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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Systems Evolution: A 21st Century Genesis Synthesis

B. Evoinformatics: A Biosemiotic Quality

Deely, John. Semiotics & Information. Spinks, C. and John Deely, eds. Semiotics 1998.. New York: Peter Lang, 1999. From this perspective, the cosmos is seen to be suffused with informative signs from its origin which then proceed to emerge and become manifest with inquisitive, sentient human life.

We thus bracket the history of the universe from the “big bang” to the present as the development from physiosemiosis, the virtual action of signs at play from the outset, to semiotics, the intellectual phenomenon wherein and by which the linguistic animal….becomes conscious of its own destiny as the formation of a community of inquirers, and becomes aware at the same time of what makes inquiry possible in the first place, namely, the action of signs. And since this action….was present from the beginnings of the universe and continues in all of its phases and parts, perhaps “semiosis” is also the proper name of what we have heretofore been labeling provisionally as “evolution.” (196-197)

Emmeche, Claus and Jesper Hoffmeyer. From Language to Nature: The Semiotic Metaphor in Biology. Semiotica. 84/1-2, 1991. An appreciation of how analogy, metaphor, and communication in biological evolution implies an understanding of life as a linguistic phenomenon.

Emmeche, Claus and Kalevi Kull, eds. Towards a Semiotic Biology: Life is the Action of Signs. London: Imperial College Press, 2011. Scientific studies across quantum and chemical to cerebral and societal stages have historically proceeded from first identifying objects, then to interconnections in between, and onto realizations that living systems are most about creative communication. In regard, such a similar textual turn is advised as a better way to understand and appreciate how organisms evolve, learn and proceed. Leading proponents such as Jesper Hoffmeyer and Terrence Deacon discuss an informational essence that is increasingly is seen to distinguish a cosmic developmental genesis of both phenotype and genotype.

A unique chapter is Semiosphere is the Relational Biosphere by the Estonian scholars Kaie Kotov and Kalevi Kull which sets this vital project in an historical context from the noosphere of Vladimir Vernadsky and Pierre Teilhard to Yuri Lotman who coined the title term in 1990. Drawing on the dynamic theories of Ilya Prigogine and others, a novel realm of information, knowledge and signification is presently seen to be enveloping and transforming the biosphere as a self-organizing system.

This book presents programmatic texts on biosemiotics, written collectively by world leading scholars in the field (Deacon, Emmeche, Favareau, Hoffmeyer, Kull, Markoš, Pattee, Stjernfelt). In addition, the book includes chapters which focus closely on semiotic case studies (Bruni, Kotov, Maran, Neuman, Turovski). According to the central thesis of biosemiotics, sign processes characterise all living systems and the very nature of life, and their diverse phenomena can be best explained via the dynamics and typology of sign relations. The authors are therefore presenting a deeper view on biological evolution, intentionality of organisms, the role of communication in the living world and the nature of sign systems. (Publisher)

Goodwin, Brian. Bateson: Biology with Meaning. Hoffmeyer, Jesper, ed. A Legacy for Living Systems: Gregory Bateson as Precursor to Biosemiotics. Berlin: Springer, 2008. Once again the Schumacher College sage provides a lucid evocation of the genesis vision, here with regard to a universal genome script. Extended quotes serve to make the case.

However, recent studies in post-genomic biology on the structure of proteomes, on genetic and metabolic networks, are leading to a new perspective on the nature of the processes involved in reading and expressing the information in the genome. These are beginning to be recognized as having the network properties of a language, so that a reading of the genetic text by an organism is a process that makes meaning of the text through the self-construction of the organism. (145)

Power laws describe the property of self-similarity in networks: a part of the network looks like and has the same connectivity structure as a larger or smaller part, and as the whole. Such structures are also described as fractals. Fractal structures are widely encountered in biological morphology, as in the branching patterns of trees, the venation patterns of leaves, and the structure of respiratory or circulatory systems. (148) These networks have evolved their complexity through gradual addition of components to core reaction pathways. It appears that they have self-organizing properties that are naturally fractal and are not a result of natural selection. (148) natural selection seems to be the fine tuner, not the initial generator of the organizational principles of living organisms, which reflect properties of order that extend beyond the living state to its physical and chemical substratum. (148)

The self-similar, self-referential properties of genetic, protein, and metabolic networks can now be seen as proto-languages whereby organisms make sense of their inheritance and their environmental contexts by generating forms (organisms of specific morphology and behaviour) that express embodied meaning in coherent wholes. (149) The result could be that indeed we become the things that dreams are made of through the imaginative power of both nature and culture, bringing into being a unified planet in which community, diversity and creativity are celebrated in a new Age of Meaning. (151)

Hendin, Yogi Hale. Meeting Report: The 18th Annual Biosemiotics Gathering. Biosemiotics. 12/2, 2019. An Erasmus University, Rotterdam philosopher reviews this UC Berkeley June convocation, organized by Terence Deacon and the author (Google title for more info and a 70 page book of abstracts). Some talks were Quantum origins of ontic emergence by Michael Epperson, Creation of the relative next by Donald Favareau, Can truth and love prevail? by Gerald Ostdick, and Do cell sing to each other? by Mark Johnson.

