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.i...@aragon.es <mailto:pcmarijuan.i...@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.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-------------------------------------------------

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