[Fis] Essential Core?
Pedro C. Marijuan
pcmarijuan.iacs at aragon.es
Fri Jul 8 14:42:05 CEST 2016
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.
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.
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. 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.
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. 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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