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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
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Organic Universe
Earth Life Emerge
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

C. Evoinformatics: Biosemiotic Code-Scripts Everywhere

    This lively image graces the home page, www.biosemiotica.it, of Marcello Barbieri’s website the University of Ferrera embryologist who into the 21st century has been a leading theorist, author and advocate of vital insights into life’s informative codes and signs in living systems. Search the site for many references. Professor Barbieri is also the founding editor-in-chief of the Springer journal Biosemiotics.


Akin to movements such as an algorithmic nature and information paradigm, since around 2000 a central presence and role for communicative aspects of living systems has gained prominence. The title term arose from the broader field of semiotics, the study of significations as they distinguish, engender, and vitalize from evolution to ecologies. A pioneer initiator was Thomas Sebeok (1920-2001) at Indiana University, where a loquacious group has since gone forth. Into the 21st century a leading sponsor has been Marcello Barbieri (see above), via an initial book The Organic Codes (2003) among many and a steady embellishment of articles.

As the endeavor grew, inspired by articulations of life’s dialogic essence, an International Society for Biosemiotic Studies formed with annual international conferences and other activities. A stream of volumes such as Biosemiotics: An Examination into the Signs of Life and the Life of Signs (2009) by Jesper Hoffmeyer, and Towards a Semiotic Biolog (2011) edited by Claus Emmeche and Kaveli Kull helped build a representative library. The London Metropolitan University scholar Wendy Wheeler has set up a Living Books about Life web page with writings by Terrence Deacon, Mary Catherine Bateson, and others, accessible from the Society home page.

By way of a Biosemiotics book series (Springer), a journal by this name, international conferences and advocates such as Marcello Barbieri and Jesper Hoffmeyer, an informational, communicative presence and role has been found and articulated for many code versions beyond genes alone. An array of microbial, cellular, metabolic sensings, signings and relative cross-talk across evolutionary organisms has been well scoped out and confirmed.

Barbieri, Marcello. Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology. Biological Theory. 14/1, 2019.
Barbieri, Marcello. The Semantic Theory of Language Biosystems. January, 2020.
Deacon, Terrence. How Molecules Became Signs. Biosemiotics. October 2021.
Lackova, Ludmila and Dan Faltynek. Can Quantitative Approaches Develop Bio/Semiotic Theory? Biosemiotics. August, 2021
Pagni, Elena and Richard Simanke, eds. Biosemiotics and Evolution: The Natural Foundations of Meaning and Symbolism. Switzerland: Springer, 2022.
Pattee, Harold. Symbol Grounding Precedes Interpretation. Biosemiotics. October, 2021.
Prosdocimi, Francisco and Savio Torres de Farias. Life and Living Beings under the Persepctive of Organic Macrocodes. Biosystems. May, 2021
Taborsky, Edwina. Rational Decision Making in Biological Systems. Biosystems. April, 2022.
Witzany, Guenther. Communication as the Main Characteristic of Life. Vera Kolb, ed. Handbook of Astrobiology, Boca Raton, FL: CRC Press, 2019.


Code Biology 2021. codebiology.org/conferences/Luznica2021. This is the website for the Seventh International Conference of the Code Biology Society which was held in September in Luznica, Croatia. The Society was founded by Marcello Barbieri and colleagues around 2010 as an offspring from a biosemiotic endeavor which is still active with a journal by this name. An extensive Abstracts book includes entries by Abir Igamberdiev (his Biosystems journal is a locus for papers in this field), Anna Aragno (NYC), Diego Gonzalez, et al (Mathematical Regularities in the Genetic Code), Elena Fimmel, Jacques Demongeot, et al and Joao Major (Jungian Archetypes). An overarching subject theme is an articulation of how much physical, natural, biological and social phases are deeply suffused by codes, signs, literary content writ large and small.

Code Biology 2022. codebiology.org/conferences/Olomouc2022. A site for this latest conference to be held at Palacky University in Olomouc, Czech Republic in June. Prior meetings with Abstracts can also be found there. More information about the society and its conceptual guide are at codebiology.org. As I update in mid June, the Abstracts are now posted on this site. Among the 29 talks we note Elena Fimmel, Ivan Fomin, Ludmila Lackova, Omar Paredes, Suren Zolyan, and Alexander Bolshoy. I found Paradigm for the Living: Evo/Devo Principles of Process and Interaction by Anna Aragno, a NYC wise woman psychoanalyst, to be of special interest. As a further note, a companion conference Gatherings in Biosemiotics 2022 is to be held at Palacky U. on June 27 to July 1.

