[Fis] How Molecules Became Signs

Sun Mar 6 16:44:11 CET 2022

More Terminology 20220306

Thanks to Francesco for inviting clarification on some terms.

Francesco:

** One must discern what is actual information (taking or shaping) or
meaning or news.*

Presently, for *‘information’* we have only *one {definition, explanation,
interpretation, understanding, word,* *algorithm, etc.}* the meaning of
which can be interpersonally communicated. The most neutral and
interpersonally acceptable *definition* is that what one reads out of
regarding the Figure depicting the Sequence *A242615**, *or the Sequence
itself. There exists a discongruence inbuilt into properties of cohesive
assemblies.

The situation is comparable to that what Lucy and her contemporaries were
confronted with as they discovered that *fire* gives warmth and does other
things. Before they could split off the finer properties of this newly
discovered, partly natural, partly in the power of humans, something they
were recognising as a separate entity, they used one and the same word for
all shades and colors of that experience.

We have discovered a powerful natural phenomenon, like Lucy *et al *have
discovered the concept of *warmth*. Warmth is something that is there or is
not there, is a property of the things, and then again can be man-made, can
be imagined and can be experienced, and we can speak about it as an
abstract concept, related to other abstract concepts, and we can observe it
to have a meaning, an aboutness, for the simplest organisms and for our
babies.

Today, we have the same situation vis-à-vis *information. *Information is
something that is there or is not there, is a property of the things, and
then again can be man-made, can be imagined and can be experienced, and we
can speak about it as an abstract concept, related to other abstract
concepts, and we can observe it to have a meaning, an aboutness, for the
simplest organisms and for our babies.

To restate in a simple fashion:

*Lucy and her contemporaries*

*We and our contemporaries*

*observed*

*observed*

lightning

fire

message

meaning

*generalised into*

*generalised into*

warmth

information

*We now think this is*

*We now think this is*

*the frequency of*

*the extent and direction of*

*displacements of things from their idealised common places*

Of this Of this explanation, only the term “idealised common places” needs
a clarification, as the other words of this composite sentence are
deictically defined.

*In Need of Terminology*

That we have not yet invented several words for realisations of the same
idea, like we managed to do it with realisations of the idea of warmth, is
a consequence of the fact that we have not noticed that the many different
forms have one common denominator. Be it Zeroes or Ones, *varietas
*that *delectat,
*magnetic repellence – attraction, chemical structures and energy balances,
the common basis is that these all are *based on alternatives*.

The basic idea of the *fundamental *existence of alternatives has to be,
well, *fundamental*. Its explanation must be such, *that a child can
understand it*, because children are able to understand fundamental truths,
upon which schools later elaborate.

You know that you have two eyes. Our brain makes one picture of what the
two eyes see. The two pictures coming from the eyes are merged by our
cleverness that is born with us. When the pictures are well merged, we have
a background in which we can draw lines, triangles and more. Being clever,
we have built a world of ideas based on the picture that is made by our
cleverness, not on the two pictures that were made by our two eyes. If you
squint a bit, you see that these are indeed two pictures.

Now what the scientists call *information *is that what becomes merged,
what makes the two pictures merged. Does it go away, after having served
its purpose of contributing to the unified picture? Well, in the human
brain, it is recycled by being broken up in smaller and smaller parts,
which then can be reused. In your dreams you meet some parts that had been
partially used, not wholly assembled into unified pictures, but these
combinations of remainders and rests are of dubious value. If there is no
recycling, it just flows away (and that process is called entropy).

In an accounting sense, it does not go away. It will neither go away in a
closed group who have many relations among each other, like a cohesive
collection or your family and friends. If you are bored and want to play
with someone, you go and find someone who has time to play with you.
Information lies both in that that you could have been hungry or sleepy and
not bored, and in that what happens to you if you go and find someone *{to
play with, to feed you, to put you to bed}. *Information lies in the fact
that it could have been, can be, could be *otherwise. *

We shall go on tomorrow talking about, and playing with dolls, an army of
dolls, and how we can exercise them, order them around and around. Maybe we
shall also use a video recorder and watch what is common among the
manoeuvres the dolls make.

Then we shall take sticks and stick them together. Then we shall fix small
sweeties on points in space onto which a doll regularly returns. After some
harrumphing, we shall say that the doll has a place it calls home, and that
we shall call that place to be his primary idealised common place. If that
place is in the Bazar, we shall see how much the dolls act as if alive,
eagerly exchanging this for that, because in their primary idealised common
place, aka home, some things are worth more, and they believe they are
still at home. But that shall be tomorrow, now go and sleep well.

*Is this a Business Idea? Any crowdfunding?*

In actual fact, this type of explanation is necessary. Please, Francesco,
give me your opinion as an economist, whether a well-written, nicely
illustrated teaching book would be a success, economically. There are very
many people who want to learn to count in twelve easy steps, once they
understand that they need to learn to count more exactly, *(by ~ 1/1092 %)*
because they need the knowledge and techniques of counting more exactly in
their jobs.

It is always a pleasure to talk to economists. In our trade, the concept of
value has the name ‘1 *util*’ and is completely dependent on circumstances.
Funny, what?

All the best

Karl

Am Fr., 4. März 2022 um 14:56 Uhr schrieb Marcus Abundis <55mrcs en gmail.com>:

> 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 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
>>
>> 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_9222692364173923574_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
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> la Universidad de Zaragoza.
> Puede encontrar toda la información sobre como tratamos sus datos en el
> siguiente enlace:
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