Re: [Fis] continuing the session molecular recognition and inviting papers on this topic

Dear FIS colleagues,

I agree with most of the comments by Luis, John and Andrei. Indeed the
conceptual paths in physics around molecular recognition are far from being
properly established yet. 'De-geometrizing' the lock and key mechanical
image of the phenomenon (as Luis proposes) and highlighting the
oscillatory/resonant/rhythmic nature of both the recognition and the
'glueing' that follows would be crucial to fabricate a simplified vision
coherent with the quantum mechanical world of underlying processes. Who
knows how, but it is there --in the fantastic molecular dynamics that
involves coulombian, hydrogen bonding, permanent and induced dipoles, van
der Waals, and hydrophobic interactions-- where a symmetry-based analysis
should tentatively put the molecular recognition phenomenon (eg, proteins)
in a proper quantum footing. In actuality, the problem of 'molecular
recognition' would be endowed with a complexity paramount, or even higher,
than the very protein-folding problem.

I disagree, however, with some further comments by Andrei on the
non-validity of the second law as a basic principle of the universe
---particularly, if one realizes that the 'entropy analysis' is among the
very few keys used by contemporary quantum cosmologists in order to make
sense of the existentialities beyond the Planck 'frontier', eg, Smolin,
Penrose, Hawking. Given that the disagreement involves the role of
principles in science (and the apparent disregard of experientia) I suggest
postponing this vast discussion until we organize an ad hoc 'information
physics' session --actually it is a long overdue discussion. In the
interim, I also refer to Igor's message (11 July 2003--fis site:
http://fis.iguw.tuwien.ac.at/mailings/) as a more ponderate version but
perhaps not so far away from these physico-semiotic views (maybe, the two
of them, Andrei and Igor could be the organizers of that focused session?).
Tom Stonier had put the relationship entropy-information in the very center
of information physics, Morowitz has suggested Pauli's exclusion, and other
parties actually take 'uncertainty' as a fundamental spacetime limit for a
unitary 'bag of bits'... It would be great that we could establish
around the concepts of information, symmetry, matter, entropy,
uncertainty, etc. a central phenomenon for information physics (a
'protophenomenon', as Goethe was calling) equivalent to molecular
recognition for the bioinformational analysis.

Because contemplating bioinformation --or the current bioinformatic debates
for that matter-- under the molecular recognition prism, opens up very
intriguing directions. For instance, the systematic relationship between
the generative (genome) and the structural (proteome), together with the
crucial role played by communication (signalome), and the supporting web of
metabolic transformations (metabolome)... The global picture is a gigantic
matrix of molecular recognition interactions, where the most significant
controlling molecules (basically, the proteome elements) are no longer mere
'catalysts' but multifunctional 'agents' endowed with principal recognition
addresses and also secondary ones (dictating the where, when, with whom,
how fast, and how long of the main functionality), all of these addresses
are based on recognition capabilities of the component protein-modules. A
non-trivial argument is that, along the eukaryotic runaway of fantastic
complexity growth, the overall evolutionary regime becomes
'transmolecular'... as the only way to explore the universe of
developmental paths.

The new keys that molecular recognition could provide about biomolecular
functions imply a very round approach to the whole informational dynamics
of life. Seemingly, a new grounding to the emerging information science
looms: in the extent to which we win a bioinformation success, "De te
fabula narratur" will apply into a constellation of information fields
(neuroinformation, socioinformation).

best regards

Pedro

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Received on Tue Sep 16 14:03:18 2003