V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

C. Evoinformatics: A Biosemiotic Code Quality

Barbieri, Marcello, ed. The Codes of Life. Berlin: Springer, 2008. This first volume in the Springer series Biosemiotics gathers 18 papers from advocates such as Eors Szathmary, Diego Gonzalez, Yair Neuman, and Romeu Guimaraes who contend in addition to selection, that realms of generative information, “natural conventions,” are creatively at work over evolution’s course. A structural guide in several places is the sequential scale of “major transitions” from molecules to language. While all the authors are men, and often use machinery metaphors, the edition is a novel window upon an intrinsically organic Copernican cosmos of dual phenotype and genotype.

The aim of the book is to show not only that a plurality of organic codes exists in nature, but also that codes exist at all levels of life, from the molecular world to the world of language. They exist in cells, embryos, nervous systems, minds, and cultures, and are fundamental components of those systems. In order to illustrate this plurality of codes at a plurality of levels, the book has been divided into four parts: (1) codes and evolution; (2) the genetic code; (3) protein, lipid, and sugar codes; and (4) neural, mental, and cultural codes. (Barbieri, x)

Brier, Soren and Cliff Joslyn. Information in Biosemiotics. Biosemiotics. Online May, 2012. An Introduction to a special issue on this topic. Papers include “Informational, Peircean and Code-Semiotic Views on Biosemiotics” by these authors, Harold Pattee’s “Epistemic, Evolutionary, and Physical Conditions for Biological Information” and “Biology needs Information Theory” by Gerard Battail. Once again, this perspective and school is trying to articulate and say in many words that an animate nature is somehow deeply suffused with and moved by creative codes.

Although semiotics emerged in efforts to scientifically investigate how signs function in language and culture, the 20th century has witnessed efforts to extend semiotic theory into the non-cultural realm, primarily in relation to living systems and computers. Resulting developments have been deployed to extend the scope of semiotics from strictly cultural communication to a “biosemiotics” that encompasses communication of all living systems from the inside of cells to the whole biosphere. Biosemiotics is thus a research program that attempts to unite the areas of nature, mind, language, human consciousness and society in an evolutionary framework, and which tries to explain the qualitative differences between these as levels of emerging qualities, and to extrapolate its consequence for science and our anthropology. (Abstract, 1)

Deacon, Terrence. How Molecules Became Signs. Biosemiotics. October, 2021. The veteran UC Berkeley bioanthropologist continues his project to explain and emphasize life’s loquacious evolution by way of an apparent codifications which manifestly appear wherever possible. For example, Fig. 7 depicts three ways that a nucleic acid template can serve to regulate a complex autogenic process. Fig. 9 shows how a recursive course between genes and proteins becomes a basis for epigenetic processes. In essence, the endeavor is seeking to parse life’s biochemical dynamics as some manner of an innate literature (liferature, iiferate).

As a target article, several critiques herein such as Does Autogenic Semiosis Underpin Minimal Cognition? by M. Garcia-Valdecasas and Data and Context by T. Dickins laud and embellish the dialogue. But a remarkable response is Symbol Grounding Precedes Interpretation by Harold Pattee (reviewed below) since Deacon casts back and dedicates this article to Pattee’s 1969 original essay, How Does a Molecule Become a Message?.

To explore this occasion I will ask: “What sort of process is necessary and sufficient to treat a molecule as a sign?” In regard I develop and specify a simple molecular model system assumes known physics and chemistry but can represent the interpretive properties of interest. Three complex variants are then sketched that parallel an “icon-index-symbol” hierarchic scaffolding logic. This analysis reverses a molecular and evolutionary biology which treats DNA and RNA as the original sources of biological information. Instead I argue that the structural characteristics of these molecules have provided semiotic affordances which the interpretive dynamics of viruses and cells have taken advantage of. (Abstract excerpt)

To summarize the argument so far: there are 5 holistic properties that even a simple autogenic system exhibits which are not reducible its physical–chemical properties of its components and emerge from the whole integrated system. They are 1. individuation (an intrinsic maintenance of a self/non-self distinction); 2. autonomy (it sustains its own boundary conditions via component processes); 3. recursive self-maintenance3 (it repairs and replicates these same critical boundary conditions); 4. normativity (it is disposed to produce these result); and 5. interpretive competence (by being able to re-present itself in new instantiations). (10)

Deacon, Terrence. Reconsidering Darwin’s “Several Powers.”. Biosemiotics. Online March, 2016. Keywords are code biology, teleology, self-organization, far-from-equilibrium and autogenesis. The UC Berkeley bioanthropologist and author of Incomplete Nature: How Mind Emerged from Matter (2011) continues his project, along with colleagues, to conceive an expanded, appropriate 21st century genesis evolutionary synthesis. Charles Darwin concluded his Origins by saying while natural selection is surely in effect, something else and more seems to be implicated, as the quote cites. Some 157 years later, via a worldwide collaboration reaching into physical and chemical sources, this prior influence is becoming understood as an innately dynamic self-organization. As the Cosmic Code and Systems Evolution chapters and references throughout attest, the “universal gestation” mindset of the mid 19th century is at last being verified and explained. Much work remains to quantify a conducive animate cosmos, whence all this phenomena could be seen as a natural genetic program.

Contemporary textbooks often define evolution in terms of the replication, mutation, and selective retention of DNA sequences, ignoring the contribution of the physical processes involved. In the closing line of The Origin of Species, however, Darwin recognized that natural selection depends on prior more basic living functions, which he merely described as life’s “several powers.” For Darwin these involved the organism’s capacity to maintain itself and to reproduce offspring that preserve its critical functional organization. In modern terms we have come to recognize that this involves the continual generation of complex organic molecules in complex configurations accomplished with the aid of persistent far-from-equilibrium chemical self-organizing and self-assembling processes. But reliable persistence and replication of these processes also requires constantly available constraints and boundary conditions. Organism autonomy further requires that these constraints and co-dependent dynamics are reciprocally produced, each by the other.

In this paper I argue that the different constraint-amplifying dynamics of two or more self-organizing processes can be coupled so that they reciprocally generate each other’s critical supportive boundary conditions. This coupling is a higher-order constraint (which can be distributed among components or offloaded onto molecular structures) that effectively constitutes a sign vehicle “interpreted” by the synergistic dynamics of these co-dependent self-organizing process so that they reconstitute this same semiotic-dynamic relationship and its self-reconstituting potential in new substrates. This dynamical co-dependence constitutes Darwin’s “several powers” and is the basis of the biosemiosis that enables evolution. (Abstract)

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)

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