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<div class="moz-cite-prefix">Dear Arturo and colleagues,<br>
<br>
I think that relating information to free energy can be a good
idea. I am not sure whether the expressions derived from Gibbs
free energy (below) have sufficient generality; at least they work
very well for chemical reactions. And it is in the biomolecular
(chemical) realm where the big divide between "animate
information" and "inanimate information" occurs. In that sense, I
include herein the scheme we have just published of prokaryotic
cells in their management of the "information flow". In a next
message I will make suggestions on how the mapping of biological
information may conduce to a more general approach that includes
the other varieties of information (anthropocentric, physical,
chemical, cosmological, etc). Biological information is the most
fundamental and radical track to unite the different approaches! <br>
<br>
Best--Pedro<br>
<br>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<span style="font-size:11.0pt;font-family:Tahoma">Pedro C.
Marijuán</span><span
style="font-size:11.0pt;font-family:Tahoma;mso-ansi-language:
EN-GB" lang="EN-GB"></span><span
style="font-size:11.0pt;font-family:Tahoma">, Jorge Navarro</span><span
style="font-size:11.0pt;font-family:Tahoma;mso-ansi-language:
EN-GB" lang="EN-GB"></span><span
style="font-size:11.0pt;font-family:Tahoma">, Raquel del Moral.
<br>
</span><span
style="font-size:11.0pt;font-family:Tahoma;mso-ansi-language:
EN-GB" lang="EN-GB"><b>How prokaryotes ‘encode’ their
environment: Systemic tools for organizing the information
flow.</b> <br>
<a href="http://www.sciencedirect.com/science/journal/03032647"
title="Go to Biosystems on ScienceDirect"><span
style="color:windowtext;
text-decoration:none;text-underline:none">Biosystems</span></a>.
October<span style="mso-spacerun:yes"> </span>2017. </span><span
style="font-size:11.0pt;font-family:Tahoma"><a
href="https://doi.org/10.1016/j.biosystems.2017.10.002"
target="doilink">https://doi.org/10.1016/j.biosystems.2017.10.002</a><o:p></o:p></span>
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<br>
<b>Abstract</b><br>
An important issue related to code biology concerns the cell’s
informational relationships with the environment. As an open
self-producing system, a great variety of inputs and outputs are
necessary for the living cell, not only consisting of matter and
energy but also involving information flows. The analysis here of
the simplest cells will involve two basic aspects. On the one
side, the molecular apparatuses of the prokaryotic signaling
system, with all its variety of environmental signals and
component pathways (which have been called 1–2-3 Component
Systems), including the role of a few second messengers which have
been pointed out in bacteria too. And in the other side, the gene
transcription system as depending not only on signaling inputs but
also on a diversity of factors. Amidst the continuum of energy,
matter, and information flows, there seems to be evidence for
signaling codes, mostly established around the arrangement of
life-cycle stages, in large metabolic changes, or in the
relationships with conspecifics (quorum sensing) and within
microbial ecosystems. Additionally, and considering the complexity
growth of signaling systems from prokaryotes to eukaryotes, four
avenues or “roots” for the advancement of such complexity would
come out. A comparative will be established in between the
signaling strategies and organization of both kinds of cellular
systems. Finally, a new characterization of “informational
architectures” will be proposed in order to explain the coding
spectrum of both prokaryotic and eukaryotic signaling systems.
Among other evolutionary aspects, cellular strategies for the
construction of novel functional codes via the intermixing of
informational architectures could be related to the persistence of
retro-elements with obvious viral ancestry.<br>
-------------------------------------------<br>
<br>
El 10/10/2017 a las 11:14, <a class="moz-txt-link-abbreviated" href="mailto:tozziarturo@libero.it">tozziarturo@libero.it</a> escribió:<br>
</div>
<blockquote
cite="mid:2028724884.4019641507626877000.JavaMail.httpd@webmail-03.iol.local"
type="cite">
<div>Dear FISers, </div>
<div>a proposal: information might stand for free energy. </div>
<div><br>
</div>
<div>Indeed, we know that, for an engine: </div>
<div>enthalpy = free energy + entropy x temperature.</div>
<div><br>
</div>
<div>At a fixed temperature, </div>
<div>enthalpy = free energy +entropy </div>
<div><br>
</div>
<div>The information detected (from an environmental object) by an
observer is not the total possible one (the enthalpy encompassed
in the object), but just a part, i.e., the part that it is not
uncertain for him (the free energy). Hence, every observer,
depending on his peculiar features, detects a different amont of
