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Wednesday, March 01, 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 biological expression

 

On Formal verses Natural systems à [206]

 

From “Paul Prueitt” to BioPAX forum

 

 

Scientific realism has many definitions, some which are very positive.  Karl Pribram (cognitive neuroscientists and one of the founders of the recent developments in quantum neuroscience) called his "philosophical viewpoint" scientific realism.

 

In Karl's sense, scientific realism states that first and foremost that there is a natural world, "out there", and that to a large extent this natural world does not depend on human beings' existence or thinking.  Period.  Definition complete. 

 

This is where "realism" starts.  But like so much else of what might (have been) valid uses of terms, the term realism is made into a series of polemics, largely to disallow the sense that I am attributing to Karl (and myself), and others. 

 

Example of polemic: "A realist position stated that there is no reason to try to improve the world because the world is going to Hell in a hand basket."  The sense here is that the realistic is someone who believes in a certain destiny.  This interpretation is nowhere close to Karl's sense of what scientific realism is. 

 

Why is this more pure sense of "realism" disallowed?  Well that is a good question, but one that leads quickly into the polemics.  So we have to endure without this discussion.  I mean, we have to ignore this interpretation. 

 

In the BioPAX case, the realist might say that the purpose of BioPAX is to communicate within a community of humans how cell and gene processes "communicate".  In both cases, the term "communicate" is something that can be interpreted quite differently depending on philosophical commitment.  If "communicate" is to have a unique meaning, as one often attempts if one is doing semantic web types of things; then the realism is about the "need for systems to know each other".  Communication is then the lock step of finite state machines working within the definitions of OWL assertions.  A different word for this might be "data interoperability", so that the term "communication" can be allowed a more full "meaning".  The "second school" would define any OWL construction to be a finite state machine with the ability to provide indexing based on first order logics and to thus contribute to data interoperability based on the assertions made with the vocabulary of this finite state machine and the inference rules.  OWL then becomes useful and not leading to an misunderstanding with natural scientists who are looking at nature and seeing non-deterministic state transitions.

 

Non-deterministic state transitions are something that a finite state machine simply cannot do.  Polemical realism would suggest that natural reality has no non-deterministic state transitions.  Scientific realism suggests that nature does not care what we humans think about such things.

 

 

As Alan is referring to, the non-precision seen in natural language is a necessary part of how human communication works.  Why would signal pathways expressing within the functioning of cells and cell environments, not require the same "multiple articulated" degeneracy?  Scientific realism would suggest that if bioinformatics moves us too far into pure reductionism, then our biological sciences will fail in sudden ways (missing completely a prediction of a real deficient reaction to an immunological agent administered to protect our population from something) for example.  In other words, the real world will not "care" if we make a fundamental mistake. 

 

Fundamental mistakes are made all the time.

 

The problem with the BioPAX definitions now given to "physicalEntityParticipant" may be that the real natural participant is at one scale of organization and that the real natural compound is at another scale of organization.  These layers of organizational interaction may be “separated” by a gap.  By “epistemic gap” we, the second school, mean a gap where no energy or mass can find stability, as in the gaps between electron shells, or the Heisenburg gap.

 

The scientific realism as represented in my work, and in Karl's work, and in the work of others; suggest that without an ontological model that accounts for the reality of emergence (from the substrate into a slower time scale level of organization) the understanding of "communication" will not map to observed reality.

 

These are my opinions, I speak for no one else.

 

 

 

PhD mathematics and quantum neuroscience



[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