Tag: Marcello Barbieri

Code Biology, Bio-Semiotics, and Relational Biology

Code Biology, Bio-Semiotics, and Relational Biology

Key Terms

  • Biosemiotics
  • Anticipatory Systems
  • Code biology
  • Relational biology
  • C.S. Peirce
  • T. Sebeok
  • Jesper Hoffmeyer
  • Marcello Barbieri
  • Robert Rosen
  • Rom Harré
  • F Schelling
  • Habits
  • Pratibha
  • Innate Ability
  • Archetypes
  • Talent
  • Character
  • Virtues
  • Caste System
  • Astrology
  • Invariance
  • Regularities
  • Periodicities
  • Sapta Rishis
  • Evolution
  • Development
  • Biology
  • Codes
  • Meaning
  • Culture
  • Nature

Archetypes and Code Biology

Source: Archetypes and code biology

As a clinical psychologist, I observe stereotyped formulas of behavior in action every day in the consulting room, despite differences in age, race, or culture; they present themselves as codified rules or typical modes of behavior in archetypical situations. Such circumstances coincide with what C.G. Jung defended: the existence of archetypes stored in an inherited/phylogenetic repository, which he called the collective unconscious – somewhat similar to the notion of an ethogram, as shown by ethology. Psychologists can use a perspective to facilitate understanding the phenomenon: the code biology perspective (Barbieri 2014). This approach can help us recognize how these phenomenological events have an ontological reality based not only on the existence of organic information but also on the existence of organic meaning.

We are not a tabula rasa (Wilson 2000): despite the explosive diversification of the brain and the emergence of conscience and intentionality, we observe the conservation of basic instincts and emotions (Ekman 2004; Damasio 2010) not only in humans but in all mammals and other living beings; we refer to the neural activity on which the discrimination behavior is based, i.e., the neural codes. The conservation of these fundamental set-of-rules or conventions suggests that one or more neural codes have been highly conserved and serves as an interpretive basis for what happens to the living being who owns them (Barbieri 2003). Thus, archetypes’ phenomenological reality can be understood not as something metaphorical but as an ontological (phylogenetic) fact (Goodwyn 2019).

Furthermore, epigenetic regulation theories present the possibility that the biomolecular process incorporates elements of the context where it takes place; something fundamental to understand our concept – the archetype presents itself as the mnesic remnant of the behavioral history of individuals who preceded us on the evolutionary scale. In short: brains are optimized for processing ethologically relevant sensory signals (Clemens et al., 2015).

From the perspective of the corporeal mind (Searle 2002), in this paper, we will show the parallels between code biology and the concept of the archetype, as Jung defended it and as it appears in clinical practice.