Over June 17–20, 2018, from dozens of countries, biosemioticians converged at the University of California, Berkeley to discuss the state of the art of Biosemiotics. The syncretic gathering, like the discipline itself, brought together scholars in natural science, social science, and the humanities, to further develop what Danish chemist and ur-biosemiotian Jesper Hoffmeyer calls “the life of signs, and the signs of life.” The conferees examined the hermeneutics of biological communication, its relevance to the Extended Evolutionary Synthesis, and went on to address primordial questions such as What is life, What Is Semiosis, and much more. (Abstract excerpt)

Hoffmeyer, Jesper. Biosemiotics: An Examination into the Signs of Life and the Life of Signs. Chicago: University of Chicago Press, 2009. In 1999, the journal Semiotica had a special issue on how nature, life, and its evolution might be most distinguished by processes of informational communication, a fledgling field dubbed ‘biosemiotics.’ Research studies have progressed to an extent that this present volume by the University of Copenhagen biologist and prime advocate can provide a cogent overview. What results, as the quotes touch on, is more than another theory, rather a “grand shift in man’s place in nature” (320) as complementary, ascendant digital and analog, genetic and organic, codes define a formative discourse of individual and societal awareness and cognizance. Be advised that the approach and this work, although accessible, can get caught up in its own jargon. But these advances are a salient contribution to a genesis universe by virtue of identifying this vital, ramifying genotype.

In contrast, those who persistently deny the oversimplified pictures that are characteristic of reductionist theories have perhaps been on the right path but have not had adequate theoretical means to create a productive alternative to reductionism. The time was not yet right for a scientific confrontation with mechanicism. However, that has changed in the last few decades, with the development of nonequilibrium thermodynamics, chaos theory, nonlinear dynamics, complexity research, and biosemiotics. (11)

The psychological concept of individuation is nowadays most often linked to the analytical psychology of C. G. Jung, where it refers to the processes through which a person comes to understand her own individuality and conceive her self as a “blended other.” However, the outline that we have given in this chapter of life’s beginnings also basically describes a process of individuation, especially if the word is understood in its broader philosophical meaning as a process through which an individual form of existence develops itself… (37)

In this chapter, I have suggested that the agency of organisms has an experience-like component, and I have sketched evolution as a perpetual increase in semiotic freedom produced through the semiogenic interactions of organisms.” (211) Accordingly, (Jacques) Monod’s idea of the human being as “a gypsy at the edge of time” may finally be dismantled – to be replaced by a conception of human beings as embedded in the general biosemiosis of living nature. Human mind is not, then, an alien element in the universe – but rather, an instantiation of evolutionary trends that penetrate the life sphere and that (I suspect) is deeply rooted in the general dynamics of the universe. (320)

Hoffmeyer, Jesper. Life and Reference. BioSystems. 60/1-3, 2001. The University of Copenhagen professor of biosemiotics finds living systems to be distinguished by complementary analog and digital or agency and communion modes or capacities. In an evolutionary context these qualities foster an intensifying individuation. Their synthesis implies a “semiotic” universe composed of this archetypal dynamic from quantum to molecular, cellular, and on to cognitive realms. This whole issue of BioSystems is entitled “The Physics and Evolution of Symbols and Codes” as a retrospective and expansion of the work of systems theorist Howard Pattee.

It is important here to stress the interdependence of the analog and the digital as two equally necessary forms of referential activity arising like twins in the individuation of that logic which we call life. (128) In this sense for instance Aristotle saw matter as individuating. What I have tried to describe here is the formation as a special kind of Aristotelian individuation, namely the formation of selfhood, or in other words a selfication. (129)

Hoffmeyer, Jesper. The Semiome: From Genetic to Semiotic Scaffolding. Semiotica. 198/11, 2014. The emeritus University of Copenhagen biolinguist is a leading philosopher of the biosemiotics ascent, search for many writings. We note this entry for its coinage of semiome, which can serve to give a genomic basis to nature’s communicative essence.

The fact that agency is an essential aspect of life introduces new explanatory avenues into the map of evolutionary thought. There is hardly any process in animate nature that is not, in one way or another, regulated communicatively, i.e., through the ability of living systems to read and interpret relevant signs in their environment. Semiotics – the science of signs – therefore ought to become a key tool for the “life sciences” in general and biology in particular. The paper analyzes the ways semiotic interactions in nature have been developed to scaffold the web of physiological, developmental, and ecological pathways. In addition to the concept of the genome we need in biology a concept of the semiome: the entirety of an organism's semiotic tool set: i.e., the means by which the organisms of this species may extract significantly meaningful content from their surroundings and engage in intra or interspecific communicative behavior. The semiome thus defines the scope of the organism's cognitive and communicative activity. The theoretical question raised in this paper is the question of the interconnectedness between genomic and semiomic changes. (Abstract)

We can define the semiome in analogy with the genome as the entirety of an organism’s semiotic tool set: i.e., the means by which the organisms of this species may extract significantly meaningful content from their surroundings and engage in intro- or interspecific communicative behavior. The semiome thus defines the scope of the organism’s cognitive and communicative activity. (28)

