[Fis] How Molecules Became Signs
Pedro C. Marijuán
pedroc.marijuan at gmail.com
Fri Feb 25 14:40:58 CET 2022
Dear Terry, Loet and All,
First, I join in the thanks to Terry for volunteering to initiate this
new discussion modality. I appreciate the 5 points in which he
summarizes his position paper.
Well, I have some disagreement with taking as a model the info
properties of human (& animal) communication, based on well developed
nervous systems, and projecting them backwards as the scheme to fit the
biological info discussion. I advocate the cellular stance, where the
signaling systems provide the capability to abduce a complex information
flow and respond appropriately to the different signals involved via
gene expression and other cytoplasmatic changes. The ad hoc changes in
the trajectory of the life cycle is the "meaning" of the concerned
signal. Once eukaryotic signaling systems are in place, everything
informational becomes possible (here we are). From this background I
comment those 5 points below (and Loet's).
Point 1. Complete agreement. Maybe I would enter the phenomenal
properties of ribosomes to transcend the world of self-replicators, as
Youri has discussed.
Point 2. Partial agreement. Though perhaps it is too general to be of
specific interest in biological information.
Point 3. It was responded in my initial paragraph. Is semiosis a
convenient approach to biological information? I think it demands more
(conceptual load) than what it gives (conceptual harvest).
Point 4. Complete agreement. I much advocate the quest for new
evolutionary explanations. So many "anomalies" and unexplained facts
have been accumulated, that the Neo Darwinian synthesis has become
outdated, and wrong in important aspects. I have discussed this in my
recent publication (doi.org/10.3390/ijms222111965). What Lou Kauffman
discussed here in the list about recursion has lead me to propose
substituting "systemic variation and adaptive recursion" by "random
variation and natural selection". Curiously, Efim Liberman had already
gone around the recursion point (the next discussion on Natural
Computation in preparation with Andrei Igamberdiev and his colleagues
will probably include this too). My views about that are in:
DOI:10.1016/j.biosystems.2022.104631.
Point 5. Complete agreement. Gunther Witzany and Luis Villarreal have
put it very eloquently: /ex virus omnia/. Without viruses our
evolutionary views are awfully incomplete. Even more, the evolution of
multicellulars and all their new biomolecular codes would be impossible
(viruses are the great code makers).
About Loet's views, partial OK (very rare!!). The caveat is that info
theory was applied to DNA sequences with great success (Lina Gatlin
pioneering work), and quite many others have followed. There was also a
very, very interesting work on a generalized application of info metrics
to whatever chemical molecules. I vaguely remember whether the link was
sent by John Holgate in late 90s (??), and the great work was done by
Michael Carlton (??), posthumously compiled. I think our list colleague
Michel Petitjean has worked on this (from a different angle).
Terry, I also appreciate your tribute to Jesper Hoffmeyer. Unfortunately
John Collier passed away last Summer (I knew not far ago) and he was a
great support of information studies and FIS in particular (already in
1995). We owe him a decent obituary.
Best--Pedro
El 25/02/2022 a las 11:52, Loet Leydesdorff escribió:
> Dear Terry, Pedro, and colleagues,
>
> Let me for the sake of the discussion posit the following. Molecules
> are structures, and structure is selective and deterministic. Assuming
> that we agree that information is a diversity measure, molecules
> cannot be both variation and selection (unless we aim at confusion).
>
> In other words, not the molecules, but the configuration of molecules
> or their probability distribution contains the information and not the
> molecules themselves. I don't see a reason to collapse the two levels.
> Information can be expressed in bits; molecules not. In other words,
> information can be measured as entropy; Shannon's H is dimensionless;
> it is a measure. One can apply this measure to a distribution. The
> latter may be a distribution of molecules. The substantive perspective
> -- different from the formal one of information theory -- can be a
> biology.
