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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

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

C. Evoinformatics: A Biosemiotic Code Quality

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)

Lackova, Ludmila and Dan Faltynek. Can Quantitative Approaches Develop Bio/Semiotic Theory? Biosemiotics. August, 2021. The Palacky University, Olomouc, Czech Republic linguists (search) introduce a dedicated collection to consider better ways to appreciate and assimilate the vital presence of organic codes and communications across life’s animate scales. Among the entries are Application of N-Gram Based Distances to Genetic Texts Comparison by Valery Kirzhner and Zena Volkovich, and A Semiotic Modern Synthesis: Quantitative Studies in Zoosemiotics by Amelia Lewis.

This special issue addresses question about the place of quantitative methods in the field of biosemiotics. Many standpoints have been taken by contributing authors to demonstrate that the answer to this question is not straightforward. Considering quantitative methods in biosemiotics is necessarily related to inclusion of other scientific fields and interdisciplinary dialogue. (Abstract)

Maran, Timo. Dimensions of Zoosemiotics. Semiotica. 198/1, 2014. An Introduction to a special double issue on this approach, a half-century after Thomas Sebeok’s entry of this term, to view creaturely, and human, signifying communication as life’s primary sustaining quality. For content, we note Zoosemiotics is the Study of Animal Forms of Knowing by Kaveli Kull, Zoo-Aesthetics: A Natural Step After Darwin by Katya Mandoki, and especially The Semiome: From Genetic to Semiotic Scaffolding by Jesper Hoffmeyer. Abstract excerpts are included for these insightful readings of nature’s creative dialogue.

Kaveli Kull This article characterizes briefly the central aims of the semiotic study of animal life. Semiotic sciences in general can be defined as approaches to the study of various forms of knowing (as different from physical sciences, which study various things in the world), considering that knowing is possible only due to semiosis. The semiosphere is the sphere of knowing (knowing being always related to learning and acting). The basic types of knowing (as well as semiosis) include the vegetative, the animal, and the cultural. Zoosemiotics is focused on the animal type of knowing. Animal knowing is characterized by its use of iconic and indexical relations, whereas the extensive use of symbols is a prerequisite of specifically human (cultural, language-based) semiosis. However, the human organism also includes animal knowing as an inevitable part of its knowing. Knowledge cannot be credible if it is exclusively symbolic; it requires that iconic and indexical semiosis be involved.

Katya Mandoki As a category, poiesis can be extended beyond the standard anthropocentric use and applied across three radically different scales: auto-poiesis in everyday self-organization of every living creature, phylo-poiesis in the shaping of a species by sexual selection across various generations and onto-poiesis as an individual's development of formal skills and creative modification of its environment. In this paper, I apply these distinctions and argue, following Darwin and Sebeok, for the possibility of considering poietic and aesthetic manifestations among various animal species in their ability of both appreciating and expressing rhythm, visual decorative patterns, and chromatic qualities. In music we can find song and equivalents to instrumental playing (cicadas and crickets), theater in representing fictitious situations (killdeer's broken wing act and playing), acrobatic skills (various types of woodcocks and paradise birds) and dancing (cranes and eleonora cockatoo).

Jesper Hoffmeyer 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. Semiotic scaffolding is only very indirectly based on genetic scaffolding. The gene products, the proteins, are not just molecules, but are always also semiotic tools, and what the genes really do is to specify the efficiency of semiotic modulators. 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.

Marijuan, Pedro, et al.. Fundamental, Quantitative Traits of the “Sociotype. Biosystems. Volume 180, 2019. Veteran researchers Pedro M., Raquel del Moral and Jorge Navarro, Aragon Health Research Institute, Sungchul Ji, Rutgers University, Marta Gil Lacruz and Juan Gomez-Quintero, University of Zaragoza (search names) press consider how such an emergent socio-genetic realm might be conceptually present in some working role akin to genotypes and phenotypes. As a result, it is advised that an optimum human grouping of social bonds seems to actually be 100 people, which is different from (Robin) Dunbar’s number of 150. See also The “Sociotype” Construct: Gauging the Structure and Dynamics of Human Sociality by this group in PLoS One (December 14, 2017).

In whatever domain of life from cells to organisms to societies, communicative exchanges underlie the formation and maintenance of the emerging collective structures. It can be clearly seen in the human social world. In the present work we have investigated the basic metrics of social bonds and communicative exchanges along the development of within our genotype-phenotype-sociotype conceptual triad. The sociotype means the relative constancy of the social world in which each individual life is developed. Other results about gender, age, and use of social Internet media highlight significant differences among the social segments, and particularly the diminished “sociotype” of the elderly. (Abstract excerpt)

Markos, Anton. The Birth and Life of Species-Cultures. Biosemiotics. Online December, 2015. The Charles University, Prague biologist and philosopher continues his endeavor (search) to discern and express a recurrent continuity across evolution and our cultural phase by way of essential semiotic scripts. Life’s development is thus akin to a gestation as well traced by learning and knowledge gains, a growing realization. But a curious issue arises in the second quote – why does a scientist in the 2010s feel it is still necessary to avoid or disown a vitalist view, an innate organic milieu that is now widely affirmed? This is the revolution in our midst that must be brought to fruition.

