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Friday, March 03, 2006


Challenge problem à

The Taos Discussion à


Generative Methodology Glass Bead Games


On the limits of the OWL standard à [184]

Reading material [1]

Reading material [2]

Reading material [3]

Summary of the discussion up to this point à [186]



On ontological modeling of expression


Subtitle: The metaphor between gene, cell and social expression



On Formal verses Natural systems à [206]


To Protégé and BioPAX forums,


I made some typos in my last communication and have fixed that up and posted to [216] .


In the recent week a number of discussions have focused on the relationship between class and individuals (instances sameAs individuals), and the nature and usefulness of what the description logic folks “call” the Open World Assumption.  What they are referring to is a partial openness to the addition of certain types of information and/or data to an existing set of OW: assertions.  The sense of hype is important to talk about, because the key unsolved problems with description logics and with the class-subclass paradigm is related to how asserted information is modified, or how two bodies of asserted information is merged. 


The BCNGroup’s focus has been on how a new category in introduced as a class.  Some call this “introduction” a “reification” of the abstraction from instances (sameAs individuals), and so our focus is properly about "signal induction" if one is talking about cellular or gene "communication".  Linguistic induction, within a social context, of new symbols and new meaning to those symbols is also part of the focus.


In pattern extraction, identification and classification (involving genetic algorithms, neural networks, stochastic algorithms or other) we want to take "data" and from the data "induct" or "abduct" some "information".


I have never liked the classical definition of induction and abduction, since two concepts do not seem to me to be needed, and neither classical definition seemed to me to be proper.  "Signal pathway induction" is a phrase that takes a while to get used it, but I encourage the use of Google and some reflection.


What is different is the clarity in the cell signal pathway induction literature about something we call “stratification”.


In this literature there is a substrate, and a separate level of response organization where the expression occurs. 


Look at




Hundreds of thousands, or millions, of “things” are interacting in the substrate and the result is a behavioral response.  So it is hard to not see the two layers of organization.  It is also hard to not mistake the sum of the parts with the “whole”. 


A metaphor is set up, and that is between gene expression, cellular expression and social expression.


In this metaphor I rely on the scientific literature about cellular expression more than the two others.  The gene has too much of the computer binary metaphor and the literature about social expression is simply too confused with hidden mindsets to be worth a second reading.


[1] http://dip.semanticweb.org/documents/ECIS2005-A-Methodology-for-Deriving-OWL-Ontologies-from-Products-and-Services-Categorization.pdf

[2] http://www.mindswap.org/2005/OWLWorkshop/sub1.pdf

[3] http://bip.cnrs-mrs.fr/bip10/rosen.pdf