Re: [Fis] bioinformation and entropy

Dear Michel and colleagues,

Thanks for the stimulus. But I am afraid the discussion on Bioinformation
contains a complexity of its own that is, at least, paramount to the
current one. Better if we devote the next focused discussion --to start
next autumn-- to the bioinfo topic. So I will be very brief.

The briefest encapsulation may be that the current 'bioinformatic'
revolution generated by molecular biology, computer sciences, and robotics,
has lead to the emergence of a series of horizontal 'omic' disciplines:
genomics, proteomics, transcriptomics, metabolomics, signaling science (or
signalomics)... all of them full of more or less homogeneous data, tons of
new data every day derived from sequencing of genomes, from protein
caracterization and networking, from RNA transcripts and processing, from
components of the cellular signaling system, from the whole degradation
machinery (degradomics). But the real biological system (or 'function') is
never organized in such a horizontal way: the lines of biological
processes systematically crisscross among all those new territories. How?
It is a crucial matter of debate. To start with, there is no consensus on
how 'information' taxonomies have to be made or considered within the whole
cellular entanglament... My personal opinion is that MOLECULAR RECOGNITION
becomes the best systematic thread to follow in the labyrinthic paths of
the cell.

Then, one needs a previous clarification on molecular recognition itself
--its specificity, affinity, etc., so much related to molecular energetics.
Entropy is a strong player in any protein-protein binding process, for
instance. Estimating the loss of translational entropy is a big word
(different approximations can be followed; eberything is heterogenous, it
is a bond-by bond analysis, and there is dozens and dozens of them). The
conceptualizations of entropy as 'disorder' are not much uninteresting
here; rather one handles the type of more naturalistic (molecular) views of
spreading (eg, Lambert) and the consideration of the global loss-gain of
degrees of freedom (what I approached as 'space-time occupancy', either
spreading and dilatation, or contraction, shrinking)...

Well, one solved a few basic points on molecular recognition, and adopting
a well axiomatized approach to information physics, firmly related to
thermodynamic entropy (and I agree about that with previous discussants
that Landauer's views are fundamental) we can develop a very original and
solid approach to the current problems on bioinformation.

In other words, the discussion right now on entropy and information may
have a lot of interest for future characterizations of biological
organization. But unfortunately I have not made it very clear in these
paragraphs!

best regards

Pedro

At 11.21 5/5/04 +0200, you wrote:
>To: <fis@listas.unizar.es>
>Subject: [Fis] bioinformation and entropy
>
>Dear Pedro, dear FISers,
>
>The most recent messages in the forum lead us to evoke the
>relations between bioinformation and entropy.
>Although I have a basic idea of what is bioinformatics,
>I do not know how is defined bioinformation.
>Could you help us, Pedro ?
>
>Michel Petitjean Email: petitjean@itodys.jussieu.fr

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Received on Wed May 5 13:58:12 2004