biosyscontext

2011-03-14T03:54:00.000-07:00

Taxonomy in the News: Taxonomy, the naming crisis

It is always a good thing to be covered by the news, so no complaint about today's article about taxonomy in the Independent.

Besides that, it is as usually depressing to read a necrology of a science that seems one to make the news with morbid reports, such as the decrease of taxonomist, the increasing underfunding, the lack of universities training taxonomists.

There is so much happening in and around taxonomy, but the speakers for taxonomy seem to be conditioned to mourn and black painting, complaining about the technophile funders. A little bit more creativity and optimism in communication of our science would not do any damage.

2011-03-06T21:39:00.000-08:00

Global Names Index (GNI)or don't we learn anything?!

The other day I was looking up Panacedechis papuanus trevorhawkeswoodi on Google to see what is known about this species and whether I can find some images. What I found was the link to the Global Names Index, I guess, because there is not so much online on this particular species.
What frustrated me immediately is, that there are just name strings. Names attached to nothing. Not even an author. And then there are name strings with an author and year, but they are not linked, not reference given, and when one clicks to the source, it is just a dead end without actually displaying the citation.
I think this is incredible for a new tool that wants to deal with all names, and is supported by the Global Biodiversity Information Facility (GBIF). We don't know what's behind a particular name in a particular publication. But now, we do not even now to what use of the name refers.
I always hoped, that especially institutions like GBIF, one of the main player in the field of biodiversity informatics, would push that names are linked to a publication in which links are provided to the materials examined that allows to understand the species concept used in this particular usage.

But no, they seem to be even more ignorant of what the Internet provides: Linkage.

I am hoping, I am wrong.

2011-03-05T23:09:00.000-08:00

Makham, Hawkeswood and Calodema: What a strange set-up

The journal Calodema has become the red herring in taxonomic publishing because of the very low standards of its publications. The editor of Calodema, Hawkeswood seems to be a very competitive fellow as is seen in this exchange from one of his papers, commenting on two letters that Chadwick mailed him:

I do not need to say much more and I will now continue with publishing papers overseas in entomological journals, without worrying any further about C.E. Chadwick and his cronies. Into the dustbin of history he and his research go!

.
The current debate in the Taxacom listserver refers to a very recent description of a new spider family, the Hawkeswoodidae Makhan & Ezzatpanah published in A new spider family, Hawkeswoodidae fam. nov. and Amrishoonops amrishi gen. et sp. nov. (Araneae) from Suriname; however, when opening the link, a different paper appears "Aschnaoonops aschnae gen. et sp. nov. from Suriname (Araneae: Oonopidae)".
But then, as Thorpe points out

Hawkeswoodidae was proposed with Amrishoonops as type genus! As it is not formed from the stem of an available generic name, it is not available [sensu ICZN 11.7.1.1. be a noun in the nominative plural formed from the stem of an available generic name] ...

When you actually read through the description, it is extremely short and makes no mention of why this species and genus is different from any existing one.

Description (male): Total length 1.8 mm. Palp with a C-shaped projection. Underside of projection strongly sclerotised, upper side soft, open and seed-like inside. Palp with large brown setae on dorsal side. Carapace brown, with brown setae, widest at posterior side. Abdomen on dorsal side light brown with brown setae, ventral side brown, with brown setae. Spinnerets light brown, with white setae. Legs light brown, with white hairs and with large thick spines.

and here the generic description

Type species: Aschnaoonops aschnae Makhan & Ezzatpanah sp. nov.
Description: Small brown species. Carapace round. Palp with a C-shaped projection. Underside of the projection strongly sclerotised and upper side soft, open and seed-like inside. Legs with large thick spines and hairs.

May be such as simple description is like Einstein's E=mc2, we just don't get it - that at least seems to be the message at the main page of Calodema

"All truth passes through three stages: first, it is ridiculed; second, it is violently opposed; third, it is accepted as self-evident!"
- Arthur Schopenhauer

"Great spirits have always encountered violent opposition from mediocre minds."
- Albert Einstein

P.S. Looking at some additional publications, it seems that Calodema is in fact the journal for highly combative authors, like Ghahari in his checklist of Iranian Braconid wasps

The results of this research indicate that the braconid fauna of north-western Iran is diverse and comprises some very interesting species. The mentioned region is very vast and includes diverse flora and fauna, and also has boundaries with Turkey, Armenia and Azerbaijan. Therefore, this small research paper, which is restricted to some areas, is not an extensive work, and the conducting of other surveys is necessary for determining many other species in this region. Since Iran is a large country with various geographical regions and climates, faunistic surveys in different regions of Iran is necessary for determining the extent of Iranian Braconidae step by step. A checklist of Iranian Braconidae was published by allahzadeh & Saghaei (2009) without perfect attention to all the resources available on Iranian Braconidae, e.g. Ghahari et al. (2009a, b, c, d) and many others. A checklist is a type of informational aid used to reduce failure by compensating for potential limits of human memory and attention.
Therefore, it is expected that a checklist would contain all the data on the subject and a checklist with deficiencies is not usable and helpful for researchers. This is main reason that all the systematic checklists must be prepared by the authorized specialists or at least edited and/or refereed by them carefully.

2011-03-05T01:30:00.000-08:00

Caught in your History, marred in Garbage

Eli Pariser made a plea at his Junk Food Algorithms and the World They Feed Us TED lecture to Google, Facebook and other social networks not to cage the users (all of us) into their own history, and essentially make them unaware of different opinions.

This is similar to an analysis of Ghaddafi and his peculiar style of dressing and acting: Nobody does tell him anymore, that this or that might be questioned.

Whilst doing so might end up close to capital punishment, Google et al seems rather stuck in a wrong philosophical approach, that somebody can be defined by few mouse clicks.

I would argue even further. Google not only puts on blinds on my eyes, it is mainly garbage that I am being fed. Most of what I really want does not show up, because the algorithms operate without context.

For example, if I want to know something about "Formica" a group (genus) of ants living in the northern temperate region, I get Formica as material but furthermore a huge array of pages that somehow end up to have Formica in them ("About 6,770,000 results").

Does this make sense? Google is the victim of its own success, and I think a very stubbern company with the same symptoms of all the succesful companies: Becoming stupid because of the insistence of its own past, the search algorithms, web crawlers and server capacity to was at the begin of its success.

So, what is missing here is context in the search.

And this might not be just Google's mistake. As long as we stick to context insensitive html, we do not deliver Google the "Food for search" they need.

Alas, we need to move into the semantic tagging of content - and that's where I believe lies the success of our approach to add domain specific elements to publishing XML, such as the NLM Journal Archiving and Interchange Tag Suite, which then becomes TaxPub, which now is used by Pensoft with all its advantages of dissemination its content as widely as possibly, and being harvested. Such a small harvester is Plazi, that allows searching within the contest of treatments (the descriptions of species, such as species of Formica) or other elements that have been tagged, resulting for example in a list of species of a particular country

2011-02-13T03:19:00.000-08:00

Kurt Pickett dead

After a long illness, my colleague and friend Kurt died a couple of days ago.

