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

Dear colleagues,

Before definitely leaving (next Wednesday) let me provide some further
arguments on this crucial theme of molecular recognition. An insight
that can be obtained from different fields related to sensory
recognition (template matching) is 'recognition by parts' versus
'recognition by wholes', its is a distinction quite strategic in visual
and acoustic processing (eg, words vs. letters).

Then, in that long list of cellular instances of molecular recognition, the
relationship between molecular partners of homogeneous nature (DNA & DNA,
RNA & RNA, DNA & RNA ) explained by 'wholistic' template matching through
the identity and complementarity cases goes fine. However, in heterogeneous
partners (DNA & protein, protein & RNA, protein & protein multiple classes)
a multiplicity of partial template matching situations arise where a new
category of 'supplementarity' (or whatever name) looks adequate. Let us
think on the promoter & DNA interaction, or the Polimerase & DNA, or the
molecular complexes in signaling pathways.The partial surfaces involved are
inherently sloppy in their specificity and have a very variable affinity.
Of course, we could keep calling 'complementarity' to this facultative and
highly variable interrelationship, but at the cost of leaving in the dark a
very interesting distinction with respect the very clean and wholistic
matching between complementary moieties (molecular fractions).

To put in literary metaphor --remembering those exchanges with Igor on
Father Brown years ago-- Mr. Gulliver could be 'matched' by identitity with
his fellows (dressing the same military uniform for instance), or by
complementarity in the relationships with his loving wife Mrs. Gulliver;
but he was also matched by a motley crew of Liliputhians who built many
kinds of 'bonds' around his bodily parts. Now, the astonishing matching
games performed by the living cell's crew is that its amino acid
Liliputhian population is coded into a genome, altered systematically (and
regularly selected), and are organized in a tremendously clever way --so
that all the 'functions' and circumstantial 'addresses' of the molecular
crews are put together into the same info bank...

The rationale may be that the cell puts together all the mol-recog. cases
integrated into a harmonious dynamics: the 'identity' implied in
polimerization and multimerization realtionships, the 'complementarity' of
the nucleic acid information-system, plus the facultative 'supplementarity'
of enzymes and proteins. They are forming together a quasi-universal system
to 'exploit' the boundary conditions at the molecular scale, recognizing
them, transforming them, and ABDUCING (?) a living process. I tried to
produce an integrated vision with most of this stuff in my paper posted at
the fis web site (resources section).

Unfortunately there is not much literature on molecular recognition as a
global phenomenon (only an unlimited panorama of ad hoc molecular
cases). It is important that we keep pondering: on the multiple different
cases, the ordering categories involved, the entropy and symmetry
implications, the existing quantum approaches to molecular recognition
('co-resonance' as a common leit motif for all forms of mol-recog.??), the
advancement of logico-molecular schemes of the living cell, the 'group
theory' transferences of multicellular order, organismic 'constraints', etc.

There could be a lot of molecular-recognition work waiting for us after
vacations (but interested parties have the list open to keep the exchanges
up ). Afterwards Jerry will convoke us for the new session on information
and ecological economics around October.

all the best

Pedro

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Received on Thu Jul 24 13:41:41 2003