Re: Data and meaning (3)

Dear colleagues,

Some brief comments on the current themes:

Cristophe --thanks for your new points. At the time being I cannot neither
disagree nor agree. In my own terms, understanding the 'proteome-genome'
(or perhaps better, 'transcriptome') interrelationship through one of your
Meaning Generator Systems might be useful to ascend towards the
computational description of further levels of complexity (tissues, organs,
systems, organisms). But the proof of the pudding is in the tasting:
although the whole cellular complexity is intractable, could you envision a
realistic MGS model (in molecular terms), for instance, of the prokaryotic
cellular signaling system (the well-known 'two component system') applied
to cellular locomotion? This system is now a fashion in alife and
autonoumous robotics. There is plenty of data and you could more or less
easily submit to the 'molecular test' your MGS computational approach... If
you consider interesting the suggestion, I would be happy to collaborate.

As for Jerry points, I find rather vague his approach to biological
optimality. Nowadays there are pretty clear biological treatments of the
theme. Stuart Kauffman 'rugged landscapes' (see At home in the universe,
1995; Investigations, 2000) are perhaps one of the most interesting
EVOLUTIONARY views about how genomes have managed to explore the
multidimensional optimization problems confronted by their phenotypes.
There is not only one maximum or a minimum, but scores of relative max-min
'peaks and valleys' that have to be charted by micro-and macro-movements of
the genetic parameters. Depending on the ruggedness of the landscape, and
the 'movements' of the environment, the ways to explore these peaks and
valleys have to change (eg, prokaryots vs. eukaryots; plants vs.
vertebrates). It is the modern version of van Valen 'Red Queen' hypothesis.
Although I disagree with Kauffman in other extremes, more or less follow
him in this overall approach to biological (and technological!) exploration
of optimality when the environment presents conflicting demands... Besides,
evidences of optimality in biological STRUCTURES, very well studied ones,
pile up in the classical literature (eg, D'Arcy Thompson): skeletons,
bones, shells, internal organs, brains, neuronal connections, plants,
leaves, flowers, widespread Fibonacci series and golden mean ratios in
morphologies, etc. In the late 80's, quite many studies of MOLECULAR
optimality were done (eg, glycogen molecular design, pentose cycle, Kelvin
cycle, metabolic control, etc.), and quite many mutational analysis were
performed --with the result that most natural enzymes are just 'optimal' to
their molecular function... FUNCTIONALLY or physiologically (pretty more
difficult terrain) there also lots of studies and controversies on
allometric relationships, grounded on optimal efficiency when metabolism,
transportation, maintenance, degradation, etc. are considered
together. The prevalence of the 3/4 power law relations in most animal
species is understood as a hallmark of the systemic quest for optimal
efficiency.

As for John, I appreciate the very elegant synthesis presented about the
different approaches (mostly non-biological ones) to extremal principles. I
am particularly intrigued by the MaxEntPro. The only additional suggestion
I would make about that principle is, What would happen if enzymes had
efficiently decoupled their 'informational' work from the thermodynamic
entropy (& free energy) requirements?

About the problem of limitation, relevance, interdisciplinarity,
overlapping of sciences, etc, (we may consider it under as many labels or
'doctrines' as we wish), it is at the very heart of the FIS mission, at
least in my view. Bringing some consistency and clarity (Enlightment as
Karl put it so elegantly weeks ago) into the mosaic of information
conceptualizations, with conflicting 'surrogates' in almost every mayor
discipline, was the initial idea behind the Madrid FIS Conference in 1994.
See the Intro to the Proceedings in our FIS home pages. Given that we are
these days involved in a philosophically oriented session, it may not look
a bad idea that we devote some discussion to this problem too.

best wishes

Pedro
Received on Wed Oct 9 14:27:27 2002