The last time I was listening to Kurt was when he presented his lecture at the meeting of the International Society of Hymenopterists in Köszeg. He wasn't able to fly and would deliver via a remote link, a lecture in which he both experimented with content and style. Even in that moment he was innovative and driven with his endless curiosity - it is sad that he is not anymore among us, an inspiring and outspoken person with a formidable mix of intellect, field- and labwork and style. I will miss him.

Kurt's lab

2011-02-12T21:44:00.000-08:00

Watch this: Zoological Nomenclature as it unfolds

There is a new flurry of debate in ICZN list (the list of the International Commission on Zoological Nomenclature or the institution that supposedly should take care of the scientific naming of zoological taxa (species, genera, etc.) and all that is related to it in order to provide stability in names) about gender of the species epithet. This is a discussion which brakes loose once and then and wouldn't be as strange, if there would actually be a system that provides the stability.

But there isn't anything like that and we have been waiting now for a long time to get there. We have Zoobank that supposedly gets yet another overhaul to be part of an even bigger system (Global Name Architecture as part of the Global Names Usage Bank. In this corner of the biodiversity informatics world exist three creeds: We need to provide the all encompassing system, the shell that can harbor all the names; there are people out there (the community of crowd) that do the work and want to chip in; The relevant stuff is in the past.

It seems to me, that this all is a misconception of Facebook, Flickr, Google which provide exactly the environment that these people envision. They all are chasing names that are legacy - but are they really that important?

Taxonomy is publishing approximately 17,000 new species and I guess ca 85,000 redescriptions per year, the biomedical field uses few 100 species names in their domain which produces millions of papers a year. But there is, with very few exceptions, no system in place that is set up so that new names are automatically collected and added to those databases.

Zoobank has at best a very tedious interface that allows adding data manually, something that does not happen as we know from a GBIF sponsored project to add Zootaxa names. Instead of spending all the effort to get this system up to date, an overhaul of Zoobank is now on its way for several years without end in sight.

There is no debate about this, but all the effort is focused on the gender agreement and similar matter. And it could not be more abstruse:

If a proper genus and species group name combination was UNIQUE and STABLE, why would we need LSID?
To a computer,
267B9A8B-372C-45EC-BFE5-661AF13CABC8
and
Stomosis arachnophila
are both UNIQUE and Stable codes.

So, why does a computer have to have a long unrecognizeable (to humans) LSID? [Chris Thompson]

(the answer is simple: so the computer knows when we talk about something for which we can not agree the proper name because we can not agree on the ending of the species epithet)

The only systematic collector of names, Zoological Record, struggles all along with, if I am right, 25 employees (zoologists etc.) to decipher the cryptic and well hidden information in our taxonomic work to produce there reference work of zoological literature.
The other large initiative, the Biodiversity Heritage Library, with an important goal to convert as much of legacy print publication into the digital world, struggles as an aside to collect names, though because of copyright issues most older than 70 years and thus irrelevant for the user on the street.

It needs something different, like PubMed and PubMed Central where the publishers submit their paper to be archived and discoverable via a form that includes all the relevant information.

We have to create something BHL-Modern for our field that does exactly this: Whenever something is being published the document is published in a form that can easily read into a dedicated database, the content be checked for validity (in case nomencaltorial acts are included) during the submission process, and then all the information will be available, including treatment, names, bibliographic records and links to external resources, such as DNA, images, etc.

We know have a system that is close to this, just the Zoobank part is missing, and probably should be dealt with differently, by just doing this part without Zoobank but either internally at BHL-Modern or Zoological Record that has the manpower to operate.
A prototype of a system is Pensoft and their suit of journals like Zookeys, Journal of Hymenoptera Research that produces taxbup NLM DTD based output with all the taxonomic elements semantically marked up that is then read in Plazi where the treatments are available for use by EOL, GBIF and whoever requests it. Zoobank is included but only through an akward interface that is being fed manually. Right now, this is not complete, but it is open for criticism: The schema can be modified, the elements to be included in the publication be defined for fulfill the purpose of ICZN, Zoological Record and others.
The good thing about this development is, that there is something alive that is growing; it is a real system that is being used, fed by authors, and paid for, and since it is open access, it is open to all sorts of experiments, but most importantly, to all the users unlimited.

2011-02-10T03:01:00.000-08:00

Collaborations in the our Field: Synergies and US Virtual Herbarium

United States Virtual Herbarium Workshop

United States Virtual Herbarium Workshop at the Missouri Botanical Garden in St Louis from February 23-25, 2010 at the Monsanto Center. (see report)

What is a National Virtual Herbarium? Well, in part that will be determined by this workshop but at the least the United States Virtual Herbarium (USVH) will support nearly all of the operations performed by a traditional herbarium. The USVH will serve as a storage and distribution center for knowledge about plants. It also must serve as a center of knowledge creation as is the case with physically located herbaria. From the information resource perspective, which of course I would take, the USVM must support the acquisition, evaluation, analysis, storage, dissemination and "weeding" of information in support of decision making for society.

Acquisition of information in herbaria is in many forms beginning with plant specimens, but including collections metadata, publications, field notes, photographs and many other materials. If there were a U.S. Virtual Herbarium it would be possible to streamline acquisition because many botanists send pieces of the same specimen to several herbaria. There is no need to redo all that data entry… like copy cataloging. There is a great opportunity for authority control and other quality control operations. There are a large number of museum digitization projects occurring throughout the country. There could be economies of scale through greater coordination of these efforts. Likewise, evaluation of information quality could be better managed. For example, if one specimen undergoes a redetermination all of its twins should be reevaluated as well wherever they are held. Likewise, georeferencing could be shared. Bryan Heidorn

This seems to be an effort worthwhile to study and copy to our domain, but also to find out what it really does and what is missing.

2011-02-08T23:09:00.000-08:00

Journal of Hymenoptera Research Open Access and taxpub based

On February 8, Pensoft published the first gold Open Access and NLM Taxpub based issue of the Journal of Hymenoptera Research. It is one of the first journals Pensoft publishes for a scientific society besides its own inhouse journals such as Zookeys. The implication are beyond changing from a traditional pdf based to a semantically enhanced taxpub NLM DTD based journal allowing immediate distribution of its content to a set of external aggregators such as Plazi, Encylopedia of Life, Wikispecied or the Global Biodiversity Information Facility, and not least PubMedCentral for archival, one of the big issues in taxonomic literature. The big question will be, how the journal will break even, will it attract more readers, and whether the members of the society will continue their annual subscription now that one of the returns is open and freely available.

I am very glad that this development keeps its momentum. The Hymenoptera taxonomist's community has and is developing very advanced tools that, if brought together, will make the field of Hymenoptera taxonomy very attractive. Norm Johnson's Hymenoptera Name Server and John Noyes Chalcidoid Database are just two very large databases with well over 100,000 names and related bibliographic records included. Antbase was spearheading the development of online domain specific digital libraries, antweb the development of standardized digital imagery, the Hymenoptera Anatomy Ontology and not least advanced systems like Norm Johnson's that allow XML publishing straight out of the databases (see an example here).

2011-02-08T01:49:00.000-08:00

What is a treatment?

On the way to define or better provide a description of treatment for the forthcoming release of taxpub, we once again stumble, as we many times did in our meetings, about the term "treatment". For us, it seemed, it was always clear that a treatment is the scientific description of a taxon including a Latinized name of the nominate taxon,followed by one or several elements such as references to older literature citing this taxon and putting it in relation (nov.comb, syn., etc.), a description (a verbatim morphological decription; that is why the element is not called description but treatment), distribution (a summary of the materials citated), materials citation (including references to the original specimen or observations used for the analysis), biology, ecology, host-relationships, etymology, etc.

