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Posts tagged ‘realism’

Weekly reading: Leonelli on classificatory theory in biology

Sabina Leonelli has authored numerous papers on bio-ontologies that relate to our Spring 2015 theme. For this week we will read:

Leonelli, S. 2013. Classificatory theory in biology. Biological Theory 7: 338-345. Available here.

Also consider my post summarizing where we are right now and might considering going.

Weekly reading: Seltmann et al. on hymenopterists’ guide to the Hymenoptera Anatomy Ontology

If it were that kind of semester, maybe it would be neat to summarize our thoughts on all the ways in which last week’s paper – one of the theoretical foundations of the OBO Foundry approach – was puzzling to us. But, so far it isn’t (that kind of semester). Just three thoughts then.

1. Many of us seem to want to be realists.

2. Whatever the merits of the theory, implementation matters too. The two need not always be entirely and reciprocally consistent. (that is putting things mildly)

3. Consider this statement by Smith (2004), top of page 79 in the publisher paper.

“Good ontologies are reality representations, and the fact that such representations are possible is shown by the fact that, as is documented in our scientific textbooks, very many of them have already been achieved, though of course always only at some specific level of granularity and to some specific degree of precision, detail and completeness.”

I think it is fair to say that this statement leaves room for both the empiricist and the realist acknowledging the importance of theories and concepts in science while not elevating them a priori to a level where they are either unassailably reliable or misguided. It is a sensible enough statement to make. Strangely, to my thinking at least, Smith takes this statement to work as something of a wedge between reality- and concept-based ontology design maxims. But the statement itself speaks more to the notion of reality (which by the way remains under-defined) and concepts being intertwined in scientific advancement. Whatever else may be said here, we concluded that following his outlined path does require ‘a strong ontological commitment’. I doubt that this message has been received and ratified by most practitioners.

Anyway, onto to more practical issues; up this week:

Seltmann, K., M. Yoder, I. Miko, M. Forshage, M. Bertone, D. Agosti, A. Austin, J. Balhoff, M. Borowiec, S. Brady, G. Broad, D. Brothers, R. Burks, M. Buffington, H. Campbell, K. Dew, A. Ernst, J. Fernandez-Triana, M. Gates, G. Gibson, J. Jennings, N. Johnson, D. Karlsson, R. Kawada, L. Krogmann, R. Kula, M. Ohl, C. Rasmussen, F. Ronquist, S. Schulmeister, M. Sharkey, E. Talamas, E. Tucker, L. Vilhelmsen, P. Ward, R. Wharton & R. Deans. 2012. A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. Available on-line here.

Weekly reading: Smith 2004 on ontology as reality representation

Last week’s paper on the merits of “realism as practiced by the BFO” left us with a sense of dissatisfaction (which cannot fairly be credited to the paper itself). First, since this was predominantly a “con” paper, it seems important to also examine the “pro” stance. And second, yes, we are getting further away from applications. We will address both issues, though necessarily in sequence. Therefore, up this week is a foundations paper on how to conceive of and construct realist (OBO-compliant) ontologies.

Smith, B. 2004. Beyond concepts: ontology as reality representation; pp. 73-84. In: Proceedings of the 3rd International Conference on Formal Ontology in Information Systems (FOIS 2004); November 4-6, 2014; Torino, Italy. IOS Press, Amsterdam. Available on-line here.

Weekly reading: Putnam on the corroboration of theories

“There is no logic of discovery – in that sense, there is no logic of testing, either; all the formal algorithms proposed for testing, by Carnap, by Popper, by Chomsky, etc., are, to speak impolitely, ridiculous; if you don’t believe this, program a computer to employ one of these algorithms and see how well it does at testing theories! There are maxims for discovery and maxims for testing: the idea that correct ideas just come from the sky, while the methods for testing them are highly rigid and predetermined, is one of the worst legacies of the Vienna Circle.” – Putnam, 1974.

Putnam offers a passionate rebuttal of logical empiricism but later on became more skeptical about metaphysical ‘evidence’ not directly linked to sensory impressions.

H. Putnam. 1974. The “corroboration” of theories; pp. 221-240. In: P.A. Schilpp, Editor. The Philosophy of Karl Popper, Volume 1. Open Court, La Salle, IL. Available (as a reprint) here.