Archetype

The Pewter Leprechaun Awards Ceremony

E. Haeckel

You may not fancy public humiliation of scientific papers (ah come on, who doesn’t?), but the Pewter Leprechaun Awards Ceremony is a fun read. If you want to know what is this all about look here.

You really need to know well your history on systematics and biogeography to fully enjoy the piece, but if you don’t you will do well in putting Google to a good use and run some searches on those names. On a side note, I do think Brazeau’s paper didn’t deserved the nomination, specially among the other contestants.

I hope they do send a pewter leprechaun to the winner (and blog about it).

Phylogenetics through videoconferencing

Last night I attended a talk in Lisbon given by Ward Wheeler at the AMNH in New York City and moderated by Frederick Matsen from his home institution in Berkeley, California. The talk was the second on a series of talks in phylogenetics held via videoconferencing.

The idea behind phyloseminar.org is to hold regular live online seminars in phylogenetic methodology open to anyone around the globe. This is a challenge given the time zone differences of the possible participants, but it does makes the whole event fun: I watched it after dinner at 9:00pm; the presenter gave it at his 4:00pm; while the moderator was there after lunch at his 1:00pm. I saw at least one person among the audience that watched it from the future after breakfast in New Zealand the next day at 10:00am. › Continue reading

Tags: Direct optimization, Dynamic homology, Frederick Matsen, phyloseminar, POY, Ward Wheeler

Patenting cladistics

Every once in a while someone comes and tries to file a patent on some of the very basic algorithms we all use to infer phylogenetic trees.
This time is a very “special” someone. The image to the left may give you a clue. Read more at Myrmecos blog.

Tags: microsoft, silly

Chris Humphries, botanist and founding fellow of the Willi Hennig Society, died on July 31st, aged 62

Photograph courtesy of Malte C. Ebach (http://urhomology.blogspot.com/)

It is our sad task to record the death of Professor Chris Humphries, merit researcher in the Botany Department until his retirement in 2007, on Friday 31st July. Chris was a leading figure in the cladistic revolution in systematics and biogeography. Without his tireless efforts, systematic botany – perhaps systematic biology – would be a very different beast.

Chris joined the Botany Department in 1972 as an assistant curator, a nearly-finished PhD student, coming directly from Vernon Heywood’s Botany Department in Reading University. With the exception of three sabbaticals – two of them at the University of Melbourne (1979-80, 1986) and a six month stay as a fellow at the Wissenschaftskolleg zu Berlin (Institute for Advanced Study, Berlin) in 1994 – Chris spent his entire career in the Museum.
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Bigger is better: the largest phylogenetic tree reconstructed.

GenBank, the standard database for genetic information maintained by National Center for Biotechnology Information, has been accumulating DNA sequences for some three decades now. Since its creation in the late 1980s, it has become the de facto repository for genetic information– genetic data must now be submitted to GenBank for a paper to be accepted for publication. Most sequence data accumulated are the result of the sum of many “local” taxonomic studies that have targeted a particular group of organism for a relatively small, but well-known collection of genes. It contents now span over hundreds of genes across all of life’s domains. So, what would happen if you were to take all the sequence information contained in GenBank and analyze it phylogenetically all together in a single, one-step study? Well, that is what Pablo A. Goloboff and coworkers just did, the results of which were published in last week’s online early edition of Cladistics, the international journal of the Willi Hennig Society.

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Tags: GenBank, James Farris, Pablo Goloboff, TNT, Willi Hennig Society

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.

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The evolution of the web

Spider web, that is.

This is an excellent example of the way systematic papers should be. In the latest issue of the Proceedings of the National Academy of Sciences (USA), Blackledge and coworkers assembled a comprehensive data set for cladistic analysis of orb web spiders that includes six different molecular loci, 143 morphological characters and behavior in the form of characters derived from web architecture.

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Tags: Direct optimization, Implied weights