V. Systems Evolution: A 21st Century Genesis Synthesis
B. Evoinformatics: A Biosemiotic Quality
Akin to movements such as an algorithmic nature and information paradigm, since circa 2000 a central presence and role for similar communicative aspects of living systems has gained prominence. The title term arose from the broader field of semiotics, the study of signs and significations as they distinguish, inform, and engender from evolution to ecologies. A pioneer initiator was Thomas Sebeok (1920-2001) at Indiana University, where a loquacious group has since arose. Into the 21st century a leading sponsor has been the University of Ferrara embryologist Marcello Barbieri, via a stream of articles and a book The Organic Codes (2003).
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)
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)
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.
Barbieri, Marcello, ed. Introduction to Biosemiotics: The New Biological Synthesis. Berlin: Springer, 2007. The proposal, initiated some three decades ago by Thomas Sebeok, that biological nature is essentially about informational content and communication has been maturing since with the result of this comprehensive volume. Contributors such as Donald Favareau, Harold Pattee, Jesper Hoffmeyer, Kalevi Kull, Stanley Salthe, Anton Markos, Ingolf Schmid-Tannwald, and others weigh in on all aspects. The conceptual shift thus implied is from a mechanical, illiterate, reduction, beyond a compromise ‘organicism,’ to “semiotics as physics of the 21st century.” By these lights, a universe to human evolution becomes inherently textual in kind, holistically suffused with signs, messages, and ‘organic codes,’ whereof the world is a ‘semiosphere.’ By what imagination might we be immersed in a ‘scripture’ waiting to be read? In his chapter, Semiotic Scaffolding of Living Systems, Hoffmeyer does allude to such an ‘ontology’ as the second “Book of Nature.” Check the publisher’s website for an extended Table of Contents.
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. 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.