On earlier publications we referred to treatment as follows:

"The presentation of names or treatments of species in taxonomic literature is not individual in the sense described above. The content of these treatments may be of high scientific value, it may be singular and new, but it derives fundamental meaning only in the context of scientific conventions that have long been established and practiced. Taxonomic treatments are formulated in a highly standardized language following highly standardized criteria. They adhere to rules and pre-defined logic.
They are not "individual", nor "original" in the sense of copyright law. They are thus data, but not "works", and therefore belong to the public domain." (Agosti & Egloff, 2009)

A key feature of this literature is the taxonomic “treatment”: publications or (more frequently) sections of publications documenting the features or distribution of a related group of organisms (called a “taxon”, plural “taxa”) in ways adhering to highly formalized conventions. Some of these are over a century old and are maintained by scientific commissions accepted by the profession. Two of the most significant are the international standard for naming animals, the International Code for Zoological Nomenclature (ICZN), and the corresponding code for plants, the International Code for Botanical Nomenclature (ICBN).(Catapano, 2010)

Winston (Winston, J. E. 1999. Describing species. Practical taxonomic procedures for biologists. Columbia University Press, New York. 518 pp) uses this term only once (p370)"...to find a monographic treatment with a key that covered all the known species". For her, treatments are "species descriptions". She doesn't present an explicit definition (at least, I haven't found it), but discusses what belongs into it on page 83:

"However, there is a common basic structure: a heading that consists of scientific name, name, author, and date, followed by a synonymy (a list of previous references to that species), and then the main body of the description, which may include etymology, diagnosis, taxonomic discussion, ecology, and distribution sections. Aftet the somewhat looser style of textbooks and research articles, taxonomic descriptions may at first seem mystifying, rather like a racetrack program in which each entering horse's form is described in tiny print and strange abbreviations. In fact, the standard taxonomic description bears a strong resemblance to the information given on each horse entered in a particular race, giving similar vital statistics (animal's name, parentage, date of "birth," description, and past performance) and packing a considerable amount of information about the organism into a very small space.
"

2011-01-26T01:47:00.000-08:00

Open Access and Publishing

The report from the SOAP Symposium provided by Derek Haank CEO from Springer (see my older posting).

The key findings of the project are:

* The number of OA articles published in “full” or “hybrid” OA journals was around 120’000 in 2009, some 8-10% of the estimated yearly global scientific output (see also http://arxiv.org/abs/1010.0506). Journals offering a “hybrid” OA option had a take-up of around 2%.
* OA journals in several disciplines (including Life Sciences, Medicine, and Earth Sciences) are of outstanding quality, and have Impact Factors in the top 1-2% of their disciplines.
* Out of some 40’000 published scholars who answered a large-scale online survey, approximately 90% are convinced that OA journals are or would be beneficial for their field. The main reasons given for this view are: benefit for the scientific community as a whole; financial issues; public good; and benefit to the individual scientist. The vast majority disagrees with the idea that OA journals are either of low quality or undermine the process of peer review.
* A separate survey of scientists who published in OA journals reveals that their drivers for this choice were the free availability of the content to readers and the quality of the journal, as well as the speed of publication and, in some cases, the fact that no fee had to be paid directly by the author.
* The main barriers encountered by 5’000 scientists who would like to publish in OA journals but did not manage to do so are funding (for 39% of them) and the lack of journals of sufficient quality in their field (for 30%).

The latter is the most often heared argument against OA in the domain of taxonomy, where authors assume that publishing is linked to no costs involved. The US authors are more used to page charges, but when it comes to pay the very modest page charges in taxonomic hybrid open access journals (eg Zootaxa) they also tend rather not to pay them. The numbers of authors paying is below 25%.

2011-01-25T02:56:00.000-08:00

"I like Wikipedia - they hate me"

Rod Page in his lecture at the recent ViBRANT Scripting Life meeting "why aren't we there yet?" talked about his encounter with Wikipedia, where he tried to link, actually automate the linking between NCBI and Wikipedia. Whilst NCBI was all for it, a live discussion developed leading to a very personal exchange on the very negative side (see slides 48-56 in Rod's talk and the actual exchange).

This is actually an interesting point, since we had the same experience trying to create for each new, and eventually all the known species a wikipedia entry. The idea is based on the notion that each species deserves an entry on Wikipedia, not just the famous hairy, feathery and flowery and that with such a service the broad community had a starting point. We could extract all this descriptive data from the original publications and this then could become the starting point to modify, rewrite, amend those descriptions, which are at the very moment the only source that exists. This would also provide a chance to he community to enhance such descriptions, whilst the original can always be seen on Plazi or similar sources.

But as in Rod's case, this idea was smashed by few editors that, in my view had little understanding no authority in the sense of understanding the issues rather then extorting their power within the Wikisystem.

Here is a visualization of what happened to one of our species, Monomorium dentatum, which can also be followed in the history of this species.

2011-01-25T00:12:00.000-08:00

Subspecies again

Charruau et al. state in their recent paper Molecular Ecology (DOI: 10.1111/j.1365-294X.2010.04986.x, Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates) on Cheetah that

Mitochondrial DNA monophyly and overall levels of genetic
differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies.

With this evidence, why aren't they treating those taxa as species, since they are not only geographically separated but obviously also genetically? It seems that there is also evidence that the Egyptian population is about 30% smaller than the subsaharan population. The did not do any morphological work.

2011-01-21T00:49:00.000-08:00

ViBRANT to provide the tools to measure decline of species within IPBES?

What follows is my reading of IPBES documents and need be followed up with a direct exchange. So, keep this in mind.

IPBES will provide global assessment of the fate of biodiversity and ecoystem services. Those will be based on the analysis of reports, that means there will be no IPBES-internal data collecting activities, but a lot of data mining and analyses of existing reports. Changes of species will only included, if their is information on them.

This is the chance for http://scratchpads.eu/. Why not provide a standard report form that suits IPBES, and link this to activties to update them according to the review cycle in IPBES. lets say, this is four year, so it would be interesting to motivate scratchpad users to make an effort to update their pages to that point in time.

It would also be an interesting experiment to see, how much information ought be available, to make statements on the distribution for the study of the global dynamic of biodiversity.

The impact might not be with those species that are widely known and ducmented, and not those that are very rare. But there ought be a middle ground that is not yet used in such exercices and that could also be recollected.

http://scratchpads.eu/ could play a role by opening up such assessemnts for groups that are not yet covered with such data. For example, if you would do ants, all the most recent publications could be taken, the treatmens and materials examined extracted and made acessible, and in a subsequent step, more material could be added through the scratchpads.

I could for example imagine, that this could complement what IUCN's SSC does by assessing the global diversity and threat of mammals, amphibians.

2011-01-14T19:35:00.000-08:00

Open Access and publishing: an interview with Derek Haank, CEO Springer Science+Business Media

Richard Poynder interviewed Derek Haank and provides an interesting overview over publishing with many provocative statements.

Almost cynic comments, with a core that points out the weakness of the academic information infrastructure and ingenuity.

