I want to call your attention to a new blog written by Kurt Pickett, a colleague and close friend of mine. Kurt and I meet at the American Museum of Natural History a few years back. He was a postdoc and I a grad student, both working with James M. Carpenter.

The blog, Apoica, is named after the genus of rare nocturnal paper-wasps (Vespidae) he studied during his Ph.D. at Ohio State University. Kurt is currently an assistant professor at the University of Vermont where he continues his research on phylogenetics and the evolution of social behavior in the paper-wasp family. We are actively collaborating on a project involving ants (of course), combining molecular and morphological data for phylogenetic analysis.

In his blog Kurt writes not about his discoveries on wasp behavior, but about another major discovery he came upon by the end of his postdoc years: he has lymphoma. He recently underwent a bone marrow transplant, the ultimate treatment for his kind of cancer. He blogs about the up and downs of his recovery with the eye of the excellent scientist he is. Kurt has a great sense of humor, but don’t expect his posts to be anything but rather dark in tone.

You will think that a blog with the name of Archetype would be very close to the root of the tree, if not being the root itself. Oh well, this blog seems to be well nested in a clade “higher up”. But look at the bright side, Archetype’s sister blog is excellent and the one that lead me into blogging in the first place.

Cretaceous African ant in amber (Courtesy of Vincent Perrichot via http://myrmecos.wordpress.com)

1. A peer-review paper gets published;
2. The media gets hold on the story;
3. The blogs react: scientists and general public fill the comments section (in the genuine tone of the internets);
4. The authors of the original paper join in the discussion.

Discussion may get heated, comments may get bitter, but the results are always rewarding for all.

It has been a highly enjoyable experience so far. My readership has grown beyond my modest expectations, currently averaging about 100 visitors a day. I have gotten the most traffic whenever one of the much more popular bloggers direct readers to this site– this has been specially so everytime I get the Myrmecos bump, but there are a few other people to thank.

When I started, I decided that if I could post at least once a week I would be satisfied (so far the case). I have thousands of Scanning Electron Micrographs from my PhD research, many that will never make it to formal publications, so I thought I would just share a nice-looking one every week to keep a constant pace. Thus the Homology Weekly series was born. But from the very first post in the series I also realized that just throwing in an image wasn’t going to be of the interest of readers and myself. The emphasis then changed from the purely visual to telling a short story about a morphological character.

It also became apparent from the very first post, however, that I wasn’t going to assemble these stories once a week. I then decided to go with the whenever-I-feel-like-it pace (also known as rate heterogeneity in molecular evolution parlance). I also decided to keep the original name of the series to remind myself that things doesn’t always turn out as you expect them to (for the good).

As for the dreaded question among bloggers of for whom do you write, I still don’t know, but I am glad to have science enthusiastic people as well as colleagues among my regular visitors.

Thank you all.

We ought not to think that a conception or definition or hypothesis that works in one part of biology must work in all others, and yet biologists themselves often behave as if this were true. That is another challenge: why is this? The answer, I believe, is that biology is both highly diverse, and also massive.

Read the rest in his post: Counterintuition: Bdelloid Rotifers « Evolving Thoughts.

On that note, Taro Eldredge is a former Cornell University undergrad that just moved to the University of Kansas to start graduate studies and just moved his blog to WordPress (btw, what would be the opposite of a double wammy?). His research interest is in staphylinid beetles of the sort that live as guest of ant and termite colonies.

Check out his blog at Myrmecoid – ??????

I just learned he is also a Ph.D. student at Pert, researching the effects of salinity levels on terrestrial arthropods. He started a clever-looking blog where he mixes photography and science. After one month posts are looking good. Besides, you know that anyone with that avatar can’t be a bad blogger.

(Hat tip to himself )

A spruced-up version of a dirty box mite. 2009 © DEWalter.

A new blog just sprung into life. Macromite’s Blog:

This blog will be devoted to mites and mite art. My original Mite Image
Gallery was hosted by the University of Queensland until I left there
in 2003. Since then it has been lying dormant on a variety of computers
in a much colder land. Many of my images continue to be available on
the web (e.g. in interactive keys) and, if you are fortunate enough to
live in Australia, you may have seen some of them at the recent
Ornamentamology exhibit created by the Jewellers and Metalsmiths Group
Queensland, but amazingly, there doesn’t seem to be a site devoted to
appreciating the often bizarre beauty of the Acari. Now there is.

This person puts me to a shame when it comes to enhancing and coloring images from scanning electron microscopy (SEM). I rarely ever mask the background out, for example, mainly because it is a pain even for simple, bare contours. I can’t imagine the work that went into masking each of those hairs on the legs and the feather-like hairs on the body to produce the image above (from this post). Notice how the true cuticle of the mite’s body peeks at varous points in salmon color through the light pink of the covering dirt, requiring a lot of masking work also.

It is not all post-production, however. Having worked extensively with scanning electron microscopy I can tell you that, giving the quality of the original images he starts with (sometimes a full set just for a single final image), there was already a lot of work in both specimen preparation and flight-hours at the microscope.

And if I stop drooling over my keyboard from looking at the images and read the text on each post, I may even learn something about mite taxonomy.

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!

———————————————————————