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Saturday, November 19, 2005

 

 The BCNGroup Beadgames

National Project à 

Challenge Problem  à

 Center of Excellence Proposal à

 

 

 

 

Discussion at ONTAC forum

 

 

 

Professor Lander

Professor of Biology, MIT

Professor of Systems Biology,    Harvard Medical School

Founding Director, The Broad    Institute of MIT and Harvard

 

With respects and appreciation for your time. 

 

My name is Dr Paul Prueitt (PhD in mathematics).

 

Might you provide some reading from your lab that would support a generalization of the notion developed by Gerald Edelman, of a response degeneracy in neuronal ensemble expression?  I need a list of the best scholarship on this issue but unfortunately mathematical degeneracy (a saddle point) is what goggle brings back, mostly.

 

And there is deep controversy over this notion of stratification of ontology (reality) in spite the evidences from quantum theory ... 

 

I am working to try to impress on computer scientists that a many to many mapping between substructural assemble and functional expression is the rule in biology.  If this point can be made, then the way is open to setting aside (what some feel are) errors being made in the Semantic Web (W3C) standards for web services supporting biology research, etc. 

 

My work is way outside the mainstream computer science discipline, and yet I still feel that my work will be seen in the future as acceptable:

 

http://www.bcngroup.org/area3/pprueitt/book.htm

 

Being now 54, this may not happen in my life time.  But I am hopeful. 

 

 

I want to develop an argument to be made to some of the ontology standards groups (GSA, NSF, DARPA) that response degeneracy is necessary to any formal modeling of process.  I want to use biological science, and ground my argument in the best work available on this issue. 

 

Part of the discussion I am having is recorded in a web log (of my own design) at:

 

http://www.ontologystream.com/beads/nationalDebate/208.htm

 

It is obvious to me, that those involved in computer science and "ontology" are not aware of the empirical bases for asserting ubiquitous function/structure degeneracy. 

 

http://www.ontologystream.com/aSLIP/files/stratification.htm

 

Perhaps you will help me, and thus "them".