Tuesday, September 18, 2007

Fish for Sale

Here is an new development of using the descriptions of new species for fundraising. This in itself can be discussed, but here is an implication for CC and a responsibility of those getting money from creating biodiversity data.

There is also the fear, that similar to the detrimental effect for collecting permits created in the late eighties by pointing out that biodiversity has to be protected, because bioprospecting will be a gold trough which did not materialize, that spending so much money on something which has no real value - there are hundreds of ants species without names only in Madagascar, and literally millions of unnamed species - could lead to the same abyss, that is the believe of the local government, that in every piece of nature there are dollars, and thus they introduce even more stringent rules to collect specimen for scientific and conservation purposes.

The original text in the official "The blue auction" Website leaves a door open to siphon off money from this auction for "other environment and biodiversity-related programs" such as running a big NGO?

Fish for Sale, Nature Sept 13, 2003

I would like to see how much money is feeding back to the actual underlying systematics, not just cool expeditions, and with that, how much money is disappearing for other purposes. Since Conservaton International is member of the Conservation Commons, I also wonder, what CI is doing to provide open access to not only the publication, but the entire data collected during this and in fact all of their expedition. A benchmark we actually could measure is when such CI data is accessible through GBIF. I will get back on this in 6 months.

here the text:
"Over the years, philanthropists have lent their names to art galleries, schools and hospitals. But in a watershed auction, the world's rich will be able to add their names to several new species of fish — all in the name of charity.

On Thursday 20 September, an auction to name ten new species of fish is being held by the Monaco-based Monaco-Asia Society, a non-profit organization devoted to Asian causes and Conservation International, based in Arlington, Virginia. The fish are a few of the dozens discovered by Conservation International during expeditions to reefs off the coast of Indonesia's Papua Province in 2006.

Bidders will arrive from around the world for a gala at Monaco's Oceanographic Museum, which sits on a bluff high above the Mediterranean Ocean. Prince Albert II will be in attendance, and auction house Christie's will oversee the bidding pro-bono.

This isn't the first auction for a species name. For example, in 2005 an anonymous online bidder won the right to name a new kind of Bolivian monkey for a charitable donation of US$650,000. But this is the first time that multiple species will be auctioned in a single event, according to Monaco-Asia Society president Francesco Bongiovanni.

There's nothing wrong with naming an animal after the rich and famous, says Andrew Polaszek, executive secretary at the International Commission on Zoological Nomenclature in London. The only technical requirements, he says, are that the name must have a generic and specific part and be published in a paper or monograph — something that Conservation International will presumably do. Species are routinely named after famous scientists, and one species of cave beetle is even named after Adolf Hitler. He says that "you can essentially name a species anything you want".

Bongiovanni says he hopes the gala will raise US$1.2-1.4 million for further expeditions and conservation efforts in the region. But is it fair to name a species after a wealthy patron, rather than the scientist who discovered or described it? Bongiovanni says yes — especially because it is all for the greater good of the fish. "At the end of the day," he says, "these species need names."

Sept. 20
here is what Piotr Nascrecki's replied:
"All data collected by CI during its surveys is, and has always been, publicly, freely accessible, both as formatted reports, which can be downloaded as PDFs in_hi_userid=122818&cached=true>, and as "raw" data , which also can be downloaded as data files.
Now it is up to GBIF to make a link to these data."

and here my reply:


Always does not exist. When (exact date) has this been made accessible.

Why it is it, that this data has "always" been accessible through Harvard, and not CI- that is why do you use not even a CI name, since the root of this address is Harvard?

Where is a link on CI to this database?

Why does the Way Back machine at archive.org not show any trace of the Site you cite? http://web.archive.org/web/*/
Conservation.org latest entry is Jul 08.

GBIF and others are not made to access pdfs, but you can communicate using a digir or Tapir protocol. And the database you have does not allow to do this. An institution like yours could use this to become a real player in the global biodiversity community.

Friday, September 14, 2007

An information revolution

The Press | Thursday, 13 September 2007

New Zealand scientists need to get aboard the coming revolution in information access, writes DAVID PENMAN.

Social networking, data modelling, real-time measurement, broadband and so on are all bound in the internet age.

It is somewhat ironic that the internet was conceived as a means to share scientific data, yet it is now an enormous vehicle for social change and commercial benefit. Somehow, the scientists have become the laggards in sharing information, yet there are enormous benefits that can come from a greater sharing of data.

