Re: [Fis] molecular discussion

From: by way of Luis Serra <collierj@nu.ac.za>
Date: Fri 11 Jul 2003 - 09:31:10 CEST

I just want to point out that the idea was originally due to James Kay and Eric Schnieder. Jorgenson's book is very derivative from their work. Kay's home page is at http://www.jameskay.ca/

Some literature:
Schneider, E.D, Kay, J.J., 1995, "Order from Disorder: The Thermodynamics of Complexity in Biology", in Michael P. Murphy, Luke A.J. O'Neill (ed), "What is Life: The Next Fifty Years. Reflections on the Future of Biology", Cambridge University Press, pp. 161-172
http://www.fes.uwaterloo.ca/u/jjkay/pubs/sch/sch.html

Schneider, E.D, Kay, J.J., 1994 "Complexity and Thermodynamics: Towards a New Ecology", Futures 24 (6) pp.626-647, August 1994
http://www.fes.uwaterloo.ca/u/jjkay/pubs/futures/tex.html

Schneider, E.D, Kay, J.J., 1994, "Life as a Manifestation of the Second Law of Thermodynamics", Mathematical and Computer Modelling, Vol 19, No. 6-8, pp.25-48.
http://www.fes.uwaterloo.ca/u/jjkay/pubs/Life_as/lifeas.pdf

I do not exactly agree with their approach in all details (they are deficient in understanding the role of information, in my opinion) but you should go to the real source.

John



At 02:17 PM 2003/07/03, you wrote:

Dear Shu-Kun and Xerman,

I have recently read a draft paper by S. E. Jorgensen on "Exergy as Orientor for the Development of Ecosystems" Exergy is a thermodynamic property that characterizes the available energy of a system with respect to the thermodynamic equilibrium. I was thinking that instead of entropy it would be more appropriate the use of exergy as a companion for the term information. In my own field of thermoeconomics we analyze how resources are distributed among the different physical processes occurring in a system (natural or artificial). Indeed, exergy together with the associated irreversibility is what we control, measure, evaluate, etc. Could the same happen in living beings at the molecular scale? Anyhow, in most biologicomolecular instances I presume that exergy differences are minimal (e.g dextro and levo compounds), so it is a quite a big challenge for any entropy or exergy approach to meaningfully characterize such tiny changes.. How can we handle and control these ! " information changes"? Excuse me for this bold speculation motivated by the L=S+I formula.

Bye,

Luis

PS:  I also join Xerman concerns about the nature of chemical bonds.

========================

At 10:34 02/07/2003 +0200, you wrote:

Dear Xerman,

Thanks for the comments. I am writing a paper using the established
methods of data compression to calculate the information theoretical entropy
and assess the stability. I am very sure this is the correct approach.
However, there is still a lot to do. What is
the relationship between energy and information related to
molecular recognition? For ideal gas system, energy divided by kT
(k is Boltzmann constant and T the temperature) gives data (information
theoretical entropy S, information I and L=S+I). How about other
cases where the considered system is not an ideal gas system?
Truly a lot to do.

Shu-Kun

"Xermán de la Fuente Leis (by way of "Pedro C. Marijuán" )" wrote:

> Hi,
>
> This is my first posting in this list. I am a chemist working on
> laser  interaction with materials. My interest on information is basically
> related to the analysis of molecular systems, so I am delighted with the
> current discussion on molecular recognition.  In my opinion, the electronic
> interactions play an essential role in any 'recognition' phenomena. Any
> instance of recognition involves changes in the electronic structure of the
> participant molecular partners: so, basically, the making or breaking of
> what we define as 'chemical bonds'.
>
> Then comes my question: do we really understand "the chemical bond"
> concept? I mean, do we have a solid theoretical bridge in between the
> principles of quantum mechanics and the simplified views of chemists
> (ionic, covalent, van der Waals, metalic... bond types)? Shouldn't this
> very classification be questioned?
>
> If we want to understand molecular recognition as a foundation of the
> informational phenomena of living beings, we have to discuss first the very
> roots of that phenomenon.
>
> Twenty years ago, like most chemists, I shared the view that chemical
> structures were all 'balls and sticks'. Now I think we have to explore a
> new (informational?) approach beyond the limitations and the very few
> 'model systems' analyzed by quantum mechanics.
>
> best regards
>
> Xerman
>
> PS. My greetings to Shu-Kun for his very interesting papers on molecular
> recognition.
>
> Xermán de la Fuente
> Instituto de Ciencia de Materiales de Aragón
> CSIC-Universidad de Zaragoza
> Laboratorio de Procesado de Materiales por Láser
> María de Luna, 3          50018  Zaragoza
> Tel. 976.76.25.27 ó 607.28.20.07
> Fax 976.76.19.57
> email: xerman@posta.unizar.es
>
> _______________________________________________
> fis mailing list
> fis@listas.unizar.es
> http://webmail.unizar.es/mailman/listinfo/fis

--
Dr. Shu-Kun Lin
Molecular Diversity Preservation International (MDPI)
Matthaeusstrasse 11, CH-4057 Basel, Switzerland
Tel. +41 79 322 3379, Fax +41 61 302 8918
e-mail: lin@mdpi.org
http://www.mdpi.org/lin


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John Collier                  collierj@nu.ac.za
Philosophy, University of Natal, Durban 4041 South Africa
T: +27 (31) 260 3248 / 260 2292       F: +27 (31) 260 3031
http://www.kli.ac.at/research.html?personal/collier
http://www.nu.ac.za/department/members/members.asp?dept=philundund&id=3248 Received on Fri Jul 11 09:31:20 2003