[Fis] CONCLUDING THE SESSION

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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Received on Wed Oct 8 14:21:25 2003