We see public sharing of financial data – the stock market, the exchange rate and interest rates – yet we see little evidence of open sharing of other information that affects our lives.

read more

Professor David Penman is Assistant Pro Vice-Chancellor (Research) in the College of Science at the University of Canterbury. He also chairs the Governing Board of the Global Biodiversity Information Facility based in Denmark.
Licences, copyright, IPR and more - some thoughts

Here some thoughts which came up whilst preparing for the TDWG meeting next week.

TDWG is about making data interoperable, thus leading, in the best case, to a seamless system of our knowledge linked to those of other domains.

This is a huge technical challenge, but by getting closer to technical solutions, other issues become relevant, such as who is generating content, how is content acknowledged and how is copyright and IPR handled.

This is especially important, since we now face for the first time a system, which aims at being the mother of all the biodiversity information, the Encyclopedia of Life which is playing the same game as the publishers of our scientific knowledge. Being corporate, they care about the copyright and IPR, and thus send out forms to transfer your rights to them. These are individual licenses which often lead to the situation, that you loose all rights, and thus we can not access our publications in an open way, be it as open access or via self archiving.

Our community has to be more vigilant the way we operate in this realm. We need to define what we want, and act accordingly. If we want to be able to have open access to our data, we should not sign contract which do not allow this. We have to negotiate individually and through whatever channels we have, such as our societies, that we only provide the publishers the right of the article for the specific publication they do, but that you can at least self archive or deposit the publications in thematic repositories, such as could be Zoobank.

Regarding access to databases, we have to be clear when we sign contracts like a Creative Commons license with institutions like EOL. Should they have the right to develop commercial products? Should they use a share a like license? If they want to produce commercial products, how is assured that the revenues are shared, or do you not mind? Should we allow individual contracts which at the end need zillions of lawyers? BHL is spending considerable amount of time to resolve all this existing contracts, so do all of the institutional repositories, and which seems clearly not something we want to initiate.

Regarding participation in initiatives which live on our data, it needs to be clear what each of the parties does. Do you build on the assumption, that you do not mind that one party is patenting some of the programs or should all what they do open source? For example, if UBIO at Woods Hole is patenting their taxonomic infrastructure, can we agree to that (search here for "Managing taxonomic information")?

We need a debate about this, and we should not let EOL go ahead, especially since many of us hope that it is a step closer to an open access infrastructure for biodiversity information. To signs right now are that we run into a lot of troubles and unease if we continue with what is happening right now, that is listen to the corporate lawyers and not of what we as a community really want.

So, before you signing any contracts, think twice. The publishers need your content, especially if it went through peer review. EOL needs our content, so you do not have to sign whatever you get offered. A discussion within bodies like TDWG would be very timely and useful.

Tuesday, September 11, 2007

A case to study to flux of information in modern science

I wonder, how important the role of open access to all the genomic information was, so that this possible cause of the collapse of bee population has been so quickly found.

Following the Editorial in the New York Times, Sept 11, 2007
A Virus Among Honeybees

Last week, scientists reported having found a possible — emphasis on possible — cause of the collapse of honeybee populations reported in the past year. What is interesting isn’t just the virus, called Israeli acute paralysis virus, but the use of new methods of genetic screening to determine what pathogens the bees in collapsed colonies had been exposed to. Researchers were able to quickly screen the DNA from all the organisms present in the bees and compare them with the DNA in genomic libraries, a catalog of known organisms. Bees from collapsed hives had the virus. Healthy bees did not.

Identifying this virus is only a first step in ascertaining the cause of colony collapse disorder, but it is a remarkable first step, a sign of how quickly new tools can be drawn from divergent scientific pursuits to track down and identify potentially global diseases.

Two other factors may also have played a role in this die-off. One is drought, which in some areas has affected the plants that bees draw nectar and pollen from. The other — still unproved — may be the commercial trucking of bees from crop to crop for pollination, a potential source of stress. These may have made bees more vulnerable to the effects of this virus.

In some ways, this newly reported research seems all the more important given all the speculation about what has been killing off the honeybees. These hive losses have inspired a kind of myth-making or magical thinking about their possible environmental origins. The suspected culprits include genetically modified crops and cellphones, to name only two.