Code Biology is the study of all codes of life with the standard methods of science. The genetic code and the codes of culture have been known for a long time. What is new is the study of all codes that came after the genetic and before cultural modes. That there are many organic codes in Nature has been an experimental fact. One implication is that most major events of macroevolution arose with the appearance of new organic codes. Another consequence is that codes involve meaning, which needs to be brought into biological studies, within the standard methods of science, In further regard, the organic codes have been highly conserved in evolution, so that they are the invariants of life, which must be perpetuated while everything else is changing. (Edited Excerpt)

Fifth International Conference in Code Biology. www.codebiology.org/conferences/Granada2018. This June in Granada, Spain 37 scientist scholars such as Pedro Marijuan, Peter Wills, Adam Kun, Branco Dragovich, Nikola Stambuk, Charles Carter, Almo Farina, along with CBs original conceiver Marcello Baribieri, spoke upon many applications such as sociotypes, major transitions and fractal ecoacoustics . The site contains abstracts for each presentation. See also the Code Biology home at www.codebiology.org for a concise explanations and resources.

Akhtar, J., et al. A Framework for Evolutionary Algorithms based on Charles Sanders Peirce’s Evolutionary Semiotics. Information Sciences. Online March, 2013. Within this computational approach, Akhtar, with coauthors Basit Koshul and Mian Muhammad Awais, Lahore University of Management Sciences (LUMS), Pakistan, contend that a Darwinian view of “blind chance and mechanistic laws” is, as increasingly being voiced, an insufficient explanation. As the Abstract details, if Charles Peirce’s (1839-1914) linguistic-logical philosophy can be properly appreciated in 21st century terms, it offers a novel, expansive guidance. Due to “dynamic semiotic processes,” life’s development then appears more as a phenomenal advance in meaningfulness. Peirce’s triad of chance, necessity, and habit-taking is thus expanded as spontaneity, necessity and a generalizing tendency. If an innate program abides and guides, as CSP glimpsed, as an Evolutionary Computation approach lately tries to evoke, a self-informing genesis might be implied. And we append Dr. Koshul’s vita as an example of the promise of international exchange, with a fine blend of science, philosophy, theology, and cultural studies. As this is logged on in March, Lahore is beset by internecine conflagrations as civilizations clash within themselves and with each other. At the same time and locale, such wise, deep contributions offer a modicum of hope via worldwide collaborations.

One of the objectives of Evolutionary Computation (EC) has been to understand the processes of natural evolution and then model them algorithmically. Hans-Paul Schwefel, in his 1997 paper on the future challenges for EC argues that the more an algorithm models natural evolution at work in the universe, the better it will perform (even in terms of function optimization). The present paper tests Schwefel’s hypothesis against Charles Sanders Peirce’s theory which places semiotics, the theory of signs, at the heart of universal evolution. This course is followed because of three primary reasons. Firstly, Peirce has not been seriously tested in EC, although there have been EA based on other theories and sub-theories. Secondly, Peirce’s universal theory, by not being restricted to biological evolution alone, qualifies for Schwefel’s hypothesis, perhaps more than most other theories that have already been modeled algorithmically. But most importantly because, in experimental terms, it warrants an original claim that Peirce’s insights are useful in improving the existing EA in computer science, as Peircean EA can potentially solve some of the major problems in this area such as the loss of diversity, stagnation, or premature convergence. This paper provides a novel framework and consequently a simple algorithm based on Peirce’s theory of evolution, and tests it extensively against a benchmark set of mathematical problems of varying dimensions and complexity. (Abstract)

Basit Koshul received his first PhD in 2003 from Drew University, specialising in the sociology of religion. He joined the School of Humanities, Social Sciences and Law at LUMS in 2006. His areas of interests include the relationship between religion and modernity, philosophy of science, philosophy of religion, the sociology of culture and the contemporary Islam-West encounter. He is especially interested in integrating the ideas of Muhammad Iqbal, Charles Peirce and Max Weber. He has co-edited a collection of essays titled Scripture, Reason and the Contemporary Islam-West Encounter: Studying the Other, Understanding the Self (Palgrave, 2007). He completed his second PhD in 2011 from the University of Virginia. The title of his dissertation was “Max Weber, Charles Peirce and the Integration of the Natur and Geisteswissenschaftern.” It goes on to show that the conversation between Weber and Peirce opens up the possibility of the conceptual integration of science, philosophy and religion.

