Re: Modern Physics, Newtonian Paradigm, and the notion of State

[Ionel <***>]

Dear Tim:

Let's look together at some more facts that do not appear to match your
proposition: a significant proportion of Robert's book on "Essays on Life
Itself.",  written much more  recently than 1973, and printed in New York,
in 2000, i.e. the latest printed work of Robert Rosen contains very
significant sections and chapters that are exactly along the lines that I
pointed out to you before about his previous work on dynamical systems. In
my view, there is nothing wrong whatsoever with that; this is what Robert
intended  to do, because this is a reasonable and fruitful way to carry out
the Relational Biology program--through modeling at several levels, not
only at ONE level. In a certain sense, such 'too restrictive' an approach
to just one level of reality would in effect be also 'reductionistic-to-
abstract-semantics-ONLY' , which in effect would be  exactly on the
opposite side of the 'reductionistic' coin, e,g. "purely
abstract 'semantics'--without real meaning", no syntax, no developmental/
numerical tools, ...and also quite sterile. This is the point that Robert
makes repeatedly throughout the 346 pages of his recent book
on "Essays ...".  A particularly clear example of this is presented in his
several chapters in this book on:  Morphogenesis in Networks (Ch.15, pp.
224-, especially pp.232-241), Genericity and especially the section
on "Dynamical Degeneracy" (Ch.12, pp. 175-186), Chapter 14 "Optimality in
Biology and Medicine (pp.201-223), Ch.16 on Order and Disorder in
Biological Control Systems (pp.246-253), and so on, and on.

Should one decide to ommit/take out such VERY important aspects as the
dynamical behavior and treatments that Robert specifically illustrates with
differential eqns., and the specific solutions of such eqns., phase
portraits, trajectories of states, etc., one would look at a much
impoverished and much less attractive book than Robert's exciting,
interesting and very readable "Essays...", the new book. The
selected, 'simple'  and complex dynamical examples that Robert provides are
really crucial to an in depth understanding of his very important work on
relational biology, with both its inter-connected aspects-- abstract and
dynamics. I do hope that you will give these points the serious
consideration that certainly Robert's "Essays..." deserve,(without
attempting to over-simplify the problem of realization to the one intended
in your paragraph cited below), which as shown in the "Essays..." is very
important indeed and cannot be/ should not be quickly "pushed under the
carpet."--  merely as :

>>>realization of these relational models, whether via sequential machine
models or via kinetic models, as attempts at interpretation/
translation/mapping from the universe of state-less atemporal relational
models into the universe of state-based models.>>

REALIZATION is much more than that: please note specifically pp. 263-269 in
Robert Rosen's "Essays... " concerning the essential need for the
realization steps, and the importance of the realization steps for
Entailment, such as in the case of (M,R)-systems. It is a key process,
connecting the 'abstract' world of relational biology to the real world in
which such models are being REALIZED! It is NOT merely a 'translation',
as the "traduttore--traditore" saying would make it to be.
It is much more than that: it's the trully complementary part that one
needs to see as a 'measure of reality' of the relational models considered.
Faithful realizations are exceedingly important for modeling in relational
biology, and practice does help, as Robert demonstrates it vividly and
clearly in his "Essays ...", many times over. Without REALIZATION,
a pseudo-'relational biology' might simply float into the abstract vacuum
of a "dolce far niente", totally remote from biological reality,
a "semantic theory" but without either real meaning or any syntax!

The realization strengthens, and is part of the relational biology theories-
-instead of detracting from them.

As Nicolas Rashevsky--the founder of relational biology-- himself pointed
out: relations in biology are quite 'general' in character: they contain
BOTH qualitative and quantitative aspects. As also he was fond of saying:
"Mathematics has been long considered the Queen of Sciences, but... she is
a democratic queen!"

In my own Qualitative Dynamics paper of 1971, (and later work) that I
posted earlier ,I have made the same points that Nicolas Rashevsky and
Robert Rosen did about the need to use both qualitative and quantitative
approaches to model dynamics in relational biology. For a more recent
reference along the same lines-- there are two substantial papers by DeJong
on Qualitative Dynamics in Biology published in BMB in 2004, one providing
the broader framework, and the other providing the application to a
specific case in great detail.

With best regards,

Ionel



On Thu, 3 Jun 2004 22:27:26 -0400, Tim Gwinn <***> wrote:

>Hi Ionel,
>
>Adding the following thoughts to my prior response to this post....
>
>>From my perspective, I draw a distinction between Rosen's relational
models
>(in his view of relational models in "Life Itself"), and the attempts at
>*realization* of such models. I consider that these relational models do
sit
>in an entirely different formal universe of discourse (for lack of a better
>phrase) from the Newtonian-paradigm formal universe of discourse; it is a
>formal universe of discourse where "systems are assigned no states, no
>environments, and there is no recursion".
>
>Generating a physical realization *from* these relational models is the
>conundrum. Certainly, it would seem likely (or at least, it seemed likely
to
>him back then (1964, 1971, 1973) that the process of realization must
>include some way to interpret/translate/map from these models to some kind
>of state-based model(s) which would tell us, among other things, how to
>physically put the parts together. I see Rosen's attempts at realization of
>these relational models, whether via sequential machine models or via
>kinetic models, as attempts at interpretation/translation/mapping from the
>universe of state-less atemporal relational models into the universe of
>state-based models.
>
>Regards,
>Tim
>
>> -----Original Message-----
>> From: ROSEN Forum [mailto:*** Behalf Of Ionel
>> Sent: Wednesday, June 02, 2004 5:33 AM
>> To: ***
>> Subject: Re: Modern Physics, Newtonian Paradigm, and the notion of State
>>
>>
>> Hi, Tim:
>>
>> I'd go along with most of your comments about (M,R)-systems, but there
are
>> some important facts that are running contrary to your sentence cited
>> below, if I understood your argumentation correctly:
>>
>> >>These functional relational models are in an entirely different formal
>> universe of discourse than a formal universe of discourse built around
>> spatiotemporal relations.>> It is, metaphorically speaking, like
>> a parallel
>> formal universe - a rather alien one to the one in which we are used to
>> doing physics in. >>....Of course, the opposite is also true: these
>> relational models have abstracted away state information entirely - they
>> have "thrown away the physics".) >>
>>
>> ---------------
>> FACTS: Both in 1971 and 1973, Robert published in BMB two substantial
>> papers in which he developed dynamic representations of (M,R)-systems
that
>> appear to be aimed at linking the Abstract (M,R)-systems approach to the
>> physical representation of such systems in terms of kinetic or dynamics
>> eqs.,etc,  e.g. attempting to avoid to "throw away the physics", such as
>> the dynamics in terms of states and state-spaces. It is clear
>> that Roberts'
>> states are not quantum states.
>> -------------
>> Regards,
>>
>> Ionel
>>
>> ...>>In TQFT, the relations represented are still between spatiotemporal
>> quantum states: the encoding has gone from the natural system to a
>> spatiotemporal encoding and then to a topological one. In Rosen's
>> relational models, the encoding goes directly from the natural system to
>> the functional relational model. This allows for representations of
>> organizational qualities that cannot be encoded into the spatiotemporal
>> encodings of the Newtonian paradigm. (Of course, the opposite is
>> also true:
>> these relational models have abstracted away state information entirely -
>> they have "thrown away the physics".)

Dear Tim: