[Top] [All Lists]

RE: [ontac-forum] taxonomy of relationships

To: "ONTAC-WG General Discussion" <ontac-forum@xxxxxxxxxxxxxx>
Cc: "Paul J. Werbos" <pwerbos@xxxxxxx>
From: "Paul S Prueitt" <psp@xxxxxxxxxxxxxxxxxx>
Date: Sat, 26 Nov 2005 11:53:26 -0700
Message-id: <CBEELNOPAHIKDGBGICBGIEIDGOAA.psp@xxxxxxxxxxxxxxxxxx>
(I may wish to edit this, so I post it also at;
http://www.ontologystream.com/beads/nationalDebate/241.htm    (01)

Examples:    (02)

First, we should state that an example is already an abstraction that
produces mental/linguistic categories, and that the abstract process was in
each case what I am referring to.  But examples are plentiful.    (03)

A chain of events in biochemistry might involve a macromolecule (complex of
proteins) that has the role of a specific catalytic environment.  This
macromolecule might have just transformed out of materials used in a
previous reaction where parts of the macromolecule were lost and parts
gained (due to the needs of the environment and due to internal properties
of the composite (whole). So there is a local history of the materials and a
more global history of the environment (say the reactions of the skin to
being cut open).    (04)

Suppose we have s(1), s(2), s(3), s(4) as a temporally ordered set of states
of a specific physical macromolecule.  Suppose that we have knowledge of a
particular environmental condition that co-caused the state s(3).  Examples
of environmental conditions are:    (05)

On set of flu
Consequences of impact injury    (06)

Each of the states, s(i), i being an index, is a state of a reaction chain
which is produced (on a regular basis) by cellular mechanisms.  The cellular
mechanisms themselves are co-produced by gene expression, etc.    (07)

The environment certainly extends out beyond the physical location of the
macromolecule.  The “non-local” influence is expressed using (actual
electromagnetic) fields (such as caused by water in the molecule).  As
elements of a compositional process come within a certain distance there is
a field interaction leading to conformational (protein folding) activities.
Degeneracy allows a selection from what is available, in order to satisfy
the "function" that the environment needs to fulfill (again the reference to
Edelman’s work).  That function is determined by several things; including
global processes.    (08)

An example of global processes is the physical support for individual
awareness of certain things in a human’s memory.  Layers of event reactions
are involved.  In each case there are global field interactions as well as
local (kinematic) reactions.  In this case, the event structure is a chain
of mental event (as in thinking).  “How thought follows” is far more complex
than classical logic would have us believe.  The same is true for business
and government interactions.  The complexity can be addressed, but only by
letting go of logical constraints, WHERE these “axiomatics” can be shown to
be the co-causes of non-interoperability in IT systems.    (09)

One MUST say that the environment co-caused the state s(3) of the
macromolecule.  How does this happen?  An answer might be that there is a
templating of environment to local protein reactions by the "needs" of the
environment.  So in each case, s(i) (where i is a ordering index) is a
representation of the state of the macromolecule in a reaction chain which
is produced (on a regular basis !) by cellular mechanisms.    (010)

For more on neural mechanisms involved in production of mental states see    (011)

pprueitt/kmbook/Chapter4.htm    (012)

also see    (013)

Levine, D. & Prueitt, P.S. (1989.) Modeling Some Effects of Frontal Lobe
Damage - Novelty and Preservation, Neural Networks, 2, 103-116.    (014)

Levine D; Parks, R.; & Prueitt, P. S. (1993.) Methodological and Theoretical
Issues in Neural Network Models of Frontal Cognitive Functions.
International Journal of Neuroscience 72 209-233.    (015)

for some work on a neural phenomenon where activity in "gated di-poles" (ie
neural assemble functional structures) leads to changes in how next states
will be processed by biological neural networks.   In these two papers, some
work is reported on a neural phenomenon where activity in "gated di-poles"
(ie neural assemble functional structures) leads to changes in how next
states will be processed by biological neural networks.  The Stephen
Grossberg category of artificial neural networks (thousands of articles and
hundreds of books/conferences) uses the "gated-dipole" model (a differential
equation) extensively to produce a search leading to pattern recognition.    (016)

