[Fis] How Molecules Became Signs

Fri Mar 4 14:56:04 CET 2022

Dear Terry:

You begin your abstract with:
>“What sort of process is necessary and sufficient to treat a molecule as a
sign?” This requires focusing on the interpreting system and its
interpretive competence.<

And later:

> . . . molecules like DNA and RNA . . .. THESE MOLECULES [my emphasis] are
not the source of biological information but are instead semiotic artifacts
<
> onto which dynamical functional constraints have been progressively
offloaded during the course of evolution. <

– My question: You are arguing SOME molecules are used as signs, no? I do
not see where you clearly distinguish between molecules as directly
functioning objects, versus molecules as signs, which leaves me wondering
if you intend ALL molecules. If you are arguing for certain 'messenger
molecules', that seems uncontroversial.
– The part '. . . onto which dynamical functional . . . ' I cannot
understand. Are there more basic terms, appropriate to an Abstract, you
might offer to clarify this?

On page 4: From previous exchanges, I still take exception to using 'closed
system' thermodynamic models (without matter exchanged) to explain 'open
system' (Life, with matter exchanged) vistas. This is especially true for
your autogen, which relies on matter exchange. Further, all four
fundamental forces break the second law's presumed entropic
symmetry/equilibrium. One wonders why science notes 'open, closed, and
isolated systems' if we are to just ignore their differences. A similar
issue plagues information studies, where people often mix/confuse/skip-over
different levels of abstraction without making clear distinctions.

On the remainder of the paper I again see your autogen model, which I have
seen before and where I have no problems.
Still, I want to amplify Christophe's note on meaning – I think this might
be a useful direction for expanding one's work. I am not sure what that
looks like but I feel certain there is ground to explore there. When I
first read your paper's title I was hoping you might begin to reductively
explore specific molecular traits (real world) and how they affect such a
system. I am unqualified to do this myself, but I look at this as the next
place where 'heavy lifting' might happen to expand our thinking on
'theories of meaning'.

As before – thanks for your work!

[image: --]
Marcus Abundis
[image: http://]about.me/marcus.abundis
<http://about.me/marcus.abundis?promo=email_sig>

On Mon, Feb 21, 2022 at 6:02 PM Terrence W. DEACON <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
>
> 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>
> 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> 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
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>>> <#m_1049423486372955379_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 list
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>
> Ud. recibe este correo por pertenecer a una lista de correo gestionada por
> la Universidad de Zaragoza.
> Puede encontrar toda la información sobre como tratamos sus datos en el
> siguiente enlace:
> https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas
> Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de
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