free energy and does not detect the uncertain part (the
entropy). </div>
<div><br>
<p class="MsoNormalCxSpFirst"
style="margin-top:12.0pt;margin-right:0cm;
margin-bottom:12.0pt;margin-left:0cm;mso-add-space:auto;text-align:justify;
line-height:115%;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size: 14px; line-height: normal; text-align:
start;"><font face="courier new, monospace"><b>Arturo Tozzi</b></font></span></p>
<p class="MsoNormalCxSpFirst"
style="margin-top:12.0pt;margin-right:0cm;
margin-bottom:12.0pt;margin-left:0cm;mso-add-space:auto;text-align:justify;
line-height:115%;mso-layout-grid-align:none;text-autospace:none"><span
style="line-height: 115%;"><font face="courier new,
monospace">AA Professor Physics, University North Texas</font></span></p>
<p class="MsoNormalCxSpFirst"
style="margin-top:12.0pt;margin-right:0cm;
margin-bottom:12.0pt;margin-left:0cm;mso-add-space:auto;text-align:justify;
line-height:115%;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size: 14px; line-height: normal; text-align:
start;"><font face="courier new, monospace">Pediatrician ASL
Na2Nord, Italy</font></span></p>
<p class="MsoNormalCxSpFirst"
style="margin-top:12.0pt;margin-right:0cm;
margin-bottom:12.0pt;margin-left:0cm;mso-add-space:auto;text-align:justify;
line-height:115%;mso-layout-grid-align:none;text-autospace:none"><span
style="font-size: 14px; line-height: normal; text-align:
start;"><font face="courier new, monospace">Comput Intell
Lab, University Manitoba</font></span></p>
<p class="MsoNormalCxSpFirst"
style="margin-top:12.0pt;margin-right:0cm;
margin-bottom:12.0pt;margin-left:0cm;mso-add-space:auto;text-align:justify;
line-height:115%;mso-layout-grid-align:none;text-autospace:none"><font
face="courier new, monospace"><a moz-do-not-send="true"
href="http://arturotozzi.webnode.it/" style="font-size:
14px; color: rgb(5, 68, 126); line-height: normal;
text-align: start;">http://arturotozzi.webnode.it/</a><span
style="font-size: 14px; line-height: normal; text-align:
start;"> </span></font><br>
</p>
</div>
<br>
<br>
<blockquote>
----Messaggio originale----<br>
Da: "Christophe Menant" <a class="moz-txt-link-rfc2396E" href="mailto:Christophe.Menant@hotmail.fr"><Christophe.Menant@hotmail.fr></a><br>
Data: 10/10/2017 11.01<br>
A: <a class="moz-txt-link-rfc2396E" href="mailto:deacon@berkeley.edu">"deacon@berkeley.edu"</a><a class="moz-txt-link-rfc2396E" href="mailto:deacon@berkeley.edu"><deacon@berkeley.edu></a><br>
Cc: <a class="moz-txt-link-rfc2396E" href="mailto:fis@listas.unizar.es">"fis@listas.unizar.es"</a><a class="moz-txt-link-rfc2396E" href="mailto:fis@listas.unizar.es"><fis@listas.unizar.es></a><br>
Ogg: [Fis] TR: Data - Reflection - Information<br>
<br>
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<div id="divRplyFwdMsg" dir="ltr">
<div><span style="font-size: 12pt;">T</span><span
style="font-size: 12pt;">hanks for these
comments Terry</span><span style="font-size:
12pt;">.</span><br>
</div>
<div><span style="font-size:12pt"><br>
</span></div>
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<p class="MsoNormal">We should
indeed be careful not to focus
too much on language because
'meaning' is not limited to
human communication. And also
because starting at basic life
level allows to address
'meaning' without the burden
of complex performances
like self-consciousness or
free will. (The existing bias
on language may come
from analytic philosophy
initially dealing with human
performances).
<br>
Interestingly, a quite similar
comment may apply to
continental philosophy where
the 'aboutness' of a mental
state was invented for human
consciousness. And this is of
some importance for us
because 'intentionality' is
close to 'meaning'. Happily
enough 'bio-intentionality' is
slowly becoming an acceptable
entity (<a
moz-do-not-send="true"
href="https://philpapers.org/rec/MENBAM-2"
id="LPlnk875013"
previewremoved="true">https://philpapers.org/rec/MENBAM-2</a>).
<br>
Regarding Peirce, I'm a
bit careful about using the
triadic approach in FIS
because non human life was not
a key subject for him and
also because the Interpreter
which creates the meaning of
the sign (the Interpretant)
does not seem that much
explicited or detailed.<br>
The divisions you propose look
interesting (<span
style="font-family:Calibri,Helvetica,sans-serif;
font-size:16px">intrinsic,
referential, normative).
Would it be possible to read
more on that (sorry if I
have missed some of your
posts)? </span></p>
<p class="MsoNormal"><span
style="font-size:12pt">Best </span><br>
</p>
<p class="MsoNormal">Christophe</p>
<p class="MsoNormal"><br>
</p>
<hr tabindex="-1"
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<div style="color:rgb(0,0,0)">
<div id="divRplyFwdMsg"
dir="ltr"><font
style="font-size:11pt"
face="Calibri, sans-serif"
color="#000000"><b>De :</b>
Fis
<a class="moz-txt-link-rfc2396E" href="mailto:fis-bounces@listas.unizar.es"><fis-bounces@listas.unizar.es></a>
de la part de Terrence W.
