biodivcontext

Citizien Scientists: A Positive View

2011-03-15T22:18:00.000-07:00

Volunteers play a vital role in ensuring that a range of valuable long-term datasets continue to survive, a team of scientists will say. [BBC online, March 15]

I am critical against the trend to engulf increasingly citizen scientists in projects and tasks traditionally scientists can not do anymore, or simple don't have the resources. A very typical example is the effort by GBIF or EOL to enlisten volunteers to help to create content (data) for there services.

It is not so much the notion that they there are not many very skillful and dedicated people out there. It is more two elements that concern me. To know, whether something is relevant or not that needs to understand the topic in a wider sense, and the reliability of the data generation in terms of commitment. A commitment that is purely driven by interest and makes these volunteers very dedicated, but at the same time certain tasks are not being done, because they are less attractive or at times that are not convenient.
This is especially of concern for long term monitoring studies, such as birders do. For collaborations, these needs its own skills to manage a crowd that you can not promise a financial reward but motivation.

The story reported in BBC and mainly reflects the work done by Earthwatch makes just the opposite point, that many of the long term observation studies only work because of the volunteers.

This is a very positive note, similar to the fact that very many taxonomists are amateurs and produce a huge wealth of knowledge.

The African Wolf: no data accessible

2011-03-14T23:43:00.000-07:00

The discovery that there is a wolf and not a jackal in Africa has recently been widely published in the news. This is based on a publication in PLoSOne by Rueness et al. There has been some older morphological evidence for the long kept secret that, despite the saying that there is no wolf in Africa, and there was always the insight from egyptian zoologist that there is a wolf population in Fayoum, that is distinct from the jackals in other places. Furthermore, the jackals also seeemed to be small relative to the rest of the population, especially those from the Qattara depression.

When I read through the article by Rueness et al., it was striking that it is impossible to find what specimens they used and from they originate. The citation leads to the master thesis by Nassef (Nassef M (2003) The Ecology and Evolution of the golden jackal (Canis aureus) Investigating a cryptid species. Master thesis. The university of Leeds.), where I can not get any further. I fist search on Google doesn't reveal the whereabout of Nassef, so I will contact the authors.

I think it is not a good policy for both PLoS-One and the authors to keep back all the observation data in a case that is clearly very important and far reaching. It is a very small data set, and I wonder, how well the samples kept in Egypt have been used to figure out that there might actually a jackal AND a wolf species living close to each other.

ICZN and Open Access, or ICZN's self-inflicted no-role

2011-03-14T21:27:00.000-07:00

This is probably the most unbelievable discussion on a thematic list serve I have come across for a long time:

I suspect you are both missing the point here. Please read the abstract once again:
http://iczn.org/content/cyclodina-aenea-girard-1857-currently-oligosoma-aeneum-reptilia-squamata-scincidae-proposed-

unfortunately, I don't have access to the whole article, only the abstract (can anyone send me the PDF, please?), but, as I understand it:

Cyclodina aenea Girard, 1857 has been found to be a junior subjective synonym of Tiliqua ornata Gray, 1843, but *both names* are in current usage (as Oligosoma aenea and O. ornata, respectively). What the authors want is to retain the usage of *both names*. Suppression of Tiliqua ornata Gray, 1843 is not going to help! The *only way* is to designate a neotype for Tiliqua ornata Gray, 1843 ...

Stephen [ICZN-list listserve, Mon 3/14/2011 11:41PM]

Here is the ICZN who faces an uphill battle to loose nomenclatorial control over the scientific names of animals, who is unable to provide lists of available names so they could offer a service to judge whether a name has already been used, and who wants to sort out errors in the naming of species. And here are the way discussions are led on their list serve, because their cases and opinions are not open access.

One of the main reasons why ICZN can not produce a list of available names is copyright. If there is no copyright for taxonomic material we could provide at least today instant access to all the nomenclatorial acts that are currently published. There are many barriers in a world where such acts are published in over 1,200 journals and books annually, but those are decreasing with the change from print only to print/electronic publishing, and especially those from non-western countries becoming open access. This process could even go faster, if the Biodiversity Heritage Library wouldn't have to run against to copyright wall.

But here is the ICZN that uses copyright and bars even those seriously interested but not attached to an institution with a subsription from reading their material. This policy is a sign far beyond nomenclature that all the discussions we lead about open access, not to speak developing technology to provide machines access to harvest its content automatically (so for example Zoobank could become more efficiently if it ever sees the light of the day), is null and void, because we believe in copyright.

Thorpe's comment is the best example how detrimental such a policy is to the discussion of internal affairs, but to the enforcement of open access. But luckily, there is an increasing move to provide and request open access from our funding bodies, so that ICZN with its publishing policies is once again maneuvered into the offside.

I wonder why ICZN can afford to add to the their loosing battle of controlling names in the electronic world another policy to play at the no role in the important nomenclatorial control of scientific names. But may be better, why it takes so long to realize what that open access is the only way out of the dark.

I am sure the reason for this business policy is that those revenues from the sale of the Bulletin is needed. If this barrier of non-access is detrimental to ICZN, I wonder whether this is the right business model to adhere to. What is clear though, is that a no-access policy is not very attractive for any funding agency.

P.S. If you are interested in reading the Bulletin, you can purchase it here

Politics Meets Conservation at Ramsar Wetland Memorial Conference

2011-03-07T05:31:00.001-08:00

UK charge d’affaires, Swedish ambassador impolite. The British charge d’affaires and the Swedish ambassador participating in the world forum on wetland in Tehran did not stand up upon the arrival of President Mahmoud Ahmadinejad. Everyone stood up as a sign of politeness when the president entered the hall except the British charge d’affaires and the Swedish ambassador. "(Shargh, March 7, 2011)

This happened at the Global Forum on Wetlands for the Future on the occasion of the 40th Anniversary of Ramsar Convention on Wetlands in Teheran, March 5-6, 2011.

There is another side of the story from insiders. When the president arrived, everybody got up, including the ambassador (not chargé d'affaires) of Britain and Sweden as was protocol. After the president moved to the lecture desk, everybody sat down. However when he left his position, most people tended to stand up and then sit down again, although not the two ambassadors who wondered why everybody was standing and sitting again at regular intervals. Since the speaker wasn't the biggest in stature, the explanation of this up and down movement was just because people wanted to see him.

Switzerland, the host country of the Ramsar Convention Secretariat, was not involved. The Swiss government decided not even to send a delegation or representative to this celebration.

From the sidelines, I wonder about the very passive attitude regarding biodiversity conservation of the Swiss government. Though there was some movement from within the Swiss science community to host the secretariat of the IPBES in Switzerland, which would complement not only Swiss science activities but profit from synergies with other similar organizations in and around Geneva, the respective federal agency took a very passive stand. This follows the absence of Switzerland in the Global Biodiversity Information Facility (GBIF), where a membership so far has been considered too costly. Switzerland is a center of global biodiversity when the importance of its scientific collections are considered, and should be a leader in opening up this extremely valuable resource.

Iranian scientists at work: an observation

2011-02-23T01:04:00.000-08:00

Yesterday, I was invited to present a lecture at the Faculty of Biological Sciences, Sharif Beheshti University, Tehran, Iran. The goal was to present the students some ideas of what I think are relevant issues regarding biodiversity. Since I had the experience of mentoring two students through their masters thesis during the last 1.5 year, I thought not to complement what I learned from them: Instead of talking about fieldwork, monitoring design and analyzes, to show them what the big, global issues in this domain are. Why is biodiversity monitoring important. The lecture "Monitoring and Measuring Biodiversity: Some Thoughts" has been attended by a large crowd in a full lecture lecture hall, including a delegation from the Tehran University.

There where interesting questions afterward and some time for catch-up in various settings.

One issue that came, and is always coming up in discussions, is the increasingly difficult situation active scientists are here in Tehran. One typical issue are deteriorating relationships between the Iranian scientists and their former, often close counterparts abroad. What they tell is, that for the last 4-6 years, their colleagues hardly reply to their emails, even in cases where the Iranian supplied tissue or other biological materials for analyses.

Similarly, local scientists complain, that publishers in the West would not even reply to submissions of their manuscripts, something that these colleagues have not been aware of until few years ago.

The feeling is that the foreign scientists complement the sanctions imposed as well as the very negative reports coming out of this country. This attitude is astonishing, since, like in the Bush-years, there were a lot of objections against an evil US government, which was always seen as something different than the US citizen or scientist. In the case of Iran, this seems not to work this way.

This is actually an observation by almost all the visitors that visit Iran for the first time: They are all very astonished how different the experience with the people they meet is, institutions they collaborate with, and in fact leave with a very positive experience.

It my humble view it would be wise to continue the relationships rather than punishing the colleagues for something they have in most cases nothing to do with; this especially in a place where those colleagues have a very high esteem for the West, very often with part of their career spent there and thus very familiar with that region of the world.

Open Data in Ecology

2011-02-15T03:23:00.000-08:00

The current Science Magazine special issue on data on Open Data in Ecology.

Abstract

Ecology is a synthetic discipline benefiting from open access to data from the earth, life, and social sciences. Technological challenges exist, however, due to the dispersed and heterogeneous nature of these data. Standardization of methods and development of robust metadata can increase data access but are not sufficient. Reproducibility of analyses is also important, and executable workflows are addressing this issue by capturing data provenance. Sociological challenges, including inadequate rewards for sharing data, must also be resolved. The establishment of well-curated, federated data repositories will provide a means to preserve data while promoting attribution and acknowledgement of its use.

This opens again the question of the illusion of adding up heterogenous data set. What can be done, what can not be done with the legacy data - data that we are going to produce for the next decennium if we do not have incentives to overcome existing research practices: to be very parsimonious on metadata and especially studying what it would need to collect data to be able to build up a larger dataset that can be used well beyond the scientists' own particular interest.

The Origin of Hackers

2011-02-12T10:01:00.000-08:00

I stumbled upon this book by Steven Levy Hackers: Heroes of the computer revolution and read it from cover to cover. It is a really interesting read, and keeping in mind that the excerpt below deals with the Hacker scene in 1982, I am stunned to become aware how "old" the issue of copyright is.

It also makes it very clear, why the problem surfaced: A switch in the business model.

The Third Generation lived with compromises in the Hacker Ethic that would have caused the likes of Greenblatt and Gosper to recoil in horror. It all stemmed from money. The bottom line of programming was ineluctably tied to the bottom line on a publisher's ledger sheet. Elegance, innovation, and coding pyrotech¬nics were much admired, but a new criterion for hacker stardom had crept into the equation: awesome sales figures. Early hackers might have regarded this as heresy: all software—all information—should be free, they'd argue, and pride should be invested in how many people use your program and how much they are impressed with it. But the Third-Generation hackers never had the sense of community of their predecessors, and early on they came to see healthy sales figures as essential to becoming winners.
One of the more onerous of the compromises in the Ethic grew out of publishers' desire to protect their sales figures. It involved intentional tampering with computer programs to prevent a program from being easily copied by users, perhaps for distribution without further payment to the publisher or author. The software publishers called this process "copy protection," but a substantial percentage of true hackers called it war.
Crucial to the Hacker Ethic was the fact that computers, by nature, do not consider information proprietary. The architecture of a computer benefited from the easiest, most logical flow of information possible. Someone had to substantially alter a computer process to make data inaccessible to certain users. Using one short command, a user could duplicate an "unprotected" floppy disk down to the last byte in approximately thirty seconds. This ease was appalling to software publishers, who dealt with it by "copy-protecting" disks: altering the programs by special rou¬tines which prevented the computer from acting naturally when someone tried to copy a disk. A digital roadblock that did not enhance the program's value to the user, but benefited the seller of the program.
The publishers had legitimate reason to resort to such unaesthetic measures. Their livelihood was invested in software. This was not MIT where software was subsidized by some institution. There was no ARPA footing the bill. Nor was this the Homebrew Computer Club, where everyone was trying to get his hardware built and where software was written by hobbyists, then freely swapped. This was an industry, and companies would go broke if no one bought software. If hackers wanted to write games free and hand them out to friends, that was their business. But the games published by On-Line and Braderbund and Sirius were not merely paper airplanes of truth released into the wind to spread computer gospel. They were products. And if a person coveted a product of any sort in the United States of America, he or she had to reach into a pocket for folding green bills or a plastic credit card in order to own it.
It drove publishers crazy, but some people refused to recognize this simple fact. They found ways to copy the disks, and did. These people were most commonly hackers.
Users also benefited from breaking disks. Some of them could rattle off a list of rationalizations, and you would hear them recited like a litany in meetings of users' groups, in computer stores, even in the letters column of Softalk. Software is too expensive. We only copy software we wouldn't buy anyway. We only do it to try out programs. Some of the rationalizations were compelling—if a disk was copy-protected, a legitimate owner would be unable to make a backup copy in case the disk became damaged. Most software publishers offered a replacement disk if ; you sent them a mangled original, but that usually cost extra, and | besides, who wanted to wait four weeks for something you already paid for?
But to hackers, breaking copy protection was as natural as breathing. Hackers hated the fact that copy-protected disks could not be altered. You couldn't even look at the code, admire tricks and learn from them, modify a subroutine that offended you, insert your own subroutine . . . You couldn't keep working on a program until it was perfect. This was unconscionable. To hackers, a program was an organic entity that had a life indepen¬dent from that of its author. Anyone who could contribute to the betterment of that machine-language organism should be wel¬come to try. If you felt that the missiles in Threshold were too slow, you should be welcome to peruse the code and go deep into the system to improve on it. Copy protection was like some authority figure telling you not to go into a safe which contains machine-language goodies . . . things you absolutely need to improve your programs, your life, and the world at large. Copy-protect was a fascist goon saying, "Hands off." As a matter of principle, if nothing else, copy-protected disks must therefore be "broken." Just as the MIT hackers felt compelled to compromise "security" on the CTSS machine, or engaged in lock hacking to liberate tools. Obviously, defeating the fascist goon copy-protect was a sacred calling and would be lots of fun.
Early varieties of copy-protect involved "bit-shifting" routines that slightly changed the way the computer read information from the disk drive. Those were fairly simple to beat. The companies tried more complicated schemes, each one broken by hackers. One renegade software publisher began selling a program called Locksmith, specifically designed to allow users to duplicate copy¬protected disks. You didn't have to be a hacker, or even a pro-grammer, to break copy protection anymore! The publisher of Locksmith assured the Apple World that his intent, of course, was only to allow users to make backup copies of programs they'd legally purchased. He insisted that users were not necessarily abusing his program in such a way that publishers were losing sales. And Buckminster Fuller announced he was becoming a With most publishers guessing that they lost more than half their business to software pirates (Ken Williams, with characteristic hyperbole, estimated that for every disk he sold, five or six were P'rated from it), the copy-protection stakes were high.

Where are you, biodiversity data?

2011-02-10T00:04:00.000-08:00

When Dave Thau presented the Google Earth Engin at the TDWG meeting in Woods Hole, I was very sceptical, and still am, with the goal of land use change detection they showed. I did some work in this field during my time as NRC fellow at the JPL and was involved in quiet many debates about the use of RADAR vs optical remote sensing data, especially when it gets to the point of creating large mosaics, or land use change detection. The problem being that all the images are taken at different times, season so the optical signal can be very different (not to speak of let's say a dry forest lost all the leaves from one shot to the next).

But never mind these thoughts, Google announced their launched of their system now called the Google Earth Engine and it presents some data and allows you to make your own analyses.

