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Re: Bob Rosen's models, sensory perception, and more
- From: Tim Gwinn <***>
- Date: Mon, 17 May 2004 08:57:19 -0400
Dr.
Baianu,
Again, sorry for
the delay in response. It has been an unexpectedly hectic week.
Thank you for
helping to "keep the flame burning"! I very much look forward to
reading your papers when they become available online - in particular the
applications of Category Theory to biological models.
Regards,
Tim
Judith Rosen
wrote:
>> However, the way my father viewed it;
function is simply
the relational nature of complexity taken to a new level
of causal
influence, which cannot be ignored in scientific study of
biological
systems. I personally feel this is why it took a
biologist to see this
particular mistake in contemporary mainstream
science... But it had to
be a biologist who had as solid a grasp of
contemporary physics as any
physicist. Because he had both perspectives, he
was able to see the
mistakenly juxtaposed concepts at the root of the
contemporary
scientific paradigm. The COMPLEXITY of biological systems
is the common
thread that ties all areas of science together, not the
material
particles that can be found in all systems. Physics has had
it
backwards from day one.>>
Before following Ms. Judith
Rosen's interesting comments about Bob Rosen's work, please allow me to
introduce myself to this group and threads:
Bob Rosen and I had a long
and fruitful correspondence by mail while I was completing my MS studies on
"Theoretical and Experimental Models in Carcinogenesis." , while studying both
in the School of Physics and the Biophysics Dept. of the School of Medicine at
Bucharest University,
between 1965 and 1969., then during the 'Cold War', I
was behind the Iron Curtain, sufferring from the restrictions typical of that
era. Bob
Rosen and Nicolas Rashevsky have both 'melted through' the Iron
Courtin a communication line to help me and my colleagues be part of
the
great progress with estabishing the programmatic fundamentals of
Complex Biological Systems, or as they were called then "Organismic
Sets"
by Nicolas Rashevsky (then at Ann Arbor in Michigan) , and later
"Metabolic-Replication-Systems" introduced by Bob Rosen, or "Organismic
Supercategories" in my own contributions to this new and growing field. As it
happened, Bob Rosen was able to come and visit with us in Bucharest and at the
famous Sigmarinen's Pelesh Castle at Predeal in Romania in 1969. Nicolas
Rashevsky then kindly invited me , and made it possible to participate at the
Mathematical Biophysics Symposium at Toledo, in Ohio, in 1970, where of course
I met again Bob Rosen, and made a new friend ,George Kareeman with whom I
remained long time friends through correspondence, after having his family in
Philadelphia.
Last week, after a long 'struggle for survival' of more
than twenty years, I was trying again to get in touch with Bob Rosen, whom I
knew to have moved to Dalhousie in Canada sometime in the 90's, and learned
with great shock and pain of his passing in 1998. This is my first
chance of offerring my belated- but most sincerely felt condolences-- to
both his family and close friends. At the same time, I had this pain doubled
by learning also that George Karreman--who was also a very,very close
friend--has passed away in 1997. Last time that George and I spoke on the
phone in the US was in 1996. I joined the stuff in Physical Chemistry at the
University of Illinois at Urbana in 1980, and met for the second time the then
US remaining Mathematical Biology 'board' with Herbert Landahl at its helm in
1984 at a SIAM meeting and dinner. At that time, I gave two talks on "Natural
Transformations in Relational and Molecular Biology." , and another on
"Molecular-Set-Variable Models in Molecular Biology.", both relevant to the
discussion here. The full texts will be available again on the web shortly on
my web sites. Till then, I am listing here several of the papers that are
relevant to this discussion, and that I am working to help continue what
Nicolas Rashevsky and Robert Rosen started,
and help 'keep the flame
burning.' As the 'youngest member' of the Relational Biology group in
the early 70s and later 80s and 90s, I hope to
be able to help others as
Nicolas Rashevsky, Bob Rosen and George Karreman helped me to develop my 'tree
branch" of the Relational Biology and Complex Systems Biological Dynamics.
Briefly, in 1985 to 1987 also had some very helpful and far-reaching
interactions with Matthew
Witten--who was also helped by Bob Rosen-- to
develop his own approach to Observation Repeatability in Biological Systems
and Medicine.
