Re: miscellanea

Dear Pedro and All:

This response has been delayed because of travel. Because of the long
delay, I have included most of Pedro's message within the response in
order to refresh the issues at at hand.

> 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.
>
The bassis of this assertion of similarity between AI and biochemistry
escapes me. The history of evolution has selected an infintesmal
fraction of all possible chemical structures and constructed a
communicative, collaborative, cooperative system from them.
 
> 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.

I presume that this is also a metaphor. All living systems are finite
in scale and in numbers of molecules. The notion of "rebellion" of
molecules is a bit anthropromorphic, isn't it? The taxonomy of all
molecules emerges from the organization of the atomic table.
Description of the behavior of molecules does not require "logical
agents", that is, something beyond the structures themselves.
>
> 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.

Counting is counting. At the O05 degree of organization, we can count
as follows: One cell grows and divides into two cells. Two cells grow
and divide into four cells. Fours cells grow and divide into eight
cells and so forth. This is "kinetic counting" without specifiying the
time units. As noted in earlier discussions, it depends on acquistion
of material from the surroundings. Yes, one can add technical terms
describing chemical reactions at degree of organization O01 or O02 or
O03. But such descriptions are in a different language and do not
influence how I count in the language of the cells and their material
relationship with the ecoment. For a few simple bacteria cells, these
'countings' are bounded by attribues of the completely determined DNA
sequences.

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 do not understand why one should limit "exhibitions of complexities
from enzymes upward". Energy flows are fundamental to sustaining life.
In living systems, most energy flows result from oxidation - reduction
reactions and reactions closely coupled to oxidation - reduction
reactions (ATP and other nucleotides.) Within a cell, oxidation -
reduction reactions involve objects at degrees of organization
O01,2,3,4. I use the term "co-laborative" because it reflects the
labor (thermodynamic work functions) among the objects of different
degrees of organization necessary to accomplish the work of growth and
division.

The reference to "inert chemicals" should be examined. Biochemicals,
taken as individuals, exhibit physical chemical attributes just as all
other chemicals. Biochemicals may also be "inert" in the sense that one
can define physical chemical conditions which no changes occur (usually!
some enyzmes are extrordinary perverse in this regard.)

So, if biochemicals are no more or no less "inert" than other chemicals,
what distinguishes them?
I suggest that biochemicals are distinguishes by history. An
evolutionary history of co-operative, collaborative and communicative
processes which results in the emergence of new degrees of organization
over the structural relationships among them.

Finally, I iterate once again that all living systems are finite in
scale and finite in numbers of molecules. The fact that large numbers
of molecules and large numbers of interactions must be counted can make
biochemistry ( and nueroanatomy!) difficult for both experimentalists
and theoreticians.
I try to separate such scientific difficulties from confusing conceptual
difficulties or from philosophical differences.

> 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).

Water is simply Hydrogen dioxide - H2O. Taxonomically, two hydrogens
and one ogygen. Two atoms of element one and one atom of element eight
in the atomic table. Agreed, watert has many many unique physical and
chemical properties - as do all other chemicals. It seems that the
description here is not about water at degree of organization O03, but
about potential relationships within a cell (O05) and with
macromolecules (O04). These are other taxonomical classes and these
other classes should play an active role in the discussion of the
cooperative and collaborative aspects of water in living processes.

(I fail to grasp the metaphor with a "actual newspaper.")

>
> 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.

I am uncertain what you are seeking to communicate here.
It is not surprizing that representations of biochemical processes by
simple strings of zeros and ones was not successful. Efforts to
compress biochemical information are seldom successful. What scientific
principle or rule suggested to you that biochemical information could be
compressed?
I certainly agree that balanced production is fundamental to cellular
growth and division and that expereimental evidence supports the
cooperative and communicative relationships amongs degrees of
organization O01,2,3,4 for normal function.

I would be very cautious about conjectures that the absence of
information is in any way "causal" in the normal usage of the word
"causal." Perhaps "absence" could be casual if one first defined the
historical habits of a system and then removed one (or more) of the
habits from the description of the system.

I have sought to illustrate how an adequate taxonomy and the notion of
degree of organization influence our conceptional of the nature of
biological information processing. It is my view that in the absence of
agreement about semiotics and semantics, our discussions simply flow
past one another rather than creating meaningful communicative
exchanges.

Cheers to All
Jerry
Received on Sun Mar 29 08:08:30 1998