Source: Code Biology 3: the study of all Codes of Life

Editorial
Overview of the third special issue in code biology

  1. Introduction
    This third special issue in Code Biology is a collection of highly different papers and their differences have two main causes. The first, the most obvious, is that Code Biology is the study of all codes that exist in living systems and the diversity of the papers is a direct consequence of the diversity of the codes. The second source of diversity is the existence of different theories. More precisely, the original theory that gave origin to Code Biology has been followed by a number of extended theories that now coexist with the original one. In Code Biology, in other words, there is pluralism but there has also been a beginning, and it is important to be clear about this starting point. The original theory of Code Biology is characterized by ideas that make it different from four major theoretical frameworks:
    1. [1] The original theory of Code Biology is different from the Modern Synthesis for two reasons. The first is the idea that evolution took place by natural selection and by natural conventions and these mechanisms are fundamentally different because natural selection is based on copying and natural conventions are based on coding. The second is the idea that the cell is not a biological computer made of genotype and phenotype but a trinity of genotype, phenotype and ribotype, where the ribotype is the ribo nucleoprotein system of the cell that functions as the codemaker of the genetic code (Barbieri 1981, 1985, 2003).
    2. [2] The original theory of Code Biology maintains that the fundamental process of life is not autopoiesis but codepoiesis (Barbieri 2012). Autopoiesis requires biological specificity and specificity comes from the genetic code, so the ancestral systems that came before that code could not have been autopoietic systems. Those ancestral systems, on the other hand, were engaged in the evolution of the genetic code and were therefore codepoietic systems. Autopoiesis, furthermore, is most evident in bacteria and bacteria have not increased their complexity and have not evolved new codes for billions of years after their appearance on Earth. It was the eukaryotes that became increasingly complex and that evolved new codes, which suggests a deep link between codes and complexity, and in particular between the origin of new codes and the origin of the great novelties of macroevolution (Barbieri 2015, 2016, 2017, 2020). Codepoiesis, on the other hand, is necessarily implemented by mechanisms, and according to the original theory of Code Biology the major mechanism that fuelled the evolution of the genetic code was the process of ambiguity reduction (Barbieri 2019a).
    3. [3] The original theory of Code Biology is different from Biosemiotics because it claims that the Peircean processes of interpretation and abduction take place in the brain but not in the cell (Barbieri 2014,2018).
    4. [4] The original theory of Code Biology is different from the Relational Biology of Robert Rosen because it assumes that the process of anticipation takes place in the brain but not in the cell (Barbieri 2019b).
  2. There are, in conclusion, four key ideas in the original theory of Code Biology:
    1. [a] Evolution took place by natural selection and by natural conventions.
      [b] The cell is a trinity of genotype, phenotype and ribotype.
      [c] The fundamental process of life is codepoiesis, not autopoiesis.
      [d] Ambiguity reduction was the major evolutionary mechanism of the genetic code.
  3. The extended theories of Code Biology differ from the original theory either because they introduce new concepts or because they reformulate some of the original concepts.
    1. [1] The first extended theory appeared when Stefan Kühn and Jan-Hendrik Hofmeyr (2014) proposed an extended definition of code, a definition where signs and meanings can be not only molecules but also biological processes. More precisely, Kühn and Hofmeyr showed that the histone code is a mapping where the signs are the marks produced on histones by acetylation or methylation processes and their meanings are the activation or the repression of particular genes.
    2. [2] A second extended theory of Code Biology has been proposed in this issue by Julie Heng and Henry Heng with the idea that the adaptors of a biological code can be “information flows”. More precisely, Heng and Heng point out that in addition to the codes that produce the components of a system there are also codes that organize those components into a working whole. The code that is used to make bricks, for example, is different from the code that is used to construct a building from those bricks. The genetic code is a code that makes bricks, i.e., proteins, but in order to arrange proteins into a living system we need an architectural code that Heng and Heng call “karyotype code”.
    3. [3] A third extended theory is presented in this issue by Omar Paredes and colleagues on the grounds that the original theory of Code Biology “raises the illusion that information has only an upward direction … whereas the current overview of cellular dynamics … illustrates that information flows freely upward and downward”. In order to overcome this limitation, the authors propose “a novel category of organic codes, the metacode”, which is defined as “an informational structure that handles the continuum of the information flow in biological systems”.

The extended theories, in short, are a reality and their existence is a testimony that there is genuine pluralism in Code Biology. The goal of this special issue, on the other hand, is to give a bird’s-eye view of the present status of Code Biology and to this purpose it has been divided into four parts, each of which is going to be illustrated in the rest of this editorial with brief presentations of its papers

My Related Posts

Semiotics, Bio-Semiotics and Cyber Semiotics

What is Code Biology?

Autocatalysis, Autopoiesis and Relational Biology

Systems Biology: Biological Networks, Network Motifs, Switches and Oscillators

Hierarchy Theory in Biology, Ecology and Evolution

System Archetypes: Stories that Repeat

On Classical Virtues

Key Sources of Research

Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology

Marcello Barbieri

Biological Theory 14 (1):21-29 (2019)

https://philpapers.org/rec/BARCBP-2

https://www.researchgate.net/profile/Marcello-Barbieri-2/publication/329325693_Code_Biology_Peircean_Biosemiotics_and_Rosen’s_Relational_Biology/links/5de18628299bf10bc3314300/Code-Biology-Peircean-Biosemiotics-and-Rosens-Relational-Biology.pdf?_sg%5B0%5D=started_experiment_milestone&origin=journalDetail

Code biology: A bird’s-eye view

Author(s): Marcello Barbieri

Gatherings in Biosemiotics XX.
(Tartu Semiotics Library 20.) Tartu: University of Tartu Press.

Issue Year: 2020 Issue No: 20 Page Range: 72-91

Lacková, Ľudmila; Rodríguez H., Claudio J.; Kull, Kalevi (eds.) 2020. 