Some of the comments, such as about the growth of OA contradict trends reported by Peter Hendriks, Springer's president STM Publishing & Marketing, that predicts OA growth rate of 20% (total article growth 3.5%) and a share of ca 25% in 2020. Obvioulsy, the CEO doesn't look very much into the future.

Q: We have focused on OA publishing or Gold OA. There is also Green OA, or self-archiving, where researchers continue publishing in subscription journals but then make copies of their papers freely available in an institutional or central repository such as PubMed Central. Some argue that this is a faster and more effective way of providing OA. And most subscription publishers consent to some form of self-archiving. As I understand it, Springer allows authors to self-archive the "author-created" versions of their papers in their institutional repository, but not Springer's PDF.
A: We have always tried to take a balanced view on this, so we are of the opinion that, in principle, author archiving is fine. Were self-archiving ever to become sufficiently professional that it began to mimic our journals, however, it could create a lot of problems. If that were to happen why would people continue to take out a subscription?

But we are such a long way from that situation today that we are very easy going about author archiving. Since we cannot see it destroying the system, we see no reason to make life miserable for our valued authors.

... on access to data

Q: Some researchers argue that OA is not enough; they also want open data. The Cambridge-based chemist Peter Murray-Rust, for instance, wants scholarly publishers not only to make research papers freely available, but all the supplementary data associated with scientific papers too, even if the paper is published in a subscription journal. Moreover, he wants that data to be made available free of copyright restrictions so that others can re-use it. Is that a reasonable request in your view?
A: I have some sympathy for the request. However, I am not convinced that, even if every publisher were to make all such data freely available tomorrow, open data would take off very quickly, not least because only a tiny minority of articles have this supplementary information.

So I am not against the principle that if we publish an article, be it subscription-based or OA—any relevant data attached to it should be made freely available.

Q: And you are happy for the data to be made available on a reuse basis so that people can, say, mash it up?
A: I am. I see very little downside to doing it, because at the end of the day, it would progress scientific research, which is what we are all here for, and from which we will all ultimately benefit. And I am not worried about the commercial aspects because in reality, we are only talking about a tiny subset of the total number of articles we publish. But it is just not a pressing issue today. Occasionally, the topic is raised, and we all say, "Yes, we should definitely do something about that"; and then the issue goes away again.

The future of print

Q: Many assumed that OA publishing would prove less expensive than subscription-based publishing. Is that not the case?
A: OA makes no material difference to pricing because most of the functions remain exactly the same. You could argue that OA allows you to dispense with print costs, but even under the subscription model, there is hardly any print any more.

Likewise, you could argue that you don't have to sell subscriptions with OA publishing. But OA requires selling institutional memberships. So whether the library pays for the system through subscriptions, or the institution pays author charges via membership schemes, it makes not a jot of difference to the overall costs in the end.

The future of OA

Q: How large a niche do you envisage OA being?
A: I expect it to remain between 5% and 10% at a maximum.

The future and reason of increasing costs

Q: Again, I doubt librarians would agree that publishers are showing price restraint. As you will know, the University of California (UC) Libraries recently released a public statement complaining that Nature was seeking to increase its license for 67 journals by 400%. For that reason, UC Libraries said, they were considering boycotting NPG.
A: I would not want to comment on this particular example; there might be a reason for it. You know, what is sometimes forgotten in discussions like this is that we operate in a growth industry: For the last couple of hundred years, we have seen a constant growth in research. More research means more researchers (because it is very labor intensive activity), and around every 2 years, each researcher produces a scientific article. That is the volume problem, and there is nothing we can do about it. So this is an enormous growth industry, and it is just not realistic to assume that there will be no price increase in the next 10 years for our growing database. One thing we have learned, however, is that the days when publishers could just say, "This is the price increase and you have to pay us" are no more.

On the amount of new output

After all, we are seeding our database with 13,000 to 14,000 new pages of information every day.

About the innovativeness and inertia of a publisher

Q: Looking to the future, what new developments can we expect from Springer?
A: Our first priority is to continue as we are. When you talk about all the new things going on, there is a temptation to forget that. But it is my job to think of what more can be done. As we have discussed, there is great pressure on the traditional library market. So we need to look at nontraditional markets.

(...)
But the first priority is to make our products more accessible. That means developing a better search engine, and improving the formatting of our data.

On the future of non library access

Q: Scholarly publishers tend to sell single articles for around $25 a time. That is not an iPad pricing model, and it is not a price I suspect many individuals would be willing to pay.
A: So maybe we will need to realign our prices there.

2011-01-11T21:51:00.000-08:00

BHL Modern

The reaction of the post on IPBES made me think why we all stick so much in the legacy literature. This is clearly a quagmire very expensive to move in what we need today, that is access to its content. To work on this needs a lot of tools that need be customized not only to different languages but different styles, fonts, almost anything one can imagine. What we experienced with our little effort to make all the ant literature available for the Malagasy ants is, that the conversion of a scanned image of a text into a semantically enhanced TaxonX is complicated and needs quiet some domain expertise. This is its own science. A science very different from publishing semantically enhanced publications from scratch.

What this really means, that besides best practices and pitfalls, working on prospective publishing is something very different. For that reason, I think we should create a BHL-Modern.

BHL-Modern would not be centered around articles but around treatments - the stuff the taxonomist and most of the users want. The main archive would not be scans of books or publications, but its content, treatments that are linked to the original source. It could also have a department of old literature that are extracted from BHL and then either linked to the digital source that is publicly available or then to BHL-Modern members only for stuff that is under copyright. Special sections would include ontologies, definitions of measurements, bibliographic records, abbreviations, some of which can be shared with BHL.

2011-01-10T22:06:00.000-08:00

IPBES a challenge to biodiversity informatics and publishing

The recent adoption by the United Nations General Assembly of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES; December 21, 2010) is an interesting challenge to the way we taxonomists publish our data: Will it be integrated into the IPBES reporting? It could, since they will base their report on the assessment of scientific paper, reports.

The IPBES will achieve this in part by prioritizing, making sense of and bringing consistency to the great variety of reports and assessments conducted by United Nations bodies, research centres, universities and others as they relate to biodiversity and ecosystem services.

I assume, that in an optimistic view, that ought be based on the assessment of publications such as taxonomic reports. With the parallel development of using publications as seeds for growing knowledge on particular taxa and publishing tools allowing such to happen, this might not just be a dream.

So we need to think of how we can demonstrate this, and how we can drew the attention of the IPBES to this potential.

See also IPCC for Nature: IPBES

2011-01-09T03:14:00.000-08:00

The Future of Taxonomic Publishing (2)

What is what the user wants?

What is the user looking for?

One clear long-term trend is that smaller pieces of information are being published. Considering just modern digital forms of publishing, there is a roughly chronological progression toward smaller publications: emails, Usenet postings, web pages, blog posts, blog comments, tweets, tags.

Terry Jones

This is followed by smaller size publishing.

A second trend is a reduction in friction. As access to easy-to-use and inexpensive publishing technology increases, it becomes economically feasible to publish smaller and less valuable pieces of content. We have reached the point where anyone with access to the Internet can easily and cheaply publish trivial, tiny pieces of information -- even single words.

