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<div class="moz-cite-prefix">Dear Terry, Loet and All,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">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.</div>
<div class="moz-cite-prefix">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).
<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Point 1. Complete agreement. Maybe I
would enter the phenomenal properties of ribosomes to transcend
the world of self-replicators, as Youri has discussed.<br>
</div>
<div class="moz-cite-prefix">Point 2. Partial agreement. Though
perhaps it is too general to be of specific interest in biological
information. <br>
</div>
<div class="moz-cite-prefix">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).</div>
<div class="moz-cite-prefix">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Neo Darwinian synthesis has become outdated, and wrong in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:<span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated">10.1016/j.biosystems.2022.104631.
<br>
</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated">Point 5. Complete
agreement. Gunther Witzany and Luis Villarreal have put it very
eloquently: <i>ex virus omnia</i>. 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).</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated"><br>
</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated">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).</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated"><br>
</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated">Terry, I also appreciate
your tribute to </span><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated">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.</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated"><br>
</span></div>
<div class="moz-cite-prefix"><span class="nova-legacy-e-link
nova-legacy-e-link--color-inherit
nova-legacy-e-link--theme-decorated">Best--Pedro<br>
</span></div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"> El 25/02/2022 a las 11:52, Loet
Leydesdorff escribió:<br>
</div>
<blockquote type="cite"
cite="mid:em3c90cb8f-eb59-4ea5-bc57-1ecf8a8b52b5@pc2014">
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<div>Dear Terry, Pedro, and colleagues, </div>
<div><br>
</div>
<div>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). </div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Best, Loet</div>
<div><br>
</div>
<div><br>
</div>
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<div id="xde210cee50534dd">
<div id="x37dfff32a36b4410ad8e891fea6bb1b8">
<p class="MsoNormal" style="line-height:normal;"
xmlns="http://www.w3.org/TR/REC-html40"><b><font
style="font-size: 9pt;" size="1" face="Times New
Roman">_______________</font></b></p>
<p class="MsoNormal" style="line-height:normal;"
xmlns="http://www.w3.org/TR/REC-html40"><b><font
style="font-size: 12pt;" size="3" face="Times New
Roman">Loet Leydesdorff</font></b></p>
<p class="MsoNormal" style="line-height:normal;"
xmlns="http://www.w3.org/TR/REC-html40"><b><font
style="font-size: 9pt;" size="1" face="Times New
Roman"><br>
</font></b></p>
<div id="x37dfff32a36b4410ad8e891fea6bb1b8">
<p class="MsoNormal"
xmlns="http://www.w3.org/TR/REC-html40"
style="line-height:normal;"><b style=""><font
style="font-size: 9pt;" size="1" face="Times New
Roman"><a
href="https://link.springer.com/book/10.1007/978-3-030-59951-5"
style="" moz-do-not-send="true">"The Evolutionary
Dynamics of Discusive Knowledge"</a>(Open Access)</font></b></p>
</div>
<p class="MsoNormal" style="line-height: normal;"
xmlns="http://www.w3.org/TR/REC-html40"><font
style="font-size: 8pt;" size="1" face="Times New Roman">Professor
emeritus, University of Amsterdam </font></p>
<p class="MsoNormal" style="line-height:normal;"
xmlns="http://www.w3.org/TR/REC-html40"><font
style="font-size: 8pt;" size="1" face="Times New Roman">
Amsterdam School of Communication Research (ASCoR)<o:p
xmlns:o="urn:schemas-microsoft-com:office:office"></o:p></font></p>
<p class="MsoNormal" style="line-height:normal;"
xmlns="http://www.w3.org/TR/REC-html40"><font
style="font-size: 8pt;" size="1" face="Times New Roman"><a
href="mailto:loet@leydesdorff.net"
title="mailto:loet@leydesdorff.net" style=""
moz-do-not-send="true">loet@leydesdorff.net </a>; <a
href="http://www.leydesdorff.net/"
title="http://www.leydesdorff.net/" style=""
moz-do-not-send="true">http://www.leydesdorff.net/</a>
<o:p xmlns:o="urn:schemas-microsoft-com:office:office"></o:p></font></p>
