Monday, October 18, 2010

Bayesian NCPA?

Hi all,
I just read Three roads diverged? Routes to phylogeographic inference by Erik W. Bloomquist, Philippe Lemey, and Marc A. Suchard, out next month in TREE and I'm confused! They review some interesting work in phylogeography, but also talk up a "Bayesian NCPA" method. However, my understanding of the method they discuss is that although it takes into account uncertainty in reconstruction of the haplotype network, it doesn't modify the inference key at all, which seemed to me to be the most problematically inscrutable part of NCPA. Have any of you folks looked at this? Is there anything fresh there?
As well- what are your impressions of the method they describe as "spatial diffusion"? My understanding from the Lemey et al 2009 paper is that it is akin to reconstructing location as a continuous character on the phylogeny under a variety of models. Have any of you tried this method? What are your thoughts?
Thanks!
Emily

Thursday, October 14, 2010

Sandwalk: Philosophers, Science, and Creationism

I don't entirely disagree with this, but...in what sense is "the supernatural did it" an explanation at all? If this is a tough question, then so is "proving naturalism couldn't do it" is also a tough question. Criticizing some particular scientific theory != no possible natural explanation is possible. It is easy to see how reasonable people might say this stuff gets beyond mere science.