Monthly Archives: May 2009

Darwinius masillae available

Finally, not letting the news fade too quickly, PloS have earned one more publicity score by adhering to the International Code of Zoological Nomenclature, by making prints available of its article on Darwinius masillae, as reported to The Loom.

If it is so difficult for e-only journals to publish taxonomic papers following the simple rules applying, no wonder that the International Commission of Zoological Nomenclature is working so hard to make it possible, and possible for everyone, not just PloS, to publish nomenclatural acts e-only.

The Commission has opened a consultation with the community about an amendment to the Code to permit e-only publishing of nomenclatural acts, posted on their website. A first round of comments has already been published.

With more than 1.8 million species named, and scientific names being the only index to this diversity, it is evident that the stability of names within the botanical and zoological nomenclatural systems is a priority for all. In its strive to take nomenclature to digital dimensions while still maintaining a system supporting stability in the short and long term, the Commission needs all advice and comments it can get from experts and practitioners.

Today’s buzz

Da buzz of today and the day before is a long-tailed almost-monkey hitting the book shelves, TV screens, all other media, and the scientific press in one sweep. If it costs USD 1 million on the fossil market, there are consequences.

Ida, also known as Darwinius masillae, a 47 million year old fossil of a
primate mammal. From Franzen et al. (2009), slightly modified.

So, where to go with taxonomy? Play show, or play low? Whereas on the one hand it is fascinating that taxonomy can be so pervasive and so hypeable, and should nourish hopes of more appreciation for this discipline which underlies all biology but also is a science on its own; the other hand is raised in warning that we can’t do science only in the headlines.

Although the article in question, about a 47 million year old primate fossil from Germany, is very nicely done, and has a fascinating history to tell, the most telling indication that things are not coming out as intended is the complete misunderstanding expressed in all headlines, “missing link between monkey and Man”. For what I understand it is more something that went extinct between lemurs and monkeys. But I see Sir David hugging a lemur in promoting the research on …. aw, yes, that’s where we are. The crucial piece in taxonomy. The scientific name. The index. The one item that is needed to find back the information about this species.

PlosOne, the publisher of the study of dear almost-monkey is an e-only journal, where authors pay to publish, but it is free to read online. There is no paper edition. For a scientific name to be available it has to be in a publication printed on paper, with simultaneously available more than one identical copies (or on other more or less durable media provided some special conditions, but web publication is not permitted). The International Code of Zoological Nomenclature is quite clear on this in its Article 8. The Code is there to keep track of the names of more than 1.5 million animal species on Earth, and thus a very important instrument in Zoology.

There is no evidence yet that this paper publication exists, and thus the intended name of the fossil, Darwinius masillae, as it appears in the online article, is reproduced here only to attract search engines to this blog.

This is somewhat embarrassing, but also sign of the times, times when roads cross at different levels and communication has glitches in changing traditions. We are going digital. Not only our toys and tools are binary and glowing like Swatch watches, but our minds have drifted away with the circuits. I was fascinated by the digital displays and remote controls on the vacuum cleaners when looking for replacement for the one that died; seems, however, the analogue version eventually purchased sucks dust with sufficient energy without displays.

I have no intention of not being absorbed by the digital tsunami. I will survive surfing. It will take some adjustments, however. E-only publishing of taxonomic matter is still counter to stability. But we have to find ways for e-only to come forth. Not to promote hype, but so we can get more papers published and more papers (read: information) more widely accessible, than is possible by paper publication. My office, my home office, are both like libraries. And still every day there is some paper-only publication that I need and cannot get. But I am immensely grateful for AnimalBase and the Biodiversity Heritage Library, and of course the Internet Archive and Google Books, for frequently saving my day.

I want all of the fishes I publish on to be on TV, and in the newspapers. I want TV personalities to enthusiastically comment on the fishes I study. But first of all, I would like to see this information society come together a little bit better, with open access, GUIDs, e-only publishing, the Global Names Architecture (GNI) and more from the informatics side, and names, descriptions, diagnoses, images, data and interpretations from the taxonomists’s side. In that context, we shall not forget to make the names nomenclaturally available.

Blog links
Ed Young
Brian Switek
Carl Zimmer

Article link

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, et al. 2009 Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. doi:10.1371/journal.pone.0005723

From sturgeons to round gobies

A while ago, I commented on the capture of a Russian sturgeon Acipenser gueldenstaedti, in southern Sweden. The fish now has a home in an aquarium at Universeum, where it moved in 5 May. Universeum is a Science center in Göteborg, located on the Swedish west coast. They have a web cam of their shark tank. I rather want to see the sturgeon!

