SemioPhenomenon - Tartu workshops, Feb. 2009

At the occasion of philosopher/phenomenologist David Abram´s visit to Estonia, two workshops will be arranged in Tartu ('The Ecology of Perception: Landscapes in Culture and Nature' and 'Animal Minds'), February 6-7 and 9-10 respectively. More information at the event webpage, SemioPhenomenon.

The events represent a meeting between a phenomenology of the sensuous and semiotics of nature (biosemiotics, ecosemiotics, zoosemiotics). Confirmed presenters, apart from Abram, include Kalevi Kull, Kati Lindström, Dario Martinelli and Morten Tønnessen.

Bodies in motion conference

The following conference will feature an introduction from Prisca Augustyn on 'Uexküll and Biosemiotics'

http://www.fau.edu/bodymindculture/Conferences.php

CFP: Distributed language group

Grounding language in perception and (inter) action
A Symposium of the Distributed Language Group

June 4-6, 2009
Gordon College, Wenham, Massachusetts USA

CALL FOR PAPERS
Abstracts due December 3, 2008
INVITED SPEAKERS
The following invited speakers have agreed to participate in the Symposium:
Philip Carr, Département d'anglais, Université Paul Valéry, Montpellier,France
Carol Fowler, Haskins Laboratories and Department of Psychology, Universityof Connecticut, Storrs, USA
Bruno Galantucci, Haskins Laboratories and Department of Psychology, Yeshiva University, New York, USA
Alexander Kravchenko, Department of Foreign Languages, Baikal National University of Economics and Law, Irkutsk, Russian Federation
Nigel Love, Department of Linguistics, University of Cape Town, South Africa
Robert Port, Departments of Linguistics and Cognitive Science, IndianaUniversity, Bloomington, USA
Joanna Raczaszek-Leonardi, Department of Cognitive Psychology, University ofWarsaw, Poland, and University of Bologna, Italy
Paul Thibault, Department of Linguistics and Media Communication, Agder University, Kristiansand, Norway
Guy Van Orden, Department of Psychology, University of Cincinnati, USA

Organizers: Bert Hodges (Gordon College) and Stephen J. Cowley (Universityof Hertfordshire)

NOTE: PLEASE FORWARD THIS CALL FOR PAPERS TO APPROPRIATE OTHERS

Abstracts due December 3, 2008
We invite original papers that contribute to the conference theme, Grounding language in perception and (inter) action.
Papers should address language(or conversing) as situated in the context of interaction, action, andperception, or, more strongly, as distributed, dialogical, and directed (i.e., intentional, normative) modes of interaction, perception, and action.
Papers may be theoretical, empirical, interpretive (e.g., reviews), and/or methodological in their focus. We especially invite papers that address ecological and dynamical accounts of perception, action, and language.
For more information about our objectives, topics, and speakers, etc., see following pages.
Paper sessions will be either about 50 minutes or 25 minutes in length. Ample time should be left for discussion. In other words, papers should be about 20 or 40 minutes long.
We cannot guarantee that we will be able to accommodate requests for preferred length, but we will take it into account in organizing the program.
Abstracts of 300- 450 words are due December 3, 2008. They will be reviewed by at least two readers and you will be notified by January 2, 2009 of theiracceptance or not. If you need to know sooner if your paper will beaccepted, please notify one of the organizers.
Send abstracts to: bert.hodges@gordon.edu or s.j.cowley@herts.ac.uk.
Gordon College is a beautiful campus about 45 minutes north of Boston on the historic North Shore, near Salem, Ipswich, Manchester-by-the-Sea, and Gloucester.

>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The Distributed Language Group (DLG) is an international, grass-roots group of scholars from a variety of disciplines (e.g., linguistics, psychology,artificial intelligence, philosophy, anthropology) that have come together to develop creative and viable alternatives to conventional accounts of language (e.g., formal, cognitive, structural) in linguistics and related disciplines. For those desiring to participate who are new to DLG, consulting the special issue of Language Sciences (2007, 29, 5), edited byStephen Cowley, may provide a starting point for contributing to our ongoingdiscussion.

Our first conference was held at Cambridge University in 2005 with the theme of "Cognitive dynamics in language" and was hosted by Stephen Cowley. In 2007 Paul Thibault hosted us at Agder University College in Grimstad, Norway in a symposium entitled "Language dynamics and the phenomenology of individual experience." Some of the papers presented at the Cambridge conference were published as a special issue of Language Sciences (2007, 29). In addition there have been several other conferences(e.g., language and robotics, external symbol grounding) and publicationssponsored by DLG that are mentioned on the group's webpage,
http://www.psy.herts.ac.uk/dlg

Roentgen semiotics

www.roentgensemiotics.net

Worth checking out this collection of articles. I've found them rather compelling since the publication of the first, at Sebeok's instigation, in 2000.

BIO/CULTURAL STUDIES

The following may be of interest. A great deal of cultural studies at the moment seems to be alighting on the 'bio', partly inspired by Agamben and, ultimately, that old chestnut, Foucault. They claim that "We are not necessarily nominalists", although, of course, they are - certainly at this stage. In general, they may be seen to be going in the right direction, albeit in a series of detours and backtracking. I flag this up to give an indication of what the prefix 'bio' is currently entailing. Announcement follows:

ANNOUNCING A SEMINAR ON BIO/CULTURAL STUDIES AT THE CULTURAL STUDIES ASSOCIATION CONFERENCE, APRIL 16-18, 2009, KANSAS CITY, MO.
Bio/Cultural Studies
[Individuals interested in participating in this Cultural Studies Association seminar should contact Bernice Hausman at bhausman@vt.edu or Brad Lewis at bl466@nyu.edu. Deadline: 14 November 2008.]
Seminar Description:
Lennard Davis and David Morris, in their “Biocultures Manifesto” that opens the summer 2007 special issue of New Literary History on Biocultures, argue that the field of intellectual endeavor encompassing biocultural studies exists but needs a name. They write, “We are not necessarily nominalists, but we do believe in the power of a name to consolidate scattered research agendas and to generate change.” Their manifesto is a clarion call to begin to reconceptualize the existing cross-fertilization of scientific investigation with cultural inquiry, broadly construed.
We are interested in a more pointed version, or subfield, of biocultures that sets cultural studies against, or into, biomedicine. Some of the more interesting variants of this field explore biopsychiatry and detail the emergence of the “neurochemical person” (N. Rose) and/or the “pharmaceutical person” (E. Martin). The bio/cultural studies approach to medicine cannot rest on a “cultural critique” of science and its objectified research paradigms. Instead, biocultures demands a kind of interpenetration of objectives from both fields, assuming that the alleviation of suffering is approached authentically in both cultural analysis (where the goal is often social justice) and medicine (where physical suffering begins the diagnostic enterprise and ending it is the goal). In this way, bio/cultural studies is about critique but also collaboration; as a paradigm it insists on new research questions that straddle the edge of the “two cultures” so famously described by C. P. Snow.
Seminar Requirements:
This seminar is for scholars and scholar-activists interested in learning more about what we are calling bio/cultural studies and in developing research questions and projects in this field. We will circulate a set of texts to seminar participants in February, and ask for brief (5-page) descriptions of projects, research areas, or developed research questions in mid-March. These will be shared with all seminar participants in late March. The object of the seminar itself will be to workshop these projects and questions to aid participants in the development of their projects, and to establish an ongoing research network of scholars. We will also discuss funding opportunities and cross-discipline collaborations that will allow research in this field to impact medical practice, biomedical research, and public health initiatives both nationally and globally. It is our belief that bio/cultural studies is not a project enclosed within academic contexts but one that should reach out to affect practices and policies worldwide.
Seminar Moderators:
Bernice L. Hausman, PhD, is professor of English at Virginia Tech and a teaching affiliate in Women’s Studies and Science and Technology Studies. Educated in feminist and critical theory, she has spent her career studying medicine, gender, sexed bodies, and motherhood. Her research addresses how human embodiment has become both a problem for, and a project of, modernity. Her books include Changing Sex: Transsexualism, Technology, and the Idea of Gender (1995) and Mother’s Milk: Breastfeeding Controversies in American Culture (2003).
Bradley Lewis, MD, PhD is an assistant professor at NYU’s Gallatin School of Individualized Study with affiliated appointments in the Department of Social and Cultural Analysis and the Department of Psychiatry. He has dual training in humanities and medicine (with a psychiatric specialty), and he writes and teaches at the interface of cultural studies, medicine, and humanities. Lewis is the author of Moving Beyond Prozac, DSM, and the New Psychiatry: Birth of Postpsychiatry and is associate editor for the Journal of Medical Humanities.
Contact information:
Bernice L. Hausman, English Dept. (0112), Virginia Tech, Blacksburg, VA 24061; 540-231-5076; bhausman@vt.edu
Bradley E. Lewis, Gallatin School of Individualized Study, New York University, 715 Broadway, 6th Floor, New York, NY 10003-6806; 212-998-7313; BL466@nyu.edu

Book on Gregory Bateson, Science and Peirce

Some of you may not have heard of this new book on Gregory Bateson as a precursor to biosemiotics:

A Legacy for Living Systems

Gregory Bateson as Precursor to Biosemiotics

Hoffmeyer, Jesper (Ed.)

Series: Biosemiotics , Vol. 2

2008, X, 290 p., Hardcover
ISBN: 978-1-4020-6705-1

Keywords:

• Biosemiotics
• Evolution
• Gregory Bateson
• Meaning
• Mind

About this book:
Gregory Bateson’s contribution to 20th century thinking has appealed to scholars from a wide range of fields dealing in one way or another with aspects of communication and epistemology. A number of his insights were taken up and developed further in anthropology, psychology, evolutionary biology and communication theory. But the large, trans-disciplinary synthesis that, in his own mind, was his major contribution to science received little attention from the mainstream scientific communities.

This book represents a major attempt to revise this deficiency. Scholars from ecology, biochemistry, evolutionary biology, cognitive science, anthropology and philosophy discuss how Bateson's thinking might lead to a fruitful reframing of central problems in modern science. Most important perhaps, Bateson's bioanthropology is shown to play a key role in developing the set of ideas explored in the new field of biosemiotics. The idea that organismic life is indeed basically semiotic or communicative lies at the heart of the biosemiotic approach to the study of life.

The only book of its kind, this volume provides a key resource for the quickly-growing substratum of scholars in the biosciences, philosophy and medicine who are seeking an elegant new approach to exploring highly complex systems.

