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Posts tagged ‘philosophy’

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: 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: Philosophy of statistical phylogenetic methods

After a long summer hiatus, our Weekly Discussion series resumes for the Fall semester of 2014 (this time also as a one-credit under-/graduate seminar course “Current Topics in Systematics”). On the menu this semester we have the theory and practice of Next Generation Sequencing, but the corresponding papers will  have to wait a few weeks to make room for 2-3 unrelated topics on which new, intriguing papers have come out over the summer.

The first of these is on the philosophical correlates of statistical phylogenetic inference!

Barker, D. 2014. Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis. Biology & Philosophy 29. (21 pp.). 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.

Weekly reading: Rieppel on the performance of morphological characters

Last week we saw that coding inapplicables is tricky; essentially one must understand the limitations of the ‘square matrix’ and utilize reductive coding in such a way that logical and biological dependencies inherent in homology assessments are not distorted by the way in which global parsimony optimization occurs. We also saw a shift from a rather clear-cut stance about the boundaries between data and inference, to a more qualified position where inferences derived from an initial matrix and analysis should caution one to re-examine ‘the evidence’. Taking this dethroning of primary observations several steps further, next week we are reading:

Rieppel, O. 2007. The performance of morphological characters in broad-scale phylogenetic analyses. Biological Journal of the Linnean Society 92: 297–308. Available here. 

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Systematics and philosophy of science: some suggested readings

This is a developing post related to a prior entry on cladistic character coding. “Systematic philosophy”, naturally (in a historical science), is a rich topic with influential contributions from various competing philosophical schools such as empiricism or realism. Often these contributions acknowledge their heritage openly, however this is not always the case.

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