John, Jamie, Pedro, Koichiro and to the list:
This email responds to the posts by John C and Jamie R. on the topic of
"Biological Computing."
Before reading this email, I would encourage readers to re-read the
excellent post of Koichiro Matsuno of June 26, 2006 and Pedro's post of
Nov. 17, 2006 in order to place my remarks in context.
First, I note that several concepts of computing exist. A computation may
be exact or inexact; the logic of computation may be either exact or
inexact. For example, I may compute the outcome of a staff meeting on
sensitive personal issues. Or, I may compute exactly the Alexander
polynomial of a particular twist knot. Or, I may compute exactly the
products of a chemical reaction. I most certainly can not compute exactly
the value of pi. The many possible usages of the concepts of computing,
both exact and inexact, should be considered when reading this post.
Finally, I note that living systems compute exactly which chemical
structures to reproduce and do so exactly; this is what is called inheritance.
John's narrative is, to me, very puzzling. I do not understand the
relation, if it exists, between the concepts used in sentences and the
notion of biological computing.
Without reference, John states:
"...Atlan's use of computational
language along with his claim that some biological (biochemical really)
stuctures have "inifinite sophistication". A structure with infinite
sophistication cannot be computed from the properties of its
components."
I find no chemical sense in this statement.
I have no idea how a chemical structure can have "inifinite sophistication".
Is either Atlan (or possibly John inadvertently) creating a false concept
of chemistry to serve a philosophical goal?
Is Atlan attempting to force the chemical sciences into a procrustean bed
of mathematical physics?
The concept of "inifinite sophistication" is dangerously close to rejecting
a basic notion of the chemical sciences, namely, that matter is composed of
multi-sets of atoms.
The concept of "computational depth" is well defined in computer science
but not in chemistry.
The chemical reference system starts with (begins with, is resourced in, is
a narrative of) parts of atoms and constructs higher order biological
structures from these parts. Chemistry is a mereologic science.
In other words, the computations of chemistry start at the deepest level,
the intangible space filling concepts of parts and constructs upward to
systems of larger size, Life itself.
What has computational depth of the computer science variety to do with
chemistry or molecular biology?
John deepens the mystery with the following paragraph:
"Here is my stab at an answer: the notion of mechanical since Goedel and
Turing (I would say since Lowenheim-Skolem, since Turing's and Goedel's
results are implicit in their theorems) breaks up into to notions,
stepwise mechanical and globally mechanical."
Is the pot calling the kettle black?
If the real number system is a mathematical structure for mechanical
computation,
stepwise mechanical is a SUBSET of global mechanical.
Or, am I missing the point?
Does John wish to imply that calculations can be made with Cantorian numbers?
A critical fact to note along this line is that living systems calculate on
how to reproduce themselves chemically and do it regularly, without help
from Cantor, Rosen or Turing.
It seems to me that if one wishes to conceptualize biological computing,
one ought to start with the notion of chemical principles as sources of
information of codes for exact chemical relations. Empirically, the
supporting facts for this conjecture has been around for more than fifty
years. I guess that the new ideas flowing into philosophy are retarded by
mechanisms that I do not understand.
Jamie writes an equally curious piece. Rather than looking at living
systems as natural objects with natural computational properties, Jamie
prefers to place mechanics of computational abstraction:
"The thema of computation is the separation of
hardware from software.
In contrast, the thema of of natural systems is
the conjoinment of 'hardware' with 'software'."
as the principle premise in his efforts to develop syllogisms. Why?
A concept, "the thema of of natural systems" is separated into two terms,
hardware and software.
For what purpose is this strawman constructed?
Stereochemistry! Really!
This leads to the conclusion:
"The 'hardware' of the metabolic step IS the
'software' .. in this example, the stereoform
acts as the specific instruction 'yes/no' or
'1/0'."
If this is the case, that the hardware is the software, why bother with
the initial premise at all?
To suggest that the information in a chemical structure is reduced to a
'yes - no' is also a very novel approach to chemical information theory.
Jamie continues:
"Adaptation" capacity is naturally intrinsic
with living cells. It will not happen unless
'imposed' - in classical computer systems.
Let me give a brief narrative that contradicts this view of computer systems.
An idealized computer system in the "idle mode" is a homostatic device.
It is structured to adapt to inputs.
Following an input, a key stroke, the computer system is perturbed and
adapts to the perturbation by changing as many electrical flows as
necessary in order to return to the 'idle' mode, to homostasis.