BIOSEMIOSIS AND CAUSATION:
DEFENDING BIOSEMIOTICS THROUGH ROSEN’S THEORETICAL BIOLOGY
OR
INTEGRATING BIOSEMIOTICS AND ANTICIPATORY SYSTEMS THEORY1

Arran Gare

Cosmos and History: The Journal of Natural and Social Philosophy, vol. 15, no. 1, 2019

https://philarchive.org/archive/GARBAC-4

A Critique of Barbieri’s Code Biology Through Rosen’s Relational Biology: Reconciling Barbieri’s Biosemiotics with Peircean Biosemiotics. 

Vega, F.

Biol Theory 13, 261–279 (2018).

https://doi.org/10.1007/s13752-018-0302-1

https://link.springer.com/article/10.1007/s13752-018-0302-1

Click to access VEGA_CUESTA_Federico_Tesis.pdf

An Integrated Account of Rosen’s Relational Biology and Peirce’s Semiosis. Part I: Components and Signs, Final Cause and Interpretation

Federico Vega

Biosemiotics (2021) 14:697–716

https://doi.org/10.1007/s12304-021-09441-z

https://link.springer.com/article/10.1007/s12304-021-09441-z

Click to access VEGA_CUESTA_Federico_Tesis.pdf

An Integrated Account of Rosen’s Relational Biology and Peirce’s Semiosis. Part II: Analysis of Protein Synthesis. 

Vega, F.

Biosemiotics 14, 717–741 (2021).

https://doi.org/10.1007/s12304-021-09438-8

https://link.springer.com/article/10.1007/s12304-021-09438-8

Click to access VEGA_CUESTA_Federico_Tesis.pdf

Peircean habits and the life of symbols

Thirty-fifth Meeting of the Semiotic Society of America October 21-24, 2010, Louisville, Kentucky

Eliseo Fernández
Linda Hall Library of Science and Technology

fernande@lindahall.org

Click to access Peirce_habits.pdf

BIOSEMIOTICS AND SELF-REFERENCE FROM PEIRCE TO ROSEN

Eliseo Fernández

Linda Hall Library of Science and Technology5109 Cherry St.Kansas City, MO 64110, USA

fernande@lindahall.org

Eighth Annual International Gatherings in Biosemiotics

University of the Aegean, Syros, Greece, June 23-28, 2008

Functional Information: Towards Synthesis of Biosemiotics and Cybernetics

Alexei A. Sharov

National Institute on Aging, 251 Bayview Boulevard, Baltimore, MD 21224, USA Alexei A. Sharov: sharoval@mail.nih.gov

Entropy (Basel). 2010 Apr 27; 12(5): 1050–1070. 

doi: 10.3390/e12051050

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3285384/

Codes: Necessary, but not sufficient for meaning-making.

Kull K. (2020)

Constructivist Foundations 15(2): 137–139.

https://constructivist.info/15/2/137

Organic Codes: A Unifying Concept for Life.

de Farias, S.T., Prosdocimi, F. & Caponi, G.

Acta Biotheor 69, 769–782 (2021).

https://doi.org/10.1007/s10441-021-09422-2

https://link.springer.com/article/10.1007/s10441-021-09422-2

A critique of Barbieri’s code Biology

Alexander V. Kravchenko
Baikal State University

https://www.researchgate.net/publication/344896397_A_critique_of_Barbieri%27s_code_Biology

Origin and evolution of the genetic code: the universal enigma

Eugene V. Koonin* and Artem S. Novozhilov
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

IUBMB Life. 2009 February ; 61(2): 99–111. doi:10.1002/iub.146.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

Code biology and the problem of emergence

Arran Gare 

Bio Systems 2021 Oct; 208:104487.

doi: 10.1016/j.biosystems.2021.104487.

https://pubmed.ncbi.nlm.nih.gov/34273444/

https://www.sciencedirect.com/science/article/abs/pii/S0303264721001349?via%3Dihub

