Re: Bob Rosen's models, sensory perception, and more

[icb <***>]

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