Archetype

Cladistics wars 2.0

There is a skirmish going on at Dechronization blog right now¹. This is a coauthored blog about phylogenetics. I like used to like this blog (its was right there on my blogroll —->²). There are surprisingly very few blogs about phylogenetic methods these days, despite the wide use that phylogenies currently have  in evolutionary biology and beyond (e.g., linguistics). I will complain that, for nine authors, they post little, sometimes not a single post during a month.

The hot post in question is a mocking of an announcement about a (to be honest, very successful) workshop in phylogenetic methods cosponsored by the Willi Hennig Society and so far held in different continents:

The Ohio State University and the Willi Hennig Society have just announced this summer’s Workshop in Phylogenetics Indoctrination in Cladistics Workshop. Some twenty students will receive fellowships to attend this workshop from the Willi Hennig Society. With these fellowships, students will be able to receive four days of instruction on the proper use of outdated methodologies for only $600.

Leaving the mocking part of the post aside, the bottom end seems to be that say poster finds objectionable the fact that model-based methods, especially Bayesian methods, will be taught by Christopher Randle who, as pointed out, has been critical of some of the aspects of how Bayesian statistics is been implemented in phylogenetic reconstruction (in particular, the possibility of establishing equal priors).

Instruction on model-based methods will be provided by Dr. Christopher Randle, whose only publications on Bayesian methods are critiques (1, 2) and whose recent publications rely either exclusively on parsimony (3) or give preference to parsimony over maximum likelihood when the two methods are largely congruent (4). I’m sure Dr. Randle is an excellent scientist, but his presence as the sole instructor of model-based methods suggests that this workshop is going to be about as balanced as Fox News.

Here are my thoughts on the issue. First I agree in that there may be no one better to teach a method or its software implementation that the person who developed it. It would be wonderful if one could learn during a workshop, say, Phylip from Joe Felsenstein and MrBayes from John Huelsenbeck. Since this type of opportunities doesn’t happen very often, I content that any systematist well familiarized with such methods is a good substitute, in the same way that I don’t need to be James Watson to teach you the structure of DNA (it’s the one with the uracil, right?). Now, I don’t know Christopher Randle personally, but I gather that as someone who has published papers criticizing Bayesian implementation in peer-reviewed journals and who’s papers have elicited published responses, he is more than qualified to teach such methods. If his papers were really far off, if he didn’t understand the theory behind the Bayesian implementations or didn’t know how to use MrBayes, they would have rather had incited the worst response there is to a scientific paper: being ignored.

As it happen, at the Ohio workshop students will get to learn parsimony based phylogenetic methods from leading authors and software programmers in the field, like TNT from Kevin Nixon and Direct Optimization (POY) from Ward Wheeler.

But regardless of your opinion about the aptness of parsimony methods in phylogenetics consider this. Parsimony methods are, literally, an elegant and simple algebraic approach to phylogenetic reconstruction. If you understand the basics of parsimony (optimization, tree search, etc), you will be able to learn model-based approaches in a breeze. You can almost reduce all phylogenetic methods to Sankoff matrices. So, even if you are only interested in model-based methods, you should know your parsimony well.

The Dechronization crew may be surprised at the sudden popularity of that particular post, but timing explains much. Just the previous day a different author posted there an interview with Jack Sullivan, editor-in-chief of the journal Systematic Biology, promising more interviews to come. This post was picked up by Noticias sobre Filogenética, a popular Latin-American blog and forum about phylogenetics widely read in the region, which recommended the blog and encouraged its readers to check out the interesting interview. Next day, blam, an acid critique intended to be humorous but that, unfortunately, reads more like a rant.

As a regular reader of Dechronization I was struck at the sudden change in tone. This is a problem of coauthored blogs. You get to read each posts as a headline of a newspaper before you know who wrote the story, if you know at all. The blog feed reader that I use doesn’t even show the author of the post. I read Dechronization blog, not the items post by Susan Perkins only, for example. Something for Dechronization to think about.

Meanwhile the comments section of that post keeps filling up quickly.

Short version of this long post: cripple fight!

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2 Comments to Cladistics wars 2.0

1

Poletarac
April 22, 2009

I am an occasional contributor to Dechronization. It’s a blog coauthored by individuals dispersed geographically and intellectually, meaning (obviously, I think) that not all authors agree on every post. Even more obviously, the comments section is as open as possible, and so as everywhere on the internet, comments are sometimes unpleasant. It goes without saying that I don’t agree with all of them.

You write:
> they post little, sometimes not a single post during a month.

This is incorrect. There have been months with few posts (Christmas Break and NSF deadline shadow), true. But we are shooting for 10-15 posts per month, and our philosophy is to err by making few good posts than post crap up in an attempt to make some arbitrary quota. I am clearly partial, but I think that many of the articles posted by my colleagues have been excellent.

My only hope is that the tone and level of discourse will (continue to) improve. While we have made mistakes, and will no doubt do so in the future, I think that the experience of the overwhelming majority of our readers will remain strongly positive.

2

Roberto Keller
April 22, 2009

My complain regarding Dechronization’s posting rate, accurate or not, should be taken as an encouragement to be more active. Again, there are too few blogs on the topic in my opinion, but many hungry readers.

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