Thus came about a substantial review , also listed here,
printed with Matthew's help in 1987, dealing with Computer modelling and
Automata
Theory in Biology and Medicine. Three important problems close to
Robert Rosen's interests were there discussed in some detail: the
algebraic
construction of Metabolic-Replication (Repair) Systems,Computer Models of
Carcinogenesis, and Computer Simulation and
'Computability' of
Complex Biological System Dynamics. This substantial review ( ~60
printed pages, 41 figures and 300 selected references)
will aslo shortly
become available at my uiuc web-site. Here follows the promised list of
references up to 1987, although I am sure it still
requires several
additions, including many of the relevant Bob Rosen's and George Karreman's
and also Nicolas Rashevsky's papers.
Hope you will also be able to add
this information in your Robert Rosen site archives, etc.
With best
regards and my very best wishes to Bob Rosen's family and friends, Rosenian
Group members, and former students and coworkers,
Ion C. Baianu,
PhD,
Professor
University of Illinois at Urbana
Urbana,
IL.61801
USA
Tel . No. 217-333-4442
Telefax:
217-244-2455
:
:
categories: APPLICATIONS to:
Automata, Biological Systems, Dynamics, Genetic and Metabolic
Networks, Human Cognitive Systems, Quantum Computers, Quantum Gravity,
Quantum Groups, Quantum Automata, Bioinformatics
Cc: <
***>
Applications of the Theory of
Categories, Functors and Natural Transformations, N-categories, Abelian or
otherwise to:
Automata Theory/ Sequential Machines, Bioinformatics,
Complex Biological Systems /Complex Systems Biology, Computer Simulations and
Modeling, Dynamical Systems , Quantum Dynamics, Quantum Field Theory, Quantum
Groups,Topological Quantum Field Theory (TQFT), Quantum Automata, Cognitive
Systems, Graph Transformations, Logic, Mathematical Modeling,
etc.
Note: This is a first attempt at
generating a Categorical Incunabula of the development of applications of the
Theory of Categories, Functors and
Natural Transformations (next...
pushouts, pullbacks, presheaves, sheaves, Categories of sheaves, Topos..,
n-valued Logic, N-categories/
higher dimensional algebra,Homotopy theory,
etc.) to an entire range of: physical, engineering, informatics,
Bioinformatics, Computer simulations, Mathematical Biology -areas that are
utilizing or developing categorical formalisms for studying complex problems
and phenomena
appearing in various types of dynamical systems,
engineering,computing, bioinformatics, biological and/or social
networks.
1. Rosen, R. 1958. The Representation of Biological
Systems from the Standpoint of the Theory of Categories." (of
sets). Bull. Math. Biophys.
20: 317-341.
2. Rosen,
Robert. 1964. Abstract Biological Systems as Sequential Machines, Bull. Math.
Biophys., 26: 103-111; 239-246; 27:11-14;28:141-148.
3. Arbib, M. 1966.
Categories of (M,R)-Systems. Bull. Math. Biophys., 28: 511-517.
4.
Cazanescu, D. 1967. On the Category of Abstract Sequential Machines. Ann.
Univ. Buch., Maths & Mech. series, 16 (1):31-37.
5. Rosen,
Robert. 1968. On Analogous Systems. Bull. Math. Biophys., 30:
481-492.
6. Baianu, I.C. and Marinescu, M. 1968. Organismic
Supercategories:I. Proposals for a General Unitary Theory of Systems. Bull.
Math. Biophys., 30: 625-635.
7. Comorosan,S. and Baianu, I.C. 1969.
Abstract Representations of Biological Systems in Supercategories. Bull.
Math. Biophys., 31: 59-71.
8. Baianu, I. 1970. Organismic
Supercategories: III. On Multistable Systems. Bull. Math. Biophys., 32:
539-561.
9. Baianu, I. 1971. Organismic Supercategories and Qualitative
Dynamics of Systems. Bull. Math. Biophys., 33: 339-354.
10.
Baianu, I. 1971. Categories, Functors and Automata Theory. The 4th Intl.
Congress LMPS, August-Sept. 1971.
11. Baianu, I. and Scripcariu, D.
1973. On Adjoint Dynamical Systems. Bull. Math. Biology., 35:
475-486.
12. Rosen, Robert. 1973. On the Dynamical realization of
(M,R)-Systems. Bull. Math. Biology., 35:1-10.
13. Baianu, I. 1973. Some
Algebraic Properties of (M,R)-Systems in Categories. Bull. Math. Biophys, 35:
213-218.
14. Baianu, I. and Marinescu, M. 1974. A Functorial
Construction of (M,R)-Systems. Rev. Roum. Math. Pures et Appl., 19:
389-392.