Contents:
Introduction: Bateson the precursor; J. Hoffmeyer
1. Angels fear revisited; M.C. Bateson
2. From thing to relation. On Bateson's bioanthropology; J. Hoffmeyer
3. What connects the map to the territory; T. Cashman
4. The pattern which connects pleroma to creature; T. Deacon, J. Sherman
5. Bateson’s method: double description; J. Hui, T. Cashman, and T. Deacon
6. Gregory Bateson's relevance to current molecular biology; L. Bruni
7. Process ecology: Creatura in an open universe; R.E. Ulanowicz
8. Connections in action – bridging implicit and explicit domains; T. Shilhab, C. Gerlach
9. Bateson: biology with meaning; B. Goodwin
10. Gregory Bateson's 'uncovery' of ecological aesthetics; P. Harries-Jones
11. Collapsing the wave function of meaning: the epistemological matrix of talk-in interaction; D. Favareau
12. Re-enchanting evolution: transcending fundamentalisms through a mythopoetic epistemology; G. Mengel
13. Bateson and Peirce on the pattern that connects and the sacred; S. Brier
14. Bateson, Peirce and the sign of the sacred; D. Eicher-Catt

From Structure to Structure-Process Duality: A Paradigm Shift in Biology

(The following excerpt is from a book manuscript which is being prepared for Springer, New York, for possible publication in 2009-2010. I thought it might be of some interest to this group because it advocates a ’triadic biology’ based on the idea that the function stems from the triad of structure, process, and mechanism, in contgrast to the traditional dyadic biology which is based on structure and function. This is reminescent of Peirce's triadic semiotics as compared to de Saussure's dyadic semiology. The excerpt is rather long, but, if you have time to read it and have any questions, comments, or suggestions for improvements, I would appreciate hearing from you.)


FROM STRUCTURE TO STRUCTURE-PROCESS DUALITY: A Paradigm Shift in Biology

Structure (e.g., DNA) and processes (e.g., gene expression) are both essential to account for life on the molecular level. In other words, structure (S) and processes (P) are fundamental to life on an equal footing, and yet contemporary biologists have been emphasizing structures over processes, probably influenced in no small measure by the discovery of DNA double helix in 1953 and its astounding successes in subsequent decades as well as by experimental constraints that favor the study of stable structures over transient, dynamic processes.

Biologists probably can learn from a similar experience that physicists went through between the 17th and 20th centuries in the form of the wave-particle duality debate on the nature of light. As is well known, the Huygens, Bohr and their followers thought that light was a wave (on the basis of interference phenomena, for example), while Newton, Einstein and their followers firmly believed that light was a stream of particles (as evidenced by the photoelectric effect). The wave-particle duality problem was not resolved until the early decades of the 20th century when the new science of quantum mechanics was established in the hands of Planck, Einstein, de Broglie, Heisenberg, Dirac, Schrődinger, Pauli, and Born. The resolution came in the form of the de Broglie equation, λ = h/p, where λ is the wavelength associated to the particle moving with momentum p. That is, quantum mechanics informs us that all particles have wave-like properties and all waves have particle-like properties. The reason macroscopic particles do now show any wave-like properties when they move is because their wavelengths calculated from de Broglie equation are too short to be detected.

Available evidence indicates to me that the 21st century biology is faced with the ‘structure-process’ duality problem that may be analogous to the ‘wave-particle’ duality paradox encountered in physics in the past century. I offer the following three examples as evidence for the need to make a transition from the traditional structure-centered perspective to a new paradigm for the biology of the coming decades that is based on ‘structure-process duality’, i.e., the perspective treating structures and processes on an equal footing.

1) Microarray experiments
With the invention of the DNA microarray technique in the mid-1990's,
biologists have been able to measure RNA levels of tens of thousands of genes simultaneously. The mistake (in my opinion [1]) that many biologists have been making unwittingly in this field over the past decade or more is this: When the microarray technique is used to measure the so-called gene expression profiles (i.e., time-dependent RNA levels) and ascribe to the genes encoding these RNAs the role for regulating their levels, biologists are measuring P (i.e., ‘changes’ in RNA levels) and reducing it to S (i.e., DNA ‘sequences’) without specifying any mechanisms. “Changes” are processes and “sequences” are structures and these cannot be connected or correlated without specific mechanisms. It is analogous to physicists who measure particle properties of an object and interpreting them in terms of waves or vice versa, under the conditions where no such interpretations are allowed by the de Broglie equation.

Interpreting the kinetics of the changes in RNA levels in terms of their DNA templates is misguided because it ignores the well-known mechanisms of the control of RNA levels inside the cell: Intracellular RNA levels are determined not by their DNA TEMPLATES but by the balance between two opposing PROCESSES – i.e., transcription and transcript degradation, and the DNA sequences serving as the templates for RNAs have little, if any, to do with transcript degradation process [1].

Just as the wave-like and particle-like properties of material objects cannot be correlated in physics outside the domain of the validity of the de Broglie equation, so structures and processes in living systems may not be correlated unless realistic physicochemical mechanisms can be found. For convenience, we may refer to interpreting P as correlated to S (or S as correlated to P) without proposing any underlying mechanisms in biology as the 'P-S conversion error'.

One way to avoid committing the ‘P-S conversion error” is to treat S and P as independent entities on an equal footing (S-P democracy ?), while acknowledging that S and P cannot be interconverted or correlated in the absence of proper mechanisms for doing so, just as physicists (after the mid-1920’s) treat particles and waves as independent entities on an equal footing, until and unless they can be correlated through the de Broglie equation.

Biologists are not alone in committing the ‘P-S conversion error’. It seems that process philosophers in the Whiteheadian tradition have eliminated S all together in favor of P, in contrast to biologists who have tended to eliminate P in favor or S. Perhaps both process philosophers and biologists can learn from each other and from what is referred to as the “rest-motion” duality (see Table 1) which appears to be a principle universally applicable to physics and biology.

Although the content of Table 1 is more or less self-explanatory, the following features are important to be pointed out.

1) The particle-wave duality and the structure-process duality may be connected through the following two identities (see Row 4 in Table 1):

Particle = structure
Wave = process

2) Particles and waves are related through motions. Examples include the oscillatory motions of atoms in molecules generating electromagnetic waves. Oscillatory motions, in turn, implicate both rest (at the position where the velocity changes its direction) and motions (in between rests). Therefore, what is common to both particle-wave duality and the structure-process duality may be construed to be the ‘rest-motion’ duality. It seems possible that the rest-motion duality is also related to the equilibrium-dissipative structure duality advocated by
Prigogine (1917-2003) at least under non-isolated (i.e., non-adiabatic) conditions (see Row 5).

3) As indicated in Row 3, the wave-particle duality may be predominantly confined to microscopic domain, whereas the structure-process duality can be applied to both microscopic (e.g., fundamental vibrational modes of enzymes leading to low-frequency conformational transitions effecting catalysis) and macroscopic (e.g., DNA sequences determining the behavior of a person).

4) ‘Mechanisms’ in biology may play the role of ’mathematical equations’ in physics (see Row 2). Although mechanisms and mathematical equations are very different in appearance, they may serve as equally valid and efficient presentations of physical laws and principles. In other words, there may be two classes of physical laws and principles – those describable in terms of mathematical equations and those that cannot. In the latter case, one way to represent them may be in terms of mechanisms, a set of processes implemented by the motions of structures. The idea of putting mechanisms on an equal footing with mathematics may be referred to as the ‘mathematics-mechanisms’ duality (MMD), in analogy to the wave-particle duality and now the structure-process duality. The conception of MMD goes against the traditional belief, probably first clearly articulated by David Hilbert in the late 19th century, that no deep problems in physical sciences can be solved without the help of mathematics, which may be analogous to the Newtons and Einsteins claiming that all wave-like properties are ultimately derivable from particles or to Huygens and Bohrs asserting that all particle-like properties are derivable from waves.


Table 1. The ‘rest-motion’ duality in physics and biology.
___________________________________________________________________

#. Parameter = Physics = Biology
___________________________________________________________________
1. Duality = particle-wave = structure-process


2. Constraint = de Broglie equation = mechanisms


3. Domain of validity = microscopic = microscopic and macroscopic


4. Connection = particle (wave) = structure (process)


5. Universality = rest-motion duality = rest-motion duality
__________________________________________________________________


2) The definition of a gene
Prior to 2007 when the results of an international research effort known as the ENCODE (Encyclopedia of DNA Elements) Project was announced, the definition of gene was simple: DNA segments encoding RNAs leading to protein synthesis [2]. But the ENCODE project has unearthed numerous new findings that cannot be readily commodated by this simple conception of a gene and a new definition of a gene is called for. The failure of the pre-ENCODE conception of a gene can be traced ultimately to the following fact: Biologists have been measuring the functions of genes (i.e., P) and reduced the results to nucleotide sequences of DNA (i.e., S) without specifying requisite mechanisms: i.e., the 'P-to-S reduction error’ again. One way to resolve the problems revealed by the ENCODE project is to postulate that there are two equally important classes of genes -- the S-genes and P-genes. The former is identified with the pre-ENCODE conception of genes (also called the Watson-Crick genes [3]) and the latter is a new class of genes called the Prigoginian genes [3]). S-genes are analogous to sheet music (or written language) and P-genes are analogous to audio music (or spoken language) [4, 5]. Just as the sheet music is converted into audio music by a pianist, so the Watson-Crick genes are postulated to be transduced into Prigoginain genes by conformons, the sequence-specific conformational strains of enzymes [3]. Thus, conformons are analogous to the de Broglie equation, since mechanisms based on conformons can convert structure (S-genes) to processes (P-genes) in cells [3, 6], just as the de Broglie equation can convert the particle-like properties of moving objects to their wave-like properties. If this analogy turns out to be true upon further theoretical scrutiny, it may be predicted that conformons will resolve the structure-process paradox in molecular cell biology in the 21st century just as the de Broglie equation solved the wave-particle paradox in particle physics in the 20th century.

3) Free radicals and human diseases
Free radicals are defined as any chemical species carrying one or more unpaired electrons. Examples include the superoxide anion free radicals (an oxygen molecule with one extra electron), nitric oxide (NO), and carbon-centered free radicals generated during air oxidation of phospholipids constituting cell membranes.

