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

From: John Collier <[email protected]>
Date: Fri 12 Sep 2003 - 16:43:28 CEST

Interesting post, Luis. I don't have anything direct to add,
but it styruck me that some work I did with Mark Burch
might be relevant. Here is a quote:

Another case involves the comparison between ethylene and butadiene (Harris and
Bertolucci 1988: 288-297). Ethylene is a double-bonded 2 carbon unit. Butadiene is a 4
carbon unit with 2 double bonds. To make all things equal, the energy of 2 molecules of
ethylene is compared with one molecule of butadiene. The butadiene is more stable by 12
kJ. The usual explanation is that the bond energy is delocalized, but it is not clear why
delocalizing something should lower its energy. Our explanation, that there is increased
cohesion in the form of harmonic entrainment of the bonds explains why the energy of
butadiene is lower.
Presumably more complex chemical systems as found in organisms increase stability
through similar nonlocality (although not through double bounds, but networks of
pathways, even though the individual molecules are not necessarily especially stable). The
thing to note is that it is the whole network that inherits the stability. We could go on
about similar issues in development, evolution and ecology, but these have been studied
extensively elsewhere (ecological studies by Robert May introduced much of the interest
in the general topic).

The quote is from SYMMETRY, LEVELS AND ENTRAINMENT, at
http://www.nu.ac.za/undphil/collier/papers/20140.pdf

John

Professor John Collier
Philosophy, University of Natal
Durban 4041 South Africa
T: +27 (31) 260 3248 / 260 2292
F: +27 (31) 260 3031
email: collierj@nu.ac.za

>>> Luis Serra <serra@unizar.es> 09/12/03 12:57PM >>>

Hello FISers,

I was willing to add a very brief comment about physical aspects of
molecular recognition. From my thermodynamic point of view (terribly
limited!) it is very difficult to find a unitary property covering the
whole "complementarity" processes involved in molecular recognition apart
from the classical thermodynamic properties: free energy, entropy,
enthalpy... For instance, the term co-resonance proposed by Pedro could do
acceptably for protein/protein recognition interactions but I think it
would fare less conveniently in most of the other cases. So, I am tempted
to suggest symmetrization as a more general alternative (in the dynamic
sense proposed by Shu Kun and Michael in their postings before vacations).

But on the other side, "resonance" is a term with a very strong
"oscillation" meaning in several field of physics, and then I think it may
be convenient in order to de-geometrize the vision of molecular processes.
I mean, bonds are seen as "sticks and balls", and recognition phenomena as
"locks and keys". That is a very impoverished approach, sadly predominant
among all my thermodynamic students and most molecular biologists, I often
realize. In general we need less "mechanical linearity" and more
"informational networks" thinking, and that is particularly needed in my
own turf of thermoeconomic analysis.
Enough philosophy for today!!!

Have a nice weekend

Luis

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Received on Fri Sep 12 16:45:26 2003

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