Re: the "realization" issue

[Judith Rosen <***>]

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:
>