Meanwhile it appears that German fishery biologists have indeed released plenty of Atlantic Sturgeon, Acipenser oxyrinchus, imported and reared from North American stock. The idea is to re-introduce an extirpated species. Without eliminating any of the adverse factors that killed the sturgeon and threatens all other life in the Baltic: fishery and pollution is just the first name. Will the introduced sturgeon become a further complication in a disturbed ecosystem or will they peacefully die away? Stay tuned.

German newspapers now report on catches (Berliner Morgenpost, 14 May 2009), and a tagged sturgeon (Acipenser oxyrinchus) was caught off Bornholm, a Danish island in the southern Baltic, on 6 May, the identification supported by newspaper photograph.

These sturgeons are apparently from a small number of large meter long sturgeons initially from Canada in 2005 but reared in Germany and recently released into the Baltic. Thousands of baby sturgeon have also been released this Spring according to the article in Berliner Morgenpost. 50 small tagged sturgeons were released in the Elbe in April. All the larger A. oxyrinchus released are tagged, and should be released again if caught — at least if you are a sturgeon fan. If the fish lacks the tag and has a very short snout, it is more likely a totally alien species; it is up to you what to do if you catch one. The expectation is that these fishes shall feed upon the rich benthic fauna in the Baltic and in ten years or so migrate up the Odra River on the border between Poland and Germany, and breed there, so re-establishing the sturgeon in the Baltic. The German Society for Saving the Sturgeon is one active organisation in this work with updated information on Sturgeon releases.

Whatever one may think of these experiments, fishing in the Baltic, always report your sturgeon, irrespective of species, to the nearest museum or other competent authority. Dead or alive there will be use for the information.

Another alien fish species is also coming up here. Last year, in July, a sport fisherman in Karlskrona, on the Baltic coast of southern Sweden, caught a strange fish which he kept in his freezer for a while. In November it was reported to the right scientist, and made some headlines. It was the first Swedish representative of the round goby, Neogobius melanostomus, a Black Sea species which has made itself at home in select locations in the Polish section of the Baltic since about 1990. Just a few days ago, the second specimen was reported, also this time near Karlskrona, which has both an important harbour and archipelago. It will be interesting to follow also the spread of this alien, which unfortunately will not go away as easily as the sturgeons may.

Neogobius melanostomus from Karlskrona, May 2009, NRM 51437.
Photo Bodil Kajrup, Swedish Museum of Natural History, CC-BY-NC.

New toy in town – GNI

Some days ago – well, maybe weeks then – I touched on the usefulness of ZooBank, Catalog of Fishes, and friends. The bigger of them all is, however, GNI, a pronounceable acronym, a component of the GNA (The Global Names Architecture), but unrelated to GNU (GNU’s Not Unix). The Global Names Index is a name aggregator for scientific names of organisms. It contains 12 million names. You will now know why it takes a special category of wizards to practice taxonomy. These gentle people are managing 12 million names, and of course they will love this new toy brought to them by GBIF and EoL. Them, because GNI seems not to have much appeal beyond the professional taxonomist and biodiversity informatician.

GNI is one necessity when trying to build large systems of biological information, because all is indexed against names of organisms. To be sure, specialized systems like FishBase realized this many, many years ago and have systems that are superior within their domain. In the long run, however, a common approach may be the only way to endorse.

GNI is ok to search already now. Try Astyanax kullanderi, a fish you have not heard of before. Does it exist? One chance in 12 million. Enter and be confirmed.

It is there, in uBio, with one NameBank record drawn from Catalogue of Life and ultimately FishBase. It has an LSID there, but this is not the ZooBank LSID. We do not want to be confused, so we make a back click to find two GBIF records, neither georeferenced. It is the holotype, catalogued in NRM 21000 and served by GBIF-Sweden, but also in the GBIF edition of FishBase, which happens to be served also by GBIF-Sweden although the entry says it is served by FishBase Philippines. And at NRM this catalog number refers four paratypes.

Amazing, no?

Of course this tool is better needed for machine use than for humans to click around in. Or as David Remsen, the architect behind this construction puts it:

GNI was developed because of the central importance of the names of organisms in the management of data about organisms. The primary users of this site are not people, but other machines, so please don’t complain because the site is boring.

