Jerry and Kevin-
This promises to be a terrific session! Already I
am using my second message for the week.
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?
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 01:39:37 2005