Many free radicals are generated in cells as the results of normal metabolism as during mitochondrial respiration responsible for generating ATP but do not cause any harm because their concentrations are strictly controlled not to exceed critical levels (reminiscent of nuclear reactors wherein nuclear chain reactions are controlled to proceed at desired rates by inserting or withdrawing graphite rods). They cause cell damages only when such control mechanisms malfunction or go awry due to environmental toxicants or pathogens. Therefore it seems reasonable to postulate that there are two kinds of free radicals in cells and tissues -- "good" and "bad" free radicals, depending on HOW MUCH of them is produced WHERE, WHEN, and for HOW LONG [6]. In other words, not all free radicals are bad (as many biologists have been assuming), since it is not the chemical structures of free radicals (i.e., S) but rather their spatiotemporally organized concentration distributions in living cells and tissues (i.e., related to P) that determine whether they are good or bad for human health. To remedy the shortcomings of the traditional paradigm in biomedical research, therefore, it appears necessary to make a transition from the traditional 'equilibrium structure-based' (i.e., S-based) paradigm to the 'equilibrium-dissipative structure duality-based' (i.e., S-P dual) paradigm. The drugs developed under the S-P dual paradigm may be referred to as the "dissipative structure-targeting drugs (DSTDs)" as compared to those developed under the traditional S-based paradigm as "equilibrium structure-targeting drugs (ESTDs)" [7]. It is possible that DSTDs will become an increasingly important form of drugs in the coming decades.


With all the best.

Sung

___________________________________________
Sungchul Ji, Ph.D.
Department of Pharmacology and Toxicology
Rutgers University
Piscataway, N.J. 08855


References:

[1] Ji, S., Chaovalitwongse, A., Fefferman, N., Yoo, W., and Perez-Ortin, J. E. (2008). Mechanism-based Clustering of Genome-wide RNA Levels in Budding Yeast: Roles of Transcription and Transcript Degradation. In: Clustering Challenges in Biological Networks (Chaovalitwongse, A., ed.) (in press).
[2] Gerstein, M. B., et al (2007). What is a gene, post-ENCODE? History and updated definition. Genome Research 17:669-681.
[3] Ji, S. (1988). Watson-Crick and Prigoginian Forms of Genetic Information. J. theoret. Biol. 130: 239-245.
[4] Ji, S. (2009). Molecular Theory of the Living Cell: Conceptual Foundations, Molecular Mechanisms, and Applications. Springer, New York (to appear) .
[5] Ji, S. (2009). Words, Sounds, and Meanings of DNA. Imperial College Press, London (in preparation under invitation from the publisher).
[6] Ji, S. (1991). Biocybernetics: A Machine Theory of Biology. In: Molecular Theories of Cell Life and Death (Ji, S., ed.), Rutgers University Press, New Brunswick. Pp. 1-237. See the section on FSDM Hypothesis of Disease Development on pp. 191-194, available at http://www.rci.rutgers.edu/~sji, under Publications.
[7] Ji, S. (2010). Cell Model-Based Pharmacotherapeutics and Toxicology (in preparation).

Biosemiotic Books

One obvious way to use this blog is to inform about new books on biosemiotics and its history, and related topics! Thus this piece of information I got:

Treasure Your Exceptions. The Science and Life of William Bateson
by Alan G. Cock and Donald R. Forsdyke (2008)

- many Biosemioticists are deeply interested in Gregory Bateson and his wife Margaret Mead. Our new biograph of Gregory's father, William Bateson, will be released by Springer, New York, in August. While far less comprehensive than David Lipset's superb biography of GB, there are some new twists that may be of interest. For more information please see http://post.queensu.ca/~forsdyke/book04.htm

Editorially

Hello!
I've been on holiday, but came back and being back I received Marcello's recent collage of correspondance (this new version of the correspondance can be downloaded here in pdf or rtf format). I sense we might be moving the discussion to the blog. Feel free to pose questions, and use comments to this post to submit questions about the use of the blog. This blog is a group blog, and we might try to help newcomers to get started. See also the intro.
Best,
Claus
.

Macro- vs. microsemiosis

Hi everybody,

I know some of you from the old OCA list, and it is good to get re-connected.

I chanced to run into the Biosemiosis blog while browsing the Internet looking for some more information on Barbieri's recent Naturwissenschaften article [Biosemiotics: a new understanding of life 95: 577-599 (2008)] which was kindly brought to my attention by Stan.

I enjoyed reading, and learned a lot from, Marcello's excellent review article, which has clearly demonstrated (at least to me) how relevant and essential it is to apply semiotic principles to biology in order to understand the phenomenon of life on the molecular, cellular and evolutionary levels.

After reading some of the discussions that followed Marcello's July 8 post, I was wondering if we could divide semiotics into three main branches based on the physical dimensions of signs on the one hand and on the materiality of signs on the other:

1) Signs divide into formal and physical signs.
2) Physical signs divide into macro and micro signs.
3) The study of formal signs ==> 'Metaphysical semiotics'.
The study of macrosigns ==> 'Macrosemiotics'.
The studyo of microsigns ==> 'Microsemiotics'.

Scheme 1. A suggested trichotomization of the field of semiotics based on i) the
materiality and ii) the size of signs.


i) By 'Metaphysical' semiotics (or semiotic metaphysics?), I mean the study of signs on the most abstract and general level, or the metaphysics of signs (in contrast to the physics of signs). Pansemiotics, and triadic metaphysics of Peirce would belong to this branch of semotics.

ii) 'Macrosemiotics' is the study of macroscopic signs (e.g., words, sentences, pictures, sculptures, sounds, etc. ) that are visible, audible, tactile, and tastable to humans and other animals. Linguistics, literary art, visual arts, musicology, archtecture, dance, anthroposemiotics, and zoosemiotics would belong here.

iii) 'Microsemiotics' can be defined as the study of signs on the microscopic level (e.g., DNA, RNA, proteins, pheromones, cells). Biosemiotics of cells and their higher-order structures (e.g., organs, including the brain) analyzed in terms of molecules as the basic building blocks would constitute the main component of this branch of semiotics. Jesper Hoffmeyers work over the years and Macello's recent review article, among ohers, have laid the foundations for the field of microsemiotics.

At the invitation of Sebeok, I attended the 25th Annual Meeting of the Semiotic Society of America in 2000 honoring Sebeok's career as a semiotician. Two papers resulted from my attending the meeting in which I developed the notions of macro- and microsemiotics. One of these papers is entitled "Isomorphism between Cell and Human Languages: Micro- and Macrosemiotics" published in "Semiotics 2000: 'Sebeoks' Century' (editied by S. simpkins and J. Deely), Legas, New York, 2001, pp. 357-373 and is available from my web site (http://www.rci.rutgers.edu/~sji) under Publications. This article starts out with the following statement by Sebeok as quotated by J. Deeely in 1994 (see my web site for the reference) which I referred to as the 'Sebeok doctrine of signs':

". . .the genetic code must be regarded as the most fundamental of all semiotic networks and therefore as the prototype for all other signaling systems used by animals, including man. From this point of view, molecules that are quantum systems, acting as physical information carriers, zoosemiotic systems, and and, finally, cultural systems, comprehending language, constitute a natural sequel of stages of ever more complex energy levels in a single universal evolution. It is possible, therefore, to describe language as well as living systems from a unified cybernetic standpoint . . . A mutual appreciation of genetics, aminal communication studies, and linguistics may lead to a full understanding of the dynamics of semiotics, and this may, in the last analysis, turn out to be no less than the definition of life."


I think the trichotomization of semiotics into microsemiotics, macrosemiotics and metaphysical semiotics suggested in Scheme 1 is fully consonant with the ideas expressed by Sebeok in this paragraph.

Marcello emphasized copying and codemaking in microsemiosis (as deinfed above). I wonder if we can trichotomize microsemiosis as well in the following manner:

i) Copying ==> iconic signs (?)
ii) Coding ==> symbolic signs (i.e., the arbitraryness of signs) (?)
iii) Transduction ==> indexical signs (e.g, free-energy driven protein
machines)(?)

Clearly, i) and ii) cannot proceed without iii), thus supporting the essentiality of the triad. Also coding (or triadicity, or the arbitraryness of signs) is not unique to transfer RNAs but also found in proteins in the form of allostery (i.e., the regulation of the geometry of enzymic acvtive sites by allosteric ligands arbitrarily related to the structure of the substrate of the enzyme).

In other words, from the point of view of microsemiotics, sign processes in the living cell may be best characterized as a triadic process implicating not only the two kinds of information transductions emphasized by Macello (i.e., copying and coding) but also energy transduction (i.e., enzymic catalysis), without which no information can be transduced.

With all the best.


Sung

Sungchul Ji, Ph.D.
Department of Pharmacology and Toxicology
Rutgers University
Piscataway, N.J. 08855

Emergence

How does 'something' become 'something different'? Not in the mechanical or computable sense where an external agent such as the wind erodes a rock, or a sculptor changes that rock.

But in an organic sense, where we observe an entity in a certain state at a particular time: x(t).

And we wonder what caused it to change to x(t + 1) one hour or one generation later. There seem to be three 'causes'.

Stochastic - which is purely accidental and not computable. This is the answer of many biologists to evolution, with their decision that random changes provide functional new properties. I have a problem with this, because by the time a random change that actually works comes along, the species would be long extinct. I am only comparing my lack of success at winning the lottery.

Deterministic - which is most certainly computable and we then have to consider the Agent of Determination. And the agenda of that Agent.
and
Choice.

(1) Choice can be by the individual alone; it can remain with the individual alone. Such as a rat biting off its tail (we won't discuss why). Such a change remains with that individual alone.

(2) Or, it can refer to the whole but local Set of a particular species (animal or plant) in a particular environmental domain. In this case, for example, the beak of a bird species will enlarge and harden to enable it to deal with a new seed in that domain.

(3) Or, it can refer to the entire non-local Set of organisms, such as all birds.

I think that Choice-2 is the most important biological property. I'd put Choice-3 as relevant to the physico-chemical realm.

Why do I use the term 'choice', a term that usually indicates a reasoning Agent? Because I think that a certain amount of Reasoning is going on. In fact, I consider Nature as a process of Reason, in that its properties and productions are not random but correlated, interactional, productive. These seem, to me, to be acts of Reason rather than non-reason.

I think that biological systems have an 'internal' informational process, a Reasoning Informational process that is held within all members of a species; and, then located within a domain. These informational processes functions as a kind of google search engine, connecting to all the realities in that ecosystem. Connecting to what is going on in that ecosystem.

As such, this internal informatonal system, which I call Strong Anticipation, comes up with hypothetical solutions to environmental concerns. Hypothetical, not actual, so that there is no destabilization of the system. It comes up with a number of such hypotheses. Any one of them would function as a solution.
But, the system itself 'chooses' ONE solution. This can be a random choice but remember, any one of them would function, because the system has 'pre-approved' all of them as informationally relevant in this domain. This then emerges as the new property of the system, and becomes dominant in the real world.