As a tool for testing the existence of names, it is already worth being bored a bit. If the result is positive, that is reassuring. If negative, apply the precautionary principle and ask your favorite taxonomist.

YouTube has this video of David Remsen explaining how the GNA works.

This is not Astyanax kullanderi, but a species of Synbranchus from Brazil,
closely related to Monopterus albus from Asia. Photo A. Kullander, CC-BY-NC

Eel out swamp eel in

Consulting the source paper for the rectum-eating eel (Siu Fai Lo, Sin Hang Wong, Lok Sang Leung, In Chak Law, Andrew Wai Chun Yip, Traumatic rectal perforation by an eel, Surgery, Volume 135, Issue 1, January 2004, Pages 110-111) where the fish is not identified further than to “eel”, it appears from the photograph there, which is very small and in low resolution, that this is not an eel at all, but more likely a swamp eel, apparently Monopterus albus, a common food fish in China where it is sold alive in the markets. This identification is suggested by the very slender tip of the tail, and somewhat inflated gular region. Thanks to Ralf Britz, expert on this order of fishes, the Synbranchiformes, for inspiring me to look at the original paper and first suggesting the identification. The swamp eel portrayed here, was never inside a human, though:

Monopterus albus, preserved. Photo Sven O Kullander, CC-BY-NC

Eel in eel out

One of my favorite sites is Matt Clarke’s web version of Practical Fishkeeping, a British aquarium journal.

Matt’s blog recently had this message: “50cm eel removed from man’s rectum”. This report building on an article in the commercial medical journal Surgery, relates that a man put up a live eel (Anguilla, species uncertain) in his rectum to remedy constipation. I guess the eel was supposed to eat away on whatever was blocking, but it was hungrier than that. That blog post has been read 10,925 times, which is probably quite good for a fish blog. I am fascinated also by the language in the comments. That is why I am never ashamed of mine Englisch. Now, see Practical Fishkeeping for more details or forget you ever saw this message …

Image: Robbie N. Cada, public domain

Nostalgic Geography

One thing that ichthyology and biodiversity informatics have in common is an interest in and need for ephemeral names of places. Names that change from one map to another, names spelt differently on different maps, and names that come an go in history. For us working with Asian, African and South American freshwater fish it more of an adventure than any non-ichthyologist can imagine.

In the case of Myanmar and Burma, it is just not the name of the nation, but I still cannot figure out what became of the Irrawaddy River — is it now Ayeyarwaddy or Ayeyarwady; maps and official websites leave me unassisted. Sandoway has become Thandwe, Tenasserim is Thanintharyi, the Salween River is now Thanlwin, Bassein became Pathein, Tavoy Dawei, Pagan Bagan, and Akyab is Sittwe. But Mandalay is still Mandalay. Check out a modern map.

In India, Madras is now Chennai, and Bombay became Mumbai (but Bollywood is not Mumywood).

Anyone long enough into South American fishes knows Barra [do rio Negro] means Manaus, and type localities in Amazonian Ecuador in the 19th Century are now in Peru (like the famous Ambyiacu of Cope = Ampiyacu, a tributary to the río Amazonas in Peru, the one called Marañón a bit upstream today as the whole river was named by the early Spanish, until el río de las Amazonas as it was called by Cristóbal de Acuña caught on.

I have been fighting with Lake Tanganyika localities for a while, starting with and Stanley, moving on to Boulenger and all the more bewildered I am for good old Kinyamkolo is today Mpulungu, and Albertville of course is Kalemie. When I read in Humphry Greenwood’s foreword to George Coulter’s Lake Tanganyika and its life (1991) that the lake was known as Uniamesi Sea in 1855, long before it was “discovered” by Europeans, I am not surprised.

Whatever happened to Tanganyika? is a book for people who find the above interesting and worth remembering. It is written by Harry Campbell (unknown to me), with a foreword by Alexander McCall Smith (The No 1 Ladies’s Detective Agency), who comes up with the term nostalgic geography. Maybe nostalgic for him. In biodiversity informatics name changes are for real and nothing to joke about. Author Campbell, however, is entertaining. When tired of being serious with name switching, this is the book that will amuse and enlight. There is 158 pages and 46 chapters, each one dedicated to a particular toponym. Your will find out about Tanganyika at the end, and you can read a little on Amazon (an online book etc. shop) to start with.