Terry Jones

Finally, this is followed by the desire the publish personal comments, both about ourselves as much as about the piece in front of us.

A solution to that is to make the content alive on the Internet, so that people can not just read it but can do things with it, like adding external links, reuse it, follow links.

Another solution is to break away from a traditional publication at all and serve the snippet the user want: A single treatment in the context of the whole.

2011-01-09T03:05:00.000-08:00

The Future of Taxonomic Publishing

Following are some thoughts about the future of taxonomic publishing.

This is a though by Hugh McGuire

Defining a book by what you cannot do

What's striking about this state of affairs -- though not surprising, given the conservative nature of the publishing business, and the complete unknowns about business models -- is that we define ebooks by a laundry list of things one cannot do with them:

* You cannot deep link into an ebook -- say to a specific page or paragraph chapter or image or table
* Indeed you cannot really "link" to an ebook, only various access points to instances of that ebook, because there is no canonical "ebook" to link to ... there is no permalink for a chapter, and no Uniform Resource Locator (url) for an ebook itself
* You (usually) cannot copy and paste text, the most obvious thing one might wish to do
* You cannot query across, say, all books about Montreal, written in 1942 -- even if they are from the same publisher

You cannot do any of these things, because we still consider that books -- the information, words, and data inside of them -- live outside of the Internet, even if they are of the e-flavor. You might be able to buy them on the Internet, but the stuff contained within them is not hooked in. Ebooks are an attempt to make it easier for people to buy and read books, without changing this fundamental fact, without letting ebooks become part of the Internet.

Many people don't want books to become part of the Internet, because we just don't know what business would look like if they were.

Unfortunately, the "many people" are not few authors and many publishers, but explicitly or implicitly a majority of the taxonomists (authors as much as users) that don't understand what it means to have a piece of a description (treatment) online with links to external resources, that can also be reused, linked to.

2010-04-20T04:50:00.000-07:00

NASA again ahead of the pack

In NYtimes Science section's Multimedia column they show the images from the "People's Camera", a program that allows people to suggest to the project scientists to take pictures of areas of the Mars they are interested in.

This program has two very appealing facts: NASA follows an open access policy with their imagery, at least to a large extend, and in this case allows not only the project scientists to choose, what they want to have covered, but the public.

I find this very appealing because projects like this have the chance to capture much more data than individual scientists ever will be able to digest, and thus using this "idle" time to capture something that is of value to somebody is very powerful and allows non "systems" persons to make use of such large endeavors and raises the chance for insights the insiders might not have.

For me this is the perfect way to complement other decision making mechanisms to select what to do: In a world very dear to me, I could imagine that the Biodiversity Heritage Library could come up with a similar mechanism that would guide them what to select next. So far, something along this line might be happening, but it is for me not clear, how such decisions, it at all are being made.

If BHL would come out and say, we are interested to redirect some of our scanning towards projects that provide improved products (essentially scans and metadata), theny this might be to their benefit - immediate use of their data that in return would be the best way for them to justify their existence and scanning into the future.

2010-03-10T22:37:00.000-08:00

Almost ironic: "Taking Stock of the Renaissance in Taxonomy: Post 2010 Capacity Building in taxonomy for the Convention on Biological Diversity"

Where is the renaissance mentioned in the title of the forthcoming CBD conference on the Global Taxonomy Initiative in Nairobi? Where are the CBD's contribution to it? Where are the taxonomists contribution, besides the courant normal? How can you talk about a renaissance when at the same time the last great initiative, the countdown 2010, bitterly failed?
At least, the BarCode of Life initiative is rapidly developing, next to a growing amount of imagery of standard shots of species that might proof as valuable.

2010-02-06T21:30:00.000-08:00

Where to make taxonomic information public?

There is once more a discussion on Taxacom about the dissemination of taxonomic information: Where should it be? EOL, Wikispecies, others?

Intellectually it is an interesting trespassing of a threshold from scholarly to general publishing that is happening. I fear, that this is happening, because of the commitment by top down organizations that receive a lot of money to provide content, and can not get content in a rate projected. I think of EOL, Scratchpads, essentially all those that want to be the mother of all the biodiversity information. Wikispecies for example stays away from this by equalizing scholarly=cited references.

Lifedesks or Scratchpads both aim as well at the citizen scientist - something we call Amateur - that can be a highly trained skilled non-professional with a professional output to the casual observer who knows something of his backyard and extrapolates this to the entire world. This is a potential source, but it must be more clearly stated what their real contribution is .

In this respect, LD, SPs etc might have a role that they offer a lot of resources that have not yet existed (literature, imaging, DNA sequences, distribution data) and thus put new input into a much better context. Also, the trend to be able to publish from SPs via a peer review process might be a good thing.

It requests though that all the information is accessible, and that is another can of worms.

such

2009-11-29T00:24:00.000-08:00

Neotype designation

In a recent revision of the Formica rufibarbis group, Seifert and Schultz designated a neotype for one of Europe's most common ant, Formica rufibarbis.

"Type material examined: F. rufibarbis: Neotype worker labelled "FRA: 44.073°N, 7.295°E, St. Martin Vesubie, Cime de la Palu, 2058 m R. Schultz 2002.05.14 -108" and "Neotype Formica rufibarbis Fabricius 1793, des. Seifert & Schultz 2009"; SMN Goerlitz. In case of destruction or loss of the neotype specimen, a replacement neotype can be designated from a series of 6 mounted workers and 14 workers in ethanol from the same nest sample, having identical sample number, kept in SMN Goerlitz and coll. RS."

There is nothing against the designation of a neotype, but it seems odd, that the authors designate a neotype, and do not place it in the Fabricius collection in Copenhagen, or at least disseminate paraneotypes to the major European ant collections that would allow comparing this new type with new material. Furthermore, I wonder why they choose not a nest series that includes all the casts, including male, queens and worker.

2008-07-20T15:44:00.000-07:00

Wilson’s Law (and Carlin’s Rant) or yet another buzzword created by Wilson

Isn't it great, that we have this great unabashed thinker that helps us to advance everything we need in this deteriorating living world we live in? And I guess, it is quiet right that such important people use their own name for baptizing fundamental laws after themselves, like the recently created "Wilson's law" by Wilson:

"His law? “If you save the living environment, the biodiversity that we have left, you will also automatically save the physical environment, too,” he said. The restorative and balancing influences of functioning ecosystems are potent and vital. But, Dr. Wilson added, “If you only save the physical environment, you will ultimately lose both.”"

Dot Earth, July 11, 2008

2008-07-20T15:30:00.000-07:00

What all you do to appear in the right light in the New York Times...

"To reach Edward O. Wilson’s office on the Harvard campus, one must first push through a door with a sign warning the public not to enter. Then, enter a creaky old elevator and press two buttons simultaneously. This counterintuitive procedure transports one into a strange realm.

It is a space that holds the world’s largest collection of ants, some 14,000 species. Curators are checking the drawers, dominated by the tall figure of Dr. Wilson, who is trying to contain his excitement: the 14,001st ant species has just been discovered in the soils of a Brazilian forest. He steamrolls any incipient skepticism about the ant’s uniqueness — the new species is a living coelacanth of ants, a primitive throwback to the first ant, a wasp that shed its wings and assigned all its descendants to live in earth, not their ancestral air. The new ant is so alien, Dr. Wilson explains, so unlike any known to earthlings, that it will be named as if it came from another planet."