Problems?

Re, Pan, and Bio

(editorial note: After somebody suggested that an email conversation (that emerged after the 8th Gatherings in Syros and Marcello's subsequent mailing his article) should be posted and continued on the blog, Marcello kindly mailed me this collage of the previous correspondance, posted here for the newcomer's information and to continue dialogue. C.E.
— note added of July 13, 2008: A newer version with more comments can be downloaded here in standard rtf)
— note added of July 20, 2008: Thanks to Marcello, a new version can be downloaded here in pdf or rtf format, as you prefer.

= = =
From: Marcello Barbieri
To: Alexander Kravchenko ; Alexei Sharov ; Almo Farina ; Andreas Weber ; Anton Markos ; Arantza Etxeberria ; Argyris Arnellos ; Arno Goudsmit ; Charbel El-Hani ; Claus Emmeche ; Cliff Joslyn ; Diego Gonzalez ; Don Favareau ; Donald Roy Forsdyke ; Edwina Taborsky ; Eörs Szathmáry ; Eugenio Andrade ; Fatima Cvrcková ; Frederik Stjernfelt ; Guenther Witzany ; Guido De Mey ; Han-liang Chang ; Hans-Joachim Gabius ; Ingolf Schmid-Tannwald ; Jean Umiker-Sebeok ; Jesper Hoffmeyer ; Joanna Raczaszek-Leonardi ; Joao Queiroz ; John Collier ; John Pickering ; Jon Umerez ; Jonathan Hope ; Jürgen Brosius ; Kalevi Kull ; Karel Kleisner ; Koichiro Matsuno ; Luis Emilio Bruni ; Luis Rocha ; Marcel Danesi ; Marcella Faria ; Marcello Barbieri ; Mario Gimona ; Mark Reybrouck ; Martien Brands ; Massimo Di Giulio ; Mehmet Ozansoy ; Mette Böll ; Morten Tønnessen ; Myrdene Anderson ; Nadir Maraldi ; Natalia Abieva ; Paul Cobley ; Peter Barlow ; Peter Cariani ; Peter Harries-Jones ; Prisca Augustyn ; Remigio Rossi ; Riin Magnus ; Ryad Benosman ; Saverio Forestiero ; Sean O'Nuallain ; Sergey Chebanov ; Søren Brier ; Stacey Ake ; Stanley Salthe ; Stephen J. Cowley ; Stephen Pain ; Susan Petrilli ; Terrence Deacon ; Thierry Bardini ; Timo Maran ; Tommi Vehkavaara ; Victoria Alexander ; Walter Riofrio ; Wendy Wheeler ; Werner Callebaut ; Winfried Nöth ; Wolfgang Hofkirchner ; Yagmur Denizhan ; Yair Neuman
Sent: Tuesday, July 08, 2008 3:07 PM
Subject: Biosemiotics

Dear Colleagues,

Please find in attachment a review article on Biosemiotics that has recently appeared in Naturwissenschaften. Comments, of course, are welcome.
Best,
Marcello

Barbieri, M. (2008) Biosemiotics: a new understanding of life. Naturwissenschaften 95, 577-599. [pdf file]

= = =
COMMENTS
= = =
(1) Stanley SALTHE

From: Stanley Salthe
Sent: Tuesday, July 08, 2008 4:49 PM
Subject: Re: Biosemiotics

Marcello- Very informative!

Well, we do differ in your restricting semiosis to life and higher levels. This difference centers on the origin of semiosis. Nothing can originate from thin air. In evolution there is always necessary a precursor system which becomes modified to give rise to the new. Generally it would be a vaguer system than the new. Therefore, on evolutionary grounds, I think we need to posit a pansemiotics. Of course, one can continue to develop biosemiotics without concern for the origin of the coding system, but it is of considerable interest, it seems to me, that there is as yet no accepted model of the origin of the genetic system. That is, the origin of biosemiosis has to be taken as completely unknown. Only a pansemiotic perspective, I think, might facilitate investigation of this origin. In my view coding could not, logically, have come about without a vaguer kind of semiosis being in place first, at a higher level, guiding this origination.
Best
STAN


= = =
(2) Marcello BARBIERI

From: Marcello Barbieri
Sent: Wednesday, July 09, 2008 8:48 AM
Subject: Re: Biosemiotics

I am sorry, Stanley, but it just isn’t true that we need pansemiotics to explain the origin of semiosis simply because nothing can originate from thin air. That is equivalent to saying that the origin of consciousness can be explained only by assuming that there is a little bit of consciousness in every atom. No, an origin is the appearance of something that did not exist before, and semiosis had a true historical origin because it did not came into existence with the Big Bang.
Semiosis is based on copying and coding and originated some 4 billion years ago when the first copymakers and codemakers (not thin air!) appeared on the primitive Earth and started producing molecular artifacts. There is a real divide between matter and life because matter is made of spontaneous objects and life is made of artifacts that cannot be formed spontaneously. The bridge was provided by the molecular machines that appeared spontaneously on the primitive Earth, and one can see that there was both continuity and discontinuity in the origin of life.
(1) The first molecular machines (bondmakers and copymakers) were spontaneous molecules, and that explains why they originated from inanimate matter.
(2) The first molecular machines started producing molecular artifacts, and that explains why they gave origin to a real divide between life and matter.
And that is true not only for the origin of life, but for the origin of all other discontinuities of life.
Explaining life means explaining the novelties of life produced by preexisting systems, and those systems can only be codemakers. That is what biosemiotics is really about and that is what pansemiotics can never hope to achieve with its appeal to infinite regress.
Yours truly
Marcello

= = =
(3) Arno GOUDSMIT

From: "Arno Goudsmit"
Sent: Wednesday, July 09, 2008 11:23 AM
Subject: Re: Biosemiotics

Hi all,
there is an interesting phenomenon named 'interpretation in retrospect' (my translation of the german 'hineininterpretieren') and it might be worthwile to consider whether this applies also to the pansemiotism - biosemiotism issue that Marcello and Stan are raising. My point is that, given a particular historical origin of something (say: semiosis), it becomes possible to assign to preceding events a quality of 'proto-something' (say: proto-semiosis). But this can only happen retrospectively.
It's like catastrophic forms such as the famous 'cusp': continuous on one dimension and discrete on another. So why not study both dimensions? I don't see why the origination of meaning (and of life) cannot be related to some value changes on some continuous dimension, and still be a discrete step. (But perhaps I will see it better retrospectively ;) )
Best,
Arno Goudsmit

= = =
(4) Edwina TABORSKY – 1

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 4:41 AM
Subject: Re: Biosemiotics

Right, I'd agree with Stan in favour of pansemiotics. My view is that the semiotic triad operates as a function where f(x)=y, which simply means that the input of matter/energy (x) is transformed by the rules of (f)..into output (y). The whole triad is a process.
What then becomes interesting is the nature of 'f', the rules of transformation or interpretation of x into y. In the physico-chemical realm, these rules the limit/constrain the formation of X-energy/matter into its morphological nature as Y, are stable. They are impervious to spatial and temporal influences. This provides a basic 'storage' of energy all over the planet.
But in the biological realm, an interesting change occurs. Those rules, f, become internalized into a specific local population; and these rules are informationally connected to the local spatial domain and temporal period in which that population exists. The rules are thus affected by the various different material species in that local domain..and therefore, the rules can change. So, you get an explosion of diversity, dependent on different spatial domains, all over the planet.
Edwina Taborsky

= = =
(5) Edwina TABORSKY – 2

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 3:05 PM
Subject: Re: Biosemiotics

Don't you think, Marcello, that it is more scientific to state that your CONCLUSION, based on your analysis of the evidence, is that..there is no such thing as pansemiosis...etc.
Instead, you make statements like 'it is true'. I think science is more open to different conclusions than that type of declaration.
I happen to believe in pansemiosis. I consider it began with the 'bigbang'. I don't describe it according to Stan's premise of regression, which I find rather linear, because I consider that all matter, including the physico-chemical realm, operates according to a triadic function f(x)=y, where the rules of f transform input data x to output interpretant y. The physico-chemical realm's 'f' or rules are 'held' within the entire SET (all hydrogen atoms) rather than within the individual particle. I don't see an atom as 'spontaneous' but as existing according to general rules.
The biological realm's switch to storing the rules within each particle or individual meant that those rules were put into a spatial area where informationally, they were in close contact to species living only in that domain. The rules were then affected by that more confined Information Set...and changed.
So, Stan's axiom is that there exists a more primitive set of rules/codes in the physico-chemical realm. My assumption is instead that this realm operates within a more general rather than primitive set of rules/codes, and those rules/codes are kept general by being exposed to all spatial zones of the planet. So, informationally, none of those rules/codes could develop a more unique style. They were always kept common.
The biological's realm's internalization of the rules/codes confined them to local rather than general space; that disabled the process of planetary generalization and moved the rules into non-common and local rules. So, we get diversity.
Plus, I don't view the biological realm as a 'machine'.
Regards,
Edwina

= = =
(6) Jesper HOFFMEYER

From: Jesper Hoffmeyer
Sent: Wednesday, July 09, 2008 1:27 PM
Subject: Re: Biosemiotics

Dear Stan, Marcello and others

I agree that "the origin of biosemiosis has to be taken as completely unknown" which however - as Marcello puts it - may also be said about consciousness. Like Marcello I don't like the idea that consciousness should be present in atoms, electrons, or quanta jump or whatever mathematicians and physicist often too easily suggest. Likewise I don't see any reason to believe that semiosis has remained the same kind of thing from the very first beginnings. I like to see semiosis as an emergent phenomenon, where the increase in semiotic freedom is indeed the one most conspiscious fact we have about organic evolution. And as some of you will know I have suggested a 5 step model for its appearence based on Stuart Kauffman's work with autonomous agents (http://www.imbf.ku.dk/MolBioPages/abk/PersonalPages/Jesper/Surfaces.html). Terrence Deacon's recent work on the autocell suggest a somewhat different approach but I take these approaches to be supplementary rather than antagonistic. Its therefore not entirely true that we have continued "to develop biosemiotics without concern for the origin of the coding system". But of course this kind of thing can never be anything but models and speculation.

Now, concerning pansemiosis, a main objection to the concept is the misunderstandings it inevitably raises. Actually, I had the feeling that this concept was always used by the opponents rather than by proponents. It smells too strongly of the German Naturphilosophie and especially of Friedrich Schelling’s conception of the world as panpsychic. And regardless of what Schelling exactly did mean by this it seems to me inappropriate to confuse natural processes with human psychology. Pansemiosis should of course not be conflated wit panpsychism, but I am sure it always will be, so for no other reason than this I would suggest that another term should be chosen for this.

