Monday, March 05, 2007

If humans can't, at least machines talk to each other

The Taxonomic Impediment, one of the main reasons why biodiversity has almost vanished from the palate of environmental issues, really has two main ingredients: We do not know most of the species, nor can we find and identify most of those known to science, and measuring their abundance is extremely complicated and thus expensive. The latter shall not be discussed here, but the former, the charting and identification of species.

The better known groups, such as the feathery, furry, scaly and flowering species tools are out there to know what species are known, and increasingly how to identify them, and to know, where they live. I am aware, that this is an optimistic view though.

But these groups are far from representing the bulk of the ca 1.5 to 1.8M species, such as ants, a single family of insects representing 12,000 species alone.

With the recent publication of “Bolton’s Catalogue of Ants of the World: 1758-2005” (CD-Rom, Harvard University Press, USD45), the authors claim that “There is no longer an excuse for nomenclatural mistakes, since all past decisions are recorded here.”. The authors must indeed be convinced about their infallibility by publishing a CD-Rom based on a Filemaker extension which does not allow entering, correcting or even exporting any data from there CD-Rom.

Although Shattuck points out some source of errors in his review of this database, he simply ignores that there is a vibrant Web-based ant systematics community out there, and in fact that ant names have been for more than four years now part of the body of names feeding into global efforts to build finally a list of the world’s species (eg. Species2000, ITIS, etc.), and it is widely used. There are not only names out there, but, unlike the citations on Bolton CD-Rom, all the citations are linked to a digital library including over 4,100 publications (excluding such copyrighted works as Wilson’s Pheidole of the World, printed like the CD at Harvard University Press), a feature used by the authors of the new CD-Rom to extract information from legacy publications.

But there is no acknowledgment on the CD-Rom, which might not have been created in such as short time had the publications to be searched in the library, nor has there been a feedback on errors found, or missing publications. This even though a Creative Commons licence in antbase.org states, that this work can be used under the following conditions: Attribution, non-commerical, and share alike.

antbase.org is based on Bolton’s first catalogue, published in 1995. But in antbase, every taxon name has an acknowledgment of the original source. Bolton and Harvard University Press did explicitly not wanted to make the catalogue of the ants of the world open access, a policy still pursued with the publication of a USD45 expensive stand alone application.

Does Shattuck’s view of the closed (CD-Rom containable) world really hold? Even if there are errors and omissions in antbase, we can now easily correct them because of this CD-Rom. At the same time we are now continually adding new names (see eg for 2006, 2007), or combination of names we discover whilst making legacy publications machine readable, and thus anybody can get all the data from the Web.

What about all those other ant communities on the web, nicely summarized by Verhaagh and Klingenberg? What about institutions like GenBank using as one of there references the antbase/Hymenoptera Name Server names to link gene sequences to names? What about antweb.org, antbase.net, anttypes.org and others using antbase.org as their taxonomic reference? What about ants helping to shape the discussion of the future of taxonomy on the web? The value off a catalogue is effectively to a much wider audience (see the red dots on the map) then to the specific taxonomists themselves. Most of the latter are from the developing world, and are not able to pay for it, even though most of the data originates is from their countries (see copyright = biopiracy?).

The good emerging property of the Web is that we no longer have to depend on this secretive and authoritative individuals and groups who want to control and sell their knowledge. Luckliy for most of us, machines do not care about self declared authorities; they just ignore them, because they are not found.

13 Comments:

Blogger Piotr Naskrecki said...

Donat,
I wish that before you go on your typical rant about how others do everything wrong, and how much you have contributed to saving the world, you had bothered to read the introduction to our catalog. In it we clearly state that the entire content of the CD will be available on the Internet. We made the right to publish the catalog freely on the web the primary condition of our agreement with HUP. While we are still evaluating the best approach to publishing this database, it is certain that it will be free, dynamically updated, linked to both images and publications, and most likely hosted by the Smithsonian Institution. The reason why you seem to be out of the loop on this is that many people are no longer interested in collaborating with you.
You also don’t seem to understand the difference between copyrighting the WORK (such as a complete package of a CD with data, its artwork, and everything else that goes into the production) and copyrighting DATA (which cannot be copyrighted.) Nobody forces anybody to purchase our WORK (the CD), and the only reason we decided to publish it was to create a permanent, always accessible (unlike antbase.org) snapshot of the state of ant taxonomy in the year 2006. This snapshot can be taken into the field on a laptop, or used in a remote location in a developing country where access to the web is still limited. None of the catalog’s authors receives any royalties or any other financial gains from the publication of this CD, and the reason the CD has a price attached to it is because the good people who produced it (HUP) have families to feed.
You also seem to forget that if it wasn’t for the original Bolton’s catalog, which you appropriated without permission and published online, and still continue to deride and criticize, there would be no antbase.org. Where is the attribution to his monumental work and years of painstaking searches on your website?
I am also curious how one can export data from the Antbase, something that you hold against our catalog?
Now, fear of competition and the desire to be in the spotlight are natural, human emotions. But the ability to control these feelings for the sake of achieving a greater goal through collaboration is a sign of maturity that you appear to have in a short supply.

