Re: [Fis] The Molecule as Text (New Session)

The Molecule as Text (New Session)Loet,

we could make an analogy between the interaction between molecules and between humans (as well as between humans talking about molecules and humans interacting with molecules). You mention "the message that the collision has taken place" which is a message between the colliding molecules as well as a message for the observer of this collission. In this case it is also a message between individuals talking about such phenomena.

As in the case of non-human biological systems, the message (in this case: your message) "collides" with different individual systems (such as my brain, pre-knowledge, using this PC etc.) but it also concerns the whole FIS community which is more than the numerical addition of its members.

We could analyze this collision(s) from a thermodynamic point of view but this would say nothing (or very little) about the matter itself we are discussing now. Is this difference a decisive one for molecules too? What are the conditions for the interactivity between "different systems of reference" and what are the "bridges" between them? Is "bridge" the right metaphor?

kind regards

Rafael

Prof. Dr. Rafael Capurro
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  ----- Original Message -----
  From: Loet Leydesdorff
  To: 'Ted Goranson' ; fis@listas.unizar.es
  Sent: Friday, November 11, 2005 9:28 AM
  Subject: RE: [Fis] The Molecule as Text (New Session)

    May I suggest that there is a difference between considering molecular information flows as a chemist or biologist and doing so in the FIS context?
  Dear Ted and colleagues,

  I have always been amazed of the direct link which some natural scientists wish to make between material flows and the information exchange. The latter is a mathematical reflection of the events with a different system of reference.

  Take, for example, the classical case of colliding balls. When the physical realization approximates the ideal case, the thermodynamic entropy vanishes, but the redistribution of momenta and energies at the macro-level becomes more pronounced (since there is less dissipation). Correspondingly, the message that the collision has taken place contains a larger amount of information. Thus, the two types of entropy can vary independently: the one may increase and the other vanish in the same event.

  The reason for this independence is that the systems of reference for the two entropies are different: thermodynamic entropy refers exclusively to the distribution of, for example, momenta and positions among particles, while the reference system for probabilistic entropy in this case is the system which conserves macroscopic momenta and energy. The two forms of entropy production (thermodynamic and probabilistic) stand orthogonally in the ideal case.

  In the case of biological systems, one does not expect independence because these systems are dissipative. However, one analytically should declare the two systems of reference first independently, in order to study their mutual information in the dissipation. Perhaps, I misunderstand this discussion, but please in that case try to explain to me why information exchange is not a mathematical construction, but would be embedded in life (or something substantively like that). It seems to me that if (following Maturana) life is defined as the exchange of molecules, the probabilistic entropy generated is not directly related with nor immediately explanatory for the phenomena. There are several in-between steps to be specified.

  These steps may be very different for different systems of reference (e.g., biological life or human culture). For example, in the latter case, I expect more anticipatory mechanisms (e.g., the sciences) to be involved than in the former and therefore a different dynamics of the entropy.

  With kind regards,

  Loet
    

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  Loet Leydesdorff
  Amsterdam School of Communications Research (ASCoR)
  Kloveniersburgwal 48, 1012 CX Amsterdam
  Tel.: +31-20- 525 6598; fax: +31-20- 525 3681
  loet@leydesdorff.net ; http://www.leydesdorff.net/

  The Knowledge-Based Economy: Modeled, Measured, and Simulated
  The Self-Organization of the Knowledge-Based Society; The Challenge of Scientometrics

    In the local context, all you have to do is invent a new science that sheds new light on phenomenon that are seen locally, namely in the molecular domain. In the FIS context, you have this seeming impossibility squared. That's because you'll be using this domain to get leverage on the larger problem of an information science that applies at all domains. And more importantly, we'd understand what flows among domains and how.

    Toward this end, I'd like to put an early suggestion for limiting the "bio" semiotic approach a bit. Several smart people here have noted the internal/external problem of meaning and intent when you scale biosemiotics down to elements that apparently cannot reason. So I am very skeptical of Peircian mechanics at the biological level.

    And yet - as with many - I find I cannot abandon the notion of meaning when using that of information.

