[Fis] Essential Core?
Michel Godron
migodron at wanadoo.fr
Fri Jul 8 16:52:21 CEST 2016
My responses are in red
Bien reçu votre message. MERCI. Cordialement. M. Godron
Le 08/07/2016 à 14:42, Pedro C. Marijuan a écrit :
> Dear FIS Colleagues,
>
> Some brief responses to the different parties:
>
> Marcus: there were several sessions dealing with info physics, where I
> remember some historical connotations with mechanics emerged. Mostly
> 1998 and 2002 chaired by Koichiro Matsuno and 2004 by Michel
> Petitjean. Afterwards the theme has surfaced relatively often. About
> the present possibilities for a UTI, my opinion is that strictly
> remaining within Shannon's and anthropocentric discourse boundaries
> there is no way out.
Yes, but it is not the same with Brillouin's information : I could
send to you a text in French which gives a demonstration of the
convergence between that information and thermodynamical neguentropy.
Since twenty years, I did not find an english review which was
interested by this problem, because I am biologist and the biological
reviews were not interested.
> I do not think that machine communication is going to advance the
> generalization either (but who knows? In conjunction with
> computational neuroscience and the "Bayesian" brain we may have
> surprises). Actually, my personal bet is for reconsidering the
> evolutionary origins, attending to the infrastructure of our cellular
> communication and to the bacterial origins of everything. I think we
> share some parts along this exploratory way, at least the curiosity.
Yes, the bacterial origins of everything is clear, but it is possible to
work with the Brillouin's information present at others scales, It was
used in an imperfect way in Forman & Godron /Landsca//pe //ecology/
(1986, Wiley).
>
> To Loet, bacteria never apologize (not much different from some
> humans, eg politicians) but chimps often do ("grooming" after
> conflicts, with the winner offering peace to the defeated). The
> restrictive use of the term communication as proposed is contrary to
> the existing body of research, not only in biology. That "biology as a
> science itself is communication" is a strange argument.
Perhaps, but "Life is a transmission of information" is not strange and
may be explained.
> For the same token it is also observation, reflection, action,
> learning, experiment, tradition... and biology, and whatever science,
> is also a form of knowledge necessarily performed by a living
> subject--so all science is "biology" following with that strange
> argument. Finally, talking about "priorities" or hierarchies in mutual
> relationships between bodies of knowledge is out of our times;
> priorities have to be won by cooperation/competence within the global
> knowledge-recombination markets of science. Rather than closing doors,
> establishing multidisciplinary teams and directions is the new mantra.
>
I fully agree !
> To Jerry, given that explicitly my approach to biological information
> /communication is based on molecular recognition, your generative
> approach to the nature of molecular information under the banner of
> electrical fields and atomic numbers looks congruent. It is a pity
> that so few biophysical approaches have been devoted to the general
> problematic of molecular recognition and molecular complexity.
I fully agree !
> The way living cells rely on different informational architectures is
> a showcase of amazing multiplicity achieved from a few model-patterns.
> But it is very difficult establishing appropriate ontologies on the
> enormous functional complexity that emerges. It relates to the last
> question of your message, I think.
>
> To Francesco, thanks, I also believe that the relationship between
> economic and biomolecular "currencies" share a similar inner logic.
> Information has "value", indeed... And finally I should clarify that
> the universals scheme proposed around bacterial communication is a
> mere initial draft --it will get worst! Actually it crystallized
> during the first days of these discussions, thinking about the limits
> of the present mechanical-Shannonian communication paradigm.
>
> Again, thanking the patience
> --Pedro
>
>
> El 07/07/2016 a las 18:44, Francesco Rizzo escribió:
>> Caro Pedro,
>> ho apprezzato moltissimo quella magnifica sintesi tra vita,
>> auto-riproduzione e comunicazione con l'ambiente nella prospettiva o
>> logica della moneta biologica. Problematica che ho affrontato più
>> volte anch'io dal punto di vista della "Nuova economia". Le pagine
>> 120-130 di "Valore e valutazioni" (FrancoAngeli, Milano, 1999) ne
>> sono una testimonianza.
>> Grazie e buone vacanze a Te e a Tutti.