Causation is a rigorous concept in science. It is vastly simpler in the popular imagination. Blaming cellphones and genetically modified crops for the death of bees is, mainly, a way of saying that we are worried — not only about the death of creatures both benign and beneficial to us, but also about technology’s effect on our world. Causation, in the nonscientific sense, is just a way of organizing our worries.

Thursday, September 06, 2007

"That's life" - is it?

In my last blog The dismal terrestrial biodiversity survey record I complained about our leaders inability to kick start a global project to survey terrestrial life.

By coincidence, in todays New York Time (Sept 6) you can read an Op-Ed contribution by EO Wilson, "That's life".

Compare this with what's written in the article about the new oceanographic campaign mentioned above.

Is this science he talks about? Is this something new? Isn't this sort of announcement of 'we create something great ... but you have to do it' exactly the recipe of disaster?

The Encyclopedia of Life is a very secretive initiative administering data collected by third parties. There is no substantial budget, nor are science plans there, to create new data. In fact, the proposed support for the affiliated Biodiversity Heritage Library has been cut - the only place, where EOL could have helped to convert existing data into a digital, all accessible and open form.

Wilson's own commitment to open access is dubious, and his credentials to develop new ways to provide access to biodiversity data are non existent.

Clearly, systematics is big science. More than 6,000 taxonomist work on describing the world in such magnificient institutions like the Natural History Museums in almost any capital of the world and hundreds of smaller insitutions. The raise of the Global Biodiversity Information Facility (an off-shoot of a OECD meagscience program) as a catalyst to make this information accesible is ongoing. But there is also a certain fatigue in the murals of these institutions, that money is not spend on creating new insights but rather to administer these data by third parties and thus siphoning the money from where it better is spent. Taxonomic aata providers which are not the large institution such as Harvard, but individuals working with very little to no support are anxious not to provide data to support institutions like EOL from which they see no return.

The faltering Countdown 2010 is just a most typical symbol. There is an international commitment to halt the loss of species by 2010. But there are not tools to measure this, because we still launch new IT initiatives and do not work on the ground, and continue talking about the terrible loss of species.

There are ways to be more efficient at very little cost.
  • Open Acccess: Assure, that all the forthcoming taxonomic and ecological literature is open access, either by the green or the gold road.

  • Commit the publishers to insert taxonomic specific tags (such as provided by taxonx the schema), so new names and descriptions can automatically be harvested.

  • Support by our government of Name Registries for all the world orgasnisms, such as IPNI and Zoobank.

  • Provide targeted access to legacy publications, digitize and mark them up, so that they can be harvested, their names, descriptions and distribution records, and provide doi or handles for all of these records.

  • Commit the members of the Conservation Commons to deliver: provide access to their data.

  • Bridge the gap between the conservation, industry and sytematics community, so that a link between data exists.

  • Implement the OECD guidelines to provide access to publicly funded scientific data.

We do not need new institutions, we need to strengthen existing one - the US unilaterist attempt in climate change is as much detrimental to the rest of the world's approach (Kyoto protocol) as is EOL to GBIF and its activities. And we really need to go out and collect data - because of empiric evidence climate change and ozone, to name a few, are on the politicians palate, and not anecdotal accounts.

Wednesday, September 05, 2007


"Facebook takes protest into whole new world" (Independent, Sept 5, 2007) is a story about using the tools the Internet provides to fight against the overwhelming power of, in this case, the industry.

Tuesday, September 04, 2007

The dismal terrestrial biodiversity survey record

'Bringing the Ocean to the World, in High-Tech' is a report in todays New York Times. It is a US $331 million program dreamed of by oceonographers and being financed by the National Science Foundation.

It has all the thrills of discovering and describing new frontiers, high tech, intersting experiments, and access to information using the Internet, and last but not least, scientists behind who drive the project.

In terrestrial and ecology we used to dream of such programs. But they all failed. It strikes me, that most of these elements have not been an integral part of the last few attempts to make such bold projects, such as the ALL species project or now the recently announced Encyclopedia of Life.

One might ask, that the reason being that oceanography like astrophysics or particle physics had traditionally been based on large research infrastructure which had to be shared.

But I would rather think, that we are in the unfortunate situation that our leaders do not have the commitment to the project needed to go through it. They do not know the nitty gritty work, the technology behind nor are they able to work for years towards a dream. It has nothing to do with creating a hypothesis and then letting others to deal with the details. But unfortunately, these people sit on the right place to initiate large initiatives, but loose them as soon as more then talk and ideas are needed. This is a real tragedy.