Barbieri, Marcello. Biosemiotics: A New Understanding of Life. Naturwissenschaften. 95/7, 2008. A succinct summary by the University of Ferrara morphologist of the view he has championed since the 1980s, lately known via the title word, that at its essence life develops, abides, and evolves by virtue of informational, semantic codes.

Barbieri, Marcello. Code Biology – A New Science of Life. Biosemiotics. Online First, April, 2012. The University of Ferrara embryologist, and main founder of this reconception of organisms via an informational essence, continues here its implications for life’s origin and macroevolution events. By this “autopoietic” view, nature’s propensity to form codes serves the formation of rudimentary ribonucleotides. Later cellular vesicles are then seen to engage in “code-creating” activities. As a result, evolution proceeds by way of self-assembly as such codes ramify and reinforce. And in closing: “Code biology is truly a new science in the making, the exploration of a vast and still largely unexplored dimension of the living world, the real new frontier of biology.” See also his 2012 posting in the same journal "The Paradigms of Biology." A 2015 book Code Biology (Springer) now provides a comprehensive survey of the central, generative role of informational programs from biochemistry to linguistics.

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 processes that are based on mathematical principles and physical laws. (Abstract)

At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (Abstract)

Barbieri, Marcello. Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology. Biological Theory. 14/1, 2019. This latest entry by the University of Ferrara biologist is a synoptic review of deepening perceptions that living, evolutionary nature is actually suffused by many generative source codes across all manner of phases and processes. By this insight, they can also each be seen to have a common affinity.

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 evidence has revealed a different reality: any codon can be associated with any amino acid. The rules of the genetic code obey the laws of physics and chemistry but are not determined by them. In the past 20 years various discoveries have shown that many other organic codes exist in living systems. These experimental facts have this theoretical implication: 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 frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is interpretation. Recently, however it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics. (Abstract)

Barbieri, Marcello. Code Biology: A New Science of Life. Berlin: Springer, 2015. The University of Ferrara theoretical biologist introduced in his 2003 book The Organic Codes the concept that in addition to the genetic script, evolutionary organisms are, must consistently be suffused with distinct prescriptive codes for every embryonic, cellular, physiologic, neural phase onto to linguistic and ecological realms. Through his steady writings (search), along with founding the journal Biosemiotics, these insights have gained a growing valid acceptance and application. This volume is his latest book length exposition. Nature is indeed graced by a semiosis of ubiquitous symbolic communications from physical and chemical informations across proteins, genes, splicing, metabolism, signal transduction, histones, tubulin, sugars, and many more instances. With notice of Erwin Schrodinger and others, a code-script is at work from life’s origin to animal signings and human cultures. An International Society of Code Biology was formed in 2012 by Jan Hofmeyr. Its site at www.codebiology.org is a concise entry point, see also its Fifth Conference in Granada, Spain herein under this name.

This book is the study of all codes of life. The genetic code and the codes of culture have been known for a long time and represent the historical foundation of this book. What is really new in this field is the study of all codes that came after the genetic code and before the codes of culture. The existence of these organic codes, however, is not only a major experimental fact, it has extraordinary theoretical implications. The first is that most events of macroevolution were associated with the origin of new organic codes, and this gives us a completely new reconstruction of the history of life. The second implication is that codes involve meaning and we need to introduce in biology not only the information but also the concept of biological meaning. The third theoretical implication comes from the fact that the organic codes have been highly conserved in evolution, which means that they are the greatest invariants of life. (Abstract)

Barbieri, Marcello. Introduction to Code Biology. Biosemiotics. Online August, 2014. For over a decade (search) the University of Ferrara morphologist and embryologist has advocated an evolutionary and biological profusion of code processes beyond genetic nucleotides, such as signal transduction and splicing codes. Akin to the major transitions view, new informational meanings are seen to foster the origins of cells, animals, neural mind, and language. An emergent ramification of an organic, animal, and human “semiosis” is then evident. By such perceptions, one might add, of the missing, immaterial array of natural programs, we may come closer to a full explanation of risen life and person. For his further contributions see What is Information? and A New Theory of Development in the Philosophical Transactions of the Royal Society A (374/2063, 2016).