>> Francesco
>>
>> 2016-07-07 13:53 GMT+02:00 Pedro C. Marijuan
>> <pcmarijuan.iacs at aragon.es <mailto:pcmarijuan.iacs at aragon.es>>:
>>
>> Dear FISers,
>>
>> [NOTE: I have just seen the new post from Marcus right now: I
>> should modify parts of the discussion below, but it is too much
>> work! Better left for a future exchange...]
>>
>> About the a priori modeling of information --and meaning-- which
>> was the focus of Marcus' presentation, putting together Shannon,
>> Bateson, and Darwin, I am not sure how that scheme would
>> translate into the "real" living stuff. Mostly thinking on the
>> work my team has done on bacterial communication for years, I
>> mentioned days ago three basic points about that: universals,
>> species-specificity, and essential cores.
>>
>> How a plurality of those information universals could be wrapped
>> or articulated around an essential core? That's the toughest
>> point in my opinion. It becomes a matter for freewheeling
>> speculation, badly needed of Schrodinger's disclaimer. Well, let
>> us consider that communication and self-production are but the
>> two inseparable sides of the bio "coin" --in order to
>> self-produce the living has to communicate with the environment,
>> and in order to communicate the living needs its flexible
>> self-production processes... (just to fabricate the meaning!)
>>
>> In bacteria, the side of communication might be seen as implying:
>>
>> --*Communication for self-production*: detection and
>> introjection/ejection of environmental substances (water, anions,
>> cations, minerals, nutrients, metabolites, waste, and toxics). In
>> bacteria this is crucial. Most of it, apart from the spontaneous
>> membrane permeability, is done by around one hundred different
>> ONE-COMPONENT SYSTEMS (1CS) and a variety of channels and
>> transporters.
>>
>> --*Communication **with****con-specifics*: in reproduction (sex
>> exchanges, plasmid exchanges); in social structures (colonies and
>> biofilms); in "differentiation" (sporulation, occasional
>> differentiated types). Around 10-20 TWO-COMPONENT SYSTEMS (2CS)
>> may be in charge, although amply swapping their functions with
>> the previous 1CSs.
>>
>> --*Ecosystem communication*: cooperation and competition with
>> other species in ecosystems; chemical arm races with fungi,
>> viruses, other bacteria, protists, etc.; symbiosis, cooperation
>> and parasitism with multicellular hosts; pathogenic switching...
>> We may find tools such as 1CS, 2CS, 3CS, special protein kinases,
>> and very complex apparatuses for pathogenesis, predation, and
>> chemical arm races.
>>
>> Not much emphasis needed in that those three items are
>> universals, species specific, and more or less
>> differentiated/entangled within the mentioned communication side
>> of the bio core.
>>
>> Thereafter, thinking about the universals side of
>> self-production, could we terribly simplify our informational
>> view of self-production, as Francis Crick's mandated with his
>> Central Dogma of molecular biology? Nonetheless it was the first
>> cogent explanation of the flow of genetic information within a
>> biological system. In any case, what we find is different
>> informational architectures --membranes and cytoskeleton
>> rudiments, nucleic acids, processing enzymes-- which are
>> respectively based on identity, complementarity, and
>> supplementarity principles (Shu-Kun Lin). They are playing
>> together the *replication, **transcription,* *translation,
>> **house-keeping*, and *degradation* functions that apparently
>> integrate the bulk of self-production...
>>
>> Summing up the obtained items, and just to close the present
>> speculation, we might have found three universals of
>> communication and another five of self-production. Indeed they
>> look very densely entangled within an essential core. At stake is
>> whether they are sufficiently congruent and ontologically robust.
>> Perhaps the most interesting aspect is that herein it becomes
>> relatively easy to upend meaning, value, knowledge-recombination
>> and other members of the conceptual cluster that usually
>> accompanies information.
>>
>> Thanking in advance for the patience!
>>
>> --Pedro
>>
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>>
>
>
> --
> -------------------------------------------------
> 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 X
> 50009 Zaragoza, Spain
> Tfno. +34 976 71 3526 (& 6818)
> pcmarijuan.iacs at aragon.es
> http://sites.google.com/site/pedrocmarijuan/
> -------------------------------------------------
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