cultural implications of biosemiotics, considering the extent to which biosemiotics constitutes an “epistemological break” with modern modes of conceptualizing the world. To some extent, the article offers a series of footnotes to points made in the work of Jesper Hoffmeyer. However, it is argued that the move towards ‘agency’ represented in biosemiotics needs to be approached with caution in light of problems of translation between the humanities and the sciences. Notwithstanding these problems, biosemiotics is found (...) |
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This article considers categorical perception (CP) as a crucial process involved in all sort of communication throughout the biological hierarchy, i.e. in all of biosemiosis. Until now, there has been consideration of CP exclusively within the functional cycle of perception–cognition–action and it has not been considered the possibility to extend this kind of phenomena to the mere physiological level. To generalise the notion of CP in this sense, I have proposed to distinguish between categorical perception (CP) and categorical sensing (CS) (...) |
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The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing systems but “meaning-making” systems. Therefore, (...) |
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The discovery of the genetic code has shown that the origin of life has also been the origin of semiosis, and the discovery of many other organic codes has indicated that organic semiosis has been the sole form of semiosis present on Earth in the first three thousand million years of evolution. With the origin of animals and the evolution of the brain, however, a new type of semiosis came into existence, a semiosis that is based on interpretation and is (...) |
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Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal (...) |
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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 (...) |
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1Center for the Philosophy of Nature and Science Studies, Blegdamsvej 17, DK-2100 Copenhagen, Denmark. Published pp. 117-124 in: Mark Bedeau, Phil Husbands, Tim Hutton, Sanjev Kumar and Hideaki Suzuki : Workshop and Tutorial Proceedings. Ninth International Conference on the Simulation and Synthesis of Living Systems. |
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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, (...) |
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A common approach in biosemiotics suggests that semiosis (any activity or process that involves signs) is a natural process embedded in evolution, which entails the production of meaningful processes. As Pattee has argued, a closer look at living systems shows that semiosis is closely related to a very specific and highly functional context of selected constraints. Symbolic control consists in 1) instituting a friction on the novelty, variability and randomness of life processes 2) allowing survival value at all levels of (...) |
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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, (...) |
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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 (...) |
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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 (...) |
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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 (...) |
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In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of (...) |
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Biological evolution is often viewed narrowly as a change of morphology or allele frequency in a sequence of generations. Here I pursue an alternative informational concept of evolution, as preservation, advance, and emergence of functional information in natural agents. Functional information is a network of signs that are used by agents to preserve and regulate their functions. Functional information is preserved in evolution via complex interplay of copying and construction processes: the digital components are copied, whereas interpreting subagents together with (...) |
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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 (...) |
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The basic premise of biosemiotics as a discipline is that there are elementary processes linking signifying strategies in all forms of animate life. Correspondingly, the discoveries of biosemiotics should, in principle, be capable of revealing new insights about human signification. In the present article, I show that this is in fact the case by constructing a biosemiotic model that links advertising strategies with corresponding structures in animal predation. The methodological framework for this model is the catastrophe theory of René Thom. (...) |
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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 (...) |
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