Re: the "realization" issue

[Ione <***>]

Dear Judith:

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".)