There are nowhere like 14,000 ant species known, rather than what we figure out are 12,451 species (see antbase.
There are no curators (a description normally used in the museum's world for a professor like position) in the collection, unfortunately.
Why to make up such stories?

Nicolas Wade, New York Times, July 15, 2008.

2008-04-28T23:39:00.000-07:00

Systematics as Cyberscience

(Systematics as Cyberscience: Computers, Change, and Continuity in Science. by Christine Hine
MIT Press: 2008. 320 pp. $35.00, £22.95)

In the current issue of Nature is a review by Kevin Kelly, chairman of (what I believed to be dead) All Species and Wired maverick (Nature 452:24, April 24, 2008).

It begins with a very bold statement:

"Taxonomy, the science of identification and classification of new species, has been one of the slowest disciplines to adopt computers. When most other scientists routinely use these number crunchers to detect patterns within large sets of data, why have taxonomists only recently started to use them?"

I am reading the book right now to prepare a review for Systematic Biology, thus I only now so far that it is mainly about a certain group of UK based systematists and, following the index and the bibliography, missing out on many relevant topics, not least by here compatriots Rod Page, Ian White, both pioneering the use of computers and challenging ongoing paradigm.

It is also clear, that you can not talk about taxonomy without their institutions, which often are very slow to adopt to this new paradigm and technological change.

It could even be argued, that it is not taxonomy itself, that is bad, but the misguided, non-operationial Mayrian biological species concept forced on taxonomist by 'hard core' biologists that sidelined taxonomy for long. Wouldn't there have been computer geeks like Chris Thomson, Norm Johnson or John Noyes and few institutions like Mobot or Kew that used computers from very early on and created content (hundred thousands of names), a quick start for initiatives like EOL would not be possible without having to invest into data creation at begin.

The problem now are not so much the taxonomists, they are still productive and could be even more so, wouldn't there be a barrier to make their data accessible, for them to work, to collect new data (see Brazil latest legislation for the Amazon basin) or us to read what they write (and most of it we paid through our taxes).
The problem are our institutions that increasingly want to generate incoming with our scientific products and thus see them a commodity that needs protection, that is exactly the opposite of what we scientists need, that is maximum usage and dissemination of our results. This mixture of commercial goal with scientific intent annhilitates a lot of rights a scientists is granted in the copyright legislation, as long as the work is not commercially oriented.
The problem are people who want to run taxonomy who do not understand it. Because of the computer and Internet, taxonomy is not about the old school' adherence to authority and final statements, but about a dynamic field that increasingly will be based on observations that can be viewed directly and challenged.

It seems to me that Kelly's introduction has been guided through being mal-informed by colleagues at ALL species like EO Wilson who exactly fits his introduction - fortunately replaced by a different reality, which hopefully the also mentioned EOL will be aware of.

need to read the book now...

2008-03-09T05:40:00.000-07:00

Who is the authority on the Encyclopedia of Live?

Gawker has a story about Wikipedia's problem with limiting who can edit = who is considered an expert in the system.

2008-02-28T00:17:00.002-08:00

Encyclopedia of Life: An interesting social experience in the sciences

EOL has been launched with huge fanfare: The best people in the world get together with a distinguished board of advisers, for biodiversity a huge award, and the backing of TED- but it faltered because the enormous amount of interest generated could not be handled (11.5M hits in the first five hours (Spiegel Online).

Insights start to trickle out on various blogs by colleagues that actually looked at EOL before it went down (Rod Page, Vince Smith) or then by slashdot whose members have a very different view on it.

It is also interesting to observe the New York Times who took down the article on EOL in my experience unusually quickly.

For all the often very crititical comments, nobody doubts we need an infrastructure like EOL which has to be an even more sophisticated and mashup engine then Google is. Many of us work since the begin of the Internet on solutions, because we all want to have access - and provide access for the public to this most thrilling knowledge.

For me the failure of the EOL start is not bad luck, but symptomatic for this approach.

Google has a huge, highly motivated and skilled staff working on their basic tools, the search engine. EOL is still looking for some of their very limited developer positions. Following the comments in slashdot, they are not up to speed with programming and producing adequate code.

EOL has a highly organized structure with directors, and various boards and distinguished scientists, overshadowed by EO Wilson. This is the typical autocratic structure, where authorities rule - each page will be authorized by a scientist, and this scientists have already blocked it seems more than a million pages, each about one species. Google has not authorities, but algorithms that do the work.

This structure does also not represent the scientific landscape. Biodiversity is marred by the problem that there zillions of small databases, most of them with very little usage beside the few creators. The institutions taking on their lead in EOL have done very little to come up with institutional support for creating a more comprehensive system with adequate metadata that would be used - similar to the large databases in astrophysics of particle physics. But more importantly, creating content is considered a voluntary contribution by the scientists - and if they don't the citizen scientists (aka amateurs) will chip in.

Megascience projects are scientific projects. You have a hypotheses you would like to falsify. It starts as a theoretical concept and then experiments are being developed and adequate tools are created to run the experiment. It can be a satellite, or cyclotron, but it includes an entire science team that can build, run, analyze and publish the findings. It take years to build up such complex endeavors. It might be worthwhile to study NASA development of new satellits for science missions. The best scientists in the field are involved, because if there is a flaw, hundreds of millions are being lost. There is a data share and archiving policy behind, allowing access to the baseline data.

Satellites and cyclotrons are not build with a letter by a 'big shot' to MacArthur, and without having thorougly reviewed written proper proposal.

This might work in traditional biological science where you could nicely summarize at the very begin of a new scientific topic, like the genetic bases of behavior (=sociobiology), and then write few article to expand into other areas like sociology; similarly "island biogeography", which are all nice catchwords, sometimes picked up by scientists sometimes not (Consilience) and sometimes causing a huge disaster (bio-prospecting), which essentially is one of the main reasons why it is extremely complicated to collect species in the wild.

The history of biodiversity informatics is then a field littered with many corpses - most of which because of misguidance, a wrong understanding of how this science works, and the pitfall of wanting to create the mother of all systems - which evidently is linked to a lot of fame.

What is what EOL want's to do? The goal is to provide the authoritative access to species information, and to stimulate research by allowing content to be exposed and open for data mining, that is the current hype about new discoveries.
But who the authorities are is already a political decisions - see for example the ant case.

What is science, and what is wikipedia or public opinion. Science is about citing. If webpages will be the element to which only authorized people can contribute and this for free (at least for now), and which are the element that ought be cited, using a doi in this case, then this means some radical changes.
What EOL ought to do is to think of innnovative ways to measure scientific accomplishment, and implement it at their own institutions. If Harvard would come up with metric for its taxonomists which includes, how often a specimen they discovered has been cited, how often an image they produced has been used, then that would have an effect. But neither is this a debate, nor is the system of 'deep citations' in place.

A scientist is measured by her productivity which is at the moment linnked to citation indeces, etc. Writing pages, and contributing to pages is not part of the system, and thus will not count, and thus contributions are very limited, even though a million odd pages are reserved already.
What is science? If you just can use a slider to get the information at your level, from basic k-12 to science, then where is the science behind - or is it just a compilation written by a skilled writer?

