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Posts tagged ‘methods’

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.

Core ASUHIC conventions for geo-referencing

An updated summary of conventions used in our insect collection to ensure consistent and accurate geo-referencing. [Prequel: Go to SCAN and log in; then proceed to “My Profile”, then “Specimen Management”, then select ASUHIC.] Blog post in development!

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Weekly reading: Next-generation sequencing platforms

…and now onto something completely different; or maybe not? We have completed the Spring 2014 circle of papers on characters, coding, homology, and philosophical implications. Here is the list again for review:

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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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Weekly reading: Coding inapplicables

For next week’s discussion in our budding coding cladistic characters series for this semester, we shall read a paper dealing with the ins and outs of coding “inapplicables”:

Strong, E.E. & D. Lipscomb. 1999. Character coding and inapplicable data. Cladistics 15: 363–371. Available here.

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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Weekly reading: Nature of cladistic data

By popular demand, the Spring 2014 weekly lab discussion series will focus on the theory and practice of coding cladistic characters, and where and why this remains an essential task of systematics. This is a broad theme that has been treated by many authors and from different perspectives. We will start with a paper that is rife with issues that merit a more nuanced discussion; but at the same time reflects a suite of topics and positions advocated in the mid t0 late 1980s when the 1st- to 2nd-generation cladistic software packages (such as Hennig86) were in use.

Pimentel, R.A. & R. Riggins. 1987. The nature of cladistic data. Cladistics 3: 201-209. Available on-line here.