In other words, from a purely mechanical perspective, an ideal computer is
an adaptive device and the narrative of adaptations for a living system and
a computational system are parallel in certain fundamental aspects of
temporal pathways of response to perturbations.
It appears to me that both Koichiro's and Pedro's narratives (cited above)
are closer to the future and that we should look to extend their
perspectives in ways that are consistent with Life itself. I note in
passing that I am working on a paper on the logic of a new relational
system, the perplex number system for atomic numbers, that I hope will
contribute to resolving some of the condundrums raised by this topic.
Cheers
Jerry
On Nov 17, 2006, at 7:44 PM,
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Today's Topics:
1. Re: Re: request - Biological Computing (James N Rose)
2. Re: Re: request - Biological Computing (John Collier)
3. what is life, logically? (Jerry LR Chandler)
From: James N Rose
<<mailto:integrity@ceptualinstitute.com>integrity@ceptualinstitute.com>
Date: November 17, 2006 9:57:14 AM EST
To: Pedro Marijuan <<mailto:marijuan@unizar.es>marijuan@unizar.es>
Cc: <mailto:fis@listas.unizar.es>fis@listas.unizar.es
Subject: Re: [Fis] Re: request - Biological Computing
Pedro,
If you will indulge me in one additional comment in this
topic also. There is a critically important analysis I
did a number of years ago on the issue of operational
differences between computer/computation practices and
natural biological/botanical systems.
Without belaboring the point is comes down to this:
The thema of computation is the separation of
hardware from software.
In contrast, the thema of of natural systems is
the conjoinment of 'hardware' with 'software'.
Every computer system has a design matrix of
information routings into-which or onto-which
instruction codes are imposed.
That does not happen in natural systems.
Let me give an example.
Stereo-chemically some molecules can be exactly the
same atomic constituents, but be mirror images in
3D structure. The levo- and dextro- rotary forms.
Because metabolic pathways rely heavily, if not
absolutely, on key-lock compatability (because of
electromagnetic 'fit' considerations), one twist
form will 'enable' a pathway step, while the
mirror form will 'block' the step.
The 'hardware' of the metabolic step IS the
'software' .. in this example, the stereoform
acts as the specific instruction 'yes/no' or
'1/0'.
This is THE KEY thematic/functional difference
between their information processings.
"Adaptation" capacity is naturally intrinsic
with living cells. It will not happen unless
'imposed' - in classical computer systems.
They approach, involve, and use 'information'
relations in quite different ways. AI - as
currently formulated/practiced - will never
perfectly emulate Life. 'Simulation' will be
only close approximations, instead of practical
duplications.
Jamie Rose
Ceptual Institute
(Please forward to list if it does not
automatically post. Thank you)
From: "John Collier" <<mailto:collierj@ukzn.ac.za>collierj@ukzn.ac.za>
Date: November 17, 2006 2:10:22 PM EST
To: <<mailto:fis@listas.unizar.es>fis@listas.unizar.es>,
<<mailto:marijuan@unizar.es>marijuan@unizar.es>
Subject: Re: [Fis] Re: request - Biological Computing
Dear colleagues,
Pedro has pointed out a real problem, I think. I have a few words to say
on it that may be of some help in sorting out the issues. They derive
partly from my trying to make sense of Atlan's use of computational
language along with his claim that some biological (biochemical really)
stuctures have "inifinite sophistication". A structure with infinite
sophistication cannot be computed from the properties of its
components. Sophistication, as far as I can tell, is a measure of
computational depth, which depends on the minimal number of
computational steps to produce the surface structure from the maximally
compressed form (Charles Bennett). Atlan has made the connection, but
also noted it is not fully clear as yet, since Bennett's measure is
purely in terms of computational steps, and is relative to maximal
compression, not components. Cliff Hooker and I noted these problems
(before we knew of Atlan's work -- well, I did, but it was presented
poorly by one of his students -- see Complexly Organized Dynamical
Systems, Open Systems and Information Dynamics, 6 (1999): 241-302. You
can find it at
<http://www.newcastle.edu.au/centre/casrg/publications/Cods.pdf>http://www.newcastle.edu.au/centre/casrg/publications/Cods.pdf).
The
question relevant to Pedro's post is why is computation relevant if
common biological systems have infinite sophistication, and thus are not
effectively computable, even if they have finite complexity?