15. Baianu, I.C. 1977. A Logical Model of Genetic Activities
in Lukasiewicz Algebras: The Non-Linear Theory., Bull. Math.
Biol.,39:249-258.
16. Baianu, I.C. 1980. Natural Transformations of
Organismic Structures. Bull.Math. Biology, 42:431-446.
17. Warner, M.
1982. Representations of (M,R)-Systems by Categories of Automata., Bull. Math.
Biol., 44:661-668.
18. Baianu, I.C.1983. Natural Transformations Models
in Molecular Biology. SIAM Natl. Meeting, Denver, CO, USA.
19. Baianu,
I.C. 1984. A Molecular-Set-Variable Model of Structural and Regulatory
Activities in Metabolic and Genetic Systems.,
Fed. Proc. Amer. Soc.
Experim. Biol. 43:917.
19. Baianu, I.C. 1987. Computer Models and
Automata Theory in Biology and Medicine. In: "Mathematical models in
Medicine.",vol.7.,
M. Witten, Ed., Pergamon Press: New York,
pp.1513-1577.
The Earliest Quantum Automata and Quantum
Dynamics in terms of Category Theory:
It is often assumed that
'Categorification' of Quantum Field Theory, or the formal use of the Theory of
Categories in Quantum Gravity and
Topological Quantum Field theories
(TQFTs) began in the 1990s. In fact, the concepts of Quantum Automata and
Quantum Dynamics represented in terms of Categories, Functors and Natural
Transformations were formally introduced as early as 1968-1973 (Bull. Math.
Biophysics, 33:339-354 (1971), and references cited therein). The
self-contained presentation in the earliest 1968 paper on Categorical
Dynamics introduce all necessary concepts for a student just entering this
'new' field. This earliest , 1968 US publication will soon become available on
the web.
I.C. Baianu, PhD,
Professor ,
University of Illinois at
Urbana,
Urbana, IL.
61801,
"I.C. Baianu" <
***>
USA
(UIUC)
At
07:36 PM 5/14/2004 -0500, you wrote:
John K. wrote: Also concepts
like "appropriate and useful in context"
seem to
unavoidably imply
some function or purpose, so function seems to be
defined in the
hierarchical relationship between a system and a
context.
The
fact, formalized by Rosen, that there are
causally-acting
feedbacks
from context to sub-system, is the
essence of organization. So
function
and organization are
related and it is impossible to speak of one
without the other,
except in a trivial or degenerate case (i.e. the
material
view).
This is exactly right. The amazing thing
to me is that so few areas of
mainstream science are either willing or
able to SEE it. The proof of
it is everywhere, yet it is denied-- As a
non-scientist, I find this
situation incomprehensible, even though I know
(intellectually) why the
situation exists. But I've always had trouble
understanding why my
father got so much flack for saying what John K. so
elegantly stated
above. And my father even went to the trouble of
"showing the work"
(i.e. how he arrived at those statements). >From my
perspective, the
statements are obvious truths and all that's required to
see it is
simple common sense.
Function is one of the concepts
that is absent or camouflaged as a
causal influence in systems that are
not alive. Life and function are
two qualities of living systems that are
either co-emergent or
connected via the kind of mutually causal
relationship that is rampant
in complex systems. To put it another way;
either "life" and "function"
are both caused by the dimension/level of
complexity that defines
living systems or they cause each other, at this
dimension/level of
complex organization. I suppose it could even be both.
But the fact
that this functional aspect is not apparent in a rock or
a
gravitational phenomenon or an electrical event-- and these are
the
systems physics has a good handle on-- I think makes it a habit
for
physics to view all systems, including biological phenomena, as
being
"free from" any functional aspect as well. Function is viewed as
an
observer overlay that taints our ability to understand "what's
really
going on"... However, the way my father viewed it; function is
simply
the relational nature of complexity taken to a new level of
causal
influence, which cannot be ignored in scientific study of
biological
systems. I personally feel this is why it took a biologist to
see this
particular mistake in contemporary mainstream science... But it
had to
be a biologist who had as solid a grasp of contemporary physics as
any
physicist. Because he had both perspectives, he was able to see
the
mistakenly juxtaposed concepts at the root of the
contemporary
scientific paradigm. The COMPLEXITY of biological systems is
the common
thread that ties all areas of science together, not the
material
particles that can be found in all systems. Physics has had
it
backwards from day
one.
Judith