Once more, the question is up, where our biodiversity observation data is that can be used to make use of these new opportunity. We could figure out, where biodiversity disappears - but can we? I haven't seen a project that specifically makes use of these RS data sets, that is not just anecdotal.

The global initiatives like GBIF or RedList do not champion new field campaigns to get data that would live up to the analysis tools we now have.

The question then remains, how could we actually make use of it.

Will Knowledge Organisation Systems kill diversity?

2011-02-09T08:42:00.001-08:00

The release of GBIF's "Recommendations for the use of Knowledge Organisation Systems by GBIF" made me think of whether the implicit drive to create the ultimate information system is not a wrong ultimately damaging approach. Such as system assumes that it models our world properly, and, ultimately that there is only one way to do so, hence the KOS for biodiversity. Essentially, this will mean, that anything that can not be packaged within the ontologies building the KOS can not be integrated - or from another perspective, we begin to look at the world from a very restrictive view - in German this would be called Scheuklappen, the little piece of leather mounted on the sides of horse eyes to avoid distractions.
This all would be not really relevant, wouldn't the organisation behind this recommendation utlimately strive to create the the bioinformatics technology standards (TDWG - Taxonomic Data Working Group, more recently changed to Biodiversity Information Standards) we all are using - better will have to use - to become part of all we hope, the seamless knowledge space.
I find this even more questionable at a moment, where this community can not even deal with something as trivial as a bibliographic citation, not to speak to build up a database of all the citations.
Or in the realm of taxonomic digital literature where we encounter on the one hand something very simple like treatments, but then are not able to define what it is - something that is now crucial to create schemas, DTDs or similar to model this domain for the purpose of creating semantically enhanced documents. The legacy data shows clearly, that there is a huge variety in how treatments are being communicated - but our goal now is to create a standard - eventually defined in one of the TDWG vocabulary that ought be more restrictive to allow reasoning and machine enabled tools to help to work through the huge amount of data we hope to open up with that move. May be, one might have to consider a definition less as something all inclusive but rather as a concept that allows a lot of flexibility in its application?

Another point is: Knowledge of what and what do we want to do with it? Bowker and Star put it this way:

Each standard and each category valorizes some point of view and silences another. This is not inherently a bad thing - indeed it is inescapable. But it is an ethical choice, and as such it is dangerous - not bad, but dangerous.

Though the others have in mind racial classification, I would argue, that we need to keep this issue of exclusion in mind.

In other words: What is the limit of what we can do with the system we create? What is the limit of the material regarding creating meaningful (as opposed to artefactual) knowledge?

This of course touching upon something very different and very negelected: Quality Control of our input data.

I wonder whether the authors provide an answer to this. The why and what questions seems to me the main stumbling block for biodiversity informatics in general.

With this in mind, I will read through this new recommendations.

CBD, IPBES and taxonomy

2011-02-07T23:35:00.000-08:00

Very quietly, unnoticed by most, at least following my channels into the taxonomy community, as part of the CBD-follow up, the Nagoya Protocol on Access and Benefit Sharing (and see comment) adopted on 29 October 2010, includes now an article that reflects that concern of the taxonomists to be able to collect with less restrictions.

ARTICLE 8
SPECIAL CONSIDERATIONS
In the development and implementation of its access and benefit-sharing legislation or regulatory requirements, each Party shall:
(a) Create conditions to promote and encourage research which contributes to the conservation and sustainable use of biological diversity, particularly in developing countries, including through simplified measures on access for non-commercial research purposes, taking into account the need to address a change of intent for such research;

The protocol must be ratified by 50 parties and would enter into force 90 days after the fiftieth ratification, according to the CBD.

IPBES and decline of taxonomists

2011-01-26T19:43:00.000-08:00

It must be a tragic coincidence that at the moment that IPBES has been created, the world largest biodiversity project, the Census of Marine Life came to an end. The legacy of this project is just not what it ought to be, a new generation of taxonomists and institutions that continue the research.

After a decade and 650 million dollars, the Census of Marine Life represents one of the largest initiatives to document biodiversity on our planet. In some regards, it was a great success, supporting 2,700 scientists to produce 2,600 new scientific publications and thousands of new species descriptions. But as the Census ends this year, no agency or organization is offering to fill the funding void previously filled by the Alfred P. Sloan Foundation.

Perhaps more importantly, the Census, like many initiatives, did not provide long-term positions and appointments for those doing taxonomic work. Many biology departments within universities no longer employ a taxonomist. The remaining positions are relegated to museums.

Wired, January 19, 2011 Craig McClain

Is the situation that tragic? Isn't this a question of the perspective? Philippe Bouchet made some points relevant to this debate in his lecture at the EDIT-5 years meeting in Paris last week: There are more taxonomists, and we know more about the gaps. He also points out that the structure of taxonomist is not just professionals, but that there are plenty of amateurs, and most of the publications are not in journals with a high impact factor. The data is from his own work on marine organisms, of which some has been published in a book chapter "The Magnitude of Marine Biodiversity".

Similarly, Sandy Knapp made a point in the discussion that we should not forget, that we need just to talk about the taxonomists: There is a huge investment into a even larger infrastructure, i.e. our herbaria and natural history collections and museums, and that there is right now a large effort being made to digitize a substantial part of these collections in the US.

One might argue, that a lot has to do with context: What do we really know, and what does it mean in context?

IPBES created by UNGA

2011-01-10T21:58:00.000-08:00

IPCC for Nature: IPBES

Press Release by UNEP:
New York/Nairobi, 21 December 2010 A new international body aimed at catalyzing a global response to the loss of biodiversity and world's economically-important forests, coral reefs and other ecosystems was born yesterday by governments at the United Nations 65th General Assembly (UNGA).

It underlines a further success of the UN's International Year of Biodiversity and should provide a boost to the International Year of Forests which begins in January 2011, and the international decade of biodiversity, also beginning in January 2011.

The adoption, by the UNGA plenary, was the last approval needed for setting up an Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES).

Governments gave a green light to its establishment in June at a meeting in Busan, Republic of Korea, coordinated by the UN Environment Programme (UNEP), but this required a resolution to be passed at the UNGA.

The independent platform will in many ways mirror the Intergovernmental Panel on Climate Change (IPCC) which has assisted in catalyzing worldwide understanding and governmental action on global warming.

The new body will bridge the gulf between the wealth of scientific knowledge on the accelerating declines and degradation of the natural world, with knowledge on effective solutions and decisive government action required to reverse these damaging trends.

Its various roles will include carrying out high-quality peer reviews of the wealth of science on biodiversity and ecosystem services emerging from research institutes across the globe in order to provide gold standard reports to governments.

This is a logic step forwards, and if the actors can get their acts together, a crucial step to bring back biodiversity as a a real item (as opposed to proxies such as area of forest lost) into the political debate. The effort needed to give the IPCC its weight is tremendous and ought not be underestimated, especially since they begun with a different social structure of the underlying scientific community.

Barcode of Life to rival GenBank? Really?

2010-06-29T05:05:00.000-07:00

Mr. Ratnasingham’s has been awarded 04-05-10 GBIF's annual prestigious Ebbe Nielsen Award for his work on BOLD. This itself is fair enough given the widespread use of of barcoding - even though it is not undisputed and has a very limited function in the rapidly developing world of whole genome sequences, the combination of morphological and DNA data for phylogenetic analyses.

What I find almost absurd is the statement by Krishtalka, the Chair of the GBIF Science Committee
"The impact and strategic significance of BOLD, according to Krishtalka, promises to rival that of Genbank. “BOLD enables a growing number of scientists to both register and access critical genomic data in a common way for complex research and research applications for science and society, both inside and outside the domains of biodiversity science.”

How can be a short sequence be a solution to complex problems? How can a short sequence solve problems of large phylogeny most of which use mutliple genes and conclude that many sequences are needed to infer a phylogenetic hypothesis that can not be easily criticized? How can Barcode make sense outside a framework of species that are also described by at least images, georeferences and some other vebatim? Clearly, a quick identification, the indication that there could be hidden species, the link between various life stages, or in the long term the identification of samples including multiple taxa is promising. But this is rather a complement to other tools, even simple visual examination of specimens that will bring ahead science and especially the applied side of it.
To consider competing with GenBank seems just the opposite what is needed: Collaborate to serve together to solve biodiversity in the interest of science and conservation with all the limited resources we have.

With such an agenda in mind of the chairman, I can not agree that this is a good choice. Sorry GBIF.

Canadian Biodiversity Information: A review

2010-06-09T22:04:00.000-07:00

Below is the executive summary of the forthcoming report on “The State of Biodiversity Information in Canada” written by Nature Serve Canada.

This is not very promising news in many respects, and an open door for all to continue to use our natural world as they please, since we do not have a really good arguments to set limits. That means conservation relies on the effort of devoted people to protect one particular piece of land, and not on the context of how this piece of land relies to the bigger pattern.

Part of the blame lays also on us taxonomists who do not provide an infrastructure users like the conservation community could rely upon.

It also shows that even Canada does rely on its southern neighbour for biodiversity information: This in fact shows the value of building a global, shared infrastructure that is of use not just for developing countries but the developed as well. Sharing also means saving, not repeating what already exists. And that is something we need to do, but it means we need learn to share.

Executive Summary

To understand the state of biodiversity in Canada, it is important to understand the state of available biodiversity information.1 Effective biodiversity information allows assessments of ecosystem health, the state of at-risk species, the location and distribution of invasive species, and changes in species numbers or distributions. Canada needs biodiversity information to manage, respond, and adapt to a variety of environmental changes (e.g., climate) through time. Such information is critical to Canada’s Biodiversity Outcomes Framework, and to meeting commitments set out in the Convention on Biological Diversity.
Biodiversity itself has intrinsic, economic, social, cultural, and evolutionary value as well as providing a variety of ecosystem services. Biodiversity occurs at local (fine) through broad scales and encompasses genetic, species, and ecosystem diversity. Primary biodiversity information identifies, locates, and communicates the status of biodiversity at different scales.
The biodiversity information required for managing species and ecosystems must be supported by accurate, consistent, science-based data, which is developed by biologists, ecologists, and other experts.
This report, which outlines the state of primary biodiversity information in Canada, is based on (1) a review of available literature including biodiversity-related legislation, policies, and initiatives; (2) known sources of Canadian biodiversity information, in particular data held by the NatureServe Canada network of conservation data centres and the Global Biodiversity Information Facility;2 and (3) interviews with selected key experts (Appendix 1).
This review found that Canada’s biodiversity information requires dramatic improvement if it is going to serve Canadian needs. Specifically, it found that:
1. Canada does not have ready access to the biodiversity information needed to understand its natural heritage or assess the shared outcomes set out in Canada’s Biodiversity Outcomes Framework.
2. Canada has significant data holdings for some taxonomic groups (e.g., birds, mammals), largely developed in response to legislative priorities or opportunistic data gathering efforts, yet, in most cases, that information is inaccessible or inconsistent.
3. Canada lacks both an understanding of its species diversity and a national inventory program designed to develop primary information for known species.
4. Canada does not have a national biomonitoring system that works across scales and builds on existing initiatives, nor the depth of interpretive expertise required to monitor ecological change.
Canada needs to invest in bio-monitoring and mapping (including remote-sensing and other related technologies).
5. Canada lacks investments in taxonomic expertise (capacity) and digitized data (presently held as “hard-copy” in Canadian collections). It is ill-prepared to respond to issues like species extinction potentials, invasive species, and climate change.
6. Canada needs to promote biodiversity information sharing and access, including one or more common repositories, and remove cultural and institutional barriers that keep information fragmented.
7. Canada needs to complete efforts to classify and map ecological communities (wetlands, grasslands, arctic tundra, etc.) as a complement to species data, and as a means of exploring and enhancing its understanding of Canadian ecosystems.
8. Canada’s approach to biodiversity information management must be based on a strategy that recognizes the shared, multi-jurisdictional mandate and responsibility for biodiversity conservation.
9. Canada needs an effective national biodiversity information partnership among federal, provincial, and territorial agencies that includes non-government, academic, aboriginal groups, and the business community.
10. Institutions in other countries, in particular the United States, publish more primary information about Canadian biodiversity than Canada does.
In the short-term, priority for discovery and biodiversity information development should be given to:
(a) regions facing rapid environmental change, where there is a lack of baseline data, particularly in Canada’s north;
(b) regions with highly valued ecosystem components, such as wetlands or other areas of high conservation value;
(c) regions with rapidly growing human populations and related development;
(d) known biodiversity “hot spots; and
(e) taxa that are poorly known in Canada.
The growing demands of Canadian society exceed the current supply of biodiversity information required to protect and conserve our natural heritage. To be effective, Canada needs an appropriately funded and staffed primary steward of biodiversity information. It needs a non-advocacy group that gathers, maintains, and provides that information, addresses legislative priorities and emerging policy issues, links economic and social development, and informs decision-making.

iPad and open access (to what we do)

2010-06-01T21:13:00.000-07:00

This June 10 issue of the New York Review of Books includes an interesting article by Sue Alpern "The iPad Revolution" about the iPad which includes a statement that confirms my worries about the Apple strategy, that is to control: Control how can produce content and applications for those gadgets. Thought this might be in the first hand too far off from what we do, but by having somebody that controls what sort of apps there are, we destroy the freedom of the Internet and with that eventually close off one of our real big chance to make our not so well known information accessible.

"The Open Source movement and Creative Commons both derive from the Internet’s essential freedom, a leveling that allows designers and filmmakers and singers and craftsmen and any number of writers, activists, politicians, artists, and entrepreneurs, many of them amateurs, to develop and disseminate their ideas. Imagine what the Internet, and our lives, would be like if, after inventing the Mosaic Web browser back in 1993, Marc Andreessen and Eric Bina not only required users to buy it but required payment for every click or download or page view. Try to imagine how a privatized, monetized Internet might have developed, and you can’t, because its evolutionary path would have been so different. Apple’s iPad apps may be ingenious. They may be fun and entertaining. They may be useful. What they can’t be is free of Apple’s control."

More of the same old stuff: the value of data/information

2010-05-30T23:16:00.000-07:00

In this context it is interesting to follow the discussion on the impact of the oil spill in the Gulf of Mexico in Democracy Now on May 28.

This is, what President Obama has said in his press conference

"I think it is a legitimate concern to question whether BP's interests in being fully forthcoming about the extent of the damage is aligned with the public interest. I mean, their interest may be to minimize the damage and, to the extent that they have better information than anybody else, to not be fully forthcoming. So, my attitude is, we HAVE TO VERIFY WHATEVER IT IS THEY SAY [my emphasis] about the damage. This is an area, by the way, where I do think our efforts fell short.
"

And here is a typical answer from the environmentalists "
JUAN GONZALEZ: This is now the largest oil spill in American history, but there was a prior even bigger oil spill off the coast of Mexico back in-I think it was 1979. Could you talk about what was learned in terms of the impact of that spill on the Gulf?

WENONAH HAUTER: Well, I THINK [my emphasis] that it takes many, many years for the species to be-to come back and that there are still impacts on the Gulf today.
"
This is not really a lot of detail of understanding what is happening comparing to the details she cites about BP etc. And the Golf is something close to the US, unlike the rest of the world where most of the biodiversity is.

It also shows, WHY it is important that we have real data as opposed to guestimates.

Loss of reality?