The above would be an example of a metabolic reaction chain that I, and
others, would like to model using a set of relationships between ontology
entities.  Half of my dissertation (1988) was on mapping between discrete
switching networks and reaction models using continuous differential
equations.  This theory is called “homology” and has many outstanding open
problems.  Perhaps these problems, as currently defined, are unsolvable
problems.  It is my claim that understanding how to re-state these problems
or to by-pass them altogether is one key to future semantic web /
anticipatory web performance.  I continue to be concerned that paradigms
acceptable to computer science builds resistance to approaches that
recognize these real problems.    (017)

Supply chain analysis has been around for many years, developed in
agriculture, and the issues are very much the same.  So a set of
relationships and specification of concepts that would the purpose of
templating biological reaction networks would also work for real problems in
supply chain modeling.    (018)

This templating approach to "process models" is advocated in hundreds of
papers, including    (019)

"Interaction Protocols as Design Abstractions for Business Processes"    (020)

by M Desai et al (special issue on interaction and state-based modeling  --
in press I think).  I am sure that many in this forum are aware of this
work.    (021)

I referred to this paper in a previous communication to the forum.    (022)

Regarding the development of ontology hubs    (023)

If I have John’s suggestion correct, the detail in each “ontology domain’
would not be shared, but there is something that can be shared.    (024)

In my examples, it is possible to not have any logic at all and no
"microtheories" or mechanisms for inference.  Merely language in the form of
controlled vocabulary and knowledge of what the terms might mean in various
references to process chains.  One needs a set of commonly useful templates
and standardization regarding data formats.    (025)

The “interaction protocols” are shared and underlying data formats are
shared, but NOT at the same time, not in the same way and not by the same
standard.  The sharing has to be responsive to use patterns that ordinary
people understand.    (026)

The point that I have been making is that reality is poorly modeled using
the types of logics that John talks about (with axiomatics being imposed, as
with many OWL ontologies).  His suggestion that hub ontology have
restrictions on the use of logic, is a suggestion that my work supports.    (027)

****    (028)

You asked this same question "MW: Can you give an example of what you mean?"
twice more.  The other two were both about stratification.    (029)

The nesting problem is one that is well discussed in the biological modeling
community.  The first step in exposing this literature's point of view is to
realize how useful biological taxonomy are; and then how limiting taxonomy
is when one gets into metabolic reactions.  The metabolic reactions can be
"abstractly treated as species" and one can try to construct a taxonomy.
But this efforts fails very quickly (for reasons that might be similar to
the failure of the ontology community to develop a upper taxonomy for
business/government).    (030)

Now I have to ask you if I have revealed enough of this so that you remember
reading about this type of things (nested class-subclass specifications) in
various books (many exists about this).    (031)

Stratified theory suggests that organizational levels develop as a natural
process of separating real energy-material interactions (so that my cells to
not interact with your consciousness).  The tri-level architecture that I
write about in my work, suggested that one cannot solve the task of
constructing a global taxonomy because of a type of relativism...
everything is ontologically relative to itself.  But everything has a set of
causes and is located within a environment where some but not all raw
materials are available to living processes that are aggregating material
(even material like quantum material in reactions like the conformational
changes in microtubule (Hameroff and Penrose).    (032)

Message Archives: http://colab.cim3.net/forum/ontac-forum/
To Post: mailto:ontac-forum@xxxxxxxxxxxxxx
Shared Files: http://colab.cim3.net/file/work/SICoP/ontac/
Community Wiki: 
http://colab.cim3.net/cgi-bin/wiki.pl?SICoP/OntologyTaxonomyCoordinatingWG    (033)
<Prev in Thread] Current Thread [Next in Thread>