Archetypes and code biology

J.C.Major

International Academy of Analytical Psychology, Portugal

Biosystems
Volume 208, October 2021, 104501

https://www.sciencedirect.com/science/article/abs/pii/S0303264721001489

The major evolutionary transitions and codes of life

Adam Kun

Bio Systems 210 2021

https://doi.org/10.1016/j.biosystems.2021.104548

Code Biology 3: the study of all Codes of Life

Edited by Marcello Barbieri

Last update 22 September 2021

3rd Special Issue in Code Biology

Bio Systems December 2021

https://doi.org/10.1016/j.biosystems.2021.104553

https://www.sciencedirect.com/journal/biosystems/special-issue/10S60V7SHC6

Code Biology 2: the study of all Codes of Life

Edited by Marcello Barbieri, Jan-Hendrik Hofmeyr

Last update 30 June 2021

Bio Systems Feb 2018

2nd Special Issue on Code Biology

https://doi.org/10.1016/j.biosystems.2019.104050

https://www.sciencedirect.com/journal/biosystems/special-issue/10Q35Z29R86

The first Special Issue on code biology – A bird’s-eye view

Jan-Hendrik S Hofmeyr 

Bio Systems 2018 Feb; 164:11-15.

doi: 10.1016/j.biosystems.2017.12.007.

Epub 2017 Dec 16.

https://pubmed.ncbi.nlm.nih.gov/29258888/

https://www.sciencedirect.com/science/article/abs/pii/S030326471730463X?via%3Dihub

https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C

GATHERINGS IN BIOSEMIOTICS

Edited by
Silver Rattasepp Tyler Bennett

TARTU SEMIOTICS LIBRARY 11

2012

Series editors: Kalevi Kull Silvi Salupere Peeter Torop

Department of Semiotics

University of Tartu
Jakobi St. 2

Tartu 51014, Estonia

https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.465.1302&rep=rep1&type=pdf

Gatherings in Biosemiotics XX

Edited by
Ľudmila Lacková Claudio J. Rodríguez H. Kalevi Kull

2020

TARTU SEMIOTICS LIBRARY 20

http://www.flfi.ut.ee/en/department-semiotics/tartu-semiotics-library

Tartu: University of Tartu Press.

Semiotic Agency: Science Beyond Mechanism

By Alexei Sharov, Morten Tønnessen

A BRIEF INTRODUCTION TO PEIRCE IN BIOSEMIOTICS

CLAUDIO J. RODR ́IGUEZ H. CLAUDIOJRODRIGUEZH@GMAIL.COM

Click to access A-Brief-Introduction-to-Peirce-in-Biosemiotics.pdf

Chapter One
Peirce in contemporary semiotics

Paul Cobley

In: The Bloomsbury Companion to Contemporary Peircean Semiotics. Jappy, Tony, ed. Bloomsbury Companions . Bloomsbury Academic, London, pp. 31-72.

2019

doi:10.5040/9781350076143.ch-001

https://eprints.mdx.ac.uk/25834/1/Chapter%201%20%20Peirce%20in%20contemporary%20semiotics%20pre-print%20.docx

Consciousness, Mind and Spirit. 

Gare, A. (2019).

Cosmos and History: The Journal of Natural and Social Philosophy, 15(2), 236–264.

Retrieved from https://mail.cosmosandhistory.org/index.php/journal/article/view/833

FROM KANT TO SCHELLING TO PROCESS METAPHYSICS: ON THE WAY TO ECOLOGICAL CIVILIZATION

Arran Gare

Cosmos and History: The Journal of Natural and Social Philosophy, vol. 7, no. 2, 2011

https://philarchive.org/archive/GARFKT-6

Toward an Ecological Civilization: The Science, Ethics, and Politics of Eco-Poiesis*

Arran Gare

PROCESS STUDIES 39.1 (2010)

Click to access GARTAE-3.pdf

Beyond Descartes and Newton: Recovering Life and Humanity

Stuart A. Kauffman and Arran Gare

Stu modification 3/11/15 Arran modification 5/17/15

Published in Progress in Biophysics and Molecular Biology, 119(3), 2017: 219-244.

Click to access GARBDA.pdf

Language and the Self-Reference Paradox

Julio Michael Stern

Cybernetics And Human Knowing. Vol. 14, no. 4, pp.71-92

Click to access STELAT-14.pdf

Overcoming the Newtonian paradigm: The unfinished project of theoretical biology from a Schellingian perspective

Arran Gare*
Philosophy, Faculty of Life and Social Sciences, Swinburne University, Melbourne, Australia

Published in Progress in Biophysics and Molecular Biology, 113, (2013): 5-24.

Click to access GAROTN.pdf

What is Code Biology?

What is Code Biology?

