Re: the "realization" issue

[Ionel <***>]

Dear Judith:

It seems I had a small problem with electronical posting.

There is a second thought that I posted today addressing the view point
differences that Tim and I have so far on the "Realization Problem' as
defined by Robert. For completeness, I am citing it below. Howard put it
very nicely in terms of : "the need for inequivalent complementary models
for adequate understanding of complex systems...", and it does have links
also with your other discussions with Dr. Howard Pattee.

Best regards, Ionel -------------------------------------------- >Hi, Tim:

A brief, and very much to the point/ appropriate response through a quote
from yesterday's posting by Dr. Howard Pattee:

>>I do claim that the need for inequivalent complementary models for
adequate understanding of complex systems is couched in terms of what Rosen
believed and expressed. Howard >>> ----------------------- Regards, Ionel>

--------------------------------------------

On Fri, 4 Jun 2004 07:20:13 -0400, Judith Rosen <***>
wrote:

>It looks to me that Tim and Ionel are talking about different things
>entirely, here. Maybe I'm getting it wrong, but Tim's use of the word
>"realization" refers to creating a living system using Rosennean models as
a >springboard. Ionel is talking about something else which is a much
smaller >side issue in Rosennean Complexity and Tim is actually in full
agreement >about not limiting science to one level of investigation... what
do you >think? > >Judith > >----- Original Message ----- >From: "Ionel"
<***> >To: <***> >Sent: Friday, June 04,
2004 7:11 AM >Subject: Re: [ROSEN] Modern Physics, Newtonian Paradigm, and
the notion of >State > > >> 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: >>



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".)


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