But I also think that the idea that world is nothing but signs - and that is I suppose what pansemiosis would mean - is strangely reductionistic, and I cannot adopt it. I know that Peirce did indeed some times speak as if he believed thus, but this was hardly his deeper intentions. On all this, you should see the very interesting exchange between John Deely and Frederik Stjernfelt in Cybernetics & Human Knowing 13,1 and 3 (2006).

I allow myself to end this with a quote from a chapter I recently wrote for The Routledge Companion of Semiotics (edited by Paul Cobley - and still in press), in which I try to explain my relation to John Deely's concept of physiosemiosis, which seems to me to be an much more acceptable idea than the idea of pansemiosis. And yet, here I explain why I prefer the more modest term proto-semiosis:

"In the evolutionary cosmology suggested here the early universe is seen as essentially indeterminate and as in a deep sense profused with proto-semiosic activity. By the term proto-semiosic activity I refer to what is nowadays called self-organizing processes, which in Peircean terminology would be "habit taking"[1]. In principle habit-taking may be seen as the most basic or general form of an interpretant, and in this sense the term physiosemiosis would indeed be a suitable way of characterizing this proto-semiosic activity. I hesitate however to use this term because it may so easily be misunderstood to imply that sign-use did indeed take place in this early universe, and I would argue strongly against such a conception. However this proto-semiosic activity would cause a gradual formation of ordered configurations of processes and thereby produce a growing deviation from equiprobability or, in other words, a growing predictability. Under the particular physical conditions that reigned at planet Earth (and possibly a great number of other locations in our universe) this growth paved the way for the appearance of a new kind of semiosic activity, biosemiosis. While protosemiosic activity refers to a profound general trend of the early universe biosemiosis may be seen as a radical potentiation of this trend brought about by the creation of concrete semiotic agents, first - as we shall see - historical agents, lineages, and later in evolution individual organisms. Stanley Salthe's specification hierarchy expresses a related conception (Salthe 1993; 2007). The appearance on our planet of biosemiosis, in short, opened a new agenda for the evolutionary process by providing entities with the agential property that is presupposed for Darwinian "striving" and thus for natural selection. At primitive levels the semiotic freedom of agents is still very low, and a bacterium for instance cannot itself chose to not swim upstream in a nutrient gradient. Therefore, at this stage of evolution semiotic freedom is primarily exhibited at the level of the lineage (the evolving species)[2]. Only later, with the evolution of brained animals would emerge a more advanced stage of biosemiosis, in which the semiosic activity is no longer a species property but also, and importantly so, an organismic property."

Cheers

Jesper


[1] The term self-organization has become standard in complexity research in spite of the inherent philosophical ambiguities connected to the us of the term 'self' as discussed by Alicia Juarrero (1999). That the self-organizing property of the early universe comes close to semiosis, since it presupposes a concept of molecular measuring processes, can be seen in Stuart Kauffman's important book Investigations (2000) (and further discussed in Hoffmeyer 2008a.)

[2] Even at this level one cannot rule out individual semiotic freedom right away though. A bacterium is a hugely complex and well tuned system of proteins and other components and although learning processes do probably not directly play a role at this level the bacterium is capable of changing its behavior by the active uptake of foreign DNA from bacteriohages.

= = =
(7) Edwina TABORSKY – 3

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 3:34 PM
Subject: Re: Biosemiotics

I think the issue of consciousness is quite different from the issue of biosemiosis vs pansemiosis. Is a plant 'conscious' in the same way that we humans are - we, who have symbolic rather than only indexical awareness and reactive capabilities?
I reject the term 'proto-semiosis' as well. I consider that the universe is completely semiotic, and my reading of Peirce is that he insisted on that as well. (I'm not using him as my authority, just pointing out that my reading of him is different from that of Jesper's).
Most certainly, the level of complexity of semiosis is different in the different realms: physico-chemical, biological, human. The most basic realm set up a universal morphology, ie, where matter is the same all over the universe ..and in this case, our planet earth. All matter operates according to a triadic process of f(x)=y. The rules or 'taking of habits' in the physico-chemical realm, f, are general (iconic) rather than bonded indexically to local matter.
I analyze what is going on by considering the interactions as informational; the particular morphological unit is engaged in an informational process with other informational systems. So, the biological realm, which internalized the coded Rules, meant that these rules were then confined to local information rather than exposed to the generalizing constraints of the full planet's information. This constraint on the ability of these rules to interact with other codes all over the planet, led to diversity of rules. And diversity increased the complexity of potential interactions and the nature of new rules.
Consciousness is something quite different from indexical interactions; it requires the ability to develop an external model of information...What becomes interesting is how much of this model is indexically formed and how much is symbolic...
Regards
Edwina Taborsky

= = =
(8) Alexei SHAROV

From: Alexei Sharov
Sent: Wednesday, July 09, 2008 4:06 PM
Subject: Re: Biosemiotics

Dear biosemioticians,

I am glad that the question of pansemiotics is open for discussion, and I totally agree with Marcello that the idea of pansemiotics is incompatible with biosemiotics. Biosemiotics assumes that life is something special (i.e., different from non-life) and this special feature is semiosis. Otherwise there is no much sense of combining "bio" - and - "semiotics".
Of course this does not mean that pansemioticians like Edvina and Stan are not welcome at biosemiotics meetings. But I think it is very important to defend the difference between biosemiotics and pansemiotics.
If any aspect of physical interaction is a semiotic interaction then either physical or semiotic description is redundant.
I understand that Stan's pansemiotic view is more complicated than this. He assumes multiple inclusive levels of the same phenomenon. For example, clay crystallization has elements of "memory" according to Cairns-Smith. Thus if he agrees that the "level of semiosis" declines to infinitely small value across the transition from life to non-life, then I would not classify his views as pansemiotic.
I prefer a different way of presenting the boundary between life and non-life by assuming that there are 2 languages for describing things: (1) physics and (2) semiotics. Non-living objects are described well by physics, whereas semiotic (=pansemiotic) description of non-living things is vague and generally non-productive (e.g., we cannot design a bicycle with just semiotics). In contrast, living things are best described with semiotics, considering purposeful behavior, living functions, etc. Physical description of living organisms does not go beyond very simple interactions (e.g., biophysics of flight, or molecular thermodynamics).
However, I assume that there is an intermediate area where both physical and semiotic description are equally relevant, and this area is the transition from non-life to life, i.e., life origin. Note, that I do not classify systems as living or non-living but talk about relevancy of 2 different languages of description.
The success of explaining life origin depends on the ability to keep both descriptions within the transition zone. Let me know if this sounds too complicated for understanding. Then I will try to explain in more details.
Alexei Sharov

= = =
(9) Edwina TABORSKY – 4

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 4:50 PM
Subject: Re: Biosemiotics

Heh, many thanks, Alexei, for your welcome of 'we pansemioticians' to meetings of biosemiotics! Of course, we'll continue to disagree! I completely reject the confinement of semiotics to living systems.

I don't think that the emotive term of 'special' (life is something special' is scientifically valid in a discussion of whether or not semiosis is found in non-biological systems. I think that the difference between the semiosis in the physico-chemical and biological realms - is the location of the 'normative habits' of each realm. You surely can't deny that normative habits function within the physico-chemical realm!

And, our knowledge of the development of the universe is that the basic chemical elements weren't all formed 'at once' but evolved in complexity over billions of years. That in itself, suggests that these normative habits of formation were 'informational'. And 'informational processes' are semiotic. After all, the various isotopes of hydrogen are examples of different codes that evolved within that element.

The difference between the two realms and their ability to change their rules is vital. I'm not disagreeing with that importance - which is why I tend to veer away from Stan's more gradual and ambiguous (I feel) relation between the physical and the biological realms. I think the difference is real and vital...and consists in the ability of the system to change its normative habits or rules.

Again, in the physico-chemical realm, the normative rules are not stored within the particular individual unit; the individual unit exists, spatially, within the rules! A complete 'flip' from the biological realm where the rules are internalized within each individual unit!
That spatial flip of where the rules are stored is vital, I think. It means that the physico-chemical realm's rules are dominant over the individual expressions of that rule..and the individual units can't gather enough 'input information' to affect those rules.

It's the opposite in the biological realm. The rules are stored within indivdiual units..and these units live within local space and time. Not all over the planet, but in local areas. They are affected, at first, by differences in temperature, water, etc...and over time..by differences in the nature of other species in that spatial area. This envt is 'an information envt'; it informs that particular unit...and this in turn 'informs' the Rules stores in that individual. This can change the rules, so a bird species in one area can be affected by a new plant in the area and develop a changed beak to enable it to gather the seeds from that new plant.

A hydrogen atom isn't affected by local space. But, I think that a physical description of molecular thermodynamics is most certainly a triadic function..and is therefore, semiotic.

Regards,

Edwina Taborsky

= = =
(10) Alexei SHAROV – 2

From: Alexei Sharov
Sent: Wednesday, July 09, 2008 5:27 PM
Subject: Re: Biosemiotics

Hi Edwina,
Thanks for reply!

Of course, we'll continue to disagree! I completely reject the confinement of semiotics to living systems.

Indeed if we agree on everything it will be boring!

You surely can't deny that normative habits function within the physico-chemical realm!

No I don't see any normative habits in physics (at least in Newton's physics). The main achievement of Newton was separation of physics from normative habits. It does not matter what is our intention of throwing a stone, but the stone follows the trajectory that does not depend on our intentions. The only thing that matters is the boundary condition (initial speed and direction) which is not equivalent to intentions.

After all, the various isotopes of hydrogen are examples of different codes that evolved within that element.
Isotopes are not codes. And I don't see any "evolution" here in biological sense. Erosion of rocks is not evolution because rocks do not remember their habits that they can reproduce when necessary. Show me a rock which has invented an adaptive response to its habitat. Show me a rock that can walk away from a steep
slope or hide in a shelter from a hurricane.

Again, in the physico-chemical realm, the normative rules are not stored within the particular individual unit; the individual unit exists, spatially, within the rules!

If they are not stored then they should not be called "normative rules" and they are not stored anywhere. Only living organisms started storing the rules. "Rules" of physics are our human rules (see below).

A hydrogen atom isn't affected by local space. But, I think that a physical description of molecular thermodynamics is most certainly a triadic function..and is therefore, semiotic.