2010-05-30T02:04:00.000-07:00

"Governments have made “positive moves” towards coming up with a plan to reduce the current loss of biodiversity, which is threatening the future of our planet. Over the past two weeks, delegates at a meeting in Nairobi have been discussing the scientific and technical aspects behind a new “big plan” to save all life on earth, the planet’s biodiversity. Scientists from IUCN, who have been taking part in the discussions, say that they’re encouraged by the commitment shown by governments to develop a new Strategic Plan for the next ten years, which would set targets to reduce the global rate of biodiversity loss." IUCN-SSC, May 23, 2010

Reading this press release together with the recent article in Science "Barometer of Live" I really wonder what these people think. Didn't the target date of Countdown 2010 just pass by? Could we say that within the last eight years the conservation community achieved something really significant towards this clearly ambitious goal? I doubt, and furthermore other competitors came up like the climate change or global financial crisis that use some of the limited resources to be used for the environment.

Now, they either hope that politicians think that this cause is important or that a philanthropist is stepping forwards to pay another 60M USD over the next few years.

I consider our biodiversity conservation a global failure. There are plenty of small initiatives that succeed, but at global level we haven't achieved anything. We still have not even a list of the species of the world, not to speak a global assessment strategy that is living up to modern standards of biodidversiy prospecting and taxonomy.

If such as failure would happen in the industry, heads would have to roll. I think, we need a new generation of leaders that are ingenious, that bring in new approaches, that include the collection of environmental data that can be used and reused; real observation data. That would mean, that we have to talk to each other, we need to build the necessary infrastructure and clever strategies on what we are going to measure, and how we are going to finance it sustainably.

As much as the biodiversity informatics community seems to luck guidance in their development, the conservation community fails the necessary scientific insights to create such a global monitoring program that would stand up to criticism. The funding agencies could steer such an endeavor into the right direction.

Star power obvioulsy is not the way to succeed. We need bold ideas and people with a vision that can be implemented and lives up to scientific rigor. It is, nevertheless the scientific methods and data that have the power to change, not good stories.

More of the same old stuff

2010-05-30T01:43:00.000-07:00

A recent article in Science The Barometer of Life arguing for increased investment in expanding the knowledge base for biodiversity, to improve our understanding of biodiversity as a key indicator of both ecological and human wellbeing and enable more effective policy decision making - authored by a group well known in this community.

The Barometer of Life is in my humble view yet an other buzzword. No doubt, we need to expand the knowledge base for biodiversity, but I strongly doubt that the approach described and the institutions have proven that they can deliver. Countdown 2010 has passed by without any real changes nor respective instruments built. More action has been announced in Nairobi (http://tinyurl.com/28hy4m2) along the same line. Conservation International’s expensive TEAM effort has not delivered the original global early warning system. SSC’s data is still not easily if at all accessible, for example linked through institutions like GBIF. The Encyclopedia of Life is far from being fully functional, nor does it generate new data. Still the number of expected 1.9M species is cited, similar to 1986 when about this estimate has been circulated for the first time. There is not even an updated list of the global species available, nor are monitoring programs in site, that would allow measuring directly changes at species level, something TEAM planned to deliver.

Whilst we now have almost 1meter resolution remote sensing data for the entire planet and a huge number of physical parameters measured, most of it open access, species are still dealt with crude “guestimates” by few experts, no system has been developed to monitor the global species properly, the underlying observational data made accessible, nor the respective collaborations between the taxonomists, conservation organizations and policy makers set up.

Unless a new approach is chosen, the estimated 60 Million US Dollars could be spent with better return, in a way that is open to such critical scrutiny like the climate data generated, and by scientists that now how to generate the necessary data.

In a world and time where remarkable changes occur in the informatics and taxonomy world, these remarkable changes should be seized. The Global Name Architecture pulling together all the existing names of the species of the world, the Biodiversity Heritage Library scanning millions pages of natural history literature and make them accessible; new publishing models in taxonomy including mark-up of relevant text and links to external resources occur (eg taxpub); numerous efforts to digitize the species at a resolution allowing the identification of an rapidly increasing number of species; DNA Barcoding allows in many areas rapid and large scale assessments with a huge potential in the future; field campaigns in various parts of the world using standardized methods run by specialists. Not least the sharing of data allows the use of this data around the globe. Unless these resources are an integral part of monitoring and content is being generated, yet another Barometer of Life will be doomed again.

Donat

Access to publicly funded research data in Switzerland

2010-04-20T05:58:00.000-07:00

A motion has been submitted to the Swiss parliament to support Open Access and Open Archives for publicly funded research publications and data with more financial resources.

Worthwhile to be watched, especially since their is support from a rather unexpected part of the right political spectrum driving this initiative.

TEAM (2): another failure

2010-03-15T02:04:00.000-07:00

When I wrote my blog about the perils of taking polluter's money, I thought that I have to go back to check on TEAM, the Tropical Ecology Assessment & Monitoring Network, a large scale initiative announced five years ago with great fanfare by Conservation Commons, one of the conservation NGO's explicitely criticized in Hari's article in the Nation. In June 2006 I wrote a comment on TEAM, and ended, specifically regarding ants " I can not see, that this (...) TEAM project has a chance to florish".

Ants are out, and do not exist anymore.

The project is far from what it wanted to be, a global monitoring project to be able to separate global from regional and local events and trends. It has now only 9 sites on three continents active abut an impressive list of 148 team members. There is even Data to be downloaded, eg. Camera Trap Data, the latest from 2006 - not really a sign of an active project. From the 9 sites there is only data from 5 to be downloaded from the "Data Query and Download" page.

If I remember right, TEAM had a stall at the last year's E-biosphere meeting in London at one of the most prominent positions.

Unfortunately, this what I consider a dismal state of such a large scale projects confirms my fears and suspicion, that Conservation International did, what it can best, attracting big funding but with little understanding of the nitty-gritty to run successfully such large scale monitoring programs. It also shows nicely what has been discussed within the Conservation Commons, that the big heavy weight members of this initiative are all but sharing data - the mission of the Conservation Commons.

2010-03-09T22:02:00.000-08:00

On the perils of taking polluter's money

Recently there has been a series of contributions about the perils of taking money from corporation involved in heavy pollution and how in the authors view is affecting the behavior of the especially the large conservation organizations. It’s worthwhile read and contribution within CC's debate in Conservation Commons on how to deal with the extracting industry.

The Real Climategate: Conservation Groups Align with World’s Worst Polluters

"Major environmental groups are coming under criticism from within their own ranks for taking positions that some say are antithetical to their stated missions of saving the planet. In the latest issue of The Nation magazine, the British journalist Johann Hari writes, “As we confront the biggest ecological crisis in human history, many of the green organizations meant to be leading the fight are busy shoveling up hard cash from the world’s worst polluters—and burying science-based environmentalism in return…In the middle of a swirl of bogus climate scandals trumped up by deniers, here is the real Climategate.”"

The Wrong Kind of Green

"Why did America's leading environmental groups jet to Copenhagen and lobby for policies that will lead to the faster death of the rainforests--and runaway global warming? Why are their lobbyists on Capitol Hill dismissing the only real solutions to climate change as "unworkable" and "unrealistic," as though they were just another sooty tentacle of Big Coal?"

Green Inc

"In this scathing indictment of the surprising profligacy and complacency of some of the world's top environmental organizations, journalist MacDonald, a former media manager at Conservation International, exposes the clubby, well-upholstered world of conservationists. The posh headquarters and six-figure compensation of top environmental leaders (from the Wildlife Conservation Society's $825,170 to the Sierra Club's $229,000) gall the author, but she's most outraged by organizations routinely accepting donations from oil, lumber and mining industries and corporate behemoths such as Wal-Mart without holding them accountable for ongoing pollution practices. MacDonald singles out BP's Beyond Petroleum campaign as a particularly egregious example of greenwashing (the label for corporations marketing themselves as green while paying lip service to environmental concerns) and lambastes Ikea for failing to ensure that the goods it imports are manufactured from sustainably harvested timber. Her lament at the loss of activist edge among top-tier environmental groups is heartfelt—MacDonald exhorts them to stop being such lapdogs and start acting like the watchdogs they were conceived to be—and her umbrage and ample evidence are impossible to ignore. (Sept.)
Copyright © Reed Business Information, a division of Reed Elsevier Inc. All rights reserved."

2009-06-04T16:09:00.000-07:00

Copyright, IPR, and no excuses

thanks to Vince Smith who bestowed me with James Boyle's latest book "The Public Domain", I cam across a very positive statement which confirms an answer I gave at the recent e-biosphere meeting in London, when somebody in the audience made the point, that laws are here to be followed:

"Contrary to what everyone has told you, the subject of intellectual property is both accessible and interesting: what people can understand, they can change - or pressure their legislator to change." [bold by me]

This should be one of the imperatives of the biodiversity community!

2009-06-01T09:13:00.000-07:00

Help wanted to write book of life: another EOL blunder

There are about 400 biodiversity informatics people from all around the world sitting here in London talking about biodiversity informatics (e-biosphere, London), talking about where we stand with the biodiversity informatics, access to biodiversity information. The way it is communicated to the outside world is, that it is the US and the UK who develop the book of life. What about all the rest? What about all the contributors needed to fill their shell?

I think this is an odd flaw in communication that should not happen. EOL with their experience in PR can not blame BBC that they did not get the point.
If I would be a EU-commissioner, I would definitely question what all the taxpayers money do, same for the Australians.

I also think, it is pretty much stressing the point that the North does it all.

BBC online, June 1, 2009

"A virtual book of all life on Earth is being created by UK and US scientists.

The online reference work will create a detailed world map of flora and fauna and track changes in biodiversity.

The database, dubbed a "macroscopic observatory', will be populated with data about local species gathered by members of the public.

Early elements of the giant database, such as automatic species identification systems, are already under construction.

Field guide

Over time the database will log shifts in species and other data such as changes in the density of forests and when plants first flower.

The backers of the idea hope that the vast, virtual book of life will eventually be comparable to the global system used to watch for and record earthquakes.

The ongoing project will constantly gather data so it can plot information about the range and abundance of plants and animals as worldwide temperature and rainfall patterns shift in response to climate change.

Details held on the database will include everything from gross anatomical details down to individual genes.

"We are creating a virtual observatory for world biodiversity, where environmental observations, specimen data, experimental results, and sophisticated modelling can be done across all levels of biodiversity - from genes to ecosystems," said James Edwards, executive director of the Encyclopedia of Life, in a statement.

The Encyclopedia, based at the Smithsonian Institution in Washington DC, and the London's Natural History Museum are the key backers of the project. The push to create the observatory was unveiled at the e-Biosphere 09 conference held from 1-3 June in London.

As well as logging long-term changes brought about by climate change, the creators of the online observatory hope it will bring more tangible benefits.

It could give early warnings about invasive species or, for example, give insights into the timing, altitude and route of bird migrations in ways that could reduce bird strike numbers on aircraft.

The observatory would also serve as a hi-tech field guide for anyone who wanted to identify animals, insects, trees or flowers they found while on holiday or near their home.

Within 10 years, expect its backers, all aspects of the database will be available. Some parts of the system, such as images of species, maps of the seas and gene sequences to help with DNA barcoding, are already in use. "

2009-05-30T17:58:00.000-07:00

e-biosphere London

I am on my way to sit on panel 6 at the forthcoming e-biosphere meeting in London. Wouter Los produced this abstract for our pannel, where we should talk about how bioinformatics is changing community policies and practices in areas such as data sharing, intellectual property rights, and open access publication.

"The worlds of Biodiversity Knowledge and of Informatics are meeting at exiting interfaces. There are the scientific and technical challenges to get a grip on the complexity of these interfaces. But especially cultural and sociological contraints put a barrier on what is technologically achievable. What works and does not in the effort to get people to share biodiversity data? What are the perspectives of the dataprovider (enablers), and what can we learn from experiences in contributing institutions?
The need and role of data publishing regimes can be discussed in facilitating increased discovery and access to primary biodiversity data. There are socio-political barriers and the question is how to overcome these. Which are the appropriate policies? We still work like twenty years ago and biodiversity informatics is not part of a biodiversity science curriculum. The science structure did not change and adopt neither to global questions nor follow globalization in science, eg Internet and digitalization and with that potential of sharing data. We will stay in the past century when there is no commitment from our institutions to collectively open up biodiversity information.
Biodiversity information and knowledge is structured and would assume a global biodiversity infrastructure created from top down. Such important initiatives were implemented in the last years. However, real innovation comes from a rapidly increasing number of individual scientists that open up their archives and often ingenious bits of software assembled from an even more incredible amount of tools that serve their best interests. They are seeing the advantage to collaborate in small but increasingly fast growing clubs that enhance their scientific process of discovery, and are willing to share their knowledge beginning with semantically enhanced, cross-linked publications. Classic intellectual property rights on information are replaced by other values.
“Community” is important to biodiversity scientists, as it is for people in general. Which are the approaches and tools that provide individual, social rewards when individuals and institutions foster broad knowledge sharing and the public good. What are the roles of cooperation, Darwinian competition, and trust in data sharing? What are the boundaries of a biodiversity research community or of traditional “owners” of information and knowledge? And do we have to consider a balance between the conditions for bottom-up and top-down approaches or just for a single straight forward solution?
"

So, what are those issues? Has biodiversity informatics really changed something in our communities, or rather enabled to continue with more of the same but in a faster way? Does this BI really change our modus operandi?

2009-05-16T09:56:00.000-07:00

Here another twist to the decade *: Is biodiversity missing out again in the current closing of the digital divide?

There are two relevant articles to this issue: one in BBC-online that states
" How ridiculous then that over the last three months, climate change has had 1,382 mentions in British national newspapers.
Yet, during the same period, biodiversity was mentioned just 115 times."

The second one in today's Tagesanzeiger, a Swiss newspaper asking the question "Gibt es in Afrika bald ein Silicon Valley" and continues" Jetzt brauchen Schulen in Timbuktu statt ganzer Bibliotheken nur noch ein paar Secondhand-Computer, um den Lernenden Zugang zum gesammelten Wissen der Welt zu verschaffen."

This refers to Jeff Sachs and his conclusions (see eg in his article "The digital war on poverty, Aug 21, 2008" in the Guardian) that the digital divide is now closing to the very great advantage of the developing world.

"Moreover, market penetration in poor countries is rising sharply. India has around 300 million subscribers, with subscriptions rising by a stunning eight million or more per month. Brazil now has more than 130 million subscribers, and Indonesia was estimated to reach 120 million. In Africa, which contains the world's poorest countries, the market is soaring, with more than 280 million subscribers."

So, we talk about getting a list of names up in the next decade or so, whilst the world around us wants content, such as publications, images, specimen and related data as starting point to find out, what is known about a species, which is a pest species, etc.

There is no discussion that each name should be linked to at least one reference specimen with a state of the domain documentation attached to it. It is clear, that creating visual documentation is not anymore a stumbling block, but it seems rather our vision to take this chance.

There is very little discussion that only names should be published unless the related information is online accessible (eg through Zoobank) thus not only delivering what the world wants from us (good for us, that we have such a huge user base that we do not need to build up) but will save us a huge amount of work to retrofit data.

We had a great chance in 1992 (Rio), but our communities and our leaders didn't had a vision to create this global system needed to make a competitive point that biodiversity is relevant but rather continued go build on their minuscule, obviously obsolete fiefdoms.

We should not let slip what Jeff Sachs observes, and end up in the next decade with the above mentioned dismal little attention observed by Gardiner - the vision to build a list of names will not do the job, nor will we get there without additional, so far non-existent support.

* This is a thought regarding an argument David Patterson stated in the Taxaxcom list serve on May 12.

2009-05-15T23:40:00.000-07:00

Tja, why is biodiversity lost?

"How ridiculous then that over the last three months, climate change has had 1,382 mentions in British national newspapers.

Yet, during the same period, biodiversity was mentioned just 115 times."

Barry Gardiner (BBC-news, May 7, 2009)

2008-11-05T06:15:00.000-08:00

More on the Global Mammal Assesment

Simon Stuart wrote a rebuttal on taxacom and conservation commons listserve, where I tried to reply. So I went back to follow all the links he provides and have to confess, that there are the shape files online available, albeit without any metadata attached to them and as zip files, and of course no primary data they just do not deal with. So I downloaded the elephant shrew data sets and opened it in ArcView to have a look at the shape files. They are very coarse, similar to what we did for our taxonomic works where we drove nice circles. From there I went to the Red List site and looked up the tiger and some of the elephant shrews. At the bottom of the page there was a template how this page would have to be cited. Fair enough.

Now, that I have the famous Mammals of East Africa by Kingdon, I thought, why not look up what he has to say about this species. And here it is: The very same map, with all the collections he checked up marked.

It seems to me odd, that somebody can just copy and paste a figure from a scientific work without citing the source (Kingdon, J. 1974. East African Mammals. An Atlas of Evolution in Africa. Vol. 2A, Academic Press, London. Page 42) and at the same time loosing data, both regarding the distribution and the populations.

Since all the distribution maps of the species pages can be downloaded - and will be downloaded by many people, the proper citation of the materials used should be given. The way it's done all the links to the original work is lost.

2008-11-03T00:35:00.000-08:00

An example of total ignorance of Conservation Commons principles: The Global Mammal Assessment.

Four years after the Global Amphibian Assessment (GAA), the Global Mammal Assessment (GMA) hit the news, this time including an impressive number of 1,700 contributing scientists, covering all the mammals of the world. It was one of the few topics that hit the press around the globe during the WCC of an otherwise rather despressive coverage of the WCC, and with it the issues of conservation. This cold be blamed to external factors such as the global financial crisis, but I think, the GMA itself might be symptomatic for the disinterest.

Why? Try to find the GMA on the web. The original Science paper is not an open access paper, and thus for most of the readers off, since you need a credit card to read it. Most of the people in the places where biodiversity disappears don’t have the means to do this. But even, when you get the paper, you can download the auxiliary materials, which refers to the original data, but does not provide access to it. The next step would be to go to IUCN, but their web site does not provide a link to it. So, why not go to SSCs? There is nothing either. A next step is to check out the Redlist web site, where there is finally a press release, but this only covering the mammals on the Red List not the GMA.
Obviously, there is no easy way to get to the anything else than press releases.

When we talked about the GAA in Bangkok four years ago, the management of the GAA stressed, that all the data will be available online. It is not yet.

During the last four years, our technology changed dramatically. One of the most striking change is the availability of remote sensing data allowing access to high resolution remote sensing data to even the most remotest corner of the world. How does the GMA approach to draw simple envelops around the know distribution records or their species live up to this resolution? There are plenty of new programs around that could produce predictive maps, and which are actually used. This approach would actually mean, that the technology is more sophisticated and a little bit more living up to what new data is offering other than essentially experts opinion. It would also allow to challenge the experts, if they would have to provide access to the observation they used to derive their conclusion.

There are well over 100M observation records available through GBIF, data that is not systematically used in the GMA. It can be argued, that there are a lot of problems with that data – but it can at least be criticized or challenged, which is part of the scientific process. Expert’s opinions can not, since their base data is not available. Probably more importantly, such experts’ data can not be used for monitoring purposes, since it is impossible to compare data over time, such as would be needed in Countdown 2010. Finally, how representative is the experts data? How well do they know their species? How has the data been collected that went into their analysis?

Since the begin of the biodiversity crisis in 1986, Redlisting has not changed. It is easier to fly around the world from meeting to meeting, to communicate via email, to use GIS and thus a wider group can be covered. But it all depends on experts – a kind of expert knowledge that can easily be challenged. What should be done is to remove the expert from providing polygons to somebody that provides point data with proper GPS records taken in the field, modeling and GIS experts, and not least an infrastructure allowing others to pick up the data and run an independent analysis. Redlisting should not be the domain of few experts, but should strive to include the widest possible community it needs to live up to this very daunting task to measure the dynamic distribution patterns and changes of our species. It should also provide the community to use the data to make their case in places where one might not expect it. Only the application of the Conservation Commons Principles will allow that.

2008-05-06T23:53:00.000-07:00

Taxonomy in Europe in the 21st century
Report to the Board of Directors
European Distributed Institute of Taxonomy

Here is what the future of taxonomy ought to be. In my humble view, it is written by people who have little insight into the day to day work of taxonomy, or at least their view is dominant. It is also written without taking into consideration the costs: DNA sequencing is becoming cheaper. Yes, it does in the medical sector which might have some impact into our world. But to have a lab that can produce sequence data for just anything, the costs will be exorbitant.

Imagine, we dream we have a MRI and genetic tools to measure every patient, that sounds great. But if there is not doctor who tells you, that you are sick of a particular kind, then this would kill the health service, because everybody would have to go through the system. Similarly, if there is no screeing in the field by experts, you fist would most likely not find your taxa you want to look for, and secondly, you can not go back to it, because you have only a gene sequence.

I wonder, whether the initiation costs to build the underlying sytem is not too high. Initiation costs is the digitization of our legacy data. You could also question the increased overhead needed to produce new data.

I also do not see a convincing case why we need taxonomy. The way I read this report is that it is assumed that taxonomy does something important. There is no scientific driver behind which would want the politicians to support taxonomy, and which would help in many cases to decide where and how money should be spent. We are again saying we do all - and that's not going to work.

The other day I "had" to accompany my son to the chocolate company "Camille-Bloch". All they do is to produce some chocolate bars. It takes close to 200 people and an amazing extremely complex array of machinery, people to produce just a single chocolate bar. In a way I was stunned to see how much it takes to produce something trivial.
But isn't what we do similar? Camille-Bloch didn't start with this complexity, but evolved, which is easily seen in some of their old machinery standing next to high-tech robots; nobody would have the investment capital to build a factory at once, but it only worked because they never lost sight of their product (ie always sold enough) and invested enough to keep up with development.

A similar case might be Amazon.com, which didn't start the couple of years ago as big and complex it is now, but grew by adding every more complexity - a complexity that is a response to their customers requirments.

I slowly think, we lost our customers, because we did not deliver. Now that we have suddenly a huge competitor for funds - the rapidly growing demand for eco-ethanol and raising food prizes - I think we lost one of our dream customer: the governments fighting biodiversity loss.

This report is a short read, and in my view it reflects exactly the problem all these top down operations like BHL and EOL face: they do not know the underlying costs of what they want to do, and thus increasingly have to become more modest and with that not that new and exciting as promised.

2008-05-02T23:33:00.000-07:00

Access to Data

I just came across two two initiatives well worth exploring

Open Government Data

This is an initiative aiming at making governmental data accessible, with its OpenDataPrinciples. I have now clue, how important this initiative is regarding having an effect.

Landsat data through USGS

Imagery for Everyone…
Timeline Set to Release Entire USGS Landsat Archive at No Charge.

Landsat scenes can be previewed and downloaded using the USGS Global Visualization Viewer at http://glovis.usgs.gov [under “Select Collection”
choose Landsat archive: L7 SLC-off (2003-present)]. Scenes can also be selected using the USGS Earth Explorer tool at
http://earthexplorer.usgs.gov [under “Select Your Dataset” choose Landsat Archive: L7 SLC-off (2003-present)]. For further information on Landsat
satellites and products, see http://landsat.usgs.gov

2008-04-06T04:44:00.000-07:00

The Power of GPS-ed Distribution Records

Here is an obvious reason why we should add to all our biodiversity observation a detailed GPS-ed record, or why it actually is done in an area that is considered highly relevant: The movement of bear JJ3 in Switzerland (Source: Blick, 20080406).

Since the Swiss are not used to such a predator, they decided to assure that his position be known at all times, which would allow to be present when he enters hamlets to frighten him off.

You could imagine to have a little application which would link your position - which is known through your mobile phone - with the one of the bear.

2008-04-02T01:15:00.000-07:00

How Google Books is Changing Academic History

An interesting blog by Tim O'Reilly regarding the power of having access to printed material, especially if it is open to computing.

2008-03-20T00:07:00.000-07:00

The future of the Web...

Sitting here at the National Digital Archive Program meeting here in Taipei is one of the most thrilling events I have taken place during the last couple of years.

It also makes me a little bit depressed looking at how little ingenious we are in the domain of biodiversity and conservation. I guess, EOL would do good to listen to this community, even it is more about humanities, libraries and social networks.

The lectures and presentation will be online, so it will be good to check out, once they are up. Especially worthwhile to start are the lecturs on Thursday afternoon to get an idea on what is happening in the Web, what people think and use.

Interesting, though in a way really trivial ideas with explosive potential is to re-construct museums to add geographic tags so that you could see content in context. Of course that means that if all the vast amount of artefacts in our collections would be marked up, the emphasis would rather be on subjects than on the museum, and thus branding of the museum might have a set back. The feeling though is, that through this, many hidden things are being discovered, and additional coverage is given to institutions through channels un-imagined before.

There is no way to stop this development, whether we like like it or not....

Here an eclectic mix of interesting topics and links to: Web2.0, calais (to extract and link content); greenstone to build up a bibliography; wordpress

2008-03-12T07:49:00.000-07:00

John Downer: Do it for nature, not to conform to standards

John Downer, an incredible animal documentary maker, is explaining in this youtube clip some of his tricks to get the proper shots to document animal behavior. One of his credos is to be guided by what you want to achieve and not how things are generally done.

2008-02-27T04:32:00.000-08:00

The Launch of Plazi.org

PLAZI.ORG - THE DIGITAL REPOSITORY FOR SPECIES DESCRIPTIONS.

Knowledge of the actual number of species on planet Earth is one of the last frontiers in science. It is not known exactly how many species have been identified and described, much less the number of as yet undescribed species.

However, the species we do know are documented in well over hundred million pages of printed scientific books and journals. – This knowledge is hidden in libraries, and no single library holds all this knowledge.

The species descriptions are very rich in data, essentially a quality controlled summary of what is known at any specific time about a particular species. In best cases, this information includes a detailed morphological description, drawings and images, a summary on behavior and ecology and a detailed list of all the specimens studied. In more recent publications, links to DNA sequences or video documentation – among other forms of data – may be provided. Recently e-publications have become available, but many of these are copyrighted and thus not generally available open to the public for perusal or use. Nor are they easily machine-searchable for discovery and re-use of contents.

Recently, the Biodiversity Heritage Library as a large scale operation to digitize this biodiversity literature has been launched. Currently, it includes major US and UK natural history libraries, with the ultimate goal of including the entire global literature. All publications will be openly accessible to the public, unless they are copyrighted -- thus most of the recent publications are still out of reach. The BHL thus falls short of optimizing the potential uses of these publications.

Tagging the “boundaries” of a species description and identifying the species dealt with, supports discovery and retrieval of data not possible through Google. Mark-up of species descriptions permits queries, such as which are the "red ant in London", a very common form of query.

Under some national copyright legislation like the Swiss, descriptions can not be copyrighted because they are through historical constraints (there are tens of millions of descriptions) and peer review standardized and listing factual, in most cases morphological data describing species, and thus they can all be made readily accessible.

Plazi.org is a new Web based service that offers access to descriptions of species and an archive to store the publications as marked up documents. GoldenGate, a dedicated editor has been developed to mark up the publications supporting the extraction of descriptions, based on a TaxonX, an XML schema modeling the logic content of these publications. The Plazi Search and Retrieval Server, building on this systematic mark-up of texts, allows powerful search functions to find species descriptions, or even simple mention of species, permitting users to answer questions like: “Which species occur together”?

Plazi.org includes already more than 3,700 description of 3,000 taxa with a goal of archiving all the forthcoming new descriptions and, contingent upon additional funding, all the descriptions of the known 12,278 ant species listed in the Hymenoptera Name Server/ antbase.org, enhanced with globally unique species numbers (LSID’s: Life Science Identifiers). While ants provide the original test case, the service is not restricted to ants but is potentially open to all groups, from Bacteria to Plants, and will support most major languages. All descriptions are machine readable and thus can be picked up for mash-ups or individual Websites.

Plazi.org is run and developed by Donat Agosti, Terry Catapano, Christiana Klingenberg and Guido Sautter, its development is supported by Grants from the US National Science Foundation (to the American Museum of Natural History: Christie Stephenson and Tom Moritz), the German Deutsche Forschungsgemeinschaft (to University of Karlsruhe: Klemens Böhm) and the Global Biodiversity Information Facility (GBIF; to Plazi.org and Zootaxa), and is collaborating with the Hymenoptera Name Server at Ohio State University (Norm Johnson), Zoobank (Richard Pyle), University of Massachusetts (Robert Morris), antweb.org (Brian Fisher) and Zootaxa (Zhi-Qiang Zhang).

Plazi.org has been released to the public at the EDIT "IPR and the web: challenges for taxonomy" meeting in London, Feb. 20, 2008

Related Links:

First descriptions of the first ant described (Linnaeus, 1758)
Recent publications with fine grained mark-up allowing extraction of specimen data and plotting automatically maps
Description in Russian:(please set encoding=utf-8 in your browser.
Description in Chinese
Fish
Bacterium
Plant
Fungi

2008-02-27T01:52:00.000-08:00

EDIT- IPR and the Web Workshop, Kew Gardens, UK, February 20, 2008

The organizers have to be thanked for taking on this important topic - IPR and copyright being a topic which all has an impact on us. It's (mis-)application is essentially one of the main culprit for biodiversity is neither on the science agenda nor a relevant issue on todays global environmental politics. "You can only protect what you know..." and with literally no access to the more than 10 Millions of descriptions, and no clear strategy yet who to do this in the current misunderstood and applied copyright framework, we fare not very well.

I was astonished that nobody from the printing industry, the law makers nor very little from the legal branch have been present. It was then very refreshing, that the representative of the legal branch, Willi Egloff had a very refreshing talk, in a way rather the opposite of what a large part of our community thinks copyright is, and whose complicated somber picture has been represented by EDIT's legal advisor (who is not a lawyer) Naomi Korn, who brought in a new term "Risk Assessment".

Practical aspects publishing side came up only at the end of my lecture, and in discussions stressing the point that we need at least self archiving (Green Road) or better find ways for open access policy, that must assure that we do not sign any contracts and give a way exclusive rights to publishers.

There was the usual discussion, based on the idea that we all continually publish in Nature and Science.... and which showed how little the same people know about contracts, such as publishing in Nature (which allows preprints in repositories).

Naomi Korn, a consultant to EDIT was speaking much more for the NHL administration then the interest of the scientists, and warned that there ar dangerous all over. The example of the danger of being sued though came from Google, or Access and Benefit Sharing issues at Kew.

Egloff gave a legal perspective (I think, he was one of the very few legal professionals in the room) which essentially would say that with his interpretation of the law descriptions can not be copyrighted, but probably the entire publications, because descriptions do not represent original, unique entities that qualify as works. It is also possible to temporarily make copies of publications for example in a process to mark them up and extract the descriptions.

