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[ontac-forum] response degeneracy in biological processes

To: <lander@xxxxxxxxxxxxx>
Cc: ONTAC-WG General Discussion <ontac-forum@xxxxxxxxxxxxxx>
From: "psp" <psp@xxxxxxxxxxxxxxxxxx>
Date: Sat, 19 Nov 2005 19:27:06 -0700
Message-id: <CBEELNOPAHIKDGBGICBGIEAGGOAA.psp@xxxxxxxxxxxxxxxxxx>
Professor Lander
Professor of Biology, MIT
Professor of Systems Biology,    Harvard Medical School
Founding Director, The Broad    Institute of MIT and Harvard    (01)

With respects and appreciation for your time.    (02)

My name is Dr Paul Prueitt (PhD in mathematics). My phone number is
703-981-2676    (03)

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 unfortuately mathematical degeneracy (a saddle
point) is what goggle brings back, mostly.    (04)

And there is deep controversy over this notion of stratification of ontology
(reality) in spite the evidences from quantum theory ...    (05)

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.    (06)

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:    (07)

http://www.bcngroup.org/area3/pprueitt/book.htm    (08)

Being now 54, this may not happen in my life time.  But I am hopeful.    (09)

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.    (010)

Part of the discussion I am having is recorded in a web log (of my own
design) at:    (011)

http://www.ontologystream.com/beads/nationalDebate/208.htm    (012)

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.    (013)

http://www.ontologystream.com/aSLIP/files/stratification.htm    (014)

Perhaps you will help me, and thus "them".    (015)

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