Here I agree with you totally. Indeed physics as description of reality is a triadic function, and it is a part of human semiotics. But physics as a language (description) is not reality itself! When we talk physics we use semiotics to describe a non-semiotic object. We develop models, measure parameters of these models (e.g., light speed, electron weight), and these models match well enough to reality so that we can successfully manipulate it. But these models are our models of the world. They are not Laws created by God to rule the universe. Models are convenient tools that work for our purposes, but they are not essences.
Non-living objects do not become semiotic simply because humans (which are semiotic systems) describe them. I hope you see my point that reality is not the same as our description of reality.

Alexei

Alexei Sharov, PhD, Staff Scientist
Lab. of Genetics, National Institute on Aging (NIA/NIH)
251 Bayview Boulevard, Suite 100, Room 10C222. Baltimore, MD 21224, USA
Phone: 410-558-8556 Fax: 410-558-8331

= = =
(11) Stanley SALTHE – 2

From: "Stanley Salthe"
Sent: Wednesday, July 09, 2008 4:53 PM
Subject: Re: Biosemiotics

Arno -- Yes, this is at least a matter of the process of discovery (leaving aside some amusing quantum mechanics possibilities related to the Anthropic Principle!). One NEVER finds what one is not looking for, and one often finds (constructs) what one is looking for. Again, this depends upon one's philosophical position. I take a materialist position, and an evolutionary position, and these positions inform my investigations. I think that in our postmodern times it is no longer possible to imagine scientific 'objectivity'.
I surmise that my position may be incongenial to those who are trying to get semiotics accepted as a scientific perspective. But, then, I am not urging that they embrace pansemioics, only pleading for it as one possible approach to semiotics. Biosemiotics can certainly stand on its own, just as cell biology can do, without inquiring into origins at all. We might note that science has never been good at origins. It deals with existents.
STAN

= = =
(12) Stanley SALTHE – 3

From: Stanley Salthe
Sent: Wednesday, July 09, 2008 4:41 PM
Subject: Re: Biosemiotics

Marcello -- Thanks for your reply. I try to answer (I will also address the later postings in other postings to the group

I am sorry, Stanley, but it just isn’t true that we need pansemiotics to explain the origin of semiosis simply because nothing can originate from thin air. That is equivalent to saying that the origin of consciousness can be explained only by assuming that there is a little bit of consciousness in every atom. No, an origin is the appearance of something that did not exist before, and semiosis had a true historical origin because it did not came into existence with the Big Bang.

S: As it happens, I do think that logic requires that there be precursors for any evolved property. It is both a materialist and an evolutionary principle. Note that I stress that these precursors would be undeveloped -- more precisely, vaguely embodied. That is, in ancestral systems we would find vague tendencies, only episodically momentarily embodied, which can be seen to supply material causes for later developments only if we look for them. I am not urging that we think that, e.g., semiosis, is functional in the early quark gluon plasma.

Semiosis is based on copying and coding and originated some 4 billion years ago when the first copymakers and codemakers (not thin air!) appeared on the primitive Earth and started producing molecular artifacts. There is a real divide between matter and life because matter is made of spontaneous objects and life is made of artifacts that cannot be formed spontaneously.
The bridge was provided by the molecular machines that appeared spontaneously on the primitive Earth, and one can see that there was both continuity and discontinuity in the origin of life.

S: But these early proto-codings can suggest both proto-semiosis and non-semiosis, depending upon one's philosophical bent. This depends upon what it one is looking for.

(1) The first molecular machines (bondmakers and copymakers) were spontaneous molecules, and that explains why they originated from inanimate matter.
(2) The first molecular machines started producing molecular artifacts, and that explains why they gave origin to a real divide between life and matter.

S: I guess I don't quite understand what is a 'molecular artifact' as opposed to other molecular configurations.

And that is true not only for the origin of life, but for the origin of all other discontinuities of life.

S: I think our philosophical difference resides in these proposed 'discontinuities'. As a generalizer, I always seek continuities. (This is no doubt a personality difference!)

Explaining life means explaining the novelties of life produced by preexisting systems, and those systems can only be codemakers. That is what biosemiotics is really about and that is what pansemiotics can never hope to achieve with its appeal to infinite regress.

S: The regress might seem infinite to, say a biologist, while it might seem to point to some quantum phenomena to a physicist. Then again, why NOT infinite?

STAN

= = =
(13) Guenther WITZANY

From: Guenther Witzany
Sent: Wednesday, July 09, 2008 7:38 PM
Subject: Re: Biosemiotics

Dear Marcello!
Nowhere in the whole universe exist machines, only on earth and these machines are constructed by humans. And for shure these machines which are constructed by humans have exciting properties except that they have any biotic features. Machines are completely different to biotic cells, so maybe another term would fit better.
Best
Guenther

= = =
(14) Edwina TABORSKY – 5

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 7:10 PM
Subject: Re: Biosemiotics

Alexei - I do think that there are codes or normative habits in physico-chemical matter. Your example of the stone being thrown is not the example I'd use, for that involves the input of the Man picking up and throwing the stone; The Stone as Itself; and the result of The Stone being moved from its first site.
But for example, matter is most certainly encoded; a Hydrogen, a Helium, a Calcium atom are all 'encoded' differently and thus, based on those codes, can interact differently with each other etc. Those atoms are existent, within normative habits of matter-organization.
The isotope is not a code; it is a morphological form, a unique result of encodement.
The erosion of a rock is an evolving process where the normative habit(s) that keep those chemical properties bound to each other start to weaken because of the intrusion of other informational data/input. (water, heat).
The codes in the physico-chemical realm ARE stored. They are stored within the entire Set. Each hydrogen atom is a particular expression of this Set.
The biological realm moved the normative codes internal to each individual expression.
But both systems most certainly store their normative codes. That's why our planet/universe contains those same elements and molecules.
No, I don't agree that the 'rules of physics' are our human deescriptions of those rules. I think that these rules, that form our universe, exist - as rules. We 'discover' them, we explain them, But we don't make them up. Of course reality is not the same as our description - for our descriptions might be inaccurate. But reality exists prior to our description, and my view of that reality is - pansemiosis.
Regards,
Edwina

= = =
(15) Stanley SALTHE – 4

From: Stanley Salthe
Sent: Wednesday, July 09, 2008 7:55 PM
Subject: Re: Biosemiotics

Jesper -- Interleaving

Dear Stan, Marcello and others
I agree that "the origin of biosemiosis has to be taken as completely unknown" which however - as Marcello puts it - may also be said about consciousness. Like Marcello I don't like the idea that consciousness should be present in atoms, electrons, or quanta jump or whatever mathematicians and physicist often too easily suggest. Likewise I don't see any reason to believe that semiosis has remained the same kind of thing from the very first beginnings. I like to see semiosis as an emergent phenomenon, where the increase in semiotic freedom is indeed the one most conspiscious fact we have about organic evolution. And as some of you will know I have suggested a 5 step model for its appearence based on Stuart Kauffman's work with autonomous agents (http://www.imbf.ku.dk/MolBioPages/abk/PersonalPages/Jesper/Surfaces.html). Terrence Deacon's recent work on the autocell suggest a somewhat different approach but I take these approaches to be supplementary rather than antagonistic. Its therefore not entirely true that we have continued "to develop biosemiotics without concern for the origin of the coding system". But of course his kind of thing can never be anything but models and speculation.

S: I think that my' vague -> increasingly more definite' trope would not be so different from these steps, except maybe for where we begin. The possibility for semiotic freedom would increase as a system of interpretance becomes more definite IF we take the freedom to refer to explicit, crisp meanings. But semiosis is often quite (even intentionally among animals) vague. Some might even think that 'vaguer' would be 'freer' (Politicians certainly think so!)

Now, concerning pansemiosis, a main objection to the concept is the misunderstandings it inevitably raises. Actually, I had the feeling that this concept was always used by the opponents rather than by proponents. It smells too strongly of the German Naturphilosophie and especially of Friedrich Schelling's conception of the world as panpsychic. And regardless of what Schelling exactly did mean by this it seems to me inappropriate to confuse natural processes with human psychology. Pansemiosis should of course not be conflated wit panpsychism, but I am sure it always will be, so for no other reason than this I would suggest that another term should be chosen for this.

S: As it happens I do take my position from Schelling, and that position does involve a hylozooic concept (as would be evident from my position of 'vague -> definite'). I am not ashamed to say that I am involved with trying to revive Natural Philosophy from the old German variety. While that seems odd to natural scientists, and possibly to those hoping for scientific acceptance of semiotics, I think one has a right to develop one's thinking where it will go logically. Partly this is driven by my distaste for the philosophical mechanicism typical of scientific discourse. The state of the world today is partly, I am convinced, a result of our weddedness to mechanistic understandings. Surely there is room within semiotics for 'many flowers to bloom'!

But I also think that the idea that world is nothing but signs - and that is I suppose what pansemiosis would mean - is strangely reductionistic, and I cannot adopt it. I know that Peirce did indeed some times speak as if he believed thus, but this was hardly his deeper intentions. On all this, you should see the very interesting exchange between John Deely and Frederik Stjernfelt in Cybernetics & Human Knowing 13,1 and 3 (2006).

S: An information only perspective is being taken up by some physicists, but it is not MY pansemiotic view. I see semiosis as involved with the physical/material world, as an aspect of it. I do not suppose either signs OR mattergy.

I allow myself to end this with a quote from a chapter I recently wrote for The Routledge Companion of Semiotics (edited by Paul Cobley - and still in press), in which I try to explain my relation to John Deely's concept of physiosemiosis, which seems to me to be an much more acceptable idea than the idea of pansemiosis. And yet, here I explain why I prefer the more modest term proto-semiosis:

"In the evolutionary cosmology suggested here the early universe is seen as essentially indeterminate and as in a deep sense profused with proto-semiosic activity. By the term proto-semiosic activity I refer to what is nowadays called self-organizing processes, which in Peircean terminology would be "habit taking"[1]. In principle habit-taking may be seen as the most basic or general form of an interpretant, and in this sense the term physiosemiosis would indeed be a suitable way of characterizing this proto-semiosic activity. I hesitate however to use this term because it may so easily be misunderstood to imply that sign-use did indeed take place in this early universe, and I would argue strongly against such a conception. However this proto-semiosic activity would cause a gradual formation of ordered configurations of processes and thereby produce a growing deviation from equiprobability or, in other words, a growing predictability. Under the particular physical conditions that reigned at planet Earth (and possibly a great number of other locations in our universe) this growth paved the way for the appearance of a new kind of semiosic activity, biosemiosis. While protosemiosic activity refers to a profound general trend of the early universe biosemiosis may be seen as a radical potentiation of this trend brought about by the creation of concrete semiotic agents, first - as we shall see - historical agents, lineages, and later in evolution individual organisms. Stanley Salthe's specification hierarchy expresses a related conception (Salthe 1993; 2007). The appearance on our planet of biosemiosis, in short, opened a new agenda for the evolutionary process by providing entities with the agential property that is presupposed for Darwinian "striving" and thus for natural selection. At primitive levels the semiotic freedom of agents is still very low, and a bacterium for instance cannot itself chose to not swim upstream in a nutrient gradient. Therefore, at this stage of evolution semiotic freedom is primarily exhibited at the level of the lineage (the evolving species)[2]. Only later, with the evolution of brained animals would emerge a more advanced stage of biosemiosis, in which the semiosic activity is no longer a species property but also, and importantly so, an organismic property."