    So I would ask you (Jerry and Kevin) if we cannot have a limited semiosis. In the following way:

    Generally, we like to think of things that have physical reality as the causal primitives in science. So we think of entities having properties as a first order concern, and those entities are the ones we can see and measure. So even though all our rudimentary physics actually operates by way of fields, we suppose those fields as assigned to or generated by entities. We go so far as to require other entities to be exchanged in field effects.

    And I see this with chemists as well. The assumption is that the molecule is what exists as the primitive agent. If information is exchanged, it must be among these "hard" entities. So we look, for instance at their shape (which I know Jerry will get to), and the structural elements Pedro mentions below.

    Can we posit that the true identity of a molecule is something information-based and that what we see is the text, a text, a representation and not something that some god started his day with? This allows me to swallow the important elements of biosemiotics, and forces me in the direction of inventing new abstractions for the primitives involved.

    And of course, these would be abstractions behind the "text" we see, and the one molecules perceive. Fields and particles then become effects, not something necessarily intrinsic to information flows and bindings.

    So then, brief responses to Jerry, Kevin, Pedro...

    Jerry:

    I am glad you gave us the history. But I think history is the enemy here. The abstractions we blindly accept today were invented in a duller context and to satisfy needs vastly less demanding than FIS requires. I fear too many contributors (one would be too many) will try to stretch one or another old principle to fit this new concern.

    But it is of extreme value in posing a candidate problem. After all, if we are creating something useful, it should solve problems more elegantly than before or describe more crisply or provide for better analytical tools.

      What are the relations between this sort of encoding and other metabolic encoding? In particular, can we imagine a catalytic - type of encoding that parallels the genetic encoding?

    And here we have it. Thanks Jerry.

    Kevin:

    I am so glad I heard your talk in Paris. So I know that when you say "Computer Science," you mean something larger than the ability to describe things algorithmically. But this notion of "natural computation" implies the logics involved are confined to the relatively simpler logics we normally code for/model within. The first order and probabilistic logics. I think that an unnecessary limitation.

      The simulation relation is central in automata theory and was recast into a category-theoretic framework by Arbib and Goguen (taking different approaches). But the notion of a mapping between a biological system and a formal system, seems to be, at first glance, a category mistake! As soon as one identifies a fragment of nature as a system, one has locked in some set of states, and it is hard to separate the true computational power of a living system from what accrues merely to our conventional state assignment. This is taken up nicely by the philosopher David Chalmers in a response to a very strong statement at the conventionality end by Hilary Putnam. (One could see this as a recasting of the debate in Plato's Cratylus in computational terms!)

      This tension between the formal and the material seems to lie at the heart of the field of natural computing.

    So we need to reinvent both, yes? Both our formal mechanics of computation and our notions of what the "material" is. In both cases we are dealing with abstraction science and unavoidably category theory, no?

    Pedro:

      This point is so important! Let me refer to arguments in my presentations ECAP 2005, and FIS 2005. I argued that as a consequence of the peculiar "embodiment" of the biomolecular agents (enzymes), in the study of their function we have to pay attention not only to the strictly functional 'what' dictated in the active site of the enzyme, but also to a series of accompanying processes distributed over different parts of the molecular structure, which may include: modulation by effectors, intracellular transportation, permanent (post-translational) modification, formation of complexes, the time-frames derived from transcription and translation, and finally degradation. So the 'what' of the functional clause should be accompanied by circumstances such as 'how fast', 'where', 'which way', 'with whom', 'when', and 'how long'. The mind-boggling factor is that almost all of these circumstances may be captured within particular parts --MODULES, DOMAINS-- of the enzyme, corresponding to DNA exons & introns, and then become amenable to evolutionary control... this is basically the source of eukaryotic organismic complexity: a "genetic algorithm" decomposable in parallel "logical" clauses that can be explored and solved in independent steps.

    As always, I'm with you, but suspect you fear going to far so don't go far enough. Why not?

    Best, Ted

-- 
__________
    Ted Goranson
    Sirius-Beta