<p class="MsoNormal" style="line-height:normal;"
xmlns="http://www.w3.org/TR/REC-html40"><a
href="http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en"
style="background-color: rgba(0, 0, 0, 0);"
moz-do-not-send="true"><font style="font-size: 8pt;"
size="1" face="Times New Roman">http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en</font></a></p>
</div>
<div id="x37dfff32a36b4410ad8e891fea6bb1b8"><span><font
style="font-size: 8pt;" size="1" face="Times New Roman">
</font></span>
<p class="MsoNormal" xmlns="http://www.w3.org/TR/REC-html40"
style="line-height:normal;background-color:rgba(0,0,0,0);"><font
style="font-size: 8pt;"><font style="font-size: 8pt;"
size="1" face="Times New Roman">ORCID: <a
href="http://orcid.org/0000-0002-7835-3098" style=""
moz-do-not-send="true">http://orcid.org/0000-0002-7835-3098</a>;
</font><span style="font-size: 10pt;"><o:p
xmlns:o="urn:schemas-microsoft-com:office:office"></o:p></span></font></p>
<span>
</span></div>
</div>
</div>
<div><br>
</div>
<div>------ Original Message ------</div>
<div>From: "Terrence W. DEACON" <<a
href="mailto:deacon@berkeley.edu" moz-do-not-send="true">deacon@berkeley.edu</a>></div>
<div>To: "fis" <<a href="mailto:fis@listas.unizar.es"
moz-do-not-send="true">fis@listas.unizar.es</a>></div>
<div>Sent: 2/21/2022 6:01:51 PM</div>
<div>Subject: Re: [Fis] How Molecules Became Signs</div>
<div><br>
</div>
<div id="xa862e70fcc1e423">
<blockquote
cite="CAOJbPRJC2JwPmVKsXpRCPPuO7YBbkmsaej=-qHvN5QTe-GroMg@mail.gmail.com"
type="cite" class="cite2">
<div dir="ltr">Dear FIS colleagues,<br>
<br>
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.<br>
<br>
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.<br>
<br>
It has a number of implications that may be of interest to
the FIS community.<br>
<br>
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).<br>
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.<br>
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.<br>
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.<br>
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.<br>
<br>
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. <br>
<br>
Thanks, Terry<br>
<div><br>
</div>
<div>In honor of the 80th birthday of our brilliant departed
colleague: Jesper Hoffmeyer</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sun, Feb 20, 2022 at
2:38 PM Terrence W. DEACON <<a
href="mailto:deacon@berkeley.edu" moz-do-not-send="true">deacon@berkeley.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear FIS colleagues,<br>
<br>
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.<br>
<br>
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. <br>
<br>
It has a number of implications that may be of interest
to the FIS community.<br>
<br>
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).<br>
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. <br>
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. <br>
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.<br>
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.<br>
<br>
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. <br>
<br>
Thanks, Terry<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Feb 19, 2022
at 1:12 PM Pedro C. Marijuán <<a
href="mailto:pedroc.marijuan@gmail.com"
moz-do-not-send="true">pedroc.marijuan@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>
<div>Dear FISers,<br>
</div>
<div><br>
</div>
<div>We are going to start the new discussion
modality based on specific publications. The
initial contribution to comment is:<br>
</div>
<div><br>
</div>
<div><b>"How Molecules Became Signs</b><b>."</b> By
<b>Terrence W. Deacon</b>, recently appeared in
Biosemiotics.<br>
</div>
<div><br>
</div>
<div>At his earlier convenience, Terry will send a
leading text to start the discussion. <br>
</div>
<div>Now, given that there is a doi <a
href="https://doi.org/10.1007/s12304-021-09453-9"
moz-do-not-send="true">https://doi.org/10.1007/s12304-021-09453-9</a>
(for freely downloading the paper), <br>
</div>
<div>interested parties may read in advance the
publication.</div>
<div><br>
</div>
<div>Best greetings to all,</div>
<div>--Pedro</div>
<div><br>
</div>
<div>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.<br>
</div>
<div
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Professor Terrence W. Deacon<br>
University of California, Berkeley</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature">Professor Terrence W.
Deacon<br>
University of California, Berkeley</div>
</blockquote>
</div>
<br>
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