Tag: Habits

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

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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