A lot of all this depends on individual cases.

Whereas Naomi would stress the point that we life in a very dangerous world, which needs a sound Risk Assessment of all we do, this point was flawed because the argument would build on cases dealt with in the courts - but there are none so far.

A further point stressed by Naomi was, that we need to protect the interest of the scientists, so that they could eventually make money with their work. This, in fact, mixes commercial with scientific use and thus disallows many exceptions in the copyright law given for scientific use. My feeling was, that Naomi, supposedly representing the interest of the scientists is much more leaning towards to administration's point of view. Her point "I have to sell a IPR policy to the administration" might not what is needed, but a convincing argument, that the administration supports the scientists point.

Egloff would take the route to feel much less constrained and make us of modern technology so it is clear to the law makers what the advantage is of having open access. So far, there is little to be seen assuming that there are 10s of millions of descriptions out there. Certainly the approach BHL is choosing helps little to make the case, since they hardly touch modern publications because of their copyright policy, and thus will not allow to build comprehensive bodies of descriptions that can be mined or used.

One problem is that our large research institutions (the natural history museums and collections) rather position them as corporations interested of selling products rather then focusing on the interest of their scientists.

Vishwas Chavan's talk about citation was one step in the direction of linking all the various pieces of data and information together, what is finally needed to represent the taxonomic knowledge as an entity as opposed to single publications and thousands for little databases nobody but the individual scientist would use.

My own presentation went along the same route, making the case that we need to make content accessible, how we could do it (see plazi.org) by providing the tools to convert legacy publications into semantically enhanced publications with an emphasis on access to descriptions, as well as the respective infrastructure to provide access to them. There will be no single way to get there, so we need to consider the Green and Gold Road to open access, and furthermore whether we want to keep publishing descriptions the same old way or whether we better make sure we can use web publications and strive for comprehensive databases and ontologies providing a more or less uniform access to the publications.

This latter point has been stressed with Vince Smith and Dave Roberts points about Scratchpads.

One point that needs be explored is the question of why we begun to talk about publications in the first hand. Clearly, if we talk about simple access to pdf copies, there is little chance to succeed, besides implementing the Green Road, but which does not allow machine readable access. What we need is a vital science curriculum that also makes use of the published material as much as it produces new material to make new discoveries by third parties, for example compiling a list of all the host-plant relationships of a given taxon. We want to introduce new metrics to show what is being how often used to measure a scientists contribution. But foremost, we have to have a strong research curriculum, and based on this ask what sort of publications we need. We all want things, but we, the systematists community, must get together more actively to show, that we develop innovative tools TOGETHER to chart the world's species. Providing open access is just one of the outcomes, which also allows the public to follow what we as scientists do.

Thus, a lot of the issues would be resolved, if the emphasis would be to come up with good science in the first hand that is built upon making use of the vast body of literature and growing databases, such as delivered through GBIF, GenBank, CBOL. That would mean that few follow some simple standards and transfer protocols.

In summary, it was a meeting that was timely, a lot of the participants left confused but still thinking that copyright is needed to protect even their right. I hope that Egloff's position will be noticed. Why not even run all the biodiversity literature operation from places like Switzerland that have the best possible legal framework to deal with? Already now, scanning takes place in the US and not the UK because of copyright law.

It is time, that the scientists go back to square one. Science is about
citations and free flow of information, and NOT copyright, which is a commercial issue. New routes are not prohibited, nor to come up with OUR strategy, and then talks including all the stakeholders.

2007-12-04T23:54:00.000-08:00

What has Hubble taught us?

Hubble has been an invaluable source of information, helping astronomers understand phenomena such as dark energy and quasars. It has even helped scientists to calculate the age of the universe. Thanks to Hubble, scientists now think that it is between 13 and 14 billion years old. Thousands of research papers have been written on the basis of information collected by Hubble, while all its data has been collected into a public archive for all to use. It has also brought us the deepest telescopic views of the universe ever produced, allowing scientists to look back in time at how the universe looked a few hundred million years after its birth

Independent, Dec. 5, 2007

2007-11-15T12:56:00.001-08:00

The oldest pirated work in Zoology?

Is the reprint of Systema Naturae 10th edition the first pirated work on the history of zoological systematics literature?

Source: TL-2 (and there search for "Linnaeus" and go to 1758.)

2007-09-18T03:22:00.000-07:00

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:

Piotr

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 http://140.247.119.145/ 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/*/http://140.247.119.145/rap/
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.

2007-09-14T02:05:00.000-07:00

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.

2007-09-14T01:28:00.000-07:00

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.

2007-09-11T14:21:00.000-07:00

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.

2007-09-06T00:39:00.000-07:00

"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.

2007-09-05T04:48:00.000-07:00

Internet-power

"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.

2007-09-04T08:43:00.000-07:00

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.

2007-08-27T00:31:00.000-07:00

Swiss Federal Court (Bundesgericht) ruling regarding usage of news media articles for the preparation of press reviews

Willi Egloff brought this important federal court ruling to my attention.

In the Bundesgerichtsentscheid (4C.73/2007, June 26, 2007, search for Prolitteris, decision 4C.73/2007, June 26, 2007) it was ruled, that the press reviews (searching for specific items and copying the relevant parts required by customer into a specific review) as a service to a third party does not breach copy right rules.

There are some interesting aspects which need detailed study:
What is the work (Werk)? Is it the entire newspaper or a separate article by a journalist?
The interest of the journalist vs the interest of the publisher?
Temporary storage of data
Preparation of press reviews for private parties (legal or personal)

The ruling, an appellation of ProLitteris against a lower court ruling (Obergericht des Kantons Zürich) has been approved, thus allowing ProLitteris to continue to provide press reviews without infringing Swiss Urberrrecht (copyright).

This is a remarkable decision which needs be studied regarding a similar usage of scientific publications, especially regarding data mining or extraction and the production of derived works.

2007-08-23T00:00:00.000-07:00

Turn away from the Earth to the Sky: Google's new star-gazing tool

Recently, Google launched a new tool in its Google Earth program: Watching the sky from Earth (see NYTimes, August 22, 2007). It is another of this mammoth tasks to stitch together more than a million of images to cover the entire sky. Google claimed, that they did it, because some of their engineers did it, because they had an interest in this, and not to generate revenues. I like this.

As a biologist though I can not get around the thought that once again biodiversity has proven to be of little attraction to the real world. This fascinating world we probably are increasingly loosing right now is somehow so elusive, that it can not catch the attention of the important people in this world.

It is elusive in a sense, that it is not easy to go out to even watch a house mouse in your backyard, not to speak of those many nocturnal or shy animals, and not to speak of understanding their population structure and dynamics. We lack just lack the time, patience, knowledge to do so. Plants are even worse. They do not move, so to watch their activity is more difficult, and then to identify them even more so. Despite the hope the BarCode of Life initiative seems to infuse, it makes the problem even more grave: We then need a hand held device to find an organism, of which we do not know how it looks like - so how will we find it in the first place?

The other day I was watching EO Wilson on Youtube presenting his 'Wish' lecture at the TED meeting. The video is 24 minutes, of which he uses about 20 minutes to tell the same old story of trivia of numbers about biodiversity, his personal involvement in this and the last few minutes he referred to some high profile institutions who are taking on his great idea of an Encyclopedia of Life, and that he now wishes that TEDsters would help. So, where is Wilson's true compassion, where can we look at it. There isn't anything visionary about what he does. It is the same content as he presented in 1987 where biodiversity became an issue. Shall we care about this?

We are rapidly approaching 2010, the year in which nearly all countries of the world came together for the World Summit on Sustainable Development to launch the countdown2010, an initiative to halt the increasing rate of loosing species (and halt species loss entirely in the EU). And the only thing we can claim in 2010, that we still do not know. And this is, because not even our leaders (see above), nor the conservation organizations are innovative or want to invest in tools to measure what is out there, nor seem they willing to share the little data they have.

There is some light in the dark by initiatives like GBIF which help to spearhead the distribution of existing data, and show the value of open access. There is EOL, which started with great fanfare to announce to provide for each species an portal of access to all the relevant information, but in the meantime became very secretive in its action despite its call to bring together all the experts. There is the conservation geo-portal, but these are all tools to disseminate existing information. They all build upon somebody collecting new data. And most of this data is very weak, because it has not been collected for the very purpose conservation needs it: to measure the change in species loss, for example. It does not live up the detail of imagery of our planet earth where we can see single trees in Madagascar.

If I would be a TEDster listening to talks from Wilson et al, I would open my handhelp or laptop and drill down in what he says. There isn't anything thrilling to see but some static images, not even text, which is still in his copyrighted book as are most of the new literature due to a strangle of the commercial publishers based on their quasi monopoly on publishing, there is no interesting, intriguing, innovative field campaign going on in his office. In more general terms, there is not even a comprehensive list of all the species of the world nor a phylogeny, which could be used, like the new map of the sky, to surf in the worlds biodiversity.

Wouldn't it be nice, if whenever a new species is described, or even found and thought to be new, an new blimp in the biodiversity sky would show up, immediately accessible with all the data around it. Such as system would bring together not only the curious engineer at Google with the field biologist, but all the many conservationists with the experts of particular taxa. All the technology to do so is here and being developed in many small little initiatives like such as Rod Pages tools or Dave Shorthouse's to visualize is spider data.

But it is not main stream, nor is it being adopted easily by the mainstream institutions. They have a problem with changing their culture, why else do they have such a big problem to sign up and implement ideas such as the Conservation Commons? Why don't invest more of their resources into generating new data rather than regurgitating the same again and again?

I think, an new generation of leaders have to raise in our fields. Leaders who understand the problems, are innovative and committed and thus solve problems rather than love to stay in limelight and rub shoulders; leaders who are not bound by all their relationships, financial constraints, and interest in star power. 20 years of mismanagement of biodiversity ought be reason enough for change. Even the 100M USD supposedly pledged for EOL over the next 10 years will do little if the underlying culture is not being changed.

2007-07-04T00:15:00.000-07:00

Methodlogy Porn

In this issue of Wired Magazine is an interesting article on how to disseminate details of methods one can not learn out of books, and I guess not entirely from videos either. But it is a great leap ahead in providing an inroad into how science works.

This is an excellent example, how innate knowledge could spread, such as the proper mounting and handling of Winkler bags, or dissecting insect genitalia. It is also an excellent vehicle to expose your own scientific work.

"YouTube Does Science, From Fruit-Fly Fight Clubs to Stem Cell Extractions Years behind the lab bench taught

Moshe Pritsker that the trickiest part of any science experiment isn't the hypothesis, it's the method. The former Harvard researcher learned this lesson back in his student days, after carefully following the instructions on a specialized kit for isolating DNA. "Surprise," Pritsker says, "no DNA!" A colleague finally showed him how to make the kit work. And that gave Pritsker an idea: methodology porn. The Web site he cofounded, the Journal of Visualized Experiments, launched last October. Now its videos of experimental procedures and techniques — from stem-cell culture prep to hippocampal dye injection — get 300 pageviews a day. The journal's still a work in progress (nothing's gone viral yet), but just wait. "No one has published results in video before," Pritsker says. "Scientists don't know how to do it." Here are a few of the journal's faves."

2007-06-19T05:15:00.000-07:00

Nature again: Access to scientific results

Once again, Nature did it. Whilst we (taxonomists) talk about LSIDs, guids, dois, Nature is offering an archive where dois and handles are given to any of your scientific work. The idea is to help to foster scientific exchange. So, you could for example add all your publications for which you didn't sign an exclusive licence to the publishers and thus it will become part of the growing digital world.

A comment is given at O'Reilly's radar

The question behind this, similar to flickr and youtube is, that these are at the end all private and commercial enterprises which lay outside our control (similar to EOL and BHL), and I wonder how wise it is from our funding fathers (science foundations etc.) to let this happen without having some sort of control mechanisms, or do it by themselves. This sort of accumulation of knowledge are certainly one of the pillars of research.

We all talk about community, democracy but with that we all work towards single institutions which are exactly the opposite of what we envision. Google is scanning an enormous amount of books at their cost, but do we really have access to its content, or can we build api to mine or use it the way we envision? No. Who can profit from our joint input into tagging things - certainly a novel feature in understanding our behavior?

Despite all this, we should make usage of this offer. Add your old publication on Nature precdings, add the bibliographic references to Connotea, but let's use this to demonstrate to our funders and our congress men and women, that these instiutions need be part of our science infrastructure, because we actually use it.

2007-06-02T08:17:00.000-07:00

A NASA insight

Editorial in June 2, 2007 New York Times

" Hot Enough in Here?

Published: June 2, 2007

Michael Griffin, administrator of the National Aeronautics and Space Administration, is renowned for speaking bluntly so it was no surprise when he stuck his foot in his mouth during a recent interview. The disturbing element is that he may have inadvertently revealed one reason the space agency has been cutting back on satellite missions to study global warming.

In an interview with National Public Radio, Mr. Griffin acknowledged that global warming is happening but then, remarkably, suggested that it might not be a problem — or at least one that had to be fixed. “I am not sure that it is fair to say that it is a problem we must wrestle with. To assume that it is a problem is to assume that the state of Earth’s climate today is the optimal climate,” he said, adding that he wasn’t sure there was any “need to take steps to make sure that it doesn’t change.”

Those comments were a jarring denial of the overwhelming scientific consensus that climate change is serious and requires mitigation. It even lagged behind the thinking of President Bush who — under strong domestic and international pressure — has now called for a long-term global goal to cut greenhouse gas emissions.

In response to the mini-furor over his comments, Mr. Griffin stressed that NASA simply collects and analyzes data; it does not make policy on issues like climate change. But the scary thing was the lens his comment provided into his innermost thoughts. The Bush administration has been justly criticized for cutting the agency’s earth sciences budget and downgrading NASA’s once-prominent goal “to understand and protect our home planet.” Tight budgets are one key reason for the cuts in earth sciences, as is the administration’s long refusal to grapple with global warming. But now it seems that Mr. Griffin’s own belief that climate change may be no big deal accounts in part for his agency’s ill-conceived retreat from environmental studies.
"

It is interesting to see, that one man with such as decisive power doesn't listen to its own scientists, and not to speak of all the others involved in the climate debate.

2007-05-31T00:29:00.000-07:00

on copyright

"The copyright system is perfect ... for people who have all the money in the world to pay lawyers."
(Lawrence Lessig's parting shot at the CISAC - International Confederation of Authors and Composers Society, Brussels, 30 - 31 May, 2007.)

An interesting, not commonly considered front against copyright holders, that is the distributors of digital content, which have a strong voice against the old fashioned copyright holders and who do not want to be help responsible for piracy happening over their nets.
There is also an intersting attack by Crett Cottle (chair of CISAC's board of directors: "Don't treat the authors like the record labels or the entertainment companies. Hollywood's Jurassic, and we're the mammals.

This comparison joins the unrest against big industry voiced at the launch of the Swiss version of the Creative Commons Licence by the two plenary speakers John Buckman (image) and Volker Grassmuck

Following some excerpts out of a report from the
The Hollywood Reporter, Leo Cendrowicz and Mark Sutherland , May 31, 2007

"BRUSSELS -- The inaugural CISAC Copyright Summit kicked off here Wednesday in with some lively initial sessions.

