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Posts tagged ‘empiricism’

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: 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.

Weekly reading: Brady on the independence of systematics

Up next week, following Rieppel’s (2007) nuanced dissection of the limits of ‘direct reference’ (Kripke’s causal theory) and emerging lessons for comparative morphologists, we shall pivot to one of the more influential and sophisticated expositions of a pattern-centric view. Ronald Brady played a sometimes under-appreciated role in conversing and shaping views with cladists at the American Museum of Natural History starting in the late 1970s.

Brady, R.H. 1985. On the independence of systematics. Cladistics 1: 113-126. Availaible here.