 

 

 

Key Terms

  • Code Biology
  • Biosemiotics
  • Charles Sanders Peirce
  • Genetic Code
  • Musical Harmony
  • Symmetry
  • Jay Kappraff
  • Gary Adamson
  • Pythagorean Triples
  • Harmonic Laws
  • Numbers
  • Geometry
  • Matrices
  • Self, Culture, Nature
  • I, We, It, Its
  • Sergey V. Petoukhov
  • Codes
  • Meaning
  • Value
  • Marcello Barbieri
  • RNA, DNA, Proteins, Cells
  • Code Semiotics
  • Ferdinand D Saussure

 

What is Code Biology?

Codes and conventions are the basis of our social life and from time immemorial have divided the world of culture from the world of nature. The rules of grammar, the laws of government, the precepts of religion, the value of money, the rules of chess etc., are all human conventions that are profoundly different from the laws of physics and chemistry, and this has led to the conclusion that there is an unbridgeable gap between nature and culture. Nature is governed by objective immutable laws, whereas culture is produced by the mutable conventions of the human mind.

In this millennia-old framework, the discovery of the genetic code, in the early 1960s, came as a bolt from the blue, but strangely enough it did not bring down the barrier between nature and culture. On the contrary, a protective belt was quickly built around the old divide with an argument that effectively emptied the discovery of all its revolutionary potential. The argument that the genetic code is not a real code because its rules are the result of chemical affinities between codons and amino acids and are therefore determined by chemistry. This is the ‘Stereochemical theory’, an idea first proposed by George Gamow in 1954, and re-proposed ever since in many different forms (Pelc and Welton 1966; Dunnil 1966; Melcher 1974; Shimizu 1982; Yarus 1988, 1998; Yarus, Caporaso and Knight 2005). More than fifty years of research have not produced any evidence in favour of this theory and yet the idea is still circulating, apparently because of the possibility that stereochemical interactions might have been important at some early stages of evolution (Koonin and Novozhilov 2009). The deep reason is probably the persistent belief that the genetic code must have been a product of chemistry and cannot possibly be a real code. But what is a real code?

The starting point is the idea that a code is a set of rules that establish a correspondence, or a mapping, between the objects of two independent worlds (Barbieri 2003). The Morse code, for example, is a mapping between the letters of the alphabet and groups of dots and dashes. The highway code is a correspondence between street signals and driving behaviours (a red light means ‘stop’, a green light means ‘go’, and so on).

What is essential in all codes is that the coding rules, although completely compatible with the laws of physics and chemistry, are not dictated by these laws. In this sense they are arbitrary, and the number of arbitrary relationships between two independent worlds is potentially unlimited. In the Morse code, for example, any letter of the alphabet could be associated with countless combinations of dots and dashes, which means that a specific link between them can be realized only by selecting a small number of rules. And this is precisely what a code is: a small set of arbitrary rules selected from a potentially unlimited number in order to ensure a specific correspondence between two independent worlds.

This definition allows us to make experimental tests because organic codes are relationships between two worlds of organic molecules and are necessarily implemented by a third type of molecules, called adaptors, that build a bridge between them. The adaptors are required because there is no necessary link between the two worlds, and a fixed set of adaptors is required in order to guarantee the specificity of the correspondence. The adaptors, in short, are the molecular fingerprints of the codes, and their presence in a biological process is a sure sign that that process is based on a code.

This gives us an objective criterion for discovering organic codes and their existence is no longer a matter of speculation. It is, first and foremost, an experimental problem. More precisely, we can prove that an organic code exists, if we find three things: (1) two independents worlds of molecules, (2) a set of adaptors that create a mapping between them, and (3) the demonstration that the mapping is arbitrary because its rules can be changed, at least in principle, in countless different ways.

 

Two outstanding examples

The genetic code

In protein synthesis, a sequence of nucleotides is translated into a sequence of amino acids, and the bridge between them is realized by a third type of molecules, called transfer-RNAs, that act as adaptors and perform two distinct operations: at one site they recognize groups of three nucleotides, called codons, and at another site they receive amino acids from enzymes called aminoacyl-tRNA-synthetases. The key point is that there is no deterministic link between codons and amino acids since it has been shown that any codon can be associated with any amino acid (Schimmel 1987; Schimmel et al. 1993). Hou and Schimmel (1988), for example, introduced two extra nucleotides in a tRNA and found that that the resulting tRNA was carrying a different amino acid. This proved that the number of possible connections between codons and amino acids is potentially unlimited, and only the selection of a small set of adaptors can ensure a specific mapping. This is the genetic code: a fixed set of rules between nucleic acids and amino acids that are implemented by adaptors. In protein synthesis, in conclusion, we find all the three essential components of a code: (1) two independents worlds of molecules (nucleotides and amino acids), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed.

