Re: [Fis] CONCLUDING THE SESSION

Dear pedro

You wrote: I also would like to argue with Soeren on autopoiesis: does
it really make molecular sense?
----------
My anser: The argument in autopoiesis is that there is a radical shift
because of the closure, and individuals are created. That does not make
sense on a molecular level. It cannot be seen from a molecular level.
There will be some downward causation from the new boudary conditions
controlling for istance the environment that determines how proteins are
folded.

"Pedro C. Mariju�n" wrote:
>
> Dear FIS colleagues,
>
> Around the end of next week (at their convenience) Jerry Chandler & Luis
> Serra will convoke us for the new session on "Information and Ecological
> Economics". During the remaining days, it would be good that invitees and
> participants in the current session on Molecular Recognition would make
> their concluding comments. In any case the list is wide open to whatsoever
> themes and suggestions.
>
> all the best
>
> Pedro
>
> PS. For travel reasons I will be unable to handle any technical problem of
> the list until next 15 October.
> _____________________________________
>
> In what follows I include some closing comments, mainly in response to
> Soeren and Loet:
>
> Considering the cell as a membrane system (Soeren) is indeed an exciting
> new research-direction. A recent issue of BioSystems is devoted to
> "membrane computing", or P-systems (from Paun, the founder of this new
> field). It appears as a very promising approach to the formal properties of
> cellular communication --quite apart from classical approaches based on
> information theory, cellular automata, Turing machine, etc.
>
> Biologically, communication means that the cell cycle itself "pops in and
> out" of the cell membrane in order to get an adaptive coupling with the
> boundary conditions of the system. As already argued, this phenomenon is
> the linchpin that distinguishes the informational coupling of life to its
> boundary conditions from the mechanical coupling (through force) of the
> inanimate. Of course, we may cut communication adrift from the reality of
> the cell-cycle (and so get it in a very simplified way, eg, Shannonian way
> as Loet suggested) but then we pay the heavy price of a complete 'meaning'
> disappearance... and we leave information only as an abstract construct or
> metrics that is definitely separated from life's own structures. Well, it
> can be done, but we renounce to a coherent informational view of the cell
> (and of other 'informational' entities).
>
> The big biomolecular challenge is in my opinion to study communication (the
> signalome) in its coordination with the cell cycle --itself a dense
> intermix of very different information architectures, mainly the sequential
> (genome, transcriptome) and the amorphous (proteome, metabolome,
> degradome). This discussion is an important part of contemporary
> bioinformatic needs, and here at fis, we have found an original path to
> contemplate the whole panorama. Starting with molecular recognition (thanks
> to Shu-Kun for his valuable insights) we can put a lot of explanatory
> weight to the three fis 'information genera'. Several schemes presented
> here, for instance, by Jerry, Karl, Michael, and quite recently by Loet,
> etc. might produce good results to study the functional mix between the
> generative and the structural--the heart of the cell cycle). And finally we
> should advance towards a new consideration of the cell cycle itself,
> conceived as a succesion of 'phases' . In the definition of these phases
> that substitute for 'states' in the biological realm, there appear further
> conceptual difficulties, mainly because of the many multiplicities of
> equi-final regimes that may be contained (my best candidate notion to
> establish the phase 'variables' would be Robert Rosen proposal in his essay
> 'what is life: the Schrodinger question 50 years later'... it is a
> particular anecdote, but this essay appeared earlier, and in a more
> complete rendering, into a Spanish Journal --in 1994, in Spanish of course)
>
> Anyhow, I am getting too long in my farewell to this exciting discussion.
> Let me add that re-reading the recent messages another future discussion to
> organize should revolve around entropy --the numerous misunderstandings,
> misconceptions, etc. surrounding it, precisely in its connection with
> Shannon (for instance, arguing with Loet, thermodynamic entropy is indeed
> 'dimensionless': it has units, but no dimensions, as 'temperature' itself
> has dimensions of energy--see John Collier excellent posting in this list
> about the subject-- and so they cancel each other). I also would like to
> argue with Soeren on autopoiesis: does it really make molecular sense?
> Maybe in the session with Jerry and Luis both entropy and autopoiesis will
> somehow reappear... it would be great returning a little to these
> bioinspired themes. best ---Pedro.
>
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-- 
Best wishes S�ren Brier
Copenhagen Business School
Dept. of Management, Politics and Philosophy 
Bl�g�rdsgade 23 B, 3. floor, room 326, DK-2200 Copenhagen N.
Telephone +45 38152208, mail sbr.lpf@cbs.dk .
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