Here is my stab at an answer: the notion of mechanical since Goedel and
Turing (I would say since Lowenheim-Skolem, since Turing's and Goedel's
results are implicit in their theorems) breaks up into to notions,
stepwise mechanical and globally mechanical. A globally mechanical
system can be represented by an algorithm that halts on all relevant
inputs (Knuth algorithm); these are computable globally. The stepwise
ones have no global solution that is effectively computable, but are
computable locally (to an arbitrarily high degree of accuracy). The
difference is similar to that between a Turing machine that halts on all
relevant inputs and one that does not. Both are machines, but only the
latter corresponds to Rosen's restricted notion of mechanical. So
computation theory can help us to understand the difference between
things that are stepwise mechanical, and things that are not. Things of
infinite sophistication are not globally mechanical. I will say without
proving that they correspond to Rosen's systems that have analytical
models but no synthetic models. They may still be mechanical in the
weaker sense. In fact I have not been able to see how they cannot be
mechanical in this way.
Consequently, there are Turing machines that are mathematically
equivalent to systems of infinite sophistication, but they do not halt.
So you are probably wondering how processes of this sort can occur in
finite time. The answer is dissipation. I'll not give the solution here,
as my coauthor on another paper just came into the room and asked me how
it was going, and I said I was writing something else that was
peripherally relevant :-) A case in point is given in my commentary on
Ross and Spurrett in Behavioral and Brain Sciences titled Reduction,
Supervenience, and Physical Emergence, BBS, 27:5, pp 629-630. It is
available at
<http://www.nu.ac.za/undphil/collier/papers/Commentary%20on%20Don%20Ross.htm>http://www.nu.ac.za/undphil/collier/papers/Commentary%20on%20Don%20Ross.htm
as well as the BBS site.
All spontaneously self-organizing systems (see the Collier and Hooker
CODS piece) are only locally mechanical. I won't prove that here, but
there is a clue in the BBS commentary.
Cheers,
John
Professor John Collier
Philosophy, University of KwaZulu-Natal
Durban 4041 South Africa
T: +27 (31) 260 3248 / 260 2292
F: +27 (31) 260 3031
email: <mailto:collierj@ukzn.ac.za>collierj@ukzn.ac.za
http://ukzn.ac.za/undphil/collier
Pedro Marijuan <<mailto:marijuan@unizar.es>marijuan@unizar.es> 11/17/06
12:22 PM >>>
Dear FISers,
I was recently asked some short views summarizing the field of
biological
computation. After several weeks delay, I finally penned a few lines.
Maybe
someone in the list can find some interest in the very rough reflections
below.
-----------------------
In my view, there is some trouble in biological computation or
bioinformation or whatever name one chooses for the field. One of the
main
inputs has traditionally come from theoretical biology, even in the 60's
(e.g., Waddington, Dancoff & Quastler, von Bertalanffy), but mostly in
late
80's and early 90's, with leading figures such as Michael Conrad and
Robert
Rosen. They both were very critical on any easy-going marriage between
computers and biology. Michael produced a very fine contraposition of
computational differences, between living cells and classical computers,
from the point of view of adaptability. On the other side, the
influences
from computer fields did crystallize into Artificial Intelligence, and
more
recently into Artificial Life (Holland, Brooks, Langton, etc.) and
perhaps
complexity theorists (Kauffman); notwithstanding important differences
among these fields , as a whole they never saw any terrible difficulty
in
the cross-fertilization, or better hybridization, between computers and
biology.
In actuality I think that around "biological computing" there is a very
tough problem --that means I am unable to produce any really convincing
argument! But the whole point may be that biological microscopic
functional
elements (say the enzyme, or the nucleic acid stretch) are not amenable
to
"sufficient" logical description in similar terms to functional
components
of computers. Structure, functionality, estrategy, etc. are in every
respect (and every "level") non-comparable, and in general
non-compatible.
The basic functionalist point of separability between hard and software
DOES NOT RULE biologically. Of course, in science one can always drop
embarrassing elements of distinction... by "disciplinary" fiat. And
then
produce flamboyant names "artif. intel.", "artif. life",
"biocomputing",
etc.
In the fis discussion list I produced several further arguments
( <http://fis.icts.sbg.ac.at/mailings/>http://fis.icts.sbg.ac.at/mailings/
), in the 2005 discussion on
molecular bionetworks.
Anyhow, thanks for the stimulus to pen these late reflections.
Pedro
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Received on Mon Nov 20 10:23:44 2006