>
> Best, Loet
>
>
> *_______________*
>
> *Loet Leydesdorff*
>
> *
> *
>
> *"The Evolutionary Dynamics of Discusive Knowledge"
> <https://link.springer.com/book/10.1007/978-3-030-59951-5>(Open Access)*
>
> Professor emeritus, University of Amsterdam
>
> Amsterdam School of Communication Research (ASCoR)
>
> loet at leydesdorff.net <mailto:loet at leydesdorff.net>;
> http://www.leydesdorff.net/ <http://www.leydesdorff.net/>
>
> http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en
> <http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en>
>
> ORCID: http://orcid.org/0000-0002-7835-3098
> <http://orcid.org/0000-0002-7835-3098>;
>
>
> ------ Original Message ------
> From: "Terrence W. DEACON" <deacon at berkeley.edu
> <mailto:deacon at berkeley.edu>>
> To: "fis" <fis at listas.unizar.es <mailto:fis at listas.unizar.es>>
> Sent: 2/21/2022 6:01:51 PM
> Subject: Re: [Fis] How Molecules Became Signs
>
>> Dear FIS colleagues,
>>
>> I am grateful to Pedro Marijuán for this opportunity to share this
>> recently published Open Access paper with all of you. I look forward
>> to this new FIS format for discussing recent publications, in
>> addition to the annual solicited discussion paper, and am honored to
>> be included. I hope this article is of interest. Here is a brief
>> introduction.
>>
>> As many scholars since the 1930s have pointed out, the concept of
>> information is regularly used in at least three distinct and nested
>> senses: a physical-statistical sense, a relational-referential sense,
>> and a pragmatic-functional sense. In the paper “How molecules become
>> signs” I show how the latter two senses can be understood in terms of
>> molecular evolution, without invoking any atypical physical-chemical
>> properties or an extrinsic observer perspective. In other words, I
>> attempt to identify the minimal systemic properties that are
>> necessary and sufficient for a physical system to be able to use a
>> molecule (such as RNA) to be “about” the relationships between other
>> molecules that are relevant to the continued existence of this same
>> capacity. This is intended to provide what amounts to a proof of
>> principle using a simple-as-possible model system, in which all
>> processes are explicitly known and fully understood, and empirically
>> testable.
>>
>> It has a number of implications that may be of interest to the FIS
>> community.
>>
>> 1. It implies that molecular template replication (such as invoked in
>> RNA-world and related replicator-first theories) cannot be understood
>> as providing intrinsically referential or functional information,
>> except as interpreted by an extrinsic observer (causing its semiotic
>> properties to appear epiphenomenal).
>> 2. It shows how the constraints on the release of energy that
>> constitutes the work required to reconstitute these same constraints
>> in new substrates is the basis of what can be described as the
>> “interpretive” capacity of a physical system.
>> 3. It demonstrates how materially “displaced” informational
>> relationships (such as in the case of DNA) depend on and grow out of
>> prior linked mutual information (iconic) and correlational
>> information (indexical) relationships, and how this can be
>> hierarchically recursive, providing a scaffolding logic for the
>> evolution of increasing informational depth.
>> 4. It suggests that Crick’s so-called “central dogma” of biological
>> information flow in organisms is the reverse of information accretion
>> in evolution - i.e. where referential-functional information flows
>> from dynamical constraints onto material constraints (e.g. molecular
>> structure), from whole to part, and thus is offloaded from dynamics
>> to structure in evolution. This may suggest new research paradigms
>> for studying the evolution of genetic information.
>> 5. It implicitly describes a mode of autonomous virus-like proto-life
>> forms that may exist in conditions that are otherwise hostile to
>> life, such as in deep petroleum deposits or other planets.
>>
>> I look forward to insights and criticisms from the FIS community. The
>> target article is also being published with commentaries, along with
>> my responses, and the journal may continue to accept commentaries
>> from the FIS community to be included in future issues.
>>
>> Thanks, Terry
>>
>> In honor of the 80th birthday of our brilliant departed colleague:
>> Jesper Hoffmeyer
>>
>> On Sun, Feb 20, 2022 at 2:38 PM Terrence W. DEACON
>> <deacon at berkeley.edu <mailto:deacon at berkeley.edu>> wrote:
>>
>> Dear FIS colleagues,
>>
>> I am grateful to Pedro Marijuán for this opportunity to share
>> this recently published Open Access paper with all of you. I look
>> forward to this new FIS format for discussing recent
>> publications, in addition to the annual solicited discussion
>> paper, and am honored to be included. I hope this article is of
>> interest. Here is a brief introduction.
