complexes and biol.organization

Dear fis colleagues,

As some of you know (ipcat members), Ray has also ignited an exciting
discussion about bioinfo in the ipcat list --sort of an "stereo" sensation
for fis & ipcat members! Should we coordinate the parallel discussion in
both lists?
Perhaps in the fis side we are emphasizing philo and general views on info.
As a provocation for us to really enter in the bio topics raised by Ray,
here it is my contribution a few minutes ago to the ipcat discussion:

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just some comments on the issues raised by Ray, Irma & Takako.

The relatively recent focus on protein complexes in signaling system and
gene expression somehow reminds what happened in late 70's and early 80's
about the phenomenon of metabolic "channeling".

The discovery of this phenomenon --protein complexes among enzymes of the
same pathway- contributed to clarify the frequent discrepancy in between
metabolic enzymes acting in vitro or in vivo conditions. It also
highlighted the sophisticated degree of space-time organization of the
"society of enzymes". One can remember the reviews by Srere (85, 87), Welch
and Clegg (87), Ovadi (91), Welch (92)...

Quite a few aspects then discussed on eg, enzymic size & surfaces,
diffusional transit, solvent capacity, free energy conservation,
cytoskeleton role, coordinate regulation (and even brand-new concepts such
as "metabolons") etc., might deserve a second look concerning the
subtitlities we are finding now in signaling pathways and gene expression
complexes. It is amazing the many parallels existing in between metabolism
("energy" intake and its subsequent transformation) and the signaling
system ("information intake" and its subsequent transformation)...

Among the host of new bioinfo topics, I find very intriguing the role of
second messengers and kinases/phosphatases chains (can we point at a new
type of "mathematical counting" in action there? Javorszky's emphasis on a
partitional bio-calculus deserves some consideration) In general, when
organizing its genuine "infostructures" (signaling system plus "DNA world"
management), the cell uses almost everything it has available: the
pervasiveness of protein degradation, proteolisis, protein folding
(chaperons involvement) both in signaling events and cell cycle control &
signaling system interfaces ("checkpoints") is but a tiny example.

Enlarging on Ray & Irma more general comments, I would say that biological
structures have a very peculiar property: they are always in the making
--and in the dismantling. Protein synthesis--protein degradation; cell
reproduction--cell necrosis and apoptosis... both coupled aspects are
necessary in almost every cell & tissue (well neurons are sort of
"eternal", but their synapsis unceasingly participate in the above dance).
It is sort of an adaptive (informationally guided) "way of existence" that
necessarily implies energy & info inputs.

For my taste, "self-organized complexity" (Per Bak) may be an interesting
point of view, among others, helping to put some overall coherence into
this wild array of new biol. phenomena. The naive mechanistic (a la Monod)
views have become so old and limited--and boring... We need more
sophisticated conceptual bioinfo frameworks.

Hope not having been too philosophical

bests

Pedro

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Pedro C. Marijuan --FAX 34 976 761 861 --TEL 34 976 761 927
Dto. Ingenieria Electronica y Comunicaciones
CPS, Universidad de Zaragoza
Zaragoza 50015, SPAIN
Received on Mon Feb 16 12:52:34 1998