CISAC -- the International Confederation of Authors and Composers Societies -- says it represents 217 copyright societies in 114 countries and 2.5 million creators and publishers in music, drama, literature, audiovisual, photography and the visual arts.

The two-day summit, attended by more than 500 delegates, goes under the banner "Creators First" and is focused on the protection of copyright in the digital age.

But in his keynote address, British Telecom CEO Ben Verwaayen issued a brutal warning to rights owners, telling them that business models that had been sustained for more than a century were coming to an end

"Your industry has not changed for 20 years, maybe 50 years. You have to rethink how you work in the digital age," he said. "Are you just a rights administrator that sends me a bill, or are you something more?"

(...)
Bragg and others called for "solidarity" among artists to help protect their income.

"The power in the creative industries is moving away from retailers and the industry toward artists and our relationships with our audiences," he said.

(...)
While attacking those who commercially exploit user-generated content, or UGC, as indulging in "sharecropping for the digital age," Lessig also told a packed conference hall that Creative Commons licenses are aimed at those who had no interest in making money from their creativity.

"There's an explosion of UGC that never wants to be part of the commercial economy," he said. "If we're arguing, it's only because you think the only model for copyright is the commercial one."

Cottle hit back: "The problem is you give credence to the general anti-copyright argument, particularly in developing countries. Don't treat the authors like the record labels or the entertainment companies. Hollywood's Jurassic, and we're the mammals."

2007-05-30T01:39:00.001-07:00

Visualizing our world

In his inaugural talk at the launch of the Swiss version of the Creative Commons licence, Volker Grasmück presented a very thoughtful lecture on the implication of copyright, and ended up with a plea for acceptance of small style piracy. More about that will follow on this site, organized by the Digitale Allmend.

In his talk he showed a slide he got from Worldmapper.org which has one cool visualizationt tool: using a mapping tool to represent each country's proportional contribution to a topic, such as the world's native plant species. This then allows to compare to the population size, science, or actual physical size.

This map shows the number of native plant species, and demonstrates a bias towards the southern hemisphere, especially the continents of South America and Africa. In contrast, Canada and North America have relatively few species (source: Worldmapper.org).

The land area of each territory is shown here.

The total land area of these 200 territories is 13,056 million hectares. Divided up equally that would be 2.1 hectares for each person. A hectare is 100 metres by 100 metres. (Source: Worldmapper.org).

In Spring 2000 world population estimates reached 6 billion; that is 6 thousand million. The distribution of the earth's population is shown in this map (Source: Worldmapper.org).

Scientific papers cover physics, biology, chemistry, mathematics, clinical medicine, biomedical research, engineering, technology, and earth and space sciences. (Source: Worldmapper.org).

This map shows the growth in scientific research of territories between 1990 and 2001. If there was no increase in scientific publications that territory has no area on the map. (Source: Worldmapper.org).

2007-05-24T01:41:00.000-07:00

Loosing control

The announcement of last week’s launch of a Nigerian telecom satellite by China is not only China’s first successful launch of a home built satellite, but it well certainly a big step in a much more efficient extraction of natural resources in the developed world by China whose foreign policy is largely driven to secure the supply of its huge need of natural resources. That means, that the exploitation of tropical resources will continue, most likely at an increased rate.

This happens at a time, where the US government creates many enemies abroad and, for conservation and taxonomy more importantly, closed down NASA’s Earth Sciences program and siphons a lot of funding into a Mars program which could not be launched at a worth time. Hopefully, the Europeans can fill in some of this gap with their ENVISAT and a series of new smaller satellites, and hopefully make at least some core data accessible for scientists and conservationists at large, similar to the current NASA policy (see eg GLCF) as partner of the Conservation Commons (A nice contradiction between White House policy and scientists concerned about conservation within NASA!).

Taxonomists better assure, that their data is quickly processed and made accessible so conservationists in the field can use it to have an impact on the increased extraction of natural resources as well as the monitoring of it. The combination of specimen data in the field, near real time remote sensing data and predictive modeling offers now a much advanced tool to support action on the place where it is most efficient. Never before was the chance to have close up images of even the remotest corner of the world (eg Google Earth, or GLCF, and increasingly, the Internet allows to supply colleagues in such places with data, and on the other hand we can get more information to do a much better job from within our own institutions.

2007-05-21T01:09:00.000-07:00

A Great Idea Lives Forever. Shouldn’t Its Copyright?

"WHAT if, after you had paid the taxes on earnings with which you built a house, sales taxes on the materials, real estate taxes during your life, and inheritance taxes at your death, the government would eventually commandeer it entirely? This does not happen in our society ... to houses. Or to businesses. Were you to have ushered through the many gates of taxation a flour mill, travel agency or newspaper, they would not suffer total confiscation.

Once the state has dipped its enormous beak into the stream of your wealth and possessions they are allowed to flow from one generation to the next. Though they may be divided and diminished by inflation, imperfect investment, a proliferation of descendants and the government taking its share, they are not simply expropriated.

That is, unless you own a copyright. Were I tomorrow to write the great American novel (again?), 70 years after my death the rights to it, though taxed at inheritance, would be stripped from my children and grandchildren. To the claim that this provision strikes malefactors of great wealth, one might ask, first, where the heirs of Sylvia Plath berth their 200-foot yachts. And, second, why, when such a stiff penalty is not applied to the owners of Rockefeller Center or Wal-Mart, it is brought to bear against legions of harmless drudges who, other than a handful of literary plutocrats (manufacturers, really), are destined by the nature of things to be no more financially secure than a seal in the Central Park Zoo."
New York Times, May 20, 2007

Seems to me to a logic argument in its own, wouldn't there be more to it then the financial side, which is almost non existant with the majority of the novels diapearing from the bookshelves and only will have a second live because the internet allows to discover them and print, if necessary, them on demand. Enforcement of copyright=ownership would though disrupt the new flow of information and development of web2.0 and similar amazing new possibilites.

2007-05-21T00:50:00.000-07:00

A mandate for open access to your publications is necessary

Empiric data from within the open access movement shows, that self archiving only works if an institutional open access mandate is in place. Obviously, this is not just a problem unique to open access but to other fields where compliance to procedures which evidently do have great advantages.

Food security:
"This isn’t simply a matter of caving in to industry pressure. The Bush administration won’t issue food safety regulations even when the private sector wants them. The president of the United Fresh Produce Association says that the industry’s problems “can’t be solved without strong mandatory federal regulations”: without such regulations, scrupulous growers and processors risk being undercut by competitors more willing to cut corners on food safety. Yet the administration refuses to do more than issue nonbinding guidelines."
Paul Krugman, New York Times, May 21, 2007

2007-05-15T22:38:00.000-07:00

Copyright = Censorship?

Tonight over a nice dinner talking about the future of taxonomy and science communication, Terry Catapano, a librarian and historian at Columbia University brought up the issue of access to information, and how it would always get out. It’s an interesting comparison between copyright of public funded research and censorship in the age of enlightenment and the former USSR.

In the age of enlightenment, the French would bar not only pornographic but other controversial books from being printed and distributed in France. So Holland and Neuchatel in Switzerland became the places where those of such barred authors like Voltaire or Descartes have been printed an then smuggled into France, where they had their impact. Similarly, the former USSR barred books by Solschenytzyn and others which then appeared in the underground Samisdad literature (with heavy penalties for the owner if caught, like those in today’s hunt for copyright infringement), illegally reproduced works distributed from one reader to the next and eventually finding its way to the West, where it got printed.

Today, copyright in our science has exactly the same effect, that is officially you there is a restriction to access by exorbitant prizing by the publishers like Elsevier, and at the same time, authors happily distribute the pdf via email to anybody who wants to have a copy, like the copied books by the Sowjet dissidents. It is an obstruction to the growth of our knowledge. On the one hand this is leading to small cells of like minded well informed people letting many of us in the dark, on the other hand, the history showed, like in the case of USSR, that such oppressive systems will disappear at some point.

2007-05-12T14:06:00.001-07:00

Electronic ark. E. O. Wilson’s idea for a Web-based encyclopedia containing all the species on Earth is now ready for launch. (Science 316: 818; May 11, 2007).

At least somebody get's the credit for all the work done for free to populate electronic ark...

2007-05-11T03:20:00.001-07:00

Access to taxonomic descriptions and names

EO Wilson's impact on the access to descriptions of new ant species in 2003. antbase.org (supported by a grant from Smithsonian's Atherton-Seidall Foundation to scan publications) allows direct access to allmost all the descriptions of the over 12,000 ant species except those copyrighted. Most of the copyrighted descriptions are those of Wilson's Pheidole revision.

In today's Nature (May 10, 2007) is a correspondence by Wheeler and Krell requiring changes in the Codes of Zoological and Botanical Nomenclature to assure that any new described species are immediately known to the universe. For that they require

- First, require such registration before a name is formally available for use.

- Second, require full text descriptions of species to be deposited by publishers or authors in a central, publicly open ‘bank’, free of charge, such as will be provided by ZooBank for zoological names (A. Polaszek et al. Bull. Zool. Nom. 62, 210–220; 2005).

- Third, require electronic publications to include a ‘hot’ link to these banks of names and descriptions. This will ensure precision in reference to names.

The call for open access to systematic literature is not new, but coincides this time with the annoucement of the Encylopedia of Life, which is building very strongly on the published record. Within the Biodiversity Heritage Library component, they plan to scan in the legacy publications. However, there is a limitation to it: Only publications out of what they consider copyright (75 years after the publication which should be in my view 75 years after the death of the author).

That does not give access the way Wheeler and Krell ask for, even if the EOL/BHL team will negotiate with individual publishers to get access, nor does it build on the open access movement green or gold road to open access. Self archiving, increasingly required by research funding bodies (such as the Swiss Science Foundation. Wellcome Trust, etc.) who singed the Berlin Declaration is just one way to go.

It is especially sad to see, that EO Wilson, the figure head of EOL, with all his star power (e.g. as spokesperson for EOL) still supports this main barrier to access to our knowledge by supporting copyright of his own recent work, even though he announced in Nature 424: (2003) "that the publisher is now putting the book online. ", which is still not the case.

- We need to rethink our own behavior. We should change the Codes, that open access to the publication is mandated, and with that that the species descriptions can be discovered online. We need at least to self archive our publications, not signing contracts with publishers which do not allow that.
- We need to convince the publishers that they enter taxonomic specific xml elements marking up the names and the boundaries of descriptions at least (using for example taxonx schema)
- We need to rethink the function of taxonomic publications: The future of systematics will be in data matrices and other databases, from which data can be extracted directly. Currently we need painfully extract information from the legacy publications. This can be avoided if publications would be instruments to control the input into these growing databases as well as to announce in a human readable form that there are new additons to the databases and matrices. It would already be sufficient, if we at least would allow mark up in the current publications so a machine readable xml version could be published at the same time the pdf comes out. PLOS-ONE is such an example, although not yet for systematics.

2007-05-10T06:32:00.000-07:00

Launch of the Encylopedia of Life

Yesterday, May 9, 2007 Jonathan D. Fanton, president of the John D. and Catherine T. MacArthur foundation, announced the launch of the Encyclopedia of Life initiative here in DC by , which clearly will affect taxonomy and provide much better access to our well hidden knowledge about our species. The project as such is supported by USD50M for the next five years, with a likely extension for another 5 years. It is great, that the money could be raised from MacArthur Foundation (with the lion0s share), the Sloan Foundation and support from the five core institutions, Harvard, The Field Museum, Smithsonian, Marin Biological Lab and Missouri Botanical Garden. The idea is to have within these 10 years for each of the 1.8M species its specific page.

In an interesting way, the participants at the official launch represent – at least for me – the main challenge of this the project: Getting content. I could hardly figure out any active scientist in the crowd. These are the people who actually are building up content, like fishbase or antbase. Populating the database is so far generally a truly bottom up movement, done by individuals and with little support from the respective institutions.

From a different angle, and also in a different time with much more digital tools at hand, the commitment from the core institutions could signal a longlasting shift in this policy, that they became aware, that building up species databases, their underlying catalogues, etc. are a quintessential element in modern research environment, and need be supported similarily to maintaining libraries, GenBank, etc.

This in turn reflects a new development, such as the OECD declaration to provide open access to publicly funded research data. This is again an initiative at top level (Governments).

What is needed now is that we define the needs for our work. We need to talk to the responsibles in these initiatives so that their decisions really reflect what we need, reflect the way we operate, so part of the outcome the EOL or OECD initiatives help us to work more efficiently, as much as it provides a much higher profile for our work. We need to assure, that the initiatives not only reflects the idea of the current core US institutions, but the needs of our colleagues in Europe or the developing world. We also need to assure, that initiatives such as GBIF, IABIN, are not being outcompeted but rather form together a superstructure. These initiatives are global, and thus affect all of us.

For example, a really important part of the project will be the Biodiversity Heritage Library. Clearly, not all the works can be digitized at once, so selection of bodies of literature should happen, to support ongoing research projects and show the benefit of it. Why not propose to scan all the journals with content on Madagascar, reef fishes or other topics, where there is a strong research and conservation community behind?

Don’t sit around, read, be pro-active and voice your concerns and wishes, use your blogs…. It is clear, that even the 100M will not suffice to satisfy all of our dreams, but it is clearly a jumping board into a new age.

2007-05-06T14:54:00.000-07:00

The impact of Internet and online libraries on how to do science

"And with the Internet, working in an out-of-the-way town like Missoula is no longer the disadvantage it once was. “People say the library is small,” said Tammy Mildenstein, a graduate student who travels between here and the Philippines to study flying foxes. “But why not get it online and watch deer out your window?”" (NYTimes, May 6, 2007)

A very nice strong statement, that access to online libraries allows to move a away from the big science centers to the places, where the questions arise, be it Montana or increasingly in the developing world. We just need to assure that all our studies are open acecss or at least in self archives.

2007-04-01T09:06:00.000-07:00

The future of data access

If we only had a guid or doi for each species and the necessary resources in the background

This figure legend
"The pattern on a building in Tokyo is filled with information that can be read by a properly programmed cellphone with a camera. The technology can also be used for many other things, like buying airline tickets. (NYTimes)"

could read like "the pattern on a food bag or sign post in a national park is filled with information that can be read by a properly programmed cellphone with a camera. The technology can also be used to provide access to all the species information of the world"

2007-03-16T01:03:00.000-07:00

Human authorities vs machine generated wisdom

In my last newspaper article in the NZZ I end up with the question

"ob nicht Websites, die allen offenstehen und über
ausgeklügelte Qualitätskontrollen für die Fakten
verfügen, besser als einzelne Spezialisten "wissen
", was wichtig und aktuell ist.
"

That is, I question whether a human expert ought be replaced by some kind of an artificial system delivering a synthesis and a metrics of how trustworthy a bit of information is. This can cover the synthesis, but could go down to the single facts upon which such an synthesis is based.

Rod in his Iphylo blog had an interesting comment about this issue, well worth reading, including Matt Cockerill's post.

I would shy away from saying, that no humans are needed, but ponder rather the idea that for knowledge based on data on Internet-accessible sources and predefined criteria, a machine might fare better.

This is certainly a hot issue regarding the measuring a scientists contribution and needs with new models of communication, such as plos one, blogs, databases the attention of those needing to judge scientists for their promotion.

