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Posts tagged ‘inference’

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: Structural complexity in ancestral ontologies

Next week’s reading in our quickly ending series on coding characters and (most recently) dynamic homology.

Ramírez, M.J. & P. Michalik. 2014. Calculating structural complexity in phylogenies using ancestral ontologies. Cladistics (Early View). Available here.

Update: Wonderful paper! Love the innovative and somewhat irreverent use of ontologies specifically to address and answer a genuine systematic question complex, outside of the “Protégé paradigm” (and in fact without formal reasoning, period). Ramírez and co-authors are onto something novel and impactful.

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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