Dear colleagues,
Thanks to Jerry and Kevin for their splendid Opening Text!
Amidst all the attractive topics raised I will select a few tidbits (there
will be plenty of time for more careful explorations).
>1. From an informational perspective what would constitute a definitive
>theory of the information content of molecular bionetworks?
>
In our times, I would say that the "bioinformational" themes have
definitely gone beyond the unitary schemes proposed after the adoption of
the information metaphor (codes, signals, translation, transduction, etc.),
for instance, the case of the so called Central Dogma of molecular biology.
In my opinion, important progress towards a more consistent vision will
depend on advancements in two strategic sub-fields: molecular recognition
on the one side, and "heterogeneous networks" on the other. What is the
information content of a single molecule? Beyond Scheider approach to DNA
sequences, based on Shannon (Lila Gatlin, in late 60's was the historical
pioneer), and I would say that some stuff presented in this list is really
promising: Shu Kun Lin on measuring "molecular similarity", and
posthumously Michael Carlton on counting the bits of non-periodic molecular
structures (John Holgate). Symmetry is a crucial avenue to advance these
conceptualizations --Michael Leyton's, Gyuri's...
>Early in the history of biology, organisms were classified based on
>categories, more or less following Aristotelian conceptualization of
>Phyphrian trees, choices of potential properties. The ten Aristotelian
>categories, the ten highest genera are listed as: substance, quantity,
>quality, relation, place, time, position, state, and action, being acted
>on. Biological function is related to these categories. I presume that a
>property of the molecular bionetwork encodes and decodes information
>concerning these genera.
>
This point is so important! Let me refer to arguments in my presentations
ECAP 2005, and FIS 2005. I argued that as a consequence of the peculiar
"embodiment" of the biomolecular agents (enzymes), in the study of their
function we have to pay attention not only to the strictly functional
‘what’ dictated in the active site of the enzyme, but also to a series of
accompanying processes distributed over different parts of the molecular
structure, which may include: modulation by effectors, intracellular
transportation, permanent (post-translational) modification, formation of
complexes, the time-frames derived from transcription and translation, and
finally degradation. So the ‘what’ of the functional clause should be
accompanied by circumstances such as ‘how fast’, ‘where’, ‘which
way’,
‘with whom’, ‘when’, and ‘how long’. The mind-boggling
factor is that
almost all of these circumstances may be captured within particular parts
--MODULES, DOMAINS-- of the enzyme, corresponding to DNA exons & introns,
and then become amenable to evolutionary control... this is basically the
source of eukaryotic organismic complexity: a "genetic algorithm"
decomposable in parallel "logical" clauses that can be explored and solved
in independent steps.
Jerry, I would appreciate if could you expand the above reference to
Aristotle. The parallel with the circumstances of the enzyme embodied
function is strikingly close!
Well, several paragraphs, in Kevin's are addressing this very problem from
a different angle. Let me remind a term used by Michael Conrad on the
"unpicturability" of the enzyme function---nevertheless it is amenable to
evolutionary control, as it is "represented" into a sequence of "symbols"
in the DNA stuff, but see better below:
>This tension between the formal and the material seems to lie at the heart
>of the field of natural computing. The work of Michael Conrad emphasized
>the special role of biological material to explain the fantastic outcomes
>of evolution, as opposed to any power inhering in the class ofrelatively
>simple Darwinian algorithms. In the mutation-absorption model of the
>enzyme, we can begin to see how computational power emerges from the
>breakdown in the simulation relation...
Kevin, in the comparison between the enzyme and the integrated circuit, say
between the cell and the computer, I wonder whether we could put into very
simple terms the crucial differences (the tradeoffs analyzed by Conrad
could be illuminating). The widespread assumption of "functionalist" thesis
on the separability between hardware and software, often translated
literally into the biological (particularly in neuronal "info
processing"--see the Churchlands) perhaps relies on the lack of robust
metaphors at the other side, on generalities raised in abstract ways... or
real cul-de-sacs (eg, autopiesis).
>One final introductory thought. In imputing computing to a fragment of
>nature -- a ribosome, say -- we should not view ourselves as reducing it
>to the apparently impoverished level of a Turing machine or a Pentium 4.
>Computer Science is in its infancy; the ribosome, the cell, the ecosystem:
>these are all better exemplars of computational wonder than our humble
>devices. If only we had a theory…
I completely agree. My contention is that we are in front of one the majors
problems of our pretended information science.
Again, Thanks for the "food for thought"!
Pedro
Received on Wed Nov 9 12:15:30 2005
