Re: [Fis] Molecular recognition and the foundamental laws of information

Dear Shu-Kun and colleagues,

I have found it very elegant the content of these two messages of yours on
molecular recognition. Coincidentally I was reading Lee Smolin ('Three
roads to quantum gravity', Weidenfeld 2000) and have found that your two
laws on information/entropy were quite meaningful there, helping me to make
some sense on the abstruse thermodynamic phenomena affecting black holes.
Perhaps only metaphorically, or maybe --reminding Bea's yesterday posting
showing support for these views from the cumulative damage field-- it
happens that good physico-informational ideas make sense in a variety of
fields...

In my own case, rather than the quantum gravity approaches of which I am
totally ignorant, these new views make a lot of sense in order to estimate
the information changes that enzymes' works introduce upon the global info
status of the cellular system. I made years ago some 'automata' models
about the enzyme work cycle, but their 'bits' were quite unclear and lacked
any systematic reference to put those minimal info changes into a global
methodological path. I talked on 'wet symmetries' and, particularly,
on 'functional voids'. Now I think that your clean formulation allows the
conceptualization of such functional voids as 'entropy outgrowths' (your
entropy of mixing--not thermodynamic entropy)... Further following this
cellular discussion would take us to the 'forbidden' abduction term, to the
life cycle organization (generative, structural, communicational info
varieties), and to the biological versions of Michael Leyton group theory
of generative processes --eg, the 'telescopic' role of Hox genes... But
all this speculative stuff should belong to the last (postvacational?) part
of the current molecular-biologic session.

So I return immediately to molecular recognition. In the brute list of
recognition phenomena I presented (a list, not a rigorous taxonomy as Jerry
was enquiring--but it has some intriguing internal order, as can easily be
appreciated), the similarity & complementarity casuistic does not look
enough: a substantial part of the biomolecular 'sexy' encounters would
demand a third category, I think. Rather than quenching a mutual 'desire'
of the molecular 'moieties' it would mean the literal involvement or
wrapping of one of the molecules (or a large part of it) by the other.
'Supplementarity' is the new term I would suggest. Supplementarity implies
a molecular involvement which can be done in many ways, putting
facultatively into action a vast panoply of atomic bonds provided for
instance (in protein complexes) by a large and very variable population of
participating amino acids. But I recognize that its is just a biological
nuance derived from the quasi-universal recognition-problem-solving
capability of the living.

"...the symmetry principle: the higher the symmetry, the more stable a
system will be. Now (only now) we can consider the molecular recognition
in details because thermodynamics is actually useless for molecular
recognition consideration. "

It looks a very challenging statement. Does everybody agree with it?

best

Pedro

_______________________________________________
fis mailing list
fis@listas.unizar.es
http://webmail.unizar.es/mailman/listinfo/fis
Received on Fri Jul 18 14:46:42 2003