2007-03-09T00:20:00.000-08:00

EO Wilson recipient of the TED award 2007 (2)

Here Wilson's wish and an excerpt from Wired's blog on Wilson lecture at the TED meeting.
"
Biologist E.O. Wilson followed Nachtwey by saying that he came on behalf of “insects and other small creatures,” to “make a plea for them.” Wilson’s wish: “I wish that we will work together to help to create the key tool we need to inspire preservation of earth’s biodiversity: The Encyclopedia of Life.” As I understand it, this would be a biological Super-Wikipedia, a collaborative project among scientists and amateurs that would contain information about all life on the planet.

“We live on a mostly unexplored planet,” Wilson emphasized. Recent years have seen the discovery of two new kinds of whales, a new kind of elephant, a distinct new kind of gorilla, and more. And on the microscopic (and smaller) scale, the earth is filled with the “dark matter of the biological world,” the bacteria, which are only beginning to be discovered.

“Our lives depend upon these creatures,” Wilson said. He estimated that 500 species of friendly bacteria live symbiotically with us in our mouths and throats, and that they probably fend of pathogenic bacteria. When it comes to species discovery, “Scientists are like explorers in a rowboat launched onto the Pacific Ocean.” (Wilson also allowed that he believes “true aliens,” creatures from outer space, might live among us on earth in the form of a bacterial species, which would have had billions of years to arrive.)

The “human juggernaut” is destroying the earth’s biodiversity, Wilson said, through habitat destruction (“including climate change”); the spread of invasive species, such as pathogenic bacteria and viruses, into every country; pollution; population expansion; and overharvesting, driving species into extinction through over-hunting and –fishing. (Wilson used the opening letter of each of these elements to create the acronym “HIPPO.”) Previous cataclysms of this sort, Wilson said, such as “the last one that ended the age of dinosaurs, took 5 to 10 million years to repair.”

In order to prevent catastrophe, Wilson said, “we need to have the biosphere properly explored.” He called for “a biological moon shot,” a project on the scale of the mapping of the human genome to map and discover the biological code of all of the life on the planet. The project, he said, could transform the science of biology and inspire a new generation of biologists to continue the quest that started for him 60 years ago: “to search for life, to understand it, and finally, above all, to preserve it.”
"

Comment: I sincerely hope that this latest initiative, together with the Encylopedia of Life project where he is honorary chair, will fly, and not end up in the same debacle as the last effort, the ALL species project. I hope, a governance model will be chosen, which is in support of the many data providers rather then us them as mere source, and one that strengthens existing global initiatives like the Global Biodiversity Information Facility rather then competes with it; one that involves, due to its global nature, the entire community and not just anglosaxon specialists, what seems to be the case right now at the EOL informatics part.

2007-03-07T05:18:00.000-08:00

A thought about the copyright of legacy publications

At last week's (March 1, 2007) „Open Access – From the principles to the implementation“ meeting, organized by the Swiss Academy of Humanities and Social Sciences (summary), Bas Savenije from Utrecht University made a very interesting comment regarding copyright of pre-digital articles.

1. Before the advent of the Internet, nobody did sign any contracts regarding the digital copies and their distribution.
2. The large publishers, ie Elsevier or Blackwell (now Wiley) scan in all their back issues without asking the individual owners, that is the authors.
3. Since they do not ask the authors, and we authors didn’t sign a respective contract, we do not need to ask the publishers to allow us using digital versions of our publications to disseminate them over the Internet.

This essentially restricts copyright of publishers for articles to a period before roughly 1996, or when the first digital publication showed up, which is also individually for each journal.

According to Peter Suber, “When this question came up in the US (for journalists, not scholars), the Supreme Court decided in favor of the authors. That is, if their old contracts didn't mention electronic rights, then the authors didn't transfer the electronic rights to the publisher”.

2007-03-06T06:13:00.000-08:00

If humans can't, at least machines talk to each other (2):

Future plans ...

The comment by Piotr Naskrecki (Director of Invertebrate Conservation at Conservation International ) about future development of the proprietary data in their recent ant catalogue CD-Rom reminded me about a blog I wrote last June TEAM initiative at Conservation International.

When I actually zoomed into their site, based on quiet some work on invertebrates, there is still no data accessible, just an announcement that there will.

TEAM is part of Conservation International, one of the lead institutions in the Conservation Commons, which signed up to make their data openly accessible.

A statement on making data accessible in another Harvard University Press based project with Piotr Nascrecki's involvement, Wilson's Pheidole, is since August 2003 up in the air with the same promise to be open access. Actions and access count, promises not.

2007-03-05T01:45:00.000-08:00

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

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

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

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

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

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

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

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

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

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

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

2007-02-22T06:30:00.001-08:00

EO Wilson recipient of the TED award 2007

On March 8, EO Wilson will receive the TED Prize. It is a very prestigious award by the 1000 thought-leaders, movers and shakers in Technology, Entertainment and Design. The winners receive USD100,000 and can formulate a wish which the members of the TED community pledged to help to fulfill.

Congratulations to Ed Wilson to yet another great award, another confirmation of his outstanding achievements!

Let’s speculate that Ed Wilson is going to fulfill his boyhood dream of an encyclopedia of life for ants. So, what would be needed to make this dream reality?

Ants are already on of the best documented group of animals in the world. There is an online catalogue of all the ants of the world updated as soon as another species is added to the currently known 11,981 species. This includes a digital library linked to from the species citations to pdfs of all the non-copyrighted descriptions. Currently, all these over 4,000 publications are being transformed to text by the Internet Archive, and the special mark-up schema, taxonx. is added for species and treatments or the descriptions of the species. There are an estimated 6,500 species documented with high resolution, magnificent standard images, even well worth printing in large scale and hanging them on your wall. Through Brian Fisher’s and Jack Longino’s superb collecting efforts in such biologically important areas as Madagascar and Costa Rica, ants have most likely one of the best documented surveys for any group of animals world wide, easily accessible online. The evolution of ants is well documented through large scale DNA-based analysis. On top of this, data aggregator such as ispecies are using mash-up technologies to collect all these information automatically – information which is added by a large, sprawling community worldwide. This infrastructure and its content already has a broad impact beyond the ant world, especially into education and other life sciences sectors

What is missing? There are three issues, that is building up and maintaining the global infrastructure, the transfer of legacy data, that is publications and specimen data into the digital realm, and the generation of new research as input into such a system, which .

TED could help make advances in each of these three areas. Most likely, the biggest impact, and one with an impact well beyond ants alone, would be to get the TED crowd to agree to build up a Digital Object Identifier (DOI) repository and resolver for all the systematics legacy publications, the descriptions of the species, the species names, and the specimens. These are the basic building blocks of systematics through which the entire information on animals and plants could be pulled together now, but especially in a semantic Web or Web2.0 environment. It would also be the best complement to the Biodiversity Heritage Library by the large US and UK natural history museums and institutions which will free knowledge hidden in millions of published literature.

Linking a statement with its evidence
Such a DOI based system would allow linking any comment made on the distribution or behavior of a species to its original observation or reference specimen with an attached Global Positioning System record. This will allow to pinpoint not only the proper name of and the specimen itself, but also its precise geographic origin which is living up to and can made the best out of high resolution satellite or map data, such as now publicly available at Google-Earth. Mash-up technologies would allow getting all additional information needed automatically, such as DNA-BarCode sequence, conservation status, studies on the biology or medical use or the increasing number of images and movies on Youtube or Yahoo as examples.

Open access to biodiversity knowlege
An agreement by the publishers to allow open access to all the articles in their journal covering the description of species, or even better biodiversity and conservation will have a similar impact as the applications of DOI’s. Alternatively, the use of specific mark-up in their journal articles, delimiting the description allowing automatic data mining and extraction and thus building up the global Encyclopedia of Life.

Imaging
Finally, taking images of all those groups of ants which are increasingly used in surveys and to measure the loss of biodiversity ought to be another priority, since images are by far the most important element to identify species. This would ideally complement ongoing world wide efforts by a rapidly increasing crowd of specialists and amateurs.

Getting this infrastructure up would enable anybody in the world, from E.O. Wilson in his little home town in Alabama to any place in the developing world to participate in this feast of knowledge and motivate more people like Awatif Omer in Khartoum to pursue the discovery of new species in such places like Sudan. The usage of all this information by the crowd, rather then expert’s opinion, would then decide what the most authoritative contributions are

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Catalogue of the ants of the World:
antbase.org (in collaboration with the Hymenoptera Name Server): literature digitized with partial support from the Atherton Seidall Foundation at the Smithsonian Institution.

Online scientific images of ants:
antweb.org
Costa Rican Ants
Ant Types at MCZ / Harvard

Mashups: ispecies

Biodiversity Heritage Library

Taxonx: an example of a systematics specific mark-up schema

An overview of the global ant community

2006-11-02T23:32:00.001-08:00

Open Access

During my research on an article on the value of "open access" I stumbled about a akward problem, that is how can I demonstrate the value of open access, which are products or research results which only are here because of open access. It seems to be a non-trivial problem, since my colleagues in the open access world, eg Peter Suber, don't have a list of examples at hand.

This list below is my dump for such examples which I hope to develop.

The wisdom of the crowds, or why more brains are more than their sum

Complex problems are more likely to be solved by many independent minds.
An initiative from a rather unexpected circle, the US Republicans, achieved that all the 48,000 boxes of documents seized since the March 2003 invasion in Iraq have been made public with the argument that "the nation's spy agencies had failed adequately to analyze the documents" and "that a wide analysis and translation of the documents (...) would reinvigorate the search for clues that Mr. Hussein had resumed his unconvetnional arms program..".
For the moment, the website "Operation Iraqi Freedom Document Portal" has been taken down because some highly sensitive articles have been found. New York Times, Nov 3, 2006 (U.S. Web Archive is Said to Reveal a Nuclear Guide)

mash-up
Mashups mix data into global service (Nature 439: 6 - 7(2005))

Open Text Mining Initiatives

This editorial from Nature gives an insight plus a couple of links.

"Editorial

Nature 440, 1090 (27 April 2006) | doi:10.1038/4401090a
Machine readability
Top of page
Abstract

A publishing initiative seems ready to make text mining simpler.

For many years Tim Berners-Lee, the inventor of the World Wide Web, has dreamed of machines being able to help humans use his creation. This would enable not only sophisticated search tools to hunt for words or phrases, but also for other engines to hunt for meanings and patterns. This 'semantic web' is being pieced together gradually. The latest step forward brings users of the scientific literature closer to that dream by enhancing computer access to the full text of the scientific literature.

Many scientists are used to the idea of data mining: the ability to plunder all the available databases to search not only for relevant nuggets, but also for unexpected combinations of data that reveal — or at least hint at — relationships and mechanisms. They are not so used to the analogous function of mining texts.

But some researchers have made a start. Biologists, for example, have developed software that explores open 'text bases', especially the PubMed database. They scan many publications in order to discover relationships based on phrases or sentences that, when analysed in combination, cumulatively link one object (such as a disease) to another (such as a molecule). At the University of California, Berkeley, the BioText project is being used to explore apoptosis, for example (http://biotext.berkeley.edu). At the University of Illinois in Chicago, the Arrowsmith software explores the causes of disease (http://arrowsmith.psych.uic.edu/arrowsmith_uic/index.html). And at the European Bioinformatics Institute near Cambridge, UK, the EBIMed retrieval engine explores protein–protein interactions (http://www.ebi.ac.uk/Rebholz-srv/ebimed/index.jsp).

But publishers have yet to develop a standard annotation of their content that allows computers access to the full text. Earlier this month, the Nature Publishing Group launched a preliminary proposal for such a standard. The proposal is not a commercial product but rather a potential service for the community. It is open for comment and is not intended to provide a competitive advantage to us: on the contrary, it will only succeed if adopted by other publishers.

The proposal is the Open Text Mining Interface (OTMI), which was first presented at the Life Sciences Conference and Expo in Boston earlier this month. A description and examples can be found at http://blogs.nature.com/wp/nascent/2006/04/open_text_mining_interface_1.html. The proposal would make coded text freely available to all. If all publishers were to adopt this or some similar standard, the entire literature would become accessible for mining.

If all publishers were to adopt this or some similar standard, the entire literature would become accessible for mining.

How does this proposal relate to publishers' various business models? 'Author pays' publishers would be able to use this approach to machine readability and help users find their content more easily. 'Subscriber pays' publishers would follow the Nature Publishing Group in making this version of the full text freely explorable by machines but unreadable by humans. (Charging for machine access across diverse publishers' firewalls would effectively make machine text-mining impossible.) The OTMI approach to encryption is to jumble up sentences, retaining semantic relationships as far as possible.

Critics will point out that this limits the machine readability too; for example, some proximity searching becomes impossible. But the subscriber-pays model is strongly supported in the marketplace. OTMI represents a potential compromise between business needs and open access. Nature and its publishers welcome feedback about this initiative, which should be sent either to nature@nature.com or to the above-mentioned blog."

2006-11-02T04:05:00.000-08:00

WTO and biodiversity (3)

Developed Countries Discuss Biodiversity IP Proposal At WTO; Peru Calls For Global Regime

At a recent World Trade Organization (WTO) meeting, Switzerland questioned an earlier proposal by Norway to link WTO intellectual property rules with the protection of biodiversity. But Peru, as one of the demanders of such a scheme, said it is highly needed.

http://www.ip-watch.org/weblog/index.php?p=442&res=1280_ff&print=0

The story includes also a link to peru’s new national, online genetic resources and traditional knowledge database http://200.121.68.202/portalCtpiWebApp/index.jsp

Source: Intellectual Property Watch (Nov 2, 2006)

2006-11-02T00:09:00.000-08:00

open access

A continuously updated news feed on open access is provided by the Open Access News
by Peter Suber.

following is a list of pro and cons re open access publications.

Pro
A reply to the "Börsenverein des Deutschen Buchhandels"

Cons
Fragen und Antworten des Börsenvereins des Deutschen Buchhandels. (in German).

General news article

I very concise description on open access has been written by Stevan Harnard in The Hindu, October 31, 2006.

2006-10-18T02:22:00.000-07:00

The importance of quality control and data maintenance in databases

Maintaining and updating a database

Examples:
Expunged criminal records and back ground checks:
".. enormous commercial databases are fast undoing the societal bargain of expungement, one that used to give people who had committed minor crimes a clean slate and a fresh start.

Most states seal at least some records of juvenile offenses. Many states also allow adults arrested for or convicted of minor crimes like possessing marijuana, shoplifting or disorderly conduct to ask a judge, sometimes after a certain amount of time has passed without further trouble, to expunge their records. If the judge agrees, the records are destroyed or sealed.

But real expungement is becoming significantly harder to accomplish in the electronic age. Records once held only in paper form by law enforcement agencies, courts and corrections departments are now routinely digitized and sold in bulk to the private sector. Some commercial databases now contain more than 100 million criminal records. They are updated only fitfully, and expunged records now often turn up in criminal background checks ordered by employers and landlords.

Thomas A. Wilder, the district clerk for Tarrant County in Fort Worth, said he had received harsh criticism for refusing, on principle, to sell criminal history records in bulk.

“How the hell do I expunge anything,” Mr. Wilder asked, “if I sell tapes and disks all over the country?”.."

New York Time, October 18, 2006

------
Biological databases.

On October 17, I found this entry of a biological specimen on Rod Pages semant blog, which was out in the sea (ants are no fish). I reported the error, and wonder how long it will take to clean it up.
Wouldn't it be much more helpful, if there would be a direct feedback mechanism, so that such errors could be corrected rountinely?