>>
>> As many scholars since the 1930s have pointed out, the concept of
>> information is regularly used in at least three distinct and
>> nested senses: a physical-statistical sense, a
>> relational-referential sense, and a pragmatic-functional sense.
>> In the paper “How molecules become signs” I show how the latter
>> two senses can be understood in terms of molecular evolution,
>> without invoking any atypical physical-chemical properties or an
>> extrinsic observer perspective. In other words, I attempt to
>> identify the minimal systemic properties that are necessary and
>> sufficient for a physical system to be able to use a molecule
>> (such as RNA) to be “about” the relationships between other
>> molecules that are relevant to the continued existence of this
>> same capacity. This is intended to provide what amounts to a
>> proof of principle using a simple-as-possible model system, in
>> which all processes are explicitly known and fully understood,
>> and empirically testable.
>>
>> It has a number of implications that may be of interest to the
>> FIS community.
>>
>> 1. It implies that molecular template replication (such as
>> invoked in RNA-world and related replicator-first theories)
>> cannot be understood as providing intrinsically referential or
>> functional information, except as interpreted by an extrinsic
>> observer (causing its semiotic properties to appear epiphenomenal).
>> 2. It shows how the constraints on the release of energy that
>> constitutes the work required to reconstitute these same
>> constraints in new substrates is the basis of what can be
>> described as the “interpretive” capacity of a physical system.
>> 3. It demonstrates how materially “displaced” informational
>> relationships (such as in the case of DNA) depend on and grow out
>> of prior linked mutual information (iconic) and correlational
>> information (indexical) relationships, and how this can be
>> hierarchically recursive, providing a scaffolding logic for the
>> evolution of increasing informational depth.
>> 4. It suggests that Crick’s so-called “central dogma” of
>> biological information flow in organisms is the reverse of
>> information accretion in evolution - i.e. where
>> referential-functional information flows from dynamical
>> constraints onto material constraints (e.g. molecular structure),
>> from whole to part, and thus is offloaded from dynamics to
>> structure in evolution. This may suggest new research paradigms
>> for studying the evolution of genetic information.
>> 5. It implicitly describes a mode of autonomous virus-like
>> proto-life forms that may exist in conditions that are otherwise
>> hostile to life, such as in deep petroleum deposits or other planets.
>>
>> I look forward to insights and criticisms from the FIS community.
>> The target article is also being published with commentaries,
>> along with my responses, and the journal may continue to accept
>> commentaries from the FIS community to be included in future issues.
>>
>> Thanks, Terry
>>
>> On Sat, Feb 19, 2022 at 1:12 PM Pedro C. Marijuán
>> <pedroc.marijuan at gmail.com <mailto:pedroc.marijuan at gmail.com>> wrote:
>>
>> Dear FISers,
>>
>> We are going to start the new discussion modality based on
>> specific publications. The initial contribution to comment is:
>>
>> *"How Molecules Became Signs**."* By *Terrence W. Deacon*,
>> recently appeared in Biosemiotics.
>>
>> At his earlier convenience, Terry will send a leading text to
>> start the discussion.
>> Now, given that there is a doi
>> https://doi.org/10.1007/s12304-021-09453-9
>> <https://doi.org/10.1007/s12304-021-09453-9> (for freely
>> downloading the paper),
>> interested parties may read in advance the publication.
>>
>> Best greetings to all,
>> --Pedro
>>
>> PS. Given that there are another three contributions
>> tentatively arranged, a time span of around 2-3 weeks could
>> be adequate. But we will see on the spot.
>>
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>> Libre de virus. www.avast.com
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>>
>>
>> <#m_-4879470826922797663_m_7595816000984545838_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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>>
>> --
>> Professor Terrence W. Deacon
>> University of California, Berkeley
>>
>>
>>
>> --
>> Professor Terrence W. Deacon
>> University of California, Berkeley
>
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