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

Dear colleagues,

Let me continue with some comments on molecular recognition. Jim's posting
on the effect of scrambling the letters in human recognition of words, and
the possible parallel in the molecular world, looks quite direct in the
case of DNA. Scrambling a promoter, for instance, leads to a diminished
expression of the gene --or in the case of an active site, to dramatically
lower kinetic rates in the functioning of the enzyme.

However, what I find fascinating is that the scrambling may also alter the
transportation destiny of the enzyme or protein, or its recognition and
anchoring into a functional complex, or its sensibility regarding some
effector, or its resistance to degradation... This actually means the
multi-stage, enlarged character of the biomolecular agent --its
transmolecularity-- that usually passes unnoticed (we only look at some
catalytic effect). In terms of the current bioinformatic discussion on
'systems biology' we might say that

genome
tanscriptome,
proteome,
metabolome,

usually obtained by separate techniques and ad hoc specialists, are linked
and intercrossed by labyrintic lines of 'process'. And there is no way to
consider any biofunction but as a complex cluster with pretty arbitrary
frontiers in most cases. Let us note that all nodes in the massive
intercrossing of events in the previous 'omes' are characterized by some
specific molecular recognition case. (en passant, I think that we are still
missing two new 'omes': the 'signalome' and the 'degradome', but is is too
long to be followed here.)

So, I am tempted to argue that the evolutionary consequences of focusing
the cellular functioning in mol. recog. terms may be rich and profound. I
think it is one of the key phenomenons that is called to produce the
theoretical breakthrough necessary to conceptualize properly the
astonishing masses of new facts that biology is producing at enormous
speed. And I also think that our classical information categories discussed
in the list ---generative, structural, communicational-- will get their
mutual dynamic relationships far clearly established if we think in terms
of the above molecular recognition matrix of events. Actually, the transfer
of the generative towards the structural in a continuous communication with
the environment ('boundary conditions') continues to be the linchpin of all
forms of life. In some theoretical realms, neat theories on 'generative
processes' or 'communication theories' have been produced: What would
happen in the generalized interplay of the above biomolecular background?
In my opinion, the paradoxical 'evanescent permanence' of life is the result.

best regards

Pedro

PS. Fis-list novelties: Around ten people from very heterogeneous
backgrounds have joined the list in recent weeks. I apologize that there is
not much info available on how this list is organized, or its discussion
style. Parsimonious posting (moderate length, no more than two postings per
week) and slow responses are encouraged. Also, here we prefer bounded
discussions with moderators (currently we are running the post-vacational
part of a session on 'molecular recognition and molecular codes', with
Shu-Kun and Sergei as central invitees and myself as moderator). But
discussion 'tangents' are always welcome in this list (well tangents, and
not necessarily 'whole geometries'). The next focused discussion will run
around the middle of next month, on "Ecological Economics and Information",
moderated by Jerry Chandler and Luis Serra. For the newcomers, some perusal
at the fis home site http://fis.iguw.tuwien.ac.at/ and
at http://fis.iguw.tuwien.ac.at/mailings/ are very recommended.
   

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Received on Tue Sep 23 14:32:43 2003