Re: Realization of (M,R)-systems, 'Artificial Life' and Dynamical Systems

[Tim Gwinn <***>]

Ionel,

Just a quick reply for the moment. I will try to get the Dejong papers this
weekend (assuming I can order and download them online) and take a look at
them, so I am more on the same page with you.

I am intrigued by your "algebraic-topological computer". I'm trying to
envision how it 'computes'...I have several probably wildy off-base ideas.
You shall have to say more about this. :)

I hope you feel better - I know when I'm sick I can't put my thoughts
together well either. :)

Regards,
Tim

> -----Original Message-----
> From: ROSEN Forum [mailto:*** Behalf Of Ionel
> Sent: Friday, June 04, 2004 9:46 PM
> To: ***
> Subject: Re: Realization of (M,R)-systems, 'Artificial Life' and
> Dynamical Systems
>
>
> Dear Tim:
>
> I appreciate your thoughtful responses concerning realization problems in
> terms of dynamics, 'Artificial Life', sequential machines/automata, etc.
> As a result of our sharper/precise/in focus discussion of the realization
> aspects, we are now getting to a very interesting part of our ongoing
> discussion of the realization problem. This lies at the heart of Robert's
> ideas on biological systems complexity and... 'Life Itself'.
>
> ----How is an (M,R)-system being entailed?----
>
> In the sections that I cited from Robert's "Essays..." in my previous
> posting, he addresses in significant detail this very important question,
> as well as the closely related question of 'AL' implementation based on
> realization strategies.
>
> It is useful to look at the problem of realization from different angles,
> or points of view, and differences of opinion are therefore naturally
> occurring; I feel that such differences in viewpoints are quite 'healthy'
> as they obviously can lead to further developments and deeper
> understanding
> of the realization process when rationally pursued. From a relational
> biology practitioner's viewpoint this as a key step.
> ----------------------
> You wrote:
>
> >>If I understand your remarks, I think you are also considering that any
> such dynamical models would have to be of the kind (e.g., non-integrable)
> that are symptomatic of a complex system. I am hesitant, though, that even
> inclusion of these kinds of dynamical models will lead to a successful
> physical realization.>>
> --------------------------------------------
> The page numbers that I quoted to you in my previous posting and that were
> from Robert Rosen's "Essays on Life Itself", are indeed concerned
> with both
> AL and the dynamic realization and entailment of (M,R)-systems. They are
> very important: they are key to developing specific applications of
> (M,R)-systems, as well as other relational biology modeling. Robert
> distinuguishes in several examples he gives in his "Essays..." between
> microstates and macrostates in a dynamical systems, but he did
> not identify
> necessarily microstates with quantum states.
>
> I, really, would like to pursue this topic with you further in a specific
> context. This is why I cited DeJong's papers in BMB (2004) that also deal
> with the connection between macro- and micro- states. His
> approach involves
> not only a computer classification of 'macrostates' in
> qualitative dynamics
> but also a relational/functional approach that might become very useful
> for realization if adequately developed. You can find them on the web at
> the BMB site (Elsevier's actually).
>
> Furthermore, I did provide 33 years ago, as well as in 1987, a third
> alternative to the 'computability'/ simulation issue for complexity and
> biological systems. Thus in agreement with Robert Rosen and Otto Rossler
> I concluded in my review on "Computer Modeling and Automata theory in
> Biology and Medicine", that despite widespread use of computers
> for 'simulating' and modeling biological systems, the recursive, or
> numerical/'digital' simulation with digital computers does not allow for
> a positive answer, also in agreement with your 'suspicions' and Robert's
> statements in response to Dr. Michael Arbib' suggestions that biological
> systems can be completely simulated by automata, or sequential machines,
> (statements made back in 1967-68 in his BMB paper on the Category of
> (M,R)-systems). However, when it comes to "computability" in general,
> things may be quite a bit different, depending on how one
> defines "computability", as discussed at length in my 1987 review that I
> cited above. For example, in one of my printed contributions in 1971, I
> introduced the concept of a symbolic-categorical 'computation' system, or
> algebraic-topological "computer" -- if you wish a hypothetical system that
> would be capable to "compute" either algebraically or
> categorically adjoint
> dynamical models of (M,R)-systems and biological systems, and
> thus 'simulate' in the strict sense of Rosen's Analogous System
> Dynamics, and my follow up "Adjoint Dynamical Systems", models of
> biological systems and functional/physiological processes. This
> concept has
> been, and still perhaps is, obviously far ahead of its time, but maybe now