Sincerely,
Piotr
http://www.hup.harvard.edu/catalog/BOLCCD.html

10:14 AM  
Blogger Donat Agosti said...

Dear Piotr

I am reading very carefully small prints. On this CD-Rom as well as on your last accompanying Wilson’s Pheidole. I I never said I am going to save the world – its being changed on an unsurpassed pace, not last because we in our community are not able to build a necessary counterweight to the drivers at work, not do we take advantage of the Internet: Sharing our data.

Being out of the loop: On February 8, 2007 I had a long talk with Gary Alpert (one of the authors of the CD-Rom) in the Ant Room at Harvard where he explained me in great detail about the origin of his cataloguing effort (typing in everything again), the usage of antbase.org’s digital library and the goal to make the database eventually accessible through the Smithsonian Institution. In 2002, at Harvard againg, we (you were actually charing the meeting) discussed the issue of a global catalogue, but then decided, since antbase/HNS was already up and running, to focus on getting all the images of the types. Obviously, you changed your mind – through other channels (antweb.org, anttypes.org, antbase.net, costa Rican ants) we are now some steps closer to this project. But on your CD-Rom there are no links, nor are there any images included – but there thousands of them laying unused around at the ant room at Harvard. With a real collaboration, we could have both – but you decided otherwise.

Access to data: There are facilities on antbase/HNS themselves where you can download all the species of a particular taxon. But you can do so also on ITIS, Species2000, GBIF, since our data feeds into these organizations. You can also download all the pdfs, which quiet few people do. And if enough people write to Norm Johnson, any such suggestion is implemented.

Acknowledgment. At the bottom of each of the taxon pages produced on the fly (e.g. Carebara coqueta) there is an acknowledgment to Bolton’s work, allowing to retrieve a full reference of Bolton’s catalogue. “Bolton, B. 1995. A new general catalogue of the ants of the world. Harvard University Press, Cambridge, MA. 504 pp.”In return, you do not credit antbase for allowing, in Gary Alpert’s own words, to check extensively legacy publications through antbase’ digital library. Or if you do not want to do so, you ought at least have given credit to Smithsonian’s Bill Brown Digital Library. This library is a collaborative project between Ted Schultz and antbase under an award of the Atherton Seidall Foundation, which accounts for about half the currently available publications. Using antbase.org underlies a Creative Commons license, and it states, that it can not be used for commercial products and it has attribution rights.

Copyright. You state that data cannot be copyrighted, but later you accuse me that I “appropriated without permission and published online” Bolton’s catalogue. This seems to be a contradiction in your argument? We also didn’t publish Bolton’s catalogue but only the data and augmented it with new records as of 1995, corrected errors, built an online interface, added almost all the original literature as pdf files. If it wasn’t our effort (antbase /Hymenoptera Name Server), Gary Alpert (in his own words) would not have started this competitive work, and we might not have any online ant catalogue as well.

Collaboration. I am not sure, what you mean by collaboration. Collaborating with you? From the downloads of our work, it seems there is at least some interest in it, and from the material I get from various authors to update the database and digital library, some people do not ignore me or at least antbase.org.

CD-Rom and updates. For the purpose of having a snapshot of what is out there (or better what your team did now at that time, since there are ten thousands more variants of names out there in the literature you haven’t harvested (see nomenclatorial sloppiness) which now are being extracted form our digital library project and its collaborations such as the Biodiversity Heritage Library, it seems fine to have a snapshot. But to claim, that such as CD-Rom will help an ecologist is not correct. He gets a product which he or she can not update, correct, export, integrate with his other field data, gene sequences, add links to images, literature. Already at the date of publication of the CD-Rom, 107 more taxa have been published in 2006 and 2007, including a revision of the Argentine ants. What you talk about is to have a copy for your safe. If you are honest, you sell the CD-Rom with an id and password allowing exactly this functionality. Anything else means that the only way to update your CD is to buy another one in a couple of years. And how can you explain, that you do not get a royalty for especially Alpert's, Bolton's and Ward's amazing search and compilations effort sells at USD45?

What we need at the end is not one or several ant-name servers, but one name server for all the taxa, as sustainable service to the community at large. We do not get his by creating small islands of knowledge. We only get this, if all our data is out and open access, and if enough people are interested in linking this data. So far we failed.
Machines are obviously needed do this job better by stripping out all kinds of wrong accusations.

2:56 AM  
Blogger James said...

Reading your comments, Piotr and Donat, I am not convinced that there is any essential disagreement between you, other than perhaps some details of the accessibility issue. Me, I actually like to make use of multiple resources when possible. It somehow makes me feel more secure about the position that I come to regarding a particular ant. While it would be good to have that ultimate, perfect, online source, I'm not sure it will ever come into being. This doesn't diminish the value of trying to create it.

As one who does not have the good fortune to be associated with an institution that has either any history of, or encouragement for, entomological research, I'm going to stay out of the quarrel and make the point that I plan to make the best possible use of all available, authoritative resources on ants that those who have such institutional support are able to muster!

Thank you both for your efforts.

James C. Trager
Shaw Nature Reserve

4:32 PM  
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