Language, mathematics, proteins, and animals are very different entities but deep down there is something in common between them. They all have (1) a ‘genetic’ algorithm that produces the objects of a potentially unlimited new world of artifacts (words, Numbers, proteins and bodies) and (2) an exploratory procedure that brings into existence additional or ‘epigenetic’ properties of the new world that were not written in the coding rules and were not present at the beginning. (1)

Barbieri, Marcello. Origin and Evolution of the Brain. Biosemiotics. Online May, 2011. The University of Ferrara biologist and advocate of “organic codes” (search) as a prime formative factor in life’s procession, as the Abstract evinces, here extends this theory onto to neural realms. In so doing, an emergent “Interpretive Brain” that progressively “represents” the world is proposed, lately facilitated by language. By this view, evolution’s three phases of creative semiosis can be identified – organic, interpretive and cultural. And may we then imagine human beings as that intended phenomenon by which a self-realizing genesis universe is trying to read, write, interpret, and conceive itself?

Modern biology has not yet come to terms with the presence of many organic codes in Nature, despite the fact that we can prove their existence. As a result, it has not yet accepted the idea that the great events of macroevolution were associated with the origin of new organic codes, despite the fact that this is the most parsimonious and logical explanation of those events. This is probably due to the fact that the existence of organic codes in all fundamental processes of life, and in all major transitions in the history of life, has enormous theoretical implications. It requires nothing less than a new theoretical framework, and that kind of change is inevitably slow. …the purpose of the present paper is to show that it can be done. More precisely, it is shown that the whole natural history of the brain can be revisited in the light of the organic codes.

The paper contains also another message. The organic codes prove that life is based on semiosis, and are in fact the components of organic semiosis, the first and the most diffused form of semiosis on Earth, but not the only one. It will be shown that the evolution of the brain was accompanied by the development of two new types of sign processes. More precisely, it gave origin first to interpretive semiosis, mostly in vertebrates, and then to cultural semiosis, in our species. (Abstract)

The parallel between life and mind, in conclusion, involves three distinct parallels: one between proteins and feelings, one between genetic code and neural code, and one between cell and animal codemaking systems. The categories that we find in the cell, in other words, are also found in animals, because at both levels we have information, code and codemaker. The details are different, and yet there is the same logic at work, the same strategy of bring absolute novelties into existence by organic coding.

Barbieri, Marcello. The Organic Codes: An Introduction to Semantic Biology. Cambridge: Cambridge University Press, 2003. A novel theory of evolution and embryology that emphasizes the information and meaning content at genetic, eukaryotic, multicellular and cultural linguistic stages. At each instance a new genetic-like code or “natural convention” complements natural selection. This is the original volume by the University of Ferrara biologist which enters these realizations of how pervasive coding functions are. A later section, Biosemiotics, now contain many entries that confirm and advance this prescient view.

The most important lesson is that language evolution was a combination of two parallel but different processes – evolution of words and evolution of grammatical rules – and this is a fitting model for the two different mechanisms of biological evolution that are proposed by the semantic theory. (237)

Barbieri, Marcello. The Semantic Theory of Language. Biosystems. January, 2020. The University of Ferrera embryologist has been a veteran contributor (search) to the biosemiotic view that living systems are most distinguished by a series of code-like activities. But this vital perspective still seems to be in a formative phase as it morphs into various interpretations. The paper opens by saying that since Aristotle language has served to link sounds and meaning by way of phonetic and cognitive aspects. As the Abstract cites, recently N. Chomsky added a nuance that Marcello doesn’t approve. In his broader scope, harking back to C. Peirce (1839-1914), the founder of a semiotic philosophy, a further revision is proposed to sort all this out into the 2020s. An emphasis is put on three main genetic, neural and symbolic codes, which are then coordinated with the unique human feature that babies are born in such an immature state that they require a long post period to mature.

Traditional linguistics was based on the idea that language links sounds and meaning. Later on due to Noam Chomsky, this view has been replaced by the idea that children learn a language because of an innate mechanism to do so. But there is still no evidence that such a device exists. Another process is the ability of higher animals to interpret what goes on in the world, which is not based on fixed rules but on a process that Charles Peirce called abduction. This allows us to generalize into the semantic view of language, a theory that language is an activity which gives meaning to sounds. This can give us a new framework for studying the origin of language without resorting to a certain device. Herein, the origin of language is compared with the origin of life and of mind, because those mega-transitions generated the three code families that we find in Nature – organic neural and cultural. (Abstract excerpt)

Abductive reasoning (also called abduction, or abductive inference), is a form of logical inference which starts with an observation or set of observations and then seeks to find the simplest and most likely explanation for the observations. This process, unlike deductive reasoning, yields a plausible conclusion but does not positively verify it.

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