 

The signal transduction codes

Signal transduction is the process by which cells transform the signals from the environment, called first messengers, into internal signals, called second messengers. First and second messengers belong to two independent worlds because there are literally hundreds of first messengers (hormones, growth factors, neurotransmitters, etc.) but only four great families of second messengers (cyclic AMP, calcium ions, diacylglycerol and inositol trisphosphate) (Alberts et al. 2007). The crucial point is that the molecules that perform signal transduction are true adaptors. They consists of three subunits: a receptor for the first messengers, an amplifier for the second messengers, and a mediator in between (Berridge 1985). This allows the transduction complex to perform two independent recognition processes, one for the first messenger and the other for the second messenger. Laboratory experiments have proved that any first messenger can be associated with any second messenger, which means that there is a potentially unlimited number of arbitrary connections between them. In signal transduction, in short, we find all the three essential components of a code: (1) two independents worlds of molecules (first messengers and second messengers), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed (Barbieri 2003).

 

A world of organic codes

In addition to the genetic code and the signal transduction codes, a wide variety of new organic codes have come to light in recent years. Among them: the sequence codes (Trifonov 1987, 1989, 1999), the Hox code (Paul Hunt et al. 1991; Kessel and Gruss 1991), the adhesive code (Redies and Takeichi 1996; Shapiro and Colman 1999), the splicing codes (Barbieri 2003; Fu 2004; Matlin et al. 2005; Pertea et al. 2007; Wang and Burge 2008; Barash et al. 2010; Dhir et al. 2010), the signal transduction codes (Barbieri 2003), the histone code (Strahl and Allis 2000; Jenuwein and Allis 2001; Turner 2000, 2002, 2007; Kühn and Hofmeyr 2014), the sugar code (Gabius 2000, 2009), the compartment codes (Barbieri 2003), the cytoskeleton codes (Barbieri 2003; Gimona 2008), the transcriptional code (Jessell 2000; Marquard and Pfaff 2001; Ruiz i Altaba et al. 2003; Flames et al. 2007), the neural code (Nicolelis and Ribeiro 2006; Nicolelis 2011), a neural code for taste (Di Lorenzo 2000; Hallock and Di Lorenzo 2006), an odorant receptor code(Dudai 1999; Ray et al. 2006), a space code in the hippocampus (O’Keefe and Burgess 1996, 2005; Hafting et al. 2005; Brandon and Hasselmo 2009; Papoutsi et al. 2009), the apoptosis code (Basañez and Hardwick 2008; Füllgrabe et al. 2010), the tubulin code (Verhey and Gaertig 2007), the nuclear signalling code (Maraldi 2008), the injective organic codes (De Beule et al. 2011), the molecular codes (Görlich et al. 2011; Görlich and Dittrich 2013), the ubiquitin code (Komander and Rape 2012), the bioelectric code (Tseng and Levin 2013; Levin 2014), the acoustic codes (Farina and Pieretti 2014), the glycomic code (Buckeridge and De Souza 2014; Tavares and Buckeridge 2015) and the Redox code (Jones and Sies 2015).

The living world, in short, is literally teeming with organic codes, and yet so far their discoveries have only circulated in small circles and have not attracted the attention of the scientific community at large.

 

Code Biology

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 and represent the historical foundation of Code Biology. 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 codes is an experimental fact – let us never forget this – but also more than that. It is one of those facts that have extraordinary theoretical implications.

The first is the role that the organic codes had in the history of life. The genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the descendants of the common ancestor into the primary kingdoms of Archaea, Bacteria and Eukarya, the splicing codes were instrumental to the origin of the nucleus, the histone code provided the rules of chromatin, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis (Barbieri 2003, 2015). The greatest events of macroevolution, in other words, were associated with the appearance of new organic codes, and this gives us a completely new understanding of the history of life.

The second great implication is the fact that the organic codes have been highly conserved in evolution, which means that they are the great invariants of life, the sole entities that have been perpetuated while everything else has been changed. Code Biology, in short, is uncovering a new history of life and bringing to light new fundamental concepts. It truly is a new science, the exploration of a vast and still largely unexplored dimension of the living world, the real new frontier of biology.