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 (individuals) 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. 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. (Abstract)

As a biologist, I might easily be accused of vitalist heresy. In spite of this, I argue that inspiration by models developed in the humanities may mark out a way towards a general
theory of evolution valid for all life. What makes all life isomorphic with what we take as human cultural features is (1) a semiotic character of individuals as well as communities rooted in the fact that they are born from similar entities, thus maintaining the continuity of lineages from ancient times. This allows both individuals and communities (2) an interpretative approach to their history – rooted in memory and experience. Moreover, it allows (3) a creative approach to their genetic endowment (“genetic script”), i.e., creation of novelties. (11)

Merrell, Floyd. Entangling Forms: Within Semiosic Processes. Berlin: De Gruyter Mouton, 2010. The Purdue University linguist, physicist, expositor of Spanish mythic literature, offers another brilliant engagement with our fantasmagorical reality that appears most of all as a textually prescriptive creation in which we intended readers have a crucial voice. This perennial view is here braced and accomplished by a unique meld of John Archibald Wheeler’s (1911-2008) cosmic physics of a “co-participatory becoming” with Charles Pierce’s (1839-1914) evocation that signification, aka semiotics, touches this deep communicative essence. Indeed its final Chapter 17 is “The Universe: A Book to be Read?” With the “Resemblance” paper above, Merrell touches truth by his rhetorical flourishes and insights from an original Taosphere to our Noosphere as Semiosphere, as phenomenal people more closely evoke the implicate presence of archetypal, gravid gender complements and familia trinities as they initiate, quicken, and move to birth themselves.

Chapter Seven suggests that the semiosic process of becoming carries the implication that everything is mutually co-participating, thus perpetuating that very process of becoming. The watchword in regard to this process is the interconnectedness of signs, worlds, meanings, and sign makers and takers. Interconnectedness call for particular focus on (1) the process of contradictory complementary coalescence, and (2) semiosic entanglement, which lie behind the notion of co-participation. Development of these topics evokes further words on what Pierce alludes to as ‘objective idealism,’ and Bohr’s complementarity. Chapter Eight interrelates semiosic entanglement with Peirce’s ‘objective idealism’ via a couple of Wheeler’s ‘thought experiments’’ that serve further to illustrate the co-participatory, self-organizing nature of signs and the world as we perceive and conceive them though our communicative channels. (xi)

Pagni, Elena and Richard Simanke, eds. Biosemiotics and Evolution: The Natural Foundations of Meaning and Symbolism. Switzerland: Springer, 2022. Federal University of Juiz De Fora, Brazil philosophers collect a wide range of authors and papers which serve to advance this present informative synthesis between living, personal systems and our pervasive communications. See for example Life Sciences and the Natural History of Signs by Franco Giorgi, Physical Intentionality: The Phenomenological Roost of Biosemiotics by Roberta Lanfredidi, and How Information Gets its Meaning by Vinciius Romanini.

This book reviews the evolution of Biosemiotics and an outlook on the future of this interdisciplinary new discipline. In this volume, the foundations of symbolism are transformed into a phenomenological, technological, philosophical and psychological discussion. The book is divided into three parts: Life, Meaning, and Information, Semiosis and Evolution, Physics, medicine, and bioenergetics. The authors shed new light on the processes underlying the origins and evolution of knowledge, the boundary between teleonomic and teleological paradigms of evolution and their possible integration, the relationship between linguistics and biological sciences, biological information and its transmission, physical and biosemiotic intentionality and models for culture, digitalization and proto-design. (Publisher)

Pattee, Harold. Symbol Grounding Precedes Interpretation. Biosemiotics. October, 2021. The entry is a response to Terrence Deacon’s entry How Molecules Become Signs in this journal (Oct. 2021, above) which was posted to honor my 1969 paper How Does a Molecule Become a Message?. In extraordinary regard, the eminent CalTech logician, physicist, and mathematician (search) is still on his message at 96 years of age. As a result, a remarkable comparison over a half century span can well illume and emphasize life’s textual articulation. Fortunately Pattee’s original paper has been reprinted in a 2012 collection, Laws, Language and Life, with many other diverse, erudite writings (search Joanna Leonardi, Polish philosopher editor).

Deacon speculates on the origin of interpretation of signs using autocatalytic origin of life models and Peircean terminology. I explain why interpretation evolved only later as a triadic intervention between symbols and actions. In all organisms the passive one-dimensional genetic informational symbol sequences are converted to active functional proteins or nucleic acids by three-dimensional folding. This symbol grounding is a direct symbol-to-action conversion. It is universal throughout all evolution. Folding is entirely a lawful physical process, leaving neither freedom nor necessity for interpretation. Similarly, the initial converse action-to-symbol conversion of sensory inputs also leaves no freedom for interpretation until after the action-to-symbol conversion. (Abstract)

Pattee, Howard. Physical and Functional Conditions for Symbols, Codes and Languages. Biosemiotics. 1/2, 2008. We cite this paper by the emeritus SUNY Binghamton physicist, biologist and logician as an entry to a lifetime of deep insights and theories that are gaining recognition such as in M. Gazzaniga’s 2018 The Consciousness Instinct. A 2012 edited volume, Laws, Language and Life, noted herein, provides a half-century collection of his writings. Their key essence is that natural reality is to be seen as graced by dual modes or phases of an animate materiality and a textual, informative quality. Within this perception, a bicameral, matter/symbol, genotype/phenotype complementary code is in evidential effect at every scale and instance. By this grand synthesis, the genetic and linguistic domains become inherently similar.

All sciences have epistemic assumptions, a language for expressing their theories or models, and symbols that reference observables that can be measured. In most sciences the language in which their models are expressed are not the focus of their attention. On the contrary, biosemiotics, by definition, cannot escape focusing on the symbol–matter relationship. Symbol systems first controlled material construction at the origin of life. At this molecular level it is only in the context of open-ended evolvability that symbol–matter systems and their functions can be objectively defined. While this partial description holds for all symbol systems, cultural languages are much too complex to be adequately described only at the molecular level. Genetic language and cultural languages have common basic requirements, but there are many significant differences in their structures and functions. (Abstract excerpt)

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