November 14, 2006
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Community Centric Service Methodology Glass Bead Games
Lobbying Congress on the Merits of the National Project
Responses are posted in order received moving from this “bead” back to the email posted at [26]
Responses:
(to www.biopax.org)
Hi Paul,
It's not clear to me what
this has to do with BioPAX, why it is relevant to the list and what
specifically you are looking for in terms of feedback.
Thanks,
Joanne
Joanne, and respected biological scientists in the www.biopax.org e-forum
As you may remember, I have a background in biomathematics, mathematical models of neural and immune function. [1] Based on my life’s work, I have been proposing that the history of biomathematics will soon see an extension of Hilbert mathematics to semi-formal models of gene, cell and social “expression”. He work by the biopax group is certainly moving science in this direction.
My past discussions within the biopax e-forum have focused on the issue of structure-function. As Allen Ruttenberg, one of the leaders in this forum, has pointed out as part of this previous discussion, the structure-function issue of gene and cell signal pathway expression may not be within the biopax mission when that mission is seen as
(paraphrasing) “to develop an ontology standard based on a modified version of OWL Full (web ontology language standard set by the W3C) that serves to integrate many of the very large existing bio-informatics databases.”
However, many members of the forum, including Alan, know that there are a specific set of issues of science that are left out of the OWL model, due to the nature of the OWL modeling construction. This does not take away from the tremendous value that the BioPax model has produced.
John Sowa is perhaps the eminent scholar on this subject, and you can review his comments at [25]. Forum members may also reflect on Steven Newcomb’s comments. The discussions over these issues are, however, difficult to achieve consensus about. So I dropped my input to the forum over six months ago.
In review of the position I presented back then: Over the past three decades, the issue of structure-function expression has been handled most often, one might claim, in a reductionist viewpoint. Clearly most of the current cell signal pathway expression and gene expression research, particularly when based in statistical methods, tend to be strongly reductionist in nature. The key issue is emergence. If emergence produces functional properties that are strongly dependant on non-localized aspects of field phenomenon, then the usual forms of reductionism seem to fail.
These are difficult issues since various empirical methods have dependencies on a categorization of substrate phenomenon as well as the expression of function. Seen in this way, ontological models have a very different nature that Hilbert mathematics, as seen in non-statistical biomathematics. A positive solution may be in how category formation is treated. Formative ontology based on a stratification of phenomenon, observed as instances of category, may be seen in ontological models more directly tied to empirical work in the lab.
I have developed the point of view that common forms of reductionism is conceptually aligned with the AI and knowledge engineering groups at the W3C and aligned with the W3C. In fact, computer science at core may be seen as biased in the direction of scientific reductionism. [2]
In common forms of the reductionist paradigm, I conjecture, causes are assumed to be completely deterministic in nature, where by “deterministic” I mean Newtonian outcomes based on action-reaction patterns. Bell’s inequality in physics appears to show that there are non-Newtonian aspects to the physical phenomenon underlying physics, and many scientists have work suggesting that non-Newtonian aspects are often seen in stirred liquids.
I have suggested to the biopax working group, early on in (2003?), that noble prize winner (in immunology) Gerald Edelman’s work [3] on response patterns identifies a type of indeterminism that ultimately may avoid categorical modeling if there is not a complete measurement of the specific reactants in a specific instance, ie where no statistical method may go.
The issue is generally framed as the issue of non-locality. [4] However, the collapse of non-locality (seen in wave-particle duality) sees to involve a determination of category through some type of “measurement”. This has been the motivation of my work on formative ontology using organizational stratification.
The relevance to the biologist in the biopax working group is this: The same structural inhibition that John Sowa and Steven Newcomb talk about is foundational to the use of OWL as an ontological modeling paradigm.
I have made the specific argument, as has one other in the biopax working group, that topic maps provides a more optimal linking of topics between complicated OWL ontologies.
The comment by one of the two original authors of the Topic Maps standard is illustrative of the feeling that I have expressed.
[1] Partial listing of publication: URL
[2] Prueitt, Paul S (1996) “Is Computation Something New?”
Chapter Two in “Foundations” URL:
http://www.bcngroup.org/area3/pprueitt/book.htm
Prueitt, Paul S. (1996a). Is Computation Something New?, published in the Proceedings of NIST Conference on Intelligent Systems: A Semiotic Perspective. Session: Memory, Complexity and Control in Biological and Artificial Systems. October 20-23.
[3] Edelman, Gerald and Gally Joseph (2001). “Degeneracy and complexity in biological systems” URL:
http://www.pnas.org/cgi/content/full/231499798v1
also see URL:
[4] Prueitt, Paul S. (2006) “Stratification and the Measurement of Non-locality”. URL” http://www.bcngroup.org/beadgames/TaosDiscussion/Stratification.htm