Hoffmeyer, Jesper. Why Do We Need a Semiotic Understanding of Life? Henning, Brian and Adam Scarfe, eds. Beyond Mechanism: Putting Life Back into Biology. Latham, MD: Lexington Books, 2013. In this chapter, the University of Copenhagen linguist and philosopher continues his project to reconceive the phenomenon of organisms via their distinctive feature of significant communication. Sections such as Origin of Agency, Semiosis, and Life; Evolution and the Growth of Semiotic Freedom; and Humanity’s Place in Nature and Nature’s Place in the Human, emphasize a genetic-like textual essence. Life’s temporal development is tracked by a nested emergence on the way to our vitalizing knowledge. And significantly, it closes with a proposal that a past existential despair can at last set aside by novel appreciations of this informative vector which people now consciously express and continue. See also his The Semiome: From Genetic to Semiotic Scaffolding in Semiotica (198/11, 2014).

We shall finish this overview of potential impacts of the semiotic understanding of nature by quoting the French molecular biologist and Nobel laureate who in his book Chance and Necessity, from 1971, concluded that “man must at last wake out of his millenary dream; and in doing so, wake to his total solitude, his fundamental isolation. Now he at last realizes that he lives on the boundary of an alien world…that is deaf to his music, just as indifferent to his hopes as it is to his suffering.” Introducing a semiotic view of nature opens for a return to a nature in which we belong. Monod’s idea of the human being as a “gypsy at the edge of time” may finally be dismantled – to be replaced by a conception of human beings as embedded in the general biosemiosis of living nature. Human mind is not an alien element in the universe – but rather, an instantiation of evolutionary trends that penetrate the life sphere and that (I suspect) is deeply rooted in the general dynamics of the universe. (163)

Hoffmeyer, Jesper, ed. A Legacy for Living Systems: Gregory Bateson as Precursor to Biosemiotics. Berlin: Springer, 2008. An evocative entry to natural and social realms as literate conversation and revelation. In this engagement, Mary Catherine Bateson, Terrence Deacon, Robert Ulanowicz, Brian Goodwin (search), Tyrone Cashman, and others seek to advance Gregory's sage perception.

Hofmeyr, Jan-Hendrik. The First Special Issue on Code Biology. BioSystems. 164/11, 2018. The Centre for Complex Systems in Transition, University of Stellenbosch, RSA systems biologist edits and introduces this edition, in collaboration with its founding biotheorist Marcello Barbieri (search). The guiding concept, which has received much exposition in Biosemiotics, is that in addition to genetic and cultural codes, life’s evolution and organic abidance contains a multitude of similar codings at each functional, metabolic instance. In these papers, a “universal genetic code” or “lingua franca” of Earth life is alluded to. See, for example, What is Code Biology? by Barbieri, On Universal Coding Events in Protein Biogenesis by Vladimir Kubyshkin, et al, How Prokaryotes Encode their Environment by Pedro Marijuan, et al, The Bioelectric Code by Michael Levin and Christopher Martyniuk (search), The Sugar Code by Hans-Joachim Gabius, Causation, Constructors and Codes by J-H. Hofmeyr, and The Evolutionary Dynamics of Language by Luc Steels and Eors Szathmary (search).

The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by matching with the acceptor units of their cognate tRNAs (“operational RNA code”) and ribosomal codon-anticodon pairing of messenger RNA (“triplet code”). A “stereochemical code” is at work between the translation dynamics, sequence composition and folding of the resulting protein. All these coding events as well as the basic chemistry of life are invariant across biological taxa due to the horizontal gene transfer (HGT) making the ‘universal genetic code’ the ‘lingua franca’ of life of earth. (Kubyshkin Abstract edits)

Lackova, Ludmila. A Biosemiotic Encyclopedia: An Encyclopedic Model for Evolution. Biosemiotics. Online May, 2018. A Palacky University, Czech Republic linguist scopes out a novel method to perceive and describe life’s oriented, developmental course. Rather than a Darwinian tree more like an alphabetic dictionary, web-like network forms could better serve and thus be an “encyclopedia of life.” As available on the home page, I gave an invited keynote to a globalization and spirituality conference in October 2005 at Palacky University in Olomouc, with fond memories of its erudite scholarship and gentle civility.

New discoveries in the life sciences have affirmed that the virtual script as well as its context-dependent reading and interpretation determine the final living creature (cell, protein or animal). An extended understanding of Darwinian Theory is crucial for understanding life as semiosis in terms of Peirce and Eco’s semiotic models. The semiosis of living systems is potentially unlimited. Genes are not static and unchangeable scripts, but can always be reinterpreted by new interpretants that illuminate them from different points of view, depending on which properties are relevant in a particular context. The encyclopedia is a term, in Umberto Eco’s semiotics, which represents the multidimensional space of semiosis that is governed by a self-sustaining production of interpretants. The paper will present the idea of understanding the Extended Synthesis in terms of a biosemiotic enyclopedia. (Abstract)

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