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

Dear Shu-Kun and colleagues,

Your idea (below) looks very good. We could try to gather some fis-related
papers and also a few invitations to interesting authors (I think at least
on Meggs and his 'biological homing'--other parties could suggest further
names to invite). Let us keep pondering upon the idea for a while.

In the physicalities involving molecular recognition, those related to
symmetry (as already partially discussed) are perhaps the most attractive
ones; but the 'glueing together' that accompanies the recognition process
puts in front of us, again, the problem of 'bonds' (Xerman). My question,
inspired by the 'coupled oscillator hypothesis' developed by JL Fox, in the
70's, in order to explain the enzymic recognition and transformation of
substrates, is the extent to which a common electromagnetic coupling
(co-resonance?) could underly the three mol.recognition categories of
similarity, complementarity and supplementarity (or heterogeneous
complementarity) in most cases. Somehow, reminding bonds commonality
itself, as some physical-chemists now are arguing. Further, there is a
pretty challenging (and short) paper by Morowitz, 2001, where he argues
that Pauli's Exclusion Principle is the genuine responsible for the
creation of all sorts of chemical information, including bonds --what I
have summarized looks awfully sketchy, but his overall idea about
physically explaining the evolutionary 'growth of information' and
complexity in the most parsimonious way might be a challenge for us to
develop a serious 'information physics' debate in a near future...

Biologically, if we could make a big taxonomy --or just a big list-- of all
kinds of mol. recognition phenomena occurring even in the simplest cells,
we would find that the very list becomes crisscrossed by a myriad of
'process' lines. Let us assume that those process lines can clearly be
grouped into functional clusters (the holy grail of present day
bioinformaticians arguing on 'systems biology'). Then, it is upon that
strange functional skeleton of life that we have to situate the big
questions about the informational characteristics of life. For instance,
the meaningfulness of the generative/structural/comunicational forms of
info (that captures and highlights, I think, the functional core of the
system); or the very peculiar cognitive relationships of the system with
respect to its own boundary conditions --the latter being an aspect
that dramatically separates life's behavior from 'dynamics', indeed.

Reductionism is mute about that strange and hiper-complex series of
recognition couplings, because it only looks at the decomposition of
processes into elements and subporcesses and not at their integration into
behavioral or functional wholes. Particularly looking at the relationship
with the boundary conditions, enacted by a multitude of adaptive
molecular-recognition events (ad hoc receptors, channels, transporters...),
followed by further adaptive changes within the inner structures, life
transcends dynamics and appears as 'informational' and not merely
'autopoietic' or 'selforganized' (secondary aspects which may also be
present in dynamic systems without the inner knowledge of life)...
therefore the living system legitimately 'abduces' (as I argued long ago)
and has 'purpose' (as James emphasized in old postings too). In other
words, once life starts, we have a new kind of entity endowed not only with
'dynamics' but also with 'infonics' (or 'infopoiesis') or whatever
'informational dynamics' term we may choose. Properly characterizing that
enlarged form of dynamics should be a crucial task.

Are these speculations cogent in any extent? Sorry for having blurred
together the bioinfo and the info physics discussion themes, but I think
this is a very defining item for our entire enterprise ---one of the few
places where we can do strategic advancements in a problem that
reverberates at great length, and untractably, into a number of
disciplinary fields.

best post-vacational wishes

Pedro

At 23.35 2/9/03 +0800, you wrote:
>Dear Pedro and other FIEers:
>
>We may organize several papers on this topic for publication as a special
>issue
>in my journal MOLECULES (http://www.mdpi.org/molecules/)
>or Molecular Diversity (http://www.kluweronline.com/issn/1381-1991).
>These two journals have been fully covered by Science Citation Index database.
>As the editor-in-chief of the printed journal Molecular Diversity
>I can have a special issue on molecular identity or molecular
>distinguishability
>which is essentially a molecular recognition topic. Could you prepare an
>overview
>f the discussions for publication as the first paper? The deadline for sending
>the papers to me might be 1 December 2003.
>
>I am still handling some of the comments made by Igor and other FIEers.
>
>Thanks, Pedro!
>
>Shu-Kun

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Received on Fri Sep 5 15:18:17 2003