miscellanea

Dear Jerry,
dear colleagues

In responding to your last two messages (sorry for the delay) I will group
the topics in four separated blocks:

1. INFORMATION AND BIOCHEMISTRY.

The problem I see with the physical and biochemical approaches to the
phenomenon of life (and of bioinfo), following your very arguments, is
largely similar to the discussions at the end of the 80's between the
practitioners of Artificial Intelligence and of Artificial Life --this was
the underlying sense of some of the questions in my previous message.

Although the "brute force" approach of the former AI was "logically"
correct, in the same sense than you have argued about biochemically
systematic counting, mapping functions and one-to one correspondence, it
turned out to be an approach scarcely relevant in order to advance the
knowledge of neuronal (bio)processing. Rodney Brooks crafted very well the
arguments on why a new computational approach (ALife) were necessary --if
the further evolution of AL has really fulfilled its initial promises and
their new strategy has been fertile is another matter. I would encapsulate
Brooks' message as the "rebellion of infinities": the AI impossible logical
management of the multiple emerging infinities in the encounter of any
logical agent with the complexities of a natural environment.

Perhaps the same is happenning here. Infinities may be found one after the
other when you try to "count" e.g. how an enzyme folds, how it "fishes" for
its substrate and transforms its electronic structures (implying in both
cases the whole panoply of electromagnetic forces, vand der Waals forces,
hydrogen bonds, hydrophobic forces, electro weak interactions, etc.!!!),
not to speak about how millions and billions of these molecules orchestrate
their individual and collective activities... (this is one of the reasons
why molecular biology remains largely empirical and pragmatic). Any
further response that one can always give a logical "kinetic counting" is
tantamount to hide the rub under the carpet. Precisely because of this very
exhibition of complexities, there may emerge, from enzymes upwards, the
amazing "info-processing abilities" of life (including neuro-processing and
intelligence). And not from any other (yet unknown) set of inert chemicals.
The fact is that "taming infinities" keeps being the regular business of
cells and of organisms (let us think on the math. graph of a trillion
interlinked neuronal processes).

I assume that you are impecable in your own exposition of the biochemical
perspective. But maybe it has the same relevance, concerning the further
organization of bioinfo, as the laws of solid-state physics have concerning
the workings of any of these clever computers around us. The biotricks to
overcome the series of infinity barriers --"abduction" of just the very few
RELEVANT traits-- would not necessarily be amenable to the brute force
(logical) approach.

2. WATER

That substance is something more than a "source of protons (as its
taxonomical bioch. role)". In a relatively recent review (in Nature, 1996),
the question on how water structures interact with macromolecules, solute
ions, and colloidal particles, largely appears as an unanswered one. The
amazing solvent, viscous, dielectric, electromagnetic, and crystalline
properties of water are continuously called into action as a means of
putting an overall GLUE (let us remember Ray4s quest) in life activities.
Water is a source of protons, but it is also the vehicle for prot. folding,
an active player in every enzymic function, a background of multiple
biophysical-electromagnectic processes, but above all it is the massive
interconnecting tool of bioinfo processes (coming back to the parallel with
computers, water solves "de gratis" the awful WIRING PROBLEM that plagues
the design of electronic VLSI circuits). Both intracellularly and
intercellularly, water becomes an actual "newspaper" that contains in its
successive pages the RELEVANT info items to search for... (and this would
lead to the story of how to analyze compositional info--but this is
becoming too long).

3. "PRESENCES VERSUS ABSCENCES"

I made, a few years ago, a very simple automaton model of a regulated
enzyme function. Its output was a binary series (just 0s and 1s) in
response to a series of binary inputs (substrate and effectors). Well,
someone argued me about the info behind every bit of the output. The "0", I
was told, represented a mere absence, so just one bit. But every "1" had
behind it all the above story about enzyme non-picturable function...

OK about the 1s, but, was it true that the "0" was almost info-free?.

My belated response was the idea of "functional voids" to be filled-in by
the productive machinery of the cell (eg. a call to protein synthesis
because the specific enzyme is out of work). So absences may have a genuine
info content in the intra and intercellular communicating games--so
implying that the "0" might be even far richer than the "1". This means, in
another words, the necessary connection of the signaling (info) processes
with the underlying productive and degradative activities of the living.
But I am affraid that, in these discussions, I have already argued about
the connection between signaling INFO - and the balanced PRODUCTION of the
own structures (the idea of self-organized criticality, and the
one-sidedness of autopiesis) and do not want to insist further.

4. THE LANGUAGE OF CELLS

Unfortunately Josi and me are at the beginning of the beginning. Our
exploration on the possibilities of "partitions" as formal descriptive
tools of cellular signaling systems has started a few months ago. But we
much thank your thoughtful comments and questions, for they have put some
of our searches in a different light.

regards from Zaragoza

Pedro

-----------------------------------------------------------
Pedro C. Marijuan --FAX 34 976 761 861 --TEL 34 976 761 927
Dto. Ingenieria Electronica y Comunicaciones
CPS, Universidad de Zaragoza
Zaragoza 50015, SPAIN
Received on Thu Mar 19 13:57:21 1998