Tuesday, December 20, 2005
Lattice of ontologies
From the Protégé OWL forum discussion
This discussion goes back several beads and is most excellent
Paul Prueitt is using foot notes to make comments aboutà 
Continuing communications between Andrea Proli and Paul Prueitt
First I would like to express my admiration for the Italian schools of information science. It is refreshing to talk with you. Thank you.
2) So that I can catch the relevant points I am going to use foot notes and then expand my comments on 
3) There was also in the time immediately after Godel some growing interest in the notion that formalization was itself subject to critic. I do not know this history, as it is not one that is easily accessable, but clearly the distinction made in the literature about the early Wittgenstein (1905 – 1917?) and the later Wittgenstein is pointing to a failure of formalism to be as “expressive” as natural language. One reason why I dislike the use of the notion of logical expressiveness in the OWL community is that the word is stolen from another connotation.
Logic is NOT expressive of the natural phenomenon. But one can not say this in the computer science community, because “they” own the word “expressive”.
The same polemic occurs with the use of the phrase “computational complexity” and formal semantics”. This phrase already makes a claim that many do not agree with. See Judith Rosen’s discussion at 
4) The way these things are talked about in some literatures, specifically those of Tarski and thousands of individuals with similar thinking, is not the same as how N Rashensky and R Rosen and others talked about these things. But this logic school, which I will associate with the AI school, made claims that they were the only ones addressing the post Godel world.
John Sowa and many others are still doing this. I have called this a form of fundamentalism simply because the school (including the work we referenced by Ian) uses natural language in a way that is simply (from my point of view) incorrect. I do not mind their use of technical terms if they are not authoritarian (as James Hendler certain is). They however, will not acknowledge the issues that are raised and pretend as if there is no legitimacy to the issue of degeneracy in metabolic signal pathway modeling as pointed out by G. Edelman, for example).
So , because they, Hendler and group, have controlled funding peer review, there is no alternative to the mainstream. They monopolize government funding and make relationships with business so that certain status quo continue to produce almost utter non-sense as our foundations to information science.
Please see: communication instrument as an example of grant proposals where Hendler, and his students, served as peer review and caused the grant to not be awarded.
5) The point is that IF there is a problem is creating precise and correct logical theories about natural processes such as human thinking, as I Prigogine points out in “End of Certainly”, then one cannot continue to impose on natural science the imposition that are imposed by this school of logic and by the mainstream of computer science. Yes?
Is this school of logic very similar to a religion? I say yes. Memetics can be used to show why the school is powerful and stable.
One has to look for something different, such as notion of “open” logic, or quasi axiomatic theory (Victor Finn): Finn, Victor (1991). Plausible Inferences and Reliable Reasoning. Journal of Soviet Mathematics, Plenum Publ. Cor. Vol. 56, N1 pp. 2201-2248
6) It is precisely this point that I, and others, am making. There are alternatives, and suggestions as to what do to in the case that medicine and other life sciences cannot be founded on classical logics. But unless the Emperors of Logic (to steal a phrase from Roger Penrose), acknowledge the complete and total incomprehensiveness of what is not done in the OWL inference engines, then we cannot start on developing these alternatives.
7) The argument is that information science must acknowledge the limitations to classical logic and quit an endless Zeno’s paradox. Our society must have good information science now, and it can not get it as long as the mainstream computer scientist is pretending as if things like 13 year development project to visualize and edit RDF / OWL is acceptable, or the two decade funding of Doug Lenat, or the four decades of massive AI funding.
8) Why are you skeptical?