S: So this goes beyond biosemiotics. I find nothing to quarrel with here! 'Proto-semiosic activity' is fine with me. So, I think that we are not VERY far apart in other than emphasis.

STAN
= = =
(16) Stanley SALTHE – 5

From: Stanley Salthe
Sent: Wednesday, July 09, 2008 8:15 PM
Subject: Re: Biosemiotics

Replying to Edwina, whose position is not very far from mine, interleaving:

I happen to believe in pansemiosis. I consider it began with the 'bigbang'. I don't describe it according to Stan's premise of regression, which I find rather linear, because I consider that all matter, including the physico-chemical realm, operates according to a triadic function f(x)=y, where the rules of f transform input data x to output interpretant y. The physico-chemical realm's 'f' or rules are 'held' within the entire SET (all hydrogen atoms) rather than within the individual particle. I don't see an atom as 'spontaneous' but as existing according to general rules.

S: I think you have misunderstood me. I would take Jesper's primitive 'protosemiosic activity' to BE triadic all the way back. One could hardly refer to Peirce (and I do) otherwise.

The biological realm's switch to storing the rules within each particle or individual meant that those rules were put into a spatial area where informationally, they were in close contact to species living only in that domain. The rules were then affected by that more confined Information Set...and changed.
So, Stan's axiom is that there exists a more primitive set of rules/codes in the physico-chemical realm. My assumption is instead that this realm operates within a more general rather than primitive set of rules/codes, and those rules/codes are kept general by being exposed to all spatial zones of the planet. So, informationally, none of those rules/codes could develop a more unique style. They were always kept common.

S: Again, we are not far apart. The primitive situation would be 'vague' (I agree with Peirce here in using vague rather than 'general' when thinking forward). So, {vague -> {more definite}} rather than {general <- {particular}}. (Although in some QM perspectives I'm sure these would be entangled.) The biological's realm's internalization of the rules/codes confined them to local rather than general space; (S: in passing, this use of 'general' I agree with - meaning 'more generally present'. It differs from the above usage, I think.) that disabled the process of planetary generalization and moved the rules into non-common and local rules. So, we get diversity.
Plus, I don't view the biological realm as a 'machine'.

S: I agree with Marcello that the genetic system, like the bacterial flagellum, etc. is very mechanistic. In the development of the world, the direction in my pansemiotic view would be from vague to more definite (= more mechanistic). However, I agree that organisms and ecosystems, etc. are NOT primarily mechanistic at those higher levels.
Edwina says:

I reject the term 'proto-semiosis' as well. I consider that the universe is completely semiotic, and my reading of Peirce is that he insisted on that as well. (I'm not using him as my authority, just pointing out that my reading of him is different from that of Jesper's).

I agree with Jesper's usage because nothing at all could be other than vague 'in the beginning', and so triadism itself would have been vague, shifting, episodic and fleeting.

STAN

= = =
(17) Edwina TABORSKY – 6

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 8:49 PM
Subject: Re: Biosemiotics

There's another important area where we disagree, Stan - with regard to both of us declaring ourselves as 'pansemioticians'.
[We also disagree on the term 'sign', for I consider an atom, a molecule, etc, to be a 'sign']
Your view of semiosis in the physico-chemical realm is that it operates in a 'vague' manner and becomes less vague in the more complex biological realm. I suggest the opposite.
Semiosic actions in the physico-chemical realm are very specific and tightly bound; there is essentially no freedom to the triadic interaction in this realm. Input of energy..as mediated by the common or universal rules..leads to a common output. This triad is closed.
But in the biological realm, since those rules are now held within the individual unit, and exposed to the informational input of local stimuli, then, an input of energy/information....can be mediated by rules that are complex and specific to the local environment, and that will provide several options...and will permit a local and diverse output.
So, freedom increases with complexity. Not decreases. The human realm has the most freedom of interpretation.
Edwina

===
(18) Stanley SALTHE – 6

From: "Stanley Salthe"
Sent: Wednesday, July 09, 2008 9:04 PM
Subject: Re: Biosemiotics

Alexei --

Dear biosemioticians,
I am glad that the question of pansemiotics is open for discussion, and I totally agree with Marcello that the idea of pansemiotics is incompatible with biosemiotics. Biosemiotics assumes that life is something special (i.e., different from non-life) and this special feature is semiosis. Otherwise there is no much sense of combining "bio" - and - "semiotics".

S: How about {pansemiosis {biosemiosis {lingustic semiosis}}} ? (the brackets have meaning as in set theory). 'Pansemiosis' could be replaced here by, simply, 'semiosis'.

Of course this does not mean that pansemioticians like Edvina and Stan are not welcome at biosemiotics meetings. But I think it is very important to defend the difference between biosemiotics and pansemiotics. If any aspect of physical interaction is a semiotic interaction then either physical or semiotic description is redundant.

S: Yes. In the pansemiotic tradition, semiosis would replace mechanistic discourse wherever a richer framework than technology is concerned -- as in Natural Philosophy!.

I understand that Stan's pansemiotic view is more complicated than this. He assumes multiple inclusive levels of the same phenomenon. For example, clay crystallization has elements of "memory" according to Cairns-Smith. Thus if he agrees that the "level of semiosis" declines to infinitely small value across the transition from life to non-life, then I would not classify his views as pansemiotic.

S: ! Hmmn. I guess it would depend upon how strong the effect of semiosis would be. I think it would be increasingly variable and vaguer (rather than increasingly weaker) as we go back into the primitive physical world, where it could only sometimes (perhaps making crucial events!) be strong.

I prefer a different way of presenting the boundary between life and non-life by assuming that there are 2 languages for describing things: (1) physics and (2) semiotics. Non-living objects are described well by physics, whereas semiotic (=pansemiotic) description of non-living things is vague and generally non-productive (e.g., we cannot design a bicycle with just semiotics).

S: I'm glad you raised this. Our style of science has been honed as a support for technology. Some might think that was quite successful, I do not - we have produced a possibly non-viable system using it. But,
leaving technology aside, what have we been missing about the physico-chemical aspects of the world with our narrow mechanistic pursuits?

In contrast, living things are best described with semiotics, considering purposeful behavior, living functions, etc. Physical description of living organisms does not go beyond very simple interactions (e.g., biophysics of flight, or molecular thermodynamics).

S: I have challenged this. I believe, e.g., that the Second Law of thermodynamics often drives our behavior. We can see this with the following specification hierarchy;
{entropy production {work {social projects}}}
All three are, or are associated with, final causes, but these are increasingly stronger higher in the hierarchy. BUT, when the stronger finalities tend to cancel each other out, the weaker, but continuously active, lower level finalities have their chance to pull the system.
I think we are often pulled into warfare by the Second Law (serving, therefore the thermodynamic
equilibration of the non-equilibrium universe).

STAN

= = =
(19) Stanley SALTHE – 7

From: Stanley Salthe
Sent: Wednesday, July 09, 2008 9:20 PM
Subject: Re: Biosemiotics

Because of the universality of historical contingency, performances are always somewhat unique, regardless of what rules and laws are in play.
Edwina is surely right in pointing to the periodic table as a system of coding.

STAN

= = =
(20) Stanley SALTHE – 8

From: Stanley Salthe
Sent: Wednesday, July 09, 2008 9:41 PM
Subject: Re: Biosemiotics

Replying to Edwina --

There's another important area where we disagree, Stan - with regard to both of us declaring ourselves as 'pansemioticians'.
[We also disagree on the term 'sign', for I consider an atom, a molecule, etc, to be a 'sign']
Your view of semiosis in the physico-chemical realm is that it operates in a 'vague' manner and becomes less vague in the more complex biological realm. I suggest the opposite.
Semiosic actions in the physico-chemical realm are very specific and tightly bound; there is essentially no freedom to the triadic interaction in this realm. Input of energy..as mediated by the common or universal rules..leads to a common output. This triad is closed.

S: Well, I think we both have some blind spots. Yours, here, if I don't misunderstand you, is your restricting yourself to the microscopic realm? The physical universe is much more than local (as you yourself have said) and it seems that it becomes increasingly less rule governed and more susceptible to contingencies the larger the scale. On my part, I guess I tend to focus more on the middle scale where the microscopic rules don't seem to contribute much per se. At this scale, I see evolution going from, say, eddies to organisms, and this brings into play more restrictive rules at that scale.

But in the biological realm, since those rules are now held within the individual unit, and exposed to the informational input of local stimuli, then, an input of energy/information....can be mediated by rules that are complex and specific to the local environment, and that will provide several options...and will permit a local and diverse output.
So, freedom increases with complexity. Not decreases. The human realm has the most freedom of interpretation.

S: This issue is important in my worldview. I think, e.g., abiotic dissipative structures have more freedom to assume different configurations than an organism does. Organisms embody more informational constraints. If they have 'more freedom', it would be in some more restrictive realm than the one where we compare them with eddies ( -- turn left / turn right, big nose / little nose, English / Arabic, etc.). This is not an easy point to make, and I am still working on it. All informational constraints are both restricting and enabling, and this is where our disagreement comes from I think.

STAN

= = =

(21) Edwina TABORSKY – 7

From: Edwina Taborsky
Sent: Wednesday, July 09, 2008 10:47 PM
Subject: Re: Biosemiotics


Well, Stan this takes more thought. I certainly consider the physico-chemical realm, as a system that transforms matter/energy to..morphological units...to be constrained quite severely by rules. A water molecule has a limited capacity to interact and 'do things', while a biological unit has increasingly more opportunities to interact in different ways.