> on the basis of Robert's notion of realization we might get very close to
> AL. The most interesting point about such a realization, is that
> if it were
> really successful--according to Robert-- there would be no valid criterion
> to call such a thing  anything but 'alive', as it would be truly
> indistinguishable from a relational biology 'viewpoint' from what we
> perceive as a living system. This is also covered by Robert in the section
> that I cited to you from his "Essays on Life Itself." Hope you'd find this
> quite interesting, but please also remember Robert's warnings... also in
> his televised interview. The topic is getting quite 'hot' in real
> possibilities. Furthermore, it may have some religious and
> ethical counter-
> current views upon the problems from a human standpoint: 'Creating life/
> cloning possibilities... etc'.
>
> I wish I could continue and complete my thougths here, but today I am
> not feeling well at all physically, and I find it very hard to concentrate
> because of being temporarily 'out of commission'. Hope to
> continue this with
> you when I feel better.  To conclude, according to Robert, realization
> does not mean neccessarily, or at all, going from complexity to "simple"
> systems such as sequential machines, etc. Hope you'd find this conclusion
> much more to your liking than the other possibilities we have discussed
> before.
>
> With best regards,
>
> Ionel
>
>
> On Fri, 4 Jun 2004 11:55:22 -0400, Tim Gwinn <***> wrote:
>
> >Hi Ionel,
> >
> >Just to clear up any possible confusion, by 'realization' I do mean what
> >Judith said: "creating a living system using Rosennean models as a
> >springboard". And, as equally stated by RR in Essays p. 263: "We want to
> >produce material systems that manifest those general attributes that we
> >associate uniquely with living organisms."
> >
> >In my remarks, I referred specifically to "Rosen's relational models (in
> his
> >view of relational models in "Life Itself")". I do not assert
> that this is
> >the only way to do relational modeling. (Rosen himself differentiates his
> >relational modeling from Rashevsky's.) I do assert that it is a primary
> >conclusion of "Life Itself" that relational models of this
> particular class
> >(such as the (M,R)-system) of a complex system cannot be
> directly or simply
> >restated into state-based model(s): "no (finite) concatenation
> of syntactic
> >models of an organism yields something which must be an organism",
> and: "the
> >abandonment of fractionability , however, means that there is no 1 to 1
> >relationship between such relational, functional organizations and the
> >structures which realize them. These are basic differences between
> organisms
> >and mechanisms or machines." [LI 280]
> >
> >Thus, I assert that the relational modeling he refers to in LI is of a
> >different formal universe from the formal universe of mechanistic
> >(state-based) models in which structures would be represented: the one
> >cannot universally be reduced to, or subsumed by, the other.
> That is all I
> >wished to convey.
> >
> >Moving to the task of realizing something like an (M,R)-system....I
> heartily
> >agree that realization - the creation of a physical specimen - from
> >something like the (M,R)-system will not simply require a
> translation from
> >the functional relational model to a dynamical representation to
> then using
> >that dynamical representation as a blueprint for manufacturing the
> specimen.
> >Sorry if I gave a wrong impression on that point. That was one of the
> points
> >I wanted to make by quoting Rosen's own instructive discussion of his
> failed
> >realization attempt in TB&C, where he tried interpreting the (M,R)-system
> as
> >a sequential machine.
> >
> >I feel that realization of a complex functional relational model like the
> >(M,R)-system is difficult because these universes of discourse are so
> >fundamentally different. I certainly do not feel that dynamical
> models are
> >to be summarily ommitted from the task of realization. I never
> made such a
> >suggestion. I do, however, have concerns about the relationship between
> >dynamical models and functional relational models of a complex system.
> >According to Life Itself, the class of systems which admit a functional
> >relational description which is also reducible to a
> state-description would
> >be 'machines' (in Rosen's specific sense of the term in LI). Clearly that
> is
> >not what we want to create in our realization, so the
> relationship between
> >between the relational and any of its dynamical models must be less
> obvious.
> >If I understand your remarks, I think you are also considering that any
> such
> >dynamical models would have to be of the kind (e.g., non-integrable) that
> >are symptomatic of a complex system. I am hesitant, though, that even
> >inclusion of these kinds of dynamical models will lead to a successful
> >physical realization.
> >
> >Regards,
> >Tim
> >
> >> -----Original Message-----
> >> From: ROSEN Forum [mailto:*** Behalf Of Ionel
> >> Sent: Friday, June 04, 2004 7:11 AM
> >> To: ***
> >> Subject: Re: 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".)