 

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CODE BIOLOGY, PEIRCEAN BIOSEMIOTICS, AND ROSEN’S RELATIONAL BIOLOGY

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 experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that 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 theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics.

 

 

Please see my related posts

Semiotics, Bio-Semiotics and Cyber Semiotics

Autocatalysis, Autopoiesis and Relational Biology

Geometry of Consciousness

Mind, Consciousness and Quantum Entanglement

 

 

Key Sources of Research:

 

Code Biology

http://www.codebiology.org

 

What is Code Biology?

Marcello Barbieri

https://www.researchgate.net/publication/320332986_What_is_Code_Biology

Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology

Marcello Barbieri

First Online:

 

 

 

Why Biosemiotics? An Introduction to Our View on the Biology of Life Itself

Kalevi Kull, Claus Emmeche and Jesper Hoffmeyer

 

 

 

BIOSEMIOTICS AND SELF-REFERENCE FROM PEIRCE TO ROSEN

Eliseo Fernández

Click to access PRfinal.pdf

 

 

 

What Does it Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics

Søren Brier & Cliff Joslyn

https://www.researchgate.net/publication/255813854_What_Does_It_Take_to_Produce_Interpretation_Informational_Peircean_and_Code-Semiotic_Views_on_Biosemiotics

Naturalizing semiotics: The triadic sign of Charles Sanders Peirce as a systems property

https://www.ncbi.nlm.nih.gov/pubmed/26276466

 

 

 

BIOSEMIOSIS AND CAUSATION: DEFENDING BIOSEMIOTICS THROUGH ROSEN’S THEORETICAL BIOLOGY OR INTEGRATING BIOSEMIOTICS AND ANTICIPATORY SYSTEMS THEORY1

Arran Gare

http://cosmosandhistory.org/index.php/journal/article/viewFile/806/1396

 

 

 

GENERALIZED GENOMIC MATRICES, SILVER MEANS, AND PYTHAGOREAN TRIPLES

Jay Kappraff

Gary W. Adamson

 

Click to access report0809-12.pdf

https://pdfs.semanticscholar.org/f641/6a1d093e77df80173ed76add159b452924b1.pdf?_ga=2.121727499.1841123216.1571671914-1769689123.1571671914

 

 

The genetic code, 8-dimensional hypercomplex numbers and dyadic shifts

 

Sergey V. Petoukhov

 

Click to access 1102.3596.pdf

 

 

 

A Fresh Look at Number

Jay Kappraff

Gary Adomson

Click to access bridges2000-255.pdf

 

 

 

SYMMETRIES IN MOLECULAR-GENETIC SYSTEMS AND MUSICAL HARMONY

G. Darvas, A.A. Koblyakov, S.V.Petoukhov, I.V.Stepanian

 

Click to access GENETIC_CODE_AND_MUSICAL_HARMONY_2012_PETOUKHOV.pdf

 

 

 

On the Semio-Mathematical Nature of Codes

Yair Neuman & Ophir Nave

Click to access On-the-Semio-Mathematical-Nature-of-Codes.pdf

 

 

GENETIC CODE AS A HARMONIC SYSTEM

Miloje M. Rakočević

 

Click to access 0610044.pdf

 

 

 

Genetic Code Table: A note on the three splittings into amino acid classes

Miloje M. Rakočević

 

Click to access 0903.4110.pdf

 

 

 

GENETIC CODE AS A HARMONIC SYSTEM: THREE SUPPLEMENTS

Miloje M. Rakočević

 

Click to access 0703011.pdf

 

 

THE GENETIC CODE INVARIANCE: WHEN EULER AND FIBONACCI MEET

Tidjani Négadi

 

Click to access 1305.5103.pdf

 

 

 

Genetic Code as a Coherent System

Miloje Rakočević

 

Click to access Genetic-Code-as-a-Coherent-System.pdf

 

 

 

A NEW GENETIC CODE TABLE

Miloje M. Rakočević

 

Click to access A-New-Genetic-Code-Table.pdf

 

 

 

Harmonically Guided Evolution

Richard Merrick

 

Click to access a084ad5ca081cf5ac00c82c77d5857795745.pdf

 

 

 

Golden and Harmonic Mean in the Genetic Code

Miloje M. Rakočević

Click to access 35c07d4f0e09a12acc2d6822a16407a14ccd.pdf