[Fis] How Molecules Became Signs

Fri Feb 25 15:42:08 CET 2022

Caro Carlo,
grazie per i "complimenti". Ma, pur nel dubbio di non avere capito bene la
Tua mail, desidero ri-fare
alcune considerazioni:
* Bisogna discernere ciò che è informazione vera e propria (prendere o dare
forma) o  significato o notizia.
* Sono informazioni non solo le merci artificiali o risorse naturali, ma
anche le persone (esseri viventi), le idee
e qualunque altra cosa.
*Anche lavorando nel campo di forma dei numeri, non possiamo superare la
distinzione-contrapposizione
tra "espressioni-proposizioni sintattiche" ed "espressioni-proposizioni
semantiche", a causa dell'indeterminazione
 o indecidibilità che riguarda la nostra esistenza e la nostra conoscenza.
Grazie anche per avermi fatto ricordare quel che ho scritto in tanti  saggi
a proposito del pensiero di Marx: La
merce ha la "forma naturale" (o artificiale) di un valore d'uso inerente al
suo essere corpo; la "forma di valore "
della merce è invece la sua "forma sociale".
 Questa è la bellezza della "forma de valore" o del "valore della forma".
Ora la pianto!
Con simpatia, Francesco Rizzo
.Dear Carlo,
thank you for the "compliments". But, also in the doubt not to have
understood well Your email, I wish to re-do
some considerations:
* One must discern what is actual information (taking or shaping) or
meaning or news.
* Information is not only man-made goods or natural resources, but also
people (living beings), ideas and anything else
and anything else.
*Even working in the field of number form, we cannot overcome the
distinction-contraposition
between "syntactic expressions-propositions" and "semantic
expressions-propositions," because of the indeterminacy
 or undecidability that affects our existence and our knowledge.
Thank you also for making me remember what I have written in many essays
about Marx's thought: The
commodity has the "natural form" (or artificial form) of a use value
inherent in its being a body; the "value form "
of the commodity is instead its "social form."
 This is the beauty of the "forma de valore" or "value form."
Now I'm going to cry it!
With sympathy, Francesco Rizzo
.

Translated with www.DeepL.com/Translator (free version)

Il giorno ven 25 feb 2022 alle ore 14:41 Pedro C. Marijuán <
pedroc.marijuan en gmail.com> ha scritto:

> 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 en leydesdorff.net ; http://www.leydesdorff.net/
>
> http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en
>
> ORCID: http://orcid.org/0000-0002-7835-3098;
>
> ------ Original Message ------
> From: "Terrence W. DEACON" <deacon en berkeley.edu>
> To: "fis" <fis en 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 en 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 en 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  (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_4180848367552026858_m_-401387228878175498_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
>
>
> _______________________________________________
> Fis mailing listFis en listas.unizar.eshttp://listas.unizar.es/cgi-bin/mailman/listinfo/fis
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> siguiente enlace:
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