What about web publications in taxonomy? The Codes does not allow it. So how do you deal with the 90% of the new species to be found out there? Since the commissioners of those codes are very slugish, will that system of Codes and some control on naming just fall apart?

Most of the information on species is published. But there is no vision in EOL on how to access this. Their interpretation of copyright rules is that they have to be very conservative and essentially do not scan in anything that is younger than 75 years, unless there is a positive evidence that they are authorized. If you think that we double out knowledge every 10 years, then what do we get having most of the newer stuff not covered?
But even, if the copyright would not be an issue, the current working model at BHL will not be able to deliver the descriptions, since they operate on a volume and side bases, so they even have a problem to know, where a publication begins and ends.
If existing nomenclators or name servers are used, then the original pages could be postulated - but all the many redescriptions would slip through, not to speak of the ca 500,000 species for which there is no nomenclator yet (so in a way, if somebody comes up with a list of 1,2M species names, they are all copies of the same - again, nobody spends the money to catalogue the last 600K species). To discover automatically species descriptions prooved so far a costly process, since it needs the involvemet of specialists. Plazi.org is on such project aimaing at solving this issue, but it comes at a cost - which might only be paid for by community involvement. But that again needs access to literature that is promising (not the old stuff that excites few taxonomists), high quality OCR and a legal framework that doesn't shy off people.

2008-02-27T00:19:00.000-08:00

The launch of the Encyclopedia of Life

Yesterday the Encyclopedia of Life has been launched. No doubt, we need this infrastructure in one way or the other.

The question though will be, do we need content they think is the right one, or do we need the potential underlying infrastructure which assembles all the relevant information for us. Google's algorithms are asked, not again the old authorities. Not talk is asked, but deliverables, and that means what is on the Web, an in a scientific context, what can be cited and thus is open accessible. And once things can be cited, we now what the community considers important.

Unfortunately, EOL is already tied to one single man, EO Wilson. Though he wrote the now widely cited article in TREE in 2003, the EOL was not his idea but came out of a meeting including Smithsonian scientists, and thus it would be better to tie EOL to the community then to one single man, especially with Wilson's track record of advocate of copyright for descriptive work, where even after five years his Pheidole revision is still copyrighted. He also never joined the movement to make taxonomic descriptions open access similar to the what happened to the gene sequences and subsequently turned out a huge scientific success.

The last two paragraphs in the New York Times coverage of the EOL just shows the problematic, authoritarian position of EOL and his founders: "... he and other ant experts will be meeting at Harvard to plan how they can take advantage of the Encyclopedia of Life." There are enough tools out to measure what's relevant in our science, we do not need to refer to the old pre-open access and pre-e-publication period, where other opinions just could be suppressed by not citing.

So, why then should Harvard with a dismal track record on the Web, and furthermore being the anachronistic champion of producing copyrighted and non-open access material be given the lead by EOL to produce authoritative content on ants? Since 2003, Wilson's Pheidole which made it even into Nature online because of its copyright issues, nor the new Bolton Catalogue is online, whilst there is a huge community out there using the existing Internet based resources on ants.
Plazi.org is just the last one, which already provides access to well over 3,500 descriptions of ants, and for the first time provides a platform for any one to get a first glimpse and entry to what is known about a species, as much as it shows the power of using LSIDs and other standards to link to external databases. There are also most of the ant systematics literature online (>4,000 pdfs) on antbase.org some of it paid for by a grant from the Smithsonian Institution. There are 184,479 records of ant specimens available through GBIF, but none from Harvard.

But there is also a huge growing community of ant taxonomists in the South. More then 300 people, among them many taxonomists, attended last November's Simpósio de Mirmecologia in São Paulo - but nobody from Harvard. There publication on Neotropical ants are online, and they are working on a new electronic catalogue of the ants of the world. There is a growing community in Asia (ANeT) with their bi-annual meeting just held in India. All this hardly mentioned in Wards recent summary on ant taxonomy in Zootaxa (Ward being closely allied to Harvard):
"The literature on ant taxonomy is highly dispersed, however, and sometimes difficult to locate. Bolton’s (2003) monograph on ant classification provides an excellent entrée into this literature, including identification guides and keys. Ant identification resources are becoming increasingly available online, through sites such as AntWeb (www.antweb.org), Antbase (www.antbase.org), Australian Ants Online (www.ento.csiro.au/science/ants), Ants of Costa Rica (http://academic.evergreen.edu/projects/ants/AntsofCostaRica.html) and Japanese Ant Image Database (http://ant.edb.miyakyo-u.ac.jp/E). Several technological developments hold the promise of facilitating ant species-level taxonomy. These include improvements in imaging (e.g., Automontage system), specimen measurement, distribution mapping, and electronic organization of data. ."

What we need are resources, especially funding to help to image all types, open up all the literature and provide platforms like Scratchpads that allow to assemble our systematics information. If this is well done, including underlying mark up, LSIDs then this can be a source for EOL, acknowledging that we systematists deliver only a fraction of what is know about a species.

We need co-operation not building further divides into a highly fractured community. EOL should provide the tools, not politics, and those tools should decide what is relevant and what not, who has something to say and who not.

2007-08-30T13:28:00.000-07:00

Whose ants?

In a recent article in the New York Times (August 28, 2007) on a crack-down on supposed biopiracy (what harm can do a scientist if you let cut down hundreds of square kilometers of forest at the same time?), a peculiar twist in the line of denying research permits was cited: "and a researcher’s request to move an ant colony was denied, supposedly because it would cause stress to the insects."

Who knows the details of this story?

Please let me know!

2007-02-15T16:08:00.000-08:00

Douplicating efforts and other questions?

"Bolton’s Catalogue of the ants of the World“ Harvard University Press, has just been released.

This is another amazing product of Harvard University Press. It is a CD-ROM selling at USD49.95 which includes all world’s ants data, such as the original citation, subsequent usage of names, the description of female, worker, larvae, karyotype and the countries where they are found, plus an actual count of the number of the world’s known ant species – which is already short of more than 80 additions in a world with over 1,600 new ant species described during the last ten years.

It is amazing, since this product, a CD-Rom is completely copyrighted, and thus does not allow to copy or export any of its data, for example non of the many references can be exported into your own bibliographic database a typical scientists maintains these days.

It also does not provide any links to all the content outside in the Internet.

And this is the critical point. Since March 2002, there is already a complete catalogue of the ants of the world online accessible at antbase.org in collaboration with the Hymenoptera Name Server: see eg Nature March 22, 2002), and not only that, it includes links to almost the entire primary literature (>4,000 publications) as pdfs and slowly growing as documents marked up in taxonx, as systematics literature specific mark up schema taxonX, which allows harvesting the specific bits of systematics publications, such as the names or the descriptions (=treatments) of individual species and to include them in mash-ups or other applications such as ispecies . Futhermore, this catalogue feeds into the global initiatives to produce lists of the world’s species (ie ITIS, Species2000 or GBIF).

In some sense, this is a redundant work. But there are two more points to it.

