----- Original Message -----
From: Igor Rojdestvenski
To: Kevin Kirby (by way of Pedro Marijuan<marijuan@unizar.es>)
Sent: Saturday, October 01, 2005 9:15 AM
Subject: Re: [FIS] Re: What is information?
Dear Kevin and others,
Very interesting post, the more interesting to argue. The ribosome does not have a function. We
assign its behavior a certain goal which we call "function". A very interesting treatise
on this can be found at
http://www.ncbi.nlm.nih.gov/entrez/utils/lofref.fcgi?PrId=3051&uid=14555626&db=PubMed&url=http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=reprint&pmid=14555626
The article is called "The fiction of function".
The existence of a network in physical sense is also highly questionable. I may seem boringly formal,
but as long as we do definitions here, we should be. There are no metabolic networks in the Nature,
but pools of interacting substances (molecules). Really physical is a molecule and interactions
between the molecules. All the rest, like chains of reactions, metabolic networks and so on -- all
this is our "model", our "explanation" certain chains of events and concomitant
interactions. It is like in the world of Feynman diagrammes some diagrammes are called
"watermelons" for their shape, but nobody expects them to really taste sweet and fruity.
----- Original Message -----
From: Kevin Kirby (by way of Pedro Marijuan<marijuan@unizar.es>)
To: fis@listas.unizar.es
Sent: Monday, September 26, 2005 6:54 PM
Subject: Re: [FIS] Re: What is information?
Dear colleagues,
The cumulative attraction of this online discussion, and now especially Pedro's posting
of 22 September, has hooked me. If you can forgive my late intrusion, I would like to try out the
following.
"The non-formal properties of information": here I believe Pedro is bringing
out something extremely important. I wish I could explain clearly why I think this is crucial to the
notion of natural computation, but I need to work at it more. Here, though, are some very crude
comments in that direction.
Look at the idea of the imposition of form on substance. What does this mean? Start with
a piece of the world. Take, say, a ribosome in a living cell. I mean a specific ribosome, this one,
here, under this microscope now. Individual. Particular. Not the type "ribosome." This
sense of "substance" I want to employ here. (The clumsy phrasing in this paragraph is me
trying to distinguish this from the Aristotelian notion of substance as an object of logical
predication.)
This ribosome has a function. Now it is a truism that "function" does not
inhere in physical objects, but arises from a network of relationships and, perhaps, an interpretive
community. We can, in a suitable frame of mind, look at a thing and ignore its function. What are we
looking at? That is, take away function from the ribosome, and what is left? "Form". (The
answer seems irresistible.) Now take away form, then what is left? "Substance" maybe? Is
that really useful? At first, that sounds like some residual meaningless metaphysical ooze-- ousia,
in fact. Isn't all of science about form anyway?
Anything on the level below form seems below scientific discourse, which seeks out form.
When we look at something as a scientist, we give it form. It may even become a "system",
with "states." In computer science, representations of things are the object of study. We
might represent an agent, a transaction, or a number, for example. (One thing you tell students in a
computer science class is that it is meaningless to speak of the complexity of testing if a number
is a prime number; you must instead speak of the complexity of testing whether a representation of a
number is a representation of a prime number. Some representations make it trivial; some make it
hard.)
But in _natural_ computation, things are different. Form, representation, system,
state-- in some way we must be able to occasionally bracket these out and speak of substance alone.
For example, an evolutionary exaptation happens when one part of a biological substance, which
served one function, is recruited for another. The semantics is broken, and re-formed. There is some
discontinuity in how we can track change in substance by change in formal representation. (I think
the philosopher Hilary Putnam hit on one part of this in his arguments against computational
functionalism.) I believe these "non-formal properties of information" are at the core of
the Conrad tradeoff between computability and amenability to evolution.
A separate observation: Pedro writes of looking at the thinker is his/her "spare
time, just when he/she is not acting in that peculiar 'scientific' way." This evokes
Wittgenstein (Philosophical Investigations 132 in particular), where he points out that the
confusions about language that vex us do not occur when language is playing its real-life role (a
non-scientific, non-philosophical role-- in Pedro's scientist's "spare time"). The
confusions only occur in when language is taken off-line, as it were, disconnected from its role in
life, set on a rack ready to be examined. [W's famous negative simile is that of language in this
mode being like "an engine idling". I just looked up the German text and there is no
"engine" mentioned directly: it's just "wenn die Sprache leerlau"ft." Not
being a native German speaker, I don't get the nuances, but the notion of language "running on
empty" seems engaging...]
The privileging of the real-life notion of information connects back to some remarks by
Hans several days ago, on the similarities between trying to define information and trying to define
energy. In fact, the art in a beautiful loose definition such as (for example) "energy is the
ability to do work" is impressive. It is invariant across different sub-notions of energy
(Gibbs free energy, Helmholtz free energy.) and changing understandings of fixed notions of energy
(pre-relativistic vs. relativistic, say). And its invocation of work hooks it in both to another set
of ordinary-life intuitions (I'm using "energy" pedaling this bicycle) and to another
physical concept (work) which can also admit further mathematical elaboration. By so neatly
injecting the concept into the web of other physical concepts, it helps one do physics. (Ok- I am
not a physicist.) This is at least as valuable as a formal definition that gives precise necessary
and sufficient conditions for something to be called "energy." Accordingly, I am a great
appreciator of definitions of information such as "reduction in uncertainty" or
"difference that makes a difference." They tie this plural concept into a scientifically
useful semantic web. If one wishes to charge into the still-dark territory of "non-formal"
information, it is definitions like these that will light the way.
Anyway, I apologize for the length of this posting, as well as its still-fuzzy content.
-- Kevin
_________________
Kevin G. Kirby
Evan Stein Professor of Biocomputing
Department of Computer Science
Northern Kentucky University, Highland Heights KY 41099 USA
kirby@nku.edu (859) 572-6544
Received on Wed Oct 5 11:20:33 2005
