FIS friends,
Thanks particularly to Ana, Giuseppina, and Michel. It is refreshing
hearing the voices from people working on the experimental side of
molecular sciences. Confronting the theoretical problems of chemistry,
biochemistry, molecular biology, etc., we should not forget that these
bodies of knowledge have been gained mostly from the experimental bench,
with all its serendipity and happenstances. Until recently, the role of
molecular-chemical theory has been very modest, and even today it is quite
frequent hearing from physical chemists about unfaithful claims built
around awkward quantum simplifications.
Arguing or exploring about an overarching "logic of chemistry" (and around
"non arithmetic" atomic numbers) as Jerry suggests, may be fertile, but one
may easily forget that chemistry has to tackle a "plurality of simultaneous
occurrences", in general involving very complex physical interactions
about, for instance, charge, spin, lattice, orbitals... where, in each one,
by large nonlinearities dominate; and where the "composite" object --eg, a
complex biomolecule-- becomes miles away from being "reduced" bona fide in
its chemical global properties down to a reasonable system of
physical-mathematical laws.
In what extent the highly composite nature of the chemical object
(manipulable only as such, experimentally) becomes a barrier to a massive
interconnection of its whole explanatory "formal procedures"? I am not
sure that this argument strait-ahead justifies the present computational
challenges mentioned by Ana and colleagues, and that new more powerful
abstractions and logic& symbolic systems would not overcome some of them;
but I would bet in favor of the non computable problems always haunting
those in charge of chemical models (think on the problems just with water,
mentioned by Michel).
Maybe the points on natural computer science raised by Kevin and Gordana
are related. We may easily take for granted that a coverage under the
umbrella of "mathematical machines" working on sophisticate topological
properties of electronic circuits, by the use of Boolean networks operating
on solid-state devices (and functionally independent), is the natural
theoretical model for any "informational or computational occurrence." Even
the world itself, not only as a theoretical object, may appear as a
gigantic computer, a la Wheeler (nope... or maybe, yes, but along a
dramatic reinterpretation of the whole three mechanics --classical,
statistical, quantum? Excuse me the wild derivation)
Anyhow, a stringent border seems necessary between let us call it
"information processing", either performed by electric currents or by means
of biomolecular networks. Between topologies of circulating electrical
currents, and myriads of molecular recognition events. Between massive
"free" Boolean constructs, and massive "adaptive" self-constructing
life-cycles... (months ago, this very theme had already surfaced, somehow
as embodiments of language, its "worldliness")... If I could bring order
into these studies, the starting point, or say one of the basic pillars of
the "information bridge" upon the biomolecular turbulent waters, in my
opinion, should be built around the characterization of molecular
recognition events, downwards and upwards.
Thanking the patience!
Pedro
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Received on Thu Nov 24 17:34:55 2005