How can Harvard University Press as one branch of Harvard undermine with such a policy to publish copyrighted material the efforts of its Natural History libraries (Botany and Museum of Comparative Zoology) which are part of the Biodiversity Heritage Library Consortium ) whose goal is to digitize their entire holding and make it open access? Its success clearly depends upon the inclusion of the most recent literature, and catalogues are needed to organize all its information. The attitude of HUP is especially questionable, since EO.Wilson’s, one of the proponents of the Encyclopedia of Life idea to produce for each species a dedicated web page, HUP-published “Pheidole” is, despite a quote in Nature (August 28, 2003) announcing releasing this monograph to the public, still copyrighted.

There is also the question of acknowledgement. The extensive cataloguing of this CD-based catalogue was only possible because of an almost complete digital library with the respective links from the species exists (partially funded by Smithsonian Atherton-Seidall Foundation). Traditionally, the usage of libraries were a given in any research. However one might argue, that in a case where digital libraries are used to build up a competitive product, they ought be cited or acknowledged, especially since there is a creative commons attribution license attached to?

To be fair, Gary Alpert, one of the authors, handed me over a free preprint version of the database as thanks for enabling him to go through all the publications using the digital library at antbase.org, and thus do all the checking and manual extraction of the names now included in this CD-Rom based database.

2006-06-21T00:25:00.000-07:00

Ant Wars

Citations in Ant Publications

It is the rule in scientific publications, that a source is given for facts and ideas, which do not belong to the authors. The number of how many ants there are belongs to this categorie. However, despite some recently published figures in some of my papers (e.g. 1, 2) , and indeed an online service providing a continuously updated known figure of ants provided through antbase/Hymenoptera Name Server, the figure is given in journals, but without a citation.

The latest example is Moreau et al.'s phylogeny of ants in Science, another by Wilson and Hölldobler on The rise of the ants: a Phylogenetic and ecological explanation in the prestigious journal Proceedings of the National Academy of Sciences.

When I asked Hölldobler about the source of the number of ants, he replied that this was just an intelligent estimate. It seems to me pretty odd to cite approx. 11,000 species, when a figure of a little more than 11,000 has been published in the mentioned sources above - a figure, which nobody could have expected, after Bolton published in his New general catalogue of the ants of the world a figure of 9536 species by 1995. Nobody would have expected a such strong surge in the discovery and descriptions of more than 1,500 new ant species or and addition of 15% of the total ant fauna. And only since we have the Internet, we have a chance to figure out the total number of taxonomists working on a partiular taxon, such as the ants (see the list of ant taxonomists. It is even difficult to keep up updating the list, for reasons see a forthcoming blog on community involvement), or the systematics publications of the last ten years.

Actually, the reason why I asked Bert Hölldobler was, that I pointed out to editor of Proceedings of the National Academy of Sciences that my name has been lost in a citation in Eusociality: Origin and consequences. The citation is the one of Ward (2000) referring to an article in a book, co-edited with four colleagues with me as senior editor. In this reference, my name as senior author suddenly did not appear. After some time, this has been corrected by PNAS (but not in the original article linked to above), and the reasons by the authors was simply, that the name has been lost when copy/pasting this citation from an earlier paper they published in the same journal.
Being cited in important journals is a very important element in one's scientific evaluation. Being deleted from a paper, which might be cited widely, could thus have an adversarial effect - a tool of the toolkits in scientific turf wars.
I must admit, I found it (and still do so) hard to believe, that exactly one noun could have been lost in the middle of a long string of words, a noun which is a name of a colleague, told explicitely to be careful about future comments on one of the authors (Wilson). The comment "you are hypersensitive!!!!!!" in a separate email by Wilson's secretary did not defuse the situation either.

2006-06-12T05:36:00.000-07:00

The last of its kind

After EO Wilson's monograph Pheidole appeared, I wrote a rather critical review of this rather unusual volume published by Harvard University Press. My core point was - and still is - that it needs to be open access. Wilson is the proponent of the Encyclopedia of Life, a project aiming at providing for each species its own web page, similar to Wikispecies or ispecies. All these depend on a global collaboration of specialists, and the 10 - 100 million of printed pages of species descriptions are the logic starting point, and thus the problem of coypright needs be resolved. Wilson's position, one of the very few in the field, is to keep the monograph copyrighted. Thus, it could not be linked to the now over 75,000 pages of systematics literature on ant currently available at antbase.org.

Within two weeks after the appearance of my review, Nature published a news article by Rex Dalton, and inhouse science journalist, in which Wilson was cited to state that the publisher is now putting the book online. After few months, I contacted Harvard University Press, where the reply simply was, that this was a misquote, and that the book remains copyrighted. When I asked Wilson directly, he just replied that it is up to Harvard University Press, and added "I ask you to be cautious in future published comments on my intentions and policies".

Still now, more than three years after the appearance of Pheidole, it is still up for USD130.00 as the only way to access its content.

In the meantime, the Encyclopedia of Life has become alive, just that it is now a proteomics initiative in the life science community. There are advances though in systematics such as the Biodiversity Heritage Library and ways to make this content accessible, such as being developed at the American Museum of Natural History. The stumbling block again is copyright, which is, ironically, supported by EO Wilson.

2006-06-12T05:11:00.000-07:00

Just a question of style?

The recent publication of an ant phylogeny in Science by Moreau et al. (Science 312(5770): 101-104 (2006) raises some serious question how this research has being done. The publication of their phylogeny caught everybody by surprise, since the US NSF Tree of Life program has awarded a grant to Phil Ward (UC-Davis), Brian Fisher (California Academy of Sciences) and Ted Schultz and Sean Bready (Smithsonian) with exactly this goal. No doubt, rivalry is an important and legitimate driving force in science. However, in this case the signs seem to point in a different direction.

The lead author, Corrie S. Moreau, a former student of one of the principle investigators of the Ant ATOL (Brian Fisher) would not inform Fisher about their intention to launch a competitive project, after her suggestions to become part of the ATOL team have not been accepted. She and her group then used tacitly information regarding the primers and specimen from the California Academy of Sciences itself (10% of their taxa) they got from the ATOL group and from her earlier work with Brian, obviously without declaring its usage.

The value of the analysis will certainly be discussed in forthcoming papers, and is questioned in here latest on Bulldog ants. An entire series of papers on ant phylogeny over the last 15 years proved just one point, that approaches like Moreau et al.’s only add some more pieces to a complex field, rather than getting a major step towards the understanding of ant phylogeny, as they claim in their general conclusion.

Doing research and publishing the results in such a clandestine way is like back-stabbing your closest allies on a long journey to figure out the diversity and evolution of planet Earth – an effort only achievable by making use of all possible collaboration and emerging synergies. But how will that happen if such a prestigious institution as Harvard, championing ideas like the community based “Encyclopedia of Life”, and its scientists behave otherwise?

2006-05-28T03:10:00.000-07:00

This blog (biosyscontext) is a part of two complimentary blogs centered around systematics and the build-up of a dedicated knowledge system. Ants serve as the model organism (see antbase). The other, conscontext, focuses on general issues arising on the way to make all data to knowledge accessible to anybody.

Ants are chosen as a model organism, to demonstrate the value of a complete comprehensive system for a group of organisms which has a dominant role in many ecoystems and thus ought to play a key role in ecological studies and conservation. At the same time, lessons learend during this transformation process, might help to implement an open access environment or commons, such as the conservation commons.

Thus, the two logs will reflect my thoughts and at the same time functions as a documentation of its development.

Links to published comments, including antbase are available at this page on antbase.