Dear Joseph and FIS collegues,

The only item I can remember formally addressing the topic is "La logique du vivant", by Francois Jacob in very early 70's. But it was perhaps more a philosophy of life than a rigorous approach or overall theoretical description of life processes. In any case it was original ("bricolage") and inspiring. Nowadays my main criticism to visions inspired in physics would run as follows: imagine we are dealing with computers; any general approach to their performances, should it be based on "solid state physics"? Nope. You would need a theoretical, brand new vision, eg Turing machine on universal computation, or something similar attending to structures of computing processes and computing machinery. It would extend completely beyond physics, as the informatics realm is situated... pure technological creativity due to software and hardware engineers (of course, always mastering and slaving natural processes at the bottom, but in "artful" ways and multilevel purposes).

Regarding bio, the new theoretical integrated or unified approach ("logic" or whatever) would be similar to the above creativity. Grounded on some central bio characteristic, in my opinion self construction, as von Neumann started with his unfinished theory of self-constructing machines. Cells (and organisms) are the only entities rigorously selfconstructing themselves. Actually biology would be the science of selfconstruction... where a new notion of info related to the impact of communication on selfconstructing processes ("meaning") would be central. It may look challenging, but without protein synthesis there is no meaning!

My criticism to current bio-doctrines extends to systems biology and other fashions (synthetic biology, bioinspired computing, artificial life...). Some ideas thrown in Inbiosa meetings could enter into the discussion too, I think.

best wishes

---Pedro escribió:
Dear Pedro,

Thank you, Pedro, for bringing up the question of logics. My suggestion of a Logic in Reality is to open the debate, rather than to claim it is the only "over-arching logic" possible. Nevertheless, it would be useful for me and perhaps others if you could make your critique more specific by pointing to at least one logic that is used biologically that addresses the dynamics of complex processes. So far, I have not identified any such logical system that is more than a metaphorical use of the term "logic" or refers to some more or less reproducible characteristics of such processes. Otherwise, logics seem to me to refer only to abstracted linguistic aspects of processes that of course follow classical propositional logic but equate to tautologies.

Because Logic in Reality is grounded in physics, it is able to express somewhat more about change, evolution, etc. than any logic of which I am aware. I would be glad to learn of other candidates for this role.

Thank you and best wishes,


    ----Ursprüngliche Nachricht----
    Datum: 11.04.2012 10:44
    An: <>
    Betreff: Re: [Fis] Physics of computing

    Dear John and colleagues,

    Nice to hear that you are OK after that dangerous intoxication
    --our best wishes for your complete recovery!
    About physical information I think that Landauer clarified the
    panorama, at least concerning the relationship between information
    theory and thermodynamics. According to his principle, any
    logically irreversible transformation of classical information is
    necessarily accompanied by the dissipation of at least k T ln(2)
    of heat per lost bit (about 3 x 10 exp -21 Joules at 300 K
    temperature), where obviously k is the Boltzmann constant and T
    the temperature. Recently this principle has been verified
    experimentally (Nature, 8 March 2012, p. 187). By the way, in his
    past message Loet enters "Watts" in a similar expression (?). To
    insist, Entropy and Information are dimensionless and do not
    explicitly incorporate any units... About the quantum management
    of info theory, it is another matter, quite more tricky.

    Beyond that immediate physicality, things get quite obscure as our
    contradictory "meaning" messages witness. The point made by Joseph
    on an overarching logic, is rather difficult to be maintained --at
    least in my small province of the biological signaling pathways.
    Too many logics are used biologically in too many different
    contexts or niches, either molecularly or neuronally... I bet that
they are not susceptible of integration in any logical system. Maybe Inbiosa parties would also disagree with me in this regard.

    best wishes to all,


    John Collier escribió:
    I have been in the hospital for almost three weeks due to
    bleeding from warfarin. I had to have three blood transfusions
    and an operation. I am only now getting my strength back. Some of
    my comments, therefore, may be dated.
    "Physical" has a variety of overlapping meanings (a
    Wittgensteinian family resemblence). For example Quine takes the
    physical to be anything accessible to the senses or inferences
    therefrom. Ladyman, Ross, Collier an Spurrett take the physical
    to be the most fundamental laws of our (part of) the universe. I
    did not agree with this, among some other crucial points, so I
    was not a primary author. Information is at least physical in
    both of these senses. Quine's approach might make it entirely
    physical. I prefer to relate it to the causal, which always has
    physical parametres, as far as we know. But there are many ways
    of approaching this issue, and disentangling them will be a major
    advance in foundations of information theory.
    My Best,

Professor John Collier Philosophy, University of KwaZulu-Natal
    Durban 4041 South Africa
    T: +27 (31) 260 3248 / 260 2292
    F: +27 (31) 260 3031
    email: <>>>> On
    2012/03/16 at 01:19 PM, in message <>,
    "Pedro C. Marijuan" <> wrote:
    Dear discussants,

    I tend to disagree with the motto "information is physical" if
    taken too strictly. Obviously if we look "downwards" it is OK,
    but in the "upward" direction it is different. Info is not only
    physical then, and the dimension of self-construction along the
    realization of life cycle has to be entered. Then the signal, the
    info, has "content" and "meaning". Otherwise if we insist only in
    the physical downward dimension we have just conventional
    computing/ info processing. My opinion is that the notion of
    absence is crucial for advancing in the upward, but useless in
    the downward.
    By the way, I already wrote about info and the absence theme in a
    1994 or 1995 paper in BioSystems...


    ---Pedro escribió:

    Thanks John and Kevin to update issues in information,
    computation, energy and reality.

     I would like point out to other articles more focused in how
    coherence and entanglement are used by living systems (far from
    thermal equilibrium):

    Engel G.S., Calhoun T.R., Read E.L., Ahn T.K., Mancal T., Cheng
    Y.C., Blankenship R.E., Fleming G.R. (2007) Evidence for
    wavelike energy transfer through quantum coherence in
    photosynthetic systems. Nature, 446(7137): 782-786.

    Collini E., Scholes G. (2009) Coherent intrachain energy in
    migration in a conjugated polymer at room temperature.  Science,
    vol. 323 No. 5912 pp. 369-373.

    Gauger E.M., Rieper E., Morton J.J.L., Benjamin S.C., Vedral V.
    (2011) Sustained Quantum Coherence and Entanglement in the Avian
    Compass. Phys. Rev. Lett., 106: 040503.

    Cia, J. et al, (2009)  Dynamic entanglement in oscillating
    molecules.  arXiv:0809.4906v1 [quant-ph]




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    Pedro C. Marijuán
    Grupo de Bioinformación / Bioinformation Group
    Instituto Aragonés de Ciencias de la Salud
    Avda. Gómez Laguna, 25, Pl. 11ª
    50009 Zaragoza, Spain
    Telf: 34 976 71 3526 (& 6818) Fax: 34 976 71 5554

Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 25, Pl. 11ª
50009 Zaragoza, Spain
Telf: 34 976 71 3526 (& 6818) Fax: 34 976 71 5554

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