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

Dear Pedro and other FISers,

Pedro's consideration of the relationship between the two parts (most cases pair-wise)
of a molecular recognition is very important.
Their relation can be always regarded as incomplete symmetry
(We can discuss this in very detail again.)

We discuss molecular recognition here because it is closely related to
information at the molecular level. Your concept - supplementarity -
might be still better considered as a kind of complementarity. Small size molecule
is supplementary to the larger one? Sometimes a metal ion,
even though the size is small, is regarded as center (or template) and a large
cyclic molecule is only regarded as a ligand.

Is the molecule wrapping the other molecule
or part of the other molecule more important? Male domination is not good,
female domination may also bad. To avoid struggling for molecular "rights", we may
use complementarity. If the two parts (host-guest) are of the same
rights, it can be regarded as a binary system and much easier to discuss
in terms of information theory.

Which one is suplementary to the other, 0 or 1, black or white?
They are complementary in certain property and the same in many other
aspects. Man and woman are all the same (both have very similar
anatomic structure: two hands, etc., and same interests, etc.).
The only difference is the sexual organs. Spin-up and spin-down are both
tiny small magnets. The only difference is their orientations (up or down).

I was in Paris in a UNESCO conference hall where the superpower USA
has the delegation seat the same size as a small country Switzerland.
UN procedures are easier if all the states are given the seat of the same size.
This might be for the same reason. Smaller country is not necessarily
a suplementary to the larger ones.

Shu-Kun

--
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
"Pedro C. Mariju�n" wrote:
> 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
>
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