RE: [Fis] The Molecule as Text (New Session)

RE: [Fis] The Molecule as Text (New Session)

From: Loet Leydesdorff <[email protected]>
Date: Fri 11 Nov 2005 - 09:28:54 CET

May I suggest that there is a difference between considering molecular
information flows as a chemist or biologist and doing so in the FIS context?

Dear Ted and colleagues,
 
I have always been amazed of the direct link which some natural scientists
wish to make between material flows and the information exchange. The latter
is a mathematical reflection of the events with a different system of
reference.
 
Take, for example, the classical case of colliding balls. When the physical
realization approximates the ideal case, the thermodynamic entropy vanishes,
but the redistribution of momenta and energies at the macro-level becomes
more pronounced (since there is less dissipation). Correspondingly, the
message that the collision has taken place contains a larger amount of
information. Thus, the two types of entropy can vary independently: the one
may increase and the other vanish in the same event.
 
The reason for this independence is that the systems of reference for the
two entropies are different: thermodynamic entropy refers exclusively to the
distribution of, for example, momenta and positions among particles, while
the reference system for probabilistic entropy in this case is the system
which conserves macroscopic momenta and energy. The two forms of entropy
production (thermodynamic and probabilistic) stand orthogonally in the ideal
case.
 
In the case of biological systems, one does not expect independence because
these systems are dissipative. However, one analytically should declare the
two systems of reference first independently, in order to study their mutual
information in the dissipation. Perhaps, I misunderstand this discussion,
but please in that case try to explain to me why information exchange is not
a mathematical construction, but would be embedded in life (or something
substantively like that). It seems to me that if (following Maturana) life
is defined as the exchange of molecules, the probabilistic entropy generated
is not directly related with nor immediately explanatory for the phenomena.
There are several in-between steps to be specified.
 
These steps may be very different for different systems of reference (e.g.,
biological life or human culture). For example, in the latter case, I expect
more anticipatory mechanisms (e.g., the sciences) to be involved than in the
former and therefore a different dynamics of the entropy.
 
With kind regards,
 
 
Loet
  
  _____

Loet Leydesdorff
Amsterdam School of Communications Research (ASCoR)
Kloveniersburgwal 48, 1012 CX Amsterdam
Tel.: +31-20- 525 6598; fax: +31-20- 525 3681
 <mailto:loet@leydesdorff.net> loet@leydesdorff.net ;
<http://www.leydesdorff.net/> http://www.leydesdorff.net/

 <http://www.leydesdorff.net/knbecon> The Knowledge-Based Economy: Modeled,
Measured, and Simulated
 <http://www.universal-publishers.com/book.php?method=ISBN&book=1581126956>
The Self-Organization of the Knowledge-Based Society;
<http://www.universal-publishers.com/book.php?method=ISBN&book=1581126816>
The Challenge of Scientometrics

 
 

In the local context, all you have to do is invent a new science that sheds
new light on phenomenon that are seen locally, namely in the molecular
domain. In the FIS context, you have this seeming impossibility squared.
That's because you'll be using this domain to get leverage on the larger
problem of an information science that applies at all domains. And more
importantly, we'd understand what flows among domains and how.

Toward this end, I'd like to put an early suggestion for limiting the "bio"
semiotic approach a bit. Several smart people here have noted the
internal/external problem of meaning and intent when you scale biosemiotics
down to elements that apparently cannot reason. So I am very skeptical of
Peircian mechanics at the biological level.

And yet - as with many - I find I cannot abandon the notion of meaning when
using that of information.

So I would ask you (Jerry and Kevin) if we cannot have a limited semiosis.
In the following way:

Generally, we like to think of things that have physical reality as the
causal primitives in science. So we think of entities having properties as a
first order concern, and those entities are the ones we can see and measure.
So even though all our rudimentary physics actually operates by way of
fields, we suppose those fields as assigned to or generated by entities. We
go so far as to require other entities to be exchanged in field effects.

And I see this with chemists as well. The assumption is that the molecule is
what exists as the primitive agent. If information is exchanged, it must be
among these "hard" entities. So we look, for instance at their shape (which
I know Jerry will get to), and the structural elements Pedro mentions below.

Can we posit that the true identity of a molecule is something
information-based and that what we see is the text, a text, a representation
and not something that some god started his day with? This allows me to
swallow the important elements of biosemiotics, and forces me in the
direction of inventing new abstractions for the primitives involved.

And of course, these would be abstractions behind the "text" we see, and the
one molecules perceive. Fields and particles then become effects, not
something necessarily intrinsic to information flows and bindings.

So then, brief responses to Jerry, Kevin, Pedro...

Jerry:

I am glad you gave us the history. But I think history is the enemy here.
The abstractions we blindly accept today were invented in a duller context
and to satisfy needs vastly less demanding than FIS requires. I fear too
many contributors (one would be too many) will try to stretch one or another
old principle to fit this new concern.

But it is of extreme value in posing a candidate problem. After all, if we
are creating something useful, it should solve problems more elegantly than
before or describe more crisply or provide for better analytical tools.

What are the relations between this sort of encoding and other metabolic
encoding? In particular, can we imagine a catalytic - type of encoding that
parallels the genetic encoding?

And here we have it. Thanks Jerry.

Kevin:

I am so glad I heard your talk in Paris. So I know that when you say
"Computer Science," you mean something larger than the ability to describe
things algorithmically. But this notion of "natural computation" implies the
logics involved are confined to the relatively simpler logics we normally
code for/model within. The first order and probabilistic logics. I think
that an unnecessary limitation.

The simulation relation is central in automata theory and was recast into a
category-theoretic framework by Arbib and Goguen (taking different
approaches). But the notion of a mapping between a biological system and a
formal system, seems to be, at first glance, a category mistake! As soon as
one identifies a fragment of nature as a system, one has locked in some set
of states, and it is hard to separate the true computational power of a
living system from what accrues merely to our conventional state assignment.
This is taken up nicely by the philosopher David Chalmers in a response to a
very strong statement at the conventionality end by Hilary Putnam. (One
could see this as a recasting of the debate in Plato's Cratylus in
computational terms!)

This tension between the formal and the material seems to lie at the heart
of the field of natural computing.

So we need to reinvent both, yes? Both our formal mechanics of computation
and our notions of what the "material" is. In both cases we are dealing with
abstraction science and unavoidably category theory, no?

Pedro:

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.

As always, I'm with you, but suspect you fear going to far so don't go far
enough. Why not?

Best, Ted

-- 
__________
Ted Goranson
Sirius-Beta
Received on Fri Nov 11 09:26:53 2005


This archive was generated by hypermail 2.1.8 on Fri 11 Nov 2005 - 09:26:53 CET