DEACON
<a class="moz-txt-link-rfc2396E" href="mailto:deacon@berkeley.edu"><deacon@berkeley.edu></a><br>
<b>Envoyé :</b> lundi 9
octobre 2017 02:30<br>
<b>À :</b> Sungchul Ji<br>
<b>Cc :</b>
foundationofinformationscience<br>
<b>Objet :</b> Re: [Fis]
Data - Reflection -
Information</font>
<div> </div>
</div>
<div>
<div dir="ltr">Against
"meaning"
<div><br>
</div>
<div>I think that there is
a danger of allowing our
anthropocentrism to bias
the discussion. I worry
that the term 'meaning'
carries too much of a
linguistic bias.</div>
<div>By this I mean that
it is too attractive to
use language as our
archtypical model when
we talk about
information.</div>
<div>Language is rather
the special case, the
most unusual
communicative adaptation
to ever have evolved,
and one that grows out
of and depends on
informationa/semiotic
capacities shared with
other species and with
biology in general.</div>
<div>So I am happy to see
efforts to bring in
topics like music or
natural signs like
thunderstorms and would
also want to cast the
net well beyond humans
to include animal calls,
scent trails, and
molecular signaling by
hormones. And it is why
I am more attracted to
Peirce and worried about
the use of Saussurean
concepts.</div>
<div>Words and sentences
can indeed provide
meanings (as in Frege's
Sinn - "sense" -
"intension") and may
also provide reference
(Frege's Bedeutung -
"reference" -
"extension"), but I
think that it is
important to recognize
that not all signs fit
this model. Moreover, </div>
<div><br>
</div>
<div>A sneeze is often
interpreted as evidence
about someone's state of
health, and a clap of
thunder may indicate an
approaching storm.</div>
<div>These can also be
interpreted differently
by my dog, but it is
still information about
something, even though I
would not say that they
mean something to that
interpreter. Both of
these phenomena can be
said to provide
reference to something
other than that sound
itself, but when we use
such phrases as "it
means you have a cold"
or "that means that a
storm is approaching" we
are using the term
"means" somewhat
metaphorically (most
often in place of the
more accurate term
"indicates").</div>
<div><br>
</div>
<div>And it is even more
of a stretch to use this
term with respect to
pictures or diagrams. </div>
<div>So no one would say
the a specific feature
like the ears in a
caricatured face mean
something.</div>
<div>Though if the drawing
is employed in a
political cartoon e.g.
with exaggerated ears
and the whole cartoon is
assigned a meaning then
perhaps the exaggeration
of this feature may
become meaningful. And
yet we would probably
agree that every line of
the drawing provides
information contributing
to that meaning.</div>
<div><br>
</div>
<div>So basically, I am
advocating an effort to
broaden our discussions
and recognize that the
term information applies
in diverse ways to many
different contexts. And
because of this it is
important to indicate
the framing, whether
physical, formal,
biological,
phenomenological,
linguistic, etc.</div>
<div>For this reason, as I
have suggested before, I
would love to have a
conversation in which we
try to agree about which
different uses of the
information concept are
appropriate for which
contexts. The classic
syntax-semantics-pragmatics
distinction introduced
by Charles Morris has
often been cited in this
respect, though it too
is in my opinion too
limited to the
linguistic paradigm, and
may be misleading when
applied more broadly. I
have suggested a
parallel, less
linguistic (and nested
in Stan's subsumption
sense) way of making the
division: i.e. into
intrinsic, referential,
and normative
analyses/properties of
information. </div>
<div><br>
</div>
<div>Thus you can analyze
intrinsic properties of
an informing medium
[e.g. Shannon etc etc]
irrespective of these
other properties, but
can't make sense of
referential properties
[e.g. what something is
about, conveys] without
considering intrinsic
sign vehicle properties,
and can't deal with
normative
properties [e.g. use
value, contribution to
function, significance,
accuracy, truth] without
also considering
referential properties
[e.g. what it is about].</div>
<div><br>
</div>
<div>In this respect, I am
also in agreement with
those who have pointed
out that whenever we
consider referential and
normative properties we
must also recognize that
these are not intrinsic
and are
interpretation-relative.
Nevertheless, these are
legitimate and not
merely subjective or
nonscientific
properties, just not
physically intrinsic. I
am sympathetic with
those among us who want
to restrict analysis to
intrinsic properties
alone, and who defend
the unimpeachable value
that we have derived
from the formal
foundations that
Shannon's original
analysis initiated, but
this should not be used
to deny the legitimacy
of attempting to develop
a more general theory of
information that also
attempts to discover
formal principles
underlying these higher
level properties
implicit in the
concept. </div>
<div><br>
</div>
<div>I take this to be the
intent behind Pedro's
list. And I think it
would be worth asking
for each of his points:
Which information
paradigm within this
hoierarchy does it
assume?</div>
<div><br>
</div>
<div>— Terry</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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</div>
</div>
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</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</blockquote>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
-------------------------------------------------
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
<a class="moz-txt-link-abbreviated" href="mailto:pcmarijuan.iacs@aragon.es">pcmarijuan.iacs@aragon.es</a>
<a class="moz-txt-link-freetext" href="http://sites.google.com/site/pedrocmarijuan/">http://sites.google.com/site/pedrocmarijuan/</a>
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