Re: Supercategories, states, Quantum Relational Biology Rosennean "Cookbook"

[Ionel <***>]

Hi, Jack:

I appreciate very much your comments on organismic supercategories and
biological system states. Your different approach to the same problems
looks to me promising, and it would be interesting to see how it can be
further developed towards specific realizations.

Also, I have now posted several recent updates/ preprints with current
coworkers both on Relational Biology applications to medicine and health,
as well as towards brain functions,  the Alegbraic Topology of Relational
Quantum Biosystems, and fundamental aspects of Quantum Fields; people who
might be interested in such recent developments could now access these
preprints on the web at the following URLs:

1. Complex System Biology and Cancer Mechanisms:

http://cdsweb.cern.ch/search.py?recid=768090&ln=en

http://arxiv.org/abs/q-bio.TO/0407006

http://bioline.utsc.utoronto.ca/archive/00001979/


2. On Quantum Algebraic Topology :

http://www.ag.uiuc.edu/~fs401/Quantum%20Algebraic%20Topology.pdf



1. On Quantum Automata and Relational Biology:

http://www.ag.uiuc.edu/~fs401/QAuto.pdf


Look forward to receiving your feedback and comments on some of these if
they fit your "CookBook".

With best regards,

Ionel



On Sat, 22 Jan 2005 11:00:13 -0800, Jack Park <***> wrote:

>Judith Rosen wrote:
>
>> *Jack Park wrote:*
>> Consider this. You have a small tribe right here. To what extent can the
>> interactions and other relations associated with this tribe be modeled
>> with Rosennean thinking?  Articulate a recipe for doing that and you've
>> got an enormously useful first cut at a cookbook.
>> *The tricky thing with applying Rosennean concepts to internet
>> informational flow is that communication is all semantics, but
>> computation is all syntax. Programming is a completely
>> different activity than using/manipulating software. I use the internet
>> all the time and I use it in a purely semantic way. I've seen many
>> connections/patterns and potential applications of my father's work in
>> this realm, but I'm not so sure that it would be of any help to you,
>> because what you want to achieve is at the programming end, isn't it?
>> Zeros and ones just don't "compute" in my head-- it makes no sense to
>> me. I'm beginning to wonder if what you're looking at is actually a
>> foundational problem with digitalization. You may have run up against
>> the limits of the syntactic medium. If so, what are the options? What
>> does that problem require?*
>> *Judith*
>
>Judith knows of my ambitions. I need to explain a few things. "The time
>has come, the whalrus said, to speak of many things..."
>
>Judith mapped my quest to something to do with the internet. I am
>reminded of Hamming's "the purpose of computing is insight, not
>numbers."  In some sense, there is, indeed, a map between my quest and
>the internet. I said so myself. It is the desire to, in some sense,
>extend Judith's BioTheory to the levels suggested by wikipedia and
>interactive portals called wikis, where people can, indeed, tell stories
>and interact with others in ways greatly different from those afforded
>by email lists. But, I think, that's a different thread.  Here, my quest
>is to find a way to articulate a "cookbook" (possibly a bad term) for
>doing science given a different (augmented) way to do science.
>
>I posed a simple inquiry: how to model this tribe.
>
>I imagine that the question "what do you mean by *model*?" will appear.
>In my case, I don't think I'm very far afield from a Rosennean model
>when I say that I'd like to understand the steps necessary to take a
>simple query and turn it into a series of "next questions" to ask and to
>answer. My background is this.
>
>I come with an analytical bent. In aero engineering, one of the
>stuctures classes, we were given a large blueprint of a landing gear
>which was coupled through an array of linkages and levers to a control
>arm which a pilot would use to extend or raise the gear. The problem was
>to plot the force required by the pilot for all positions of the landing
>gear as it rotates between fully extended to tucked up in the fuselage.
>All the other students began drawing lines on the blueprint and making
>measurements, while I wrote a small set of simultaneous equations, one
>for each lever, and achieved the result in less than an hour. I like to
>solve problems analytically. Rosennean stuff strikes me as rich in
>opportunities. What, then, are the steps involved?  There is one aspect
>of that question that rings of someone who doesn't know the math. True.
>That's not what I am asking.
>
>I am rereading I.C. Baianu's papers "Natural Transformation Models in
>Molecular Biology" and "Organismic Supercategories and Qualitative
>Dynamics of Systems" this morning and I am seeing hints of that which I
>seek. Both of those papers take the time to articulate the flow of
>thought processes involved. Ayten Aydin's paper "Shrinking versus
>Expanding TIME within Time's Arrow" (available at BioTheory) is equally
>stimulating.
>
>My recent background involves something derived from the artificial
>intelligence thread called qualitative physics: qualitative process
>theory.  From that, my instincts tell me that one approach to take in
>modeling this tribe is to ask these questions:
> who/what are the actors?
> what are their relationships?
> what are the states involved?
> what are the process rules involved?
>"states" being that n-tuple of observables mentioned in "Organismic
>Supercategories."
>
>I suppose I might rephrase my questions in this way:
> who/what are the actors? (what are the components)
> what do those actors entail?
>I still might ask to enumerate the observable states.
>
>That methodology is implemented in a program I and colleagues wrote in
>the early 90's, called The Scholar's Companion (r) (TSC).  That program
>got its name because it was always intended to augment the thinking
>ability of its user, not to replace the user. That methodology has been
>applied to a variety of problem spaces, from polymer curing to molecular
>biology and hyperbaric immunology. Outside my own program, QP theory is
>finding wide application.
>
>My quest, in some sense, is to determine the mappings necessary to morph
>QP Theory into RR Theory. My intuitions suggest that this should be
>possible.
>
>My program adds a different dimension to computation from that which a
>"calculator" brings forth; the dimension of discovery. Think of TSC as a
>kind of spreadsheet where "what if" questions can be asked. With TSC,
>the program, itself, has the ability to "play" with the numbers
>(concepts), to perform mutations, conceptual combinations, on objects
>stored as symbols (an actor or a relation is a symbol), and to then
>return to perform modeling computations on the mutated concept. This is
>called evolutionary programming. The "conjectures" offered by the
>program may, or may not, stimulate cognitive processes in the user.
>That's the point.
>
>What does it mean to "perform computations" in QPtheory? It means this.
>Entailments in QP Theory are called "process rules." TSC allows a user
>to "set a stage" with actors, relations and states (initial conditions).
>Process rules are then collected to and "fired". That's the equivalent
>of a "script" being read. Some rules fire, states/relations/actors
>change, and you form a new stage setting.
>
>Some readers on this list might be antagonized by the image I am
>painting, since it reminds them strongly of reductionist methodology. I,
>personally, don't see much difference between what I just described and
>Figure 2 in "Organismic Supercategories." A profound difference exists
>in the fact that TSC is operating in plain old set theory, and Dr.
>Baianu's discourse applies category theory. I suspect that TSC can be
>morphed to perform similar functions under topological algebras. There
>exist a few programs which already do pieces of that.
>
>To return to my quest for a "cookbook", I suppose that all I am really
>asking for is concrete articulation of ways in which one "sets the
>stage". After all, the stove and oven will do the rest. n'est-ce pas?
>
>Having explained my quest in such terms, how would Rosennean thinkers
>approach the task of modeling this tribe? What questions would they ask?
>What analytics would they apply to those questions?
>
>Jack

Dear Park: