Sunday, November 04, 2007

Graduate studies in Comparative Biology

Some months ago, the American Museum of Natural History (AMNH) in New York City was granted official authority to award its own Ph.D. degrees. What this means is that, starting in the Fall of 2008, a first generation of graduate students will be able to pursue a full state-of-the-art program in Comparative Biology at the best setting possible: an institution devoted to collection-based science.

The AMNH has already a long history in graduate level education through its join programs with Columbia University, NYU, CUNY and Cornell University. Many courses are already taught right in situ by the Museum's curators, and the students enjoy use of the various resources for their research (besides the collections, there are molecular laboratories, digital imaging with a SEM facility, and the fastest computer clusters for phylogenetic analysis ever assemble, just to name a few). However, further governing autonomy will surely create a more cohesive atmosphere and save a few headaches to its students. Nevertheless, as far as I know, the AMNH will keep its join programs with the universities.

This post was prompted by the launching of the new Ph.D. program website. The application deadline is December 28, 2007. I highly recommend anyone interested to contact some of the curators and apply for this or subsequent academic years.

Thursday, October 25, 2007

IISE Planet Bob: bringing Taxonomy to the public

This week the International Institute for Species Exploration (IISE), a new research institute based at Arizona State University, released Planet Bob. This short, humorous film is the first effort within the IISE's commitment in educating and bringing the science of Taxonomy closer to the public. It does a good job in shaking off Taxonomy's reputation as a dead science and in describing the field's central role in biodiversity studies.

Watching the clip reminded me how unbelievable it seems that ants entered the realm of cybertaxonomy more than 10 years ago with the creation of antbase by Donat Agosti.

Tuesday, October 09, 2007

Publication of species names on the Web

I recently found a letter Donat Agosti, Jim Carpenter and I sent to the journal Science some years ago. The letter was prompted by the journal's publication of a new species of a pre-Cambrian bilaterian fossil. The issue was that no introduction of a new scientific name was to be found in the printed version of the article, since this had been relegated to the electronic, on-line only, supplemented materials. The fossil, thus, remain unnamed in accordance to the Zoological Code of Nomenclature.

Our letter never got published, but we did receive a reply from the journal some months later. I for one was pleasantly surprised that the editors consider the matter and cared to write us back. It is very interesting. You can read both our original letter and Science's reply below.

The issue of electronic publishing of scientific names for organism continues unsolved, but great progress has been made by the International Commission on Zoological Nomenclature itself with initiatives like ZooBank.

(Submitted to Science magazine on July 13, 2004)
The report on the oldest bilaterian fossils by Chen and co-workers (“Small Bilaterian Fossils from 40 to 50 Million Years Before the Cambrian,” 9 July, p. 218) invites reexamination not only of current theories of metazoan evolution but of the rules of zoological nomenclature as well. Although the interpretation of the fossils and discussion of the relevance of the discovery appeared in both the printed and online versions of this journal, the systematic paleontology section introducing the new generic and specific names appeared as an online supplement only. The International Code of Zoological Nomenclature (ICZN), regulating the application of scientific names of animals, is yet to regard as valid publication of “text or illustrations distributed by electronic signals (e.g., by means of the World Wide Web)” (Art. 9.8.) exclusively. No scientific name for the new bilaterian fossils is thus yet available.

It is worth quoting Art. 8.6. of the ICZN as it also pertains online publication: “For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.” The explicit rejection by the International Commission on Zoological Nomenclature of the WWW as a mean of publication responds to valid concerns regarding the permanence of such electronic media. The growing popularity of exclusively electronic, peer-reviewed, scientific journals is a welcome trend, and there is no reason why publication of scientific names for organism shouldn’t follow in that direction. However, permanence of electronic-only published scientific research should be a universal concern and not just an issue of zoological nomenclature. Greater discussion and involvement in this area by the scientific community and the publishers can result in a successful model that will prompt the ICZN to modify its rules to allow the use of electronic media as a valid form of publication for the purpose of scientific nomenclature.

Roberto A. Keller, Donat Agosti and James M. Carpenter
Division of Invertebrate Zoology, American Museum of Natural History, Central Park west at 79th Street, New York, NY 10024, USA

(reply by Science on April 27, 2005)
Dear Dr. Keller,

Thank you for your letter regarding the policies of the International Code of Zoological Nomenclature (ICZN) regarding publication of new generic and specific names on the WWW. We were unaware of that policy. We feel that the publication of electronic only information has reached a level of sophistication such that we are confident in the ability of libraries, of HighWire Press (our online publisher), and other non profit institutions to maintain copies of our electronic only publications in perpetuity. Sciences online version is the journal of record and multiple redundant copies are held at HighWire Press and at numerous libraries. Science has been published since 1880 and is fully confident that its archives from the first issue indefinitely onward will be available for future scholars. Thus we disagree with the premise of the ICZNs policy and would urge them to revisit it.

Nevertheless, we will keep the ICZNs view in mind in the future when reporting new species in the pages of Science.

Best wishes,

Katrina L. Kelner, PhD
Deputy Editor, Life Sciences

Since the bilaterian fossil publication, I have not seen new species published in Science magazine where the nomenclature does not appear in the printed version. I will always wonder how much our letter played a role in that.

Wednesday, September 12, 2007

Iberian Ants

It seems that updated its interface last March (2007). The site is devoted to the ants of the Iberian Peninsula (Spain and Portugal) and its curated by Kiko Gómez and Xavier Espadaler. It is now a site easier to navigate and its data is now handled with a proper built-in database. It is also a pleasant-looking site with a simply design.

Looking at their ClustrMaps site counter it is interesting to note that the bulk of the site's hits come from Latin America. This is not surprising given that the site is one of the few such sources in Spanish. The general information on ants provided by is of universal use of course (classification, glossary on ant anatomy, etc). However it does shows the need for such sites and web-resources for Spanish-speakers interested in the native ants of the vast and species rich Latin American region.

Tuesday, September 04, 2007

Incoming Book: Ants of North America

Schedule to be released in November 2007:

Brian L. Fisher and Stefan P. Cover
Ants of North America
A Guide to the Genera
$34.95, £19.95 paperback

* New keys to the 73 North American ant genera illustrated with 250 line drawings ensure accurate identification
* 180 color images show the head and profile of each genus and important species groups
* Includes a glossary of important terms

You can read more at The University of California Press' website.

Thursday, August 30, 2007

antbase useage

ClustrMaps - our tool to visualize the geographic origin of our users - is now running for exactly one year showing almost 110.000 visits on antbase, in most cases to use the digital library and as starting point for the Ant Name Server (Hymenoptera Name Server).
I am glad we can offer a service to a truly global user community.

Friday, August 24, 2007

Nomenclatorial sloppiness (5) and a solution

Christiana Klingenberg suggested being more constructive in this blog about typos and others misspelled names, and to offer my own little personal tool to the community.

Here it is. I once made two files for my MS-Word spell checker, one including all the species terms we have an the Hymenoptera Name Server for ants (of about 2002: ) and a second one for all the morphological and anatomical terminology of social insects in Torre Bueno.

And here how you use it: Save the files best directly in the location where MS World hast the spell check custom.dic file. This is in my case c:\Documents and Settings\donat\Application Data\Microsoft\Proof. Then open MS Word, Tools, Options, Spelling and Options, Custom Dictionary and add it.

The species file is not up to date, so I will figure out a way to get a new one – but for the moment, here it is.

Thursday, April 12, 2007

iPod + Taxonomy = Taxon-podcast

During a recent visit by Brian Fisher I showed him some Scanning Electron Micrographs from my work on ant morphology that I had stored on my iPod as a curiosity. While these gray-scale SEMs look already very good on the iPod screen, we decided to upload some full-color images from AntWeb. The results were fantastic.

Then the idea came of some sort of taxon-podcast. One can, for example, load into the iPod the ants of Arizona before going into the field or all the species of Pogonomyrmex
before sitting at the microscope in the Museum. However, for the regular AntWeb user the only way to currently upload sets of ant images into an iPod is to painstakingly save into one’s hard-drive each image individually from the desired biogeographic or taxonomic set to have iTunes read the resulting folder. Ideally taxon-podcasts could be automatically produced the way now AntWeb capably produces field guides in pdf format.

One drawback is that the iPod doesn’t have the same capabilities for dealing with images the way it can deal with a collection of audio and video files by way of hierarchical categories (artist, album, genres, composers, etc) and playlists. One can turn to Pocket PCs that are “proper” computers with touch screen interfaces. In fact, Kevin Nixon from Cornell University has had a fully functional version of WinClada for such devices for some years now, including a powerful algorithm to manage identification keys in matrix format with the ability to include images. However the idea here is to utilize the most popular electronic device to date for research and education.

Such taxon-podcasts are not going to be needed when wireless networks become global and iPhone type devices with full web capabilities become common, so we can tap directly into antbase and AntWeb. For now, with 100m units sold, iPod seems the logical choice.

Thursday, March 22, 2007

The Importance of Ants...

I have always suspected that ants are not just very important in any ecosystem in the world, but in our scientific world as well. Nature's bibliography project "Connotea" confirms this suspicion with hard facts: Formicidae are more important than HIV and cancer.

Thanks to Jochen Bihn's work, almost all of the digital versions of the ant taxonomic publications are now also accessible through Connotea, a bibliographic tool aimed at the general science audience.

Check it out, add you own tags, and let us known for innacuracies, wishes and more

Thursday, March 15, 2007

rss feeds and new names alerts

I just discovered the new UBio RSS-Nomina Nova feed for new names. This is much more professional then what we have at, but it also has a different function, that is to discover new names in the literature. And of course, that's what we are out for to secure we have a catalogue as complete as possible.

If you compare the results from NominaNova and with our still simple "New Taxa Notifyer" for the year 2006, the results are very different: 5 publications when searching for "Formicidae" of which one is counted twice, and 105 species described (including those in the NominaNova publictions) on our system, plus two more publications or10 species for 2007 .

As a collector of new names, I would like to be NominaNova to be complete, and in return, I would like to have the possibilty to send a feedback, if I discover a publication, that is not in their feed. This is my personal interest.

But there is also a wide service to the community, since other Website providers are using the UbioRSS-feed on their website to inform their audiences about new publications (eg antweb, the ant of the cachoeira nature reserve.

There is an additional suggestion. Since all the new ant systematics publications are read, the names checked for whether they are already in the Hymenoptera Name Server, and if not, the the name is linked to an existing name and a decision is made, of what kind the relation is and then entered into the HNS, it would be ideal, if this could flow directly into the Ubio system as well - which I hope Norm Johnson at the Hymenoptera Name Server, where the ant data reside as well, and UBio can sort it out?

Monday, March 05, 2007

Nomenclatorial sloppiness (4) and a stinking dead cow

Sloppiness and a dead cow

Another paper I entered recently which make me think of the value of entering names into our databases so we could in future read all our publications by machines. But it needs somebody going through often confusing prose....

here the problems I encountered in Collingwood and Van Harten's "Additions to the ant fauna of Yemen":

Pachycondyla senaarensis; ought to be sennaarensis
Cardiocondyla yemene: ought to be Cardiocondyla yemeni
Cardiocondyla schuckardi: ought to be shuckardi
Crematogaster flaviventris Santchi, clandestinely raised to species in this paper
Monomorium phoenicium: ought be phoenicum (see quadrinomen below). But originally described as Monomorium salomonis subopacum var. phoenicia by Emery 1908: 677, then cited as Monomorium (Xeromyrmex) subopacum v. phoenica Emery in Santschi 1927 in his listing of Monomorium (Xeromyrmex) subopacum v. phoenicum
Monomorium wahibiense: ought to be wahibense
Technomyrmex bruneipes Forel: clandestinely raised to species
Camponotus spissinodis Forel: clandestinely raised to species
Lepisiota opaciventris (Finzi): clandestinely raised to species

Quadrinomen, a (stinking) dead cow

I am not sure, but it was Bolton who decided to get rid of quadrinomen by just dimissing them. The Code allows to disregard quadrinomen, and so, tacitly, the first author using the name at least as trinomen becomes the author. But many of them, like Santschi in the case of Monomorium phoenicum (and more recent authors as well), didn’t care, and implicitly accept the type of the new species as the one belonging to the quadrinomen and so fixed unintentionally, thus the new species is not valid, since no type species has been fixed properly. So, following suit of Bolton's iron broom, we ought to dismiss all the subsequently raised taxa.

But this is only part of the story: If we want to collect all the names though the Biodiversity Heritage Library and Ubio, then we need somebody sitting here, like I right now, curating all these names. I have the priviledge to have a system, where I can look up all the original literature, but spend nevertheless on the above document so much time, that I think twice about the value I am getting out of this. Clearly, getting the name is only one part - and in fact none with which I can get any scientific cridentials. It only begins to add up, once I can access all the localities mentioned in this paper - but this is yet another nut to crack, and a huge time investment.

So, when I think about building up an Encyclopedia of Life project which has hardly any money for this kind of work - work that can not be done by machine nor by untrained people - I just wonder where we end up. And this Yemen paper is just a simple paper....

Tuesday, February 20, 2007

Nomenclatorial slopiness (3) - a positive note

Entering all of Seifert's Cardiocondyla revision is like day and night to the publication I critized earlier. Reading through the former is very easy, and most of the spelling of the original combinations is actually following the original citation. Also, it is very clear, what nomenclatorial action is being taken.

Both Seifert's and Alex Wild's revision of Linepithema (including the notorious Argentine ant) include also a list of citation of the species by various authors which is opening yet another cattle of fish: taxonomic concepts.

Ubio is currently the leader in collecting all species names ever published, from the original scientific - they get from specific namer servers - to identifications used in non-taxonomic works to vernacular names, which are especially important in feathery and fury taxa. If we really do want to build up a global digital library of our legacy data (such as the Biodiversity Heritage Library might provide), then we need also to make sure, that we list these taxonomic concepts once we know the proper name of the voucher specimens used in earlier work. Only this way (through the experts opinion) crosswalks using species names can be produced. So, please make sure you add them in your systematics work!

Monday, February 19, 2007

Nomenclatorial slopiness (2) - a positive note

Csösz et al.s paper recently published paper "Taxonomic revision of the Palaearctic Tetramorium chefketi species complex (Hymenoptera: Formicidae)" in Zootaxa 1405 is a nice example, where all the names can easily be found and if not present, added to a Name Server, in this case the Hymenoptera Name Server.

Norm Johnson has created a set of online data entry tools which allows entering new citations and data from any remote place to anybody who has an interest to collaborate.

In the case of Csösz' paper, I am opening up the paper, just copy and paste the respective elements and it shows up in most cases immediately up and I can view the changes through The HNS has even the feature allowing to subsribe to an alert to become aware of such changes. This way, the system is kept up to date as much as possible, of course depending also, whether we are aware of the papers published around the world and in places one would not expect to find new descriptions.

The advantage of Zootaxa paper over Myremcological News is, that once a pdf is available (Myrmecological News provides open access, Zootaxa only on a pay per artcile base), one can easily copy and paste any text, which is not possible generally from Myrmecological News, with the exceptions, when they provide publications with taxonomic content to be included in

Nomenclatorial slopiness

Cataloging and entering nomenclatorial relevant data is best done by machine (if not even better generated by machine and coded accordingly). However, this needs some discipline by the authors to allow at least semiautomatic processing.

Right now, I am looking at Seiferts paper on west Palaearctic Myrmica species where he raises two subspecies to species and makes some synonymies. At least that what he mentions in the abstract.

When you actually read the paper you are overwhelmed by extensive measurements, but very incomplete information on the specimens he used to derive his conclusions. In other words, nobody could reproduce this paper- a standard scientific expectation.

Within the paper he has for some of the taxa a section header, so it is clear he talks about a particular taxon for which he at least provides a list of the taxa he is including (and only from the abstract does one knows that he is actually synonymizing them). It would be much easier for any one abstracting this paper, not to speak of the computer, if there would be a simple acronomy ".n.syn.". But then, for Myrmica spinosior, it is completely implicit that he is rasising this taxon to species level.

There is also the issue about the original citation. For example, he lists "Myrmica lobicornis var. lobulicornis Nylander" as "Myrmica lobicornis lobulicornis" which is a simple detail not necessary for the computer, but an inconsistency because in other places he is using the original citations. When I asked him about another case he just replied that I would surely know what he meant, and that he might have confused this name with what was written on the label. This has no nomenclatorial consequences, as he points out, but it means a lot more work and a lot of hassle for Zoorecord or us who actually try to keep a record of what is being published. And it makes it very difficult to write programs like GoldenGATE, which actually ought to help to transfer our systematics knowledge into a digital world, where all our colleagues could take advantage of. For a taxonomist, who now has allmost all the publications available as pdf, this might be just one step to actually check the original publication and extract the proper original combinations.

In the next case though, it might have consequences. He lists "Myrmica lobicornis lobicornis var. lissahorensis" Stärcke as synonym of Myrmica lobicornis. But this is a quadrinomen, and thus not an available name. The name has been made available by Stitz in 1939:100. Furthermore, in this case, Seifert hasn't looked at the type, but the description only.