I am guessing that you are thinking of things like tornadoes and tsunamis etc when you refer to an 'abiotic dissipative structure'.
I don't think that these are any different, frankly! A tornado, as itself, has a limited capacity to do anything different. It cannot, as can a clam, develop a larger shell so that in future, all tornadoes will have 'larger shells'. It cannot, like a bird, develop a tougher beak so that in future, etc etc. All it can do, is function as a tornado, small or large. It can't evolve new knowledge and store it..as a tornado!

My point is that the physico-chemical realm ...forms 'morphological units'. That can be an atom, a molecule or a tornado. But the formal template, the code, so to speak, that makes that 'morphological unit' is pretty rigid. It doesn't have that openness to forming a new template that the biological realm has.

The biological realm has its own constraints; the first one, of course, comes from the basic physico-chemical matter it has to work with. Then, I think that other constraints come from the nature of its contextual situation - is the species operating where there is a lot or a little water, hot or cold, lots of other species or organisms...and so on. In other words, is the matter/energy content of the situation 'rich' or 'low'? And, there are its own normative rules developed over its historical devt that act as another constraint on it. The rules function as constraints - and the question is - how /if the species can change those rules and enable that species to interact constructively with its local envt.. The biological realm has a great capacity to change its rules and evolve.

I think that the human species has the most freedom, because they have moved into defining information within symbols. So, instead of physically developing wings, we build a physical unit that we attach to ourselves: airplanes. Neat. Not quite the Harry Potter tactic.. but...

Edwina

= = =
(22) Stanley SALTHE – 9

From: Stanley Salthe
Sent: Thursday, July 10, 2008 4:41 PM
Subject: Re: Biosemiotics

Edwina -

Well, Stan this takes more thought. I certainly consider the physico-chemical realm, as a system that transforms matter/energy to..morphological units...to be constrained quite severely by rules. A water molecule has a limited capacity to interact and 'do things', while a biological unit has increasingly more opportunities to interact in different ways.
I am guessing that you are thinking of things like tornadoes and tsunamis etc when you refer to an 'abiotic dissipative structure'.
I don't think that these are any different, frankly! A tornado, as itself, has a limited capacity to do anything different. It cannot, as can a clam, develop a larger shell so that in future, all tornadoes will have 'larger shells'. It cannot, like a bird, develop a tougher beak so that in future, etc etc. All it can do, is function as a tornado, small or large. It can't evolve new knowledge and store it..as a tornado!

S: When I compare abiotic dissipative structures with biotic ones, I focus on the fact of fewer informational constraints being operative compared to the possible configurations they might take.We have trouble visualizing these latter because they are vaguer than the possible configurations for biotic dissipative structures. It could be argued that vortices and the like are so vague. This question of vagueness is looming. Organisms are ague as well, but the vagueness here (say the position of long air from moment to moment) seems unimportant in comparison with what WE consider important. When you say that the tornado 'cannot do anything different', I think you are not considering its momentary embodiment compared to that of an organism. But even with the latter, are we prepared to catalog every conceivable conformation a body might assume? We get around this by imposing categories -- standing, siting, lying down etc. But in doing this we are dismissing a lot of interest to informational entropy.

My point is that the physico-chemical realm ...forms 'morphological units'. That can be an atom, a molecule or a tornado. But the formal template, the code, so to speak, that makes that 'morphological unit' is pretty rigid. It doesn't have that openness to forming a new template that the biological realm has.

S: I don't agree with 'pretty rigid' because the boundary conditions bearing upon abiotic systems re JUST AS MANY as upon living ones (e.g., temperature, exact locale, heat flux, etc., etc.)

The biological realm has its own constraints; the first one, of course, comes from the basic physico-chemical matter it has to work with. Then, I think that other constraints come from the nature of its contextual situation - is the species operating where there is a lot or a little water, hot or cold, lots of other species or organisms...and so on.
I think that the human species has the most freedom, because they have moved into defining information within symbols. So, instead of physically developing wings, we build a physical unit that we attach to ourselves: airplanes. Neat. Not quite the Harry Potter tactic.. but...

S: I can only repeat that a system with more constraints bearing must be more bounded by rules. Such rules enable kinds of behaviors not available to the less constrained. This is essentially a matter of being able to make finer distinctions -- a hand with fingers can play the piano, etc. -- but in the BIG picture (my theoretical interest) this seems a triviality. It is kind of like inventing new dimensions, and it IS exactly inventing new degrees of freedom. These new degrees do not erase the older ones, still in place, still supporting and enabling the newer one
STAN

= = =
(23) Charbel EL HANI

From: Charbel El-Hani
Sent: Thursday, July 10, 2008 3:05 PM
Subject: Re: Biosemiotics

Dear Marcello and other friends,
What we should talk about, about our models about the world, or about what the world is...? I do not think scientific knowledge is about discovering what is and what is not. But it is about building models, and exploring them to see what they can give us in terms of explanatory, predictive, and heuristic powers. It seems that we have a basic epistemological disagreement here....
Cheers
Charbel El-Hani

= = =
(24) Stanley SALTHE – 10

From: "Stanley Salthe"
Thursday, July 10, 2008 9:46 PM
Subject: Re: Biosemiotics

Charbel –

Dear Marcello and other friends,
What we should talk about, about our models about the world, or about what the world is...? I do not think scientific knowledge is about discovering what is and what is not. But it is about building models, and exploring them to see what they can give us in terms of explanatory, predictive, and heuristic powers. It seems that we have a basic epistemological disagreement here....

S: This is a good point, and relates to my discussion with Edwina concerning the number of informational constraints acting upon systems. If we consider, for example, a hurricane, we have various measurements that are taken relative to our knowledge of thermodynamics, fluid dynamics, hydrology, meteorology and the like, and from this we can construct a model. The shape of the equations and the number and placement of the constants reflects the theory. But there might be another theory, with fewer constraints, or more, and each might have a different 'purpose'. Likely we would NOT include knowledge of chemistry, quantum mechanics or materials science, as these would be held to be too far in scale from the phenomenon of interest. A similar general kind of understanding could be undertaken with an organism, using knowledge of its anatomy and size (I doubt if there are any similar equations in this realm).
Here again, microscopic information (proteins, genes) would NOT be relevant to the project at hand. But this kind of thing is not found in biology, and probably not even in professional dance discourse. So, in these cases we are really comparing, as they say, apples with oranges. The hurricane is relatively vague, the organism is more definite. We might more likely be able to discern particular configurations in organisms than in hurricanes. But could they be countable? I doubt it. We would simplify the field according to our interests, classifying different stances (as in ballet). With the hurricane we take just a very few measurements, reflecting what we think are our interests (but maybe our 'success' in predicting them relates to the simplified knowledge we have constructed concerning them). I think this comparison might serve to focus the discussion of the relation between 'pan' and 'bio' (or, indeed, ANY) semiotics.
STAN

= = =
(25) Walter RIOFRIO

From: "Walter Riofrio"
Sent: Thursday, July 10, 2008 1:45 AM
Subject: Re: Biosemiotics

Dear Marcello,

Because in your paper you said:

"...a semiotic system is a whole set of signs and meanings that are linked together by all the various
conventions that make up a code...(they) do not come into existence of their own. There is always an 'agent'
that produces them, and that agent can be referred to as a codemaker..."

I have these questions:

- First, how we can understand the nature of signs in natural and biological terms? Do you could accept a
mater-energy variation (MEV) as the "carrier of signs" and only inside the semiotic system this MEV would
become in a sign due to some pre-requisites or conditions imposed by this system, by its natural way to exist?

- On the other hand, the naturalistic core of a meaning in biosemiotics (and I would like to call it
"bio-meaning") has its origins, also, because certain conditions are in biological (and prebiotic) systems?
What would the minimal be?

- It means, both signs and meanings are relational terms emerging inside biological systems and ruled by
natural laws (physicochemistry, chemistry, physics) because they arises in naturalistic terms (without any
"addition" of our metaphysics, epistemology or any other human believe...)?

- Finally, could you say something about what is your proposal on a low level emergence of first 'biological or
prebiotic codes', in its most minimal expression? Always in natural terms?

Thank you very much.
Sincerely,
Walter

Walter Riofrio
Theoretical and Evolutionary Biology Researcher
Associate Professor; Peruvian University Cayetano Heredia.
Chercheur Associé; Complex Systems Institute (ISC-PIF).

= = =
(26) Natalia ABIEVA

From: Natalia Abieva
Sent: Thursday, July 10, 2008 12:56 PM
Subject: Re: Biosemiotics

Dear Marcello,

I find your paper not only very informative (as Stan has formulated it) but very important for the present state of semiotics, and biosemiotics in particular. Your attempt to sum up the situation in the biosemiotic research is quite timely. Numerouos papers in the field reveal great interest in the subject, but unfortunately we witness an undiscriminate use of scientific terms and main concepts of it.
I quite agree that the time has come to unite all efforts and to give rise to a new discipline of biosemiotics ( I'm all for this name that discloses the true sense of the research - the information processes in the organic world as opposed to all sort of inorganic matter, which processes are regulated by physics, as Alexei Sharov has rightly stated it). I cannot take the term 'pansemiotics' seriously for its ambiguity - embracing everything and nothing in particular. Actually it reminded me of Romantic philosophers and the concept of Oversoul (they loved so much) that permeated everything and everyone on Earth according to them. Biosemiotics must possess the status of a natural science, but in that case its theoretical issues must be formulted: the subject, object of research, main principles and techniques - all are to be carefully sorted out and agreed upon. The last but not the least, - the terminology: a lot of confusion and misunderstanding arise from the lack of the unified system of terms. I would say we all need a dictionary, but maybe I'm unaware of it already being under preparation.

I'm afraid I cannot review your paper in full here but I want to point to some things I find really important not only for biosemiotics but cognitive science in general. Firstly, you've stressed upon the fact that both genes and proteins are manufactured molecules, and you described the two mechanisms that are employed - a) copying and the origin of copymakers; b) coding and the origin of codemakers. I find your reasoning quite convincing here and, as I see it, you have succeded in tracing the dual coding of information (earlier raised by A. Paivio and J. Hoffmeyer in the microrealm). The asymmetry of the human brain that functions in two modes - analogue-imagistic and vebal-propositioning - receives in that case certain grounding in the evolutionary perspective, and the translatability as the basic principle as well.
Secondly, I find your conclusion that 'life is artifact-making' very promising also - it may help to bridge human cultures and other biological species habitats (see also LLaland et al.2000).
But there is something I miss in your paper. I believe you have not quite succeeded in describing the elements of consciousness on that level. Though you have attributed reasonable 'behaviour' to codemakers, you have not explained how the meaning is extracted.
Nevertheless I really enjoyed reading your paper.
Best regards

Natalia Abieva

= = =