Wednesday, June 28, 2006

TreeBASE rocks

I gave a talk today ("Dude, where's my tree?") at the Evolution 2006 meeting at Stony Brook. It was intended as a somewhat tongue-in-check overview of some issues concerning TreeBASE, and broader areas of biodiversity informatics, making use of ants as an example (see my SemAnt project).
Michael Donoghue took me aside after the talk and made some interesting points. He was a little tired — understandably — of hearing that "TreeBASE sucks" (e.g., my CIPRES talk), and felt that my constantly saying this was counter productive. It could also lead to people not putting their data in TreeBASE because they'd heard that it "sucks".
There is an element of social responsibility here, I guess. I resolutely avoid politics. I don't mean this in a pejorative sense, it's just that I don't have the temperament or skill for it, unlike Michael himself (Lee Belbin is another person in this area who strikes me as a very skilled manager).
Now, my talk was intended to be fun, and I was taking the piss out of myself as much as anything. I also think the things we criticise are the things we value the most. But that said, let be make it clear that TreeBASE is very important. As editor of Systematic Biology I've made authors submit data to it. I have a lot of respect for the work Michael, Bill Piel, and Mike Sanderson put into TreeBASE. If you have phylogenetic data — submit it to TreeBASE. It's the best we have. It's just that, well, as a community, we could do better.


Anonymous said...


Thanks for clarifying your position. Since I was at the CIPRES talk, and not the later one, I can only speak to that event. While the intent of your talk was clear in some ways, and made some interesting points, it also showed a rather limited understanding of why TreeBASE was created, and how many of its own goals it actually achieved with very little resources. This accomplishment was possible only through an extraordinary amount of personal commitment by the people you mentioned specifically in your blog (the same names you seemed to ridicule in your CIPRES talk).

Currently TreeBASE II is under development, as you well know, and the CIPRES team has endeavoured to make itself available for constructive user input. It would be really great if you actually participated with us in constructing future TreeBASE versions through a reasoned dialogue. If you feel you must focus your talks on criticism of existing databases, perhaps it would be more sensible to start by focusing on those that have more than adequate resources to respond to your critiques, such as those created by acts of federal governments. Still better, perhaps you should get to know and work constructively with the people involved in these projects as well, and to influence their behavior by the time-honored method of cogent persuasion.

We will be happy to hear your requests/feedback regarding TreeBASE and consider whether they can be accommodated in the context of the deliverables we have committed to for TreeBASE II. All you need to do is present them to us in a spirit of cooperation.


Mark A. Miller

Roderic Page said...


Well, maybe I deserved some of this for being so flippant, but I think your response is a little over the top (if not to say somewhat patronising).

I certainly didn't (knowingly) ridicule anybody in my talk at CIPRES, and if you'd been at the Evolution talk you'd have see me send myself up more than anything (c'mon, I had a slide saying "Rod Page sucks"). I have a pretty clear idea of why TreeBASE was created, and I've played a small part in its development through TreeView (used as a viewer), and the mincut supertree algorithm (now off line due to a recent hacking incident). I've consistently supported it in editorial board meetings, and now as editor of Systematic Biology where I require authors to submit their data to TreeBASE. I've also had very fruitful interactions with Bill Piel over the years (and Bill's been very patient with my comments). Lastly, as a journal editor I suggest I know more than enough about "personal commitment".

A lot of my recent work on Life Science Identifiers, federated search engines (doi:10.1186/1471-2105-6-48), and has been motivated by issues directly to do with TreeBASE. I feel this is the best way I can contribute to developing a truly useful phylogenetic database.

Now, you may feel this is not the way to do things, but I value the freedom of being able to say what I think. In other words, I like being a gadfly. For me, "reasoned dialog" includes criticism, whether it be private or public (in talks or blogs). If I wasn't actively working on solutions (see above) then, sure, maybe your criticism would be justified. But I think I'm doing more than just saying "TreeBASE sucks".

And, I hate to say it, but for me the sentence "We will be happy to hear your requests/feedback regarding TreeBASE and consider whether they can be accommodated in the context of the deliverables we have committed to for TreeBASE II " encapsulates everything wrong with this approach to science. This is management-speak, not science.