2006-10-17T13:44:00.000-07:00

On understanding flows

If wine makers can understand how the workflow, energy and waste management go along the creation of a bottle of wine, we ought to be able to do the same for understanding the flow of information in conservations projects. A case study from Italy, reported in the New York Time, October 17, 2006.

2006-10-11T06:26:00.000-07:00

WTO and Biodiversity (2)

some more on the discussion on biodiversity (genetic resources, indegenous knowledge) and its impact at WTO. The part below has been written by Tove Iren S. Gerhardsen (original source Intellectual Property Watch) October 10, 2006.

WTO TRIPS Council To Discuss Biodiversity (...)

By Tove Iren S. Gerhardsen
Developing countries say they will push their proposal on biodiversity and the European Union is sharply stepping up its call for enforcement, but otherwise the preliminary agenda of an upcoming World Trade Organization meeting on intellectual property seems to be reserved for “housekeeping” issues, according to sources.

The meeting of the Council of the WTO Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) is planned for 25-26 October.

As the overall free-trade talks arising from the 2001 WTO ministerial in Doha, Qatar have been in limbo since July, the issues in the TRIPS Council related to these talks are not expected to move, a developing country source said.

“Everything is quiet,” a Thai official told Intellectual Property Watch, adding that “even in the TRIPS Council” there seems to be a “mode of wait and see.” Little is expected to happen in the TRIPS Council until the general talks move in the area of agriculture and non-agricultural market access, the source said, adding, “I hope [the TRIPS Council meeting will be] short and sharp.”

A developed country official said that this likely would be a meeting on “housekeeping” issues, while an EU official said that many of the issues are “ongoing business” from previous meetings.

TRIPS Biodiversity Issue Returns

But another developing country official told Intellectual Property Watch that the six developing countries that tabled a proposal in May on the relationship between the Convention on Biological Diversity (CBD) and the TRIPS agreement regarded the upcoming council meeting as an opportunity to “bring the issue back” (IPW, WTO/TRIPS, 1 June 2006).

The official said that the six countries had not discussed the issue since the collapse of the talks.

The Thai official said that there are “lots of problems with biopiracy in Thailand,” despite the introduction of national laws two years ago, showing the need for international regulation.

The May proposal suggests adding a new Article 29bis to the TRIPS agreement. TRIPS Article 29 covers disclosure requirements of inventions for patent applicants.

The proposal suggests that it should become mandatory to disclose, in the application form, the source of biological resources and/or associated traditional knowledge, as well as show that authorisation has been given and that a benefit-sharing scheme for possible economic gain is in place.

At the moment, there is little these developing countries could trade this off with in a “quid-pro-quo” fashion, a source said. Some countries have suggested issues related to digital copyrights, which have been debated at the World Intellectual Property Organization, but some developing countries are not ready for that trade off, the source said.

The Thai official said developed countries had asked for proof of the occurrence of biopiracy.

2006-09-19T03:04:00.000-07:00

The Fourth Force:

Another Conservation International discovery of eden, this time underwater from the Bird's Head Seascape of Papua.

This seems to me to be a good example for the discussion about what supporters of the Conservation Commons ought to do. Is there an access point to sharing the underlying scientific and conservation data or information on CI's Web sites? I would say not at all.

I read in today’s Independent about this discovery and went to Conservation International’s Web site, and there it is featured on the home page.

It is a highly professional Website, nicely written and with all the necessary links to send free eCards, watch a video, links to older success stories, to see the spread of this report in the international news and requests for donations and to join CI, but there is nowhere a link to share data. In fact, getting access to data is impossible, such as to get a simple record of the species collected, the remote sensing data most likely analyzed to decide where to collect, not to speak of a way a machine could read it. Furthermore, the images are copyrighted and not under a Creative Commons license or under Conservation Commons principles.

I do not want to discuss the commercial appearance, but I question whether this can be made for a member of the conservation commons. This might be the moment, where the spirit of the Conservation Commons should show up. At the same time all the downloads and other PR material is being prepared, all the scientific and conservation data ought to be prepared as well and made accessible (together with all the reminder of CI’s conservation data), either on CI’s prime site, on CABS site, or any one ought to find. Without such a commitment, I wonder whether the Conservation Commons can seriously talk to anybody in the developing world to make their data accessible.

Conservation International or a report in the Independent

2006-09-14T02:05:00.000-07:00

Access related events to be watched

Broadcast Treaty
In Geneva this week, Gwen Hinze from EFF is presenting a joint statement from podcasters from around the world. This piece of internet history is an attempt to make sure that the development of the Broadcast Treaty into internet broadcast/netcast/webcast does not wipe out grassroots podcasting. More... [14. Sept.2006]

2006-08-28T00:54:00.000-07:00

Do not believe the industry and your government?

In the following, I am trying to collect reports on adverse developments for the environment hidden or only reluctantly reported.

GMOs:

Rice contaminated by GM has been on sale for months: US has been knowingly shipping banned food here [UK] all year. But only now do they tell us. Independent, 28 August 2006. [Aug. 28. 06]

GMO contaminated long corn rize appears in Switzerland. It is LL 601, which is even banned in the US. The large retail chains Migros and COOP stop selling contaminated rize. Neue Zürcher Zeitung, 13. Sept. 06 [Sept. 14, 2006]

Documents obtained by the Independent Newspaper show that the UK Watchdog might have given green light to supermarkets to sell 'illegal' genetically modified rice (LL601) dispite its annoucements to the public that the rice should not go on sale. Independent, 17. September 2006. [Sept 17, 2006]

Access to Content or the Idea of a Commons

Puneet Kishor makes an interesting point about the rise of commons (Babel of Licences) leading to a complete chaos doing the opposite of what it aimed for: open access and sharing within communities. There is also another side to it: subscribing to a commons, but never live up to it (see The Fourth Force).

Here an example.
Recently, sometimes in August 2008, Zoobank had a soft launch of their new Website relying entirely on Thomson Scientific, the owner of Zoo Record, a commercial publisher. There is an undisputed need for a comprehensive authoritative list of all the species on our planet, and there were many discussions with Thomson, so they would know what the specs for such a service are. There are now plenty of Name Servers out there, allowing scrutinizing for pitfalls but also commonalities.

Instead of being proud to be one of the world's foremost provider of biodiversity information, Thomson released in collaboration with the International Commission on Zoological Nomenclature an unbelievable crumy first version fraud with errors and clear unwillingness to even serve a complete scientific reference.

This shows view points. ZooRecord has a very poor name server with many errors in it, and thus shows the need of a body of scientists cleaning it up - a work it clearly is unable to do. ZooRecord is using the cooperation with ICZN to foster their own commercial goals: There is much better data within ZooRecord, but they are not even willing to share a complete reference, not to speak of the adequate one. It seems very odd to display few (incomplete) referenecs which have nothing to do with systematics, which must be considered teasers indicating that ZooRecord has more to offer once you enter their business site. There is certainly more information in it, but the service is not complete, since it doesn't cover all the publications and there is no up to date name server.

Without doubt, the lack of a comprehensive list of the name of the Earth's organism has to do with the complexity of the task. Great names do not solve this problem, nor computing technoloy and business. The scientific community needs to be brought together into the task. This needs tools to allow collaborations, to find new ways to give credit to be put into your CV, and it needs funding agencies which do invest into a bottom up approach aiming at populating specific databases and linking them up, not only between the specific databases, but also with the rest of our scientific knowledge. Mashups, such as Rod Page's ispecies might be a way to go. We need also to come to grips to realize the potential of systematics as megascience, that is more than 6,000 specialists working on charting the species of planet Earth. If the scientists would pool their knowledge, Thomson could not act the way they do right now. [Sept. 06, 06]

Cimate change and the extracting industry

The UK Royal Society contents that EXXON MOBILe is spreading „inaccurate and misleading“ information about climate change and is financing goups that misinform the public on the issue. New York Times, September 21, 2006 [Sept. 22, 2006]

Environmental Record: unlikely candidates

"It sounds an unlikely scenario: a couple of prominent Hollywood liberals honouring Wal-Mart, the world's largest retailer and much-criticised corporate bogeyman, for its contributions to the environment.

And yet that is what transpired on Monday. Lee Scott, Wal-Mart's chief executive, found himself fêted at a dinner reception at New York's Rockefeller Plaza courtesy of Bob and Harvey Weinstein, who called him "a great role model for those of us who care about the environment".

Independent, October 25, 2006 (posted October 25, 2006)

Extracting industry

Rio Tinto

"The business-friendly Malagasy government, led by the self-made millionaire Marc Ravalomanana, has recently given the mining giant Rio Tinto permission to start work in the region [Ilakaka], a move described by the director of Friends of the Earth, Tony Juniper, as "very sad and very bad news for the people of Madagascar"." Independent, Nov 3, 2006: Kim Sengupta

2006-08-27T14:33:00.000-07:00

The new piracy: how West 'steals' Africa's plants

The article in todays Observer (Sunday, August 27, 2006; article) on biopiracy is quiet revealing in terms of the industries position (or at least those cited in the article).

First, one of the companies cited (Phytopharm) claimed, that the specific tribe was already extint, and then its CEO makes the point of what a pitty it would be, if this traditional knowledge would die out as these people become westernised.

Five years ago The Observer became the first newspaper to reveal how the British drug firm Phytopharm had patented an active ingredient in a plant called hoodia. This is a cactus-like African plant that is used by the San bushmen in South Africa to ward off hunger before hunting trips. Phytopharm has linked with Unilever to market this product, now being developed, as a diet drug. Unilever has agreed to pay up to £21m to Phytopharm, which originally claimed the tribe was extinct.

'In any case it takes a huge effort and a lot of money from recognising a particular property in a plant and developing it into a drug. It can cost between $200m and $500m [£100m-£250m]. If companies could not get the protection of a patent then they simply would not bother. Then what would happen is that the traditional knowledge of these communities would die out with the people or be lost as they become westernised.'

2006-07-13T01:38:00.000-07:00

Biopiracy and music piracy

What has biopiracy and music (or internet) piracy in common? Both have to do with the volatility and uncontrollability of their products, a gene and a digital medium respectively.

Once a gene is discovered, its origin can hardly be identified, and derivatives can be produced and sold far beyond the source of its origin. One a piece of music is on the Web, its dissemination can not be controlled. And in both cases, the "owner" fight tough battles to keep control to secure financial returns.

Just the roles of the players is changed. Whilst big industry is trying to fight an all out war against music piracy down to ruining individual students with well publicized court cases, big industry is opposing strenuously the declaration of the sources of genetic material. They even risk to have this as a cause that the current WTO Doha round is failing.

2006-07-11T04:48:00.000-07:00

Blackwell Launches 3000 Years of Digitized Journal Backfiles

The current issue of Blackwell Publishing Journal News (July 2006, page 15) has an article about their strategy to opne up their huge archive.

As much as it is advantageous to have more and more digital journals, the more the divide between those having something and those having nothing widens, since hardly any of the content is free. Furhtermore, having access to 3,000 years of journals means, that in fact Blackwell opened for themselves another stream of income, this time not claiming copyright but the effort spent to digitize the content. In fact, this has the same effect as copyright.

Since Blackwell asks individual societies for paying the costs of scanning, if they want to have their journals open access, one could argue at the same time, that Blackwell ought to pay each society a royalty if they sell an article. All the content has not been generated by Blackwell, and thus this is not a fair deal. It might be there is more language hidden in contracts, but this is not to be found in the article.

I would also argue, that this development is undermining the success of the Biodiversity Heritage Library.

Finally, the advantage of open access is only on a very short time access to
pdfs: the real impact will yield tools such as open text mining, which are prevented by Blackwell's behavior - a behavior that could or ought to be changed.

An additional comment regarding open access is on Peter Suber's open access blog

2006-07-06T02:03:00.000-07:00

Should you open your mouth?

Read Noss recently made the point at the Society for Conservation Biology meeting in San Jose (California), that conservationists should approach law makers and suggest policies. Not everybody agreed, but about 70% of the participants questioned supported it. The reminder objected because good conservation and science is what is changing the world (Nature 442, July 6, 2006)

If conservation would be perfect science, and its policy suggestions would immediately become law, then conservationists ought to be very restrained in entering the field of policy making. However, there are so many other forces entering the path of the creation of a new law, that it is rather important, that policies should be drafted and entered from the conservation community. They even ought to be present and sreening emerging new laws on its impact on the environment. Why else is lobbying such an important instrument in policy making?

Within this process, it is clear, that poor science or biased conservation has its own corrective. If the industry or any body else can pick apart an initiative easily, the creator of it will loose quickly his credibility - one she had to build up over the years and of which she is probably very protective. Again, the conservationists do not have the huge financial interests and the necessary resources to be present in the policy making arena, which furthermore limits the influx of environmental interests: thus if one has the urge, one should go ahead.

2006-06-29T06:43:00.000-07:00

Marsh Arabs, Island Biogeogrpahy and the importance of details

In a recent paper, Richardson and Hussain (Bioscience Vol.56(6), June 2006, pp. 477 - 489) discuss the current situation of the Marshes in Southern Iraq. Besides the humanitarian and environmental disaster, their report has some details of interest for the discussion on biogeography, conservation and restoration biology.

In the introduction, the authors state, that the entire 15,000 square kilometers of marshes have been destroyed under Saddam Hussein. This is not entirely true.

Saddam could only succeed in this project, because the Eurphrat had extremely low water caused by massive damns in Turkey, and water diversion by Syria. The capacity of the turkish reservoir is about 5.5 times the annual amound of Euphrates discharge. And thus the future of the Marshes depends on politics as well, not just snow.

Unlike the authors mention, the marshes have not been entirely destroyed, about 5% always left according to satellite data (see also the area in the Norteast of the satellite picture on page 478). So, the idea, that there was nothing left is not right from begin. But the data is all from satellites with a resolution of 28meter - what about all the small fragments? From a European perspective, exactly these sorts of minute habitats are important. The hedges or the many small isolated ponds for the survival of Amphibians. Only when they disappear, the genetic pools diminishes. In none of the reports on Iraq, this is an issue.

The repopulation of the 39% of the marshes is also interesting from the point of view of Island Biogeography, where at 90% of destruction roughly 50% of the species ought to disappear. But this is not the case here in Iraq, nor in Central Europe or the Atlantic Forest in Brazil. Obviously, the simple, mathematical representation of island species numbers does not real take into consideration heterogenous landscapes. If, as the other mention, the entire ecosystem has gone, then there should be nothing left.

The presence of the species they observe ought then rather be an indication, that for proper ecological studies we need more focus on minute fragments and most likely heavily degraded bits, or, like it is the case in the Semien mountains in Ethiopia, the small sanctuaries including leftovers of native vegetation around sacral sites. But this, acknowledgingly, is difficult to do in Iraq, where moving around seems only be possible at great risks.

2006-06-29T04:52:00.000-07:00

Blagging in the blogosphere, or why bloging is necessary and good

Richard Ladle compiles often heard points about the blogosphere trying to sort out whether blogs are good or bad in a recent contribution to the Green Room at BBC-. He looks essentially at the green environmental sphere. He argues from the point of view of a very well established news group (the BBC), a point of view, which could easily be taken from the science or conservation itself.

He concludes, that if the established journalists don't act quick "we run the risk of creating a generation of eco-illiterate consumers and voters at a crucial time for the Earth's diminishing resources." But isn't that, what the media does with us anyway? There is very little coverage in the news about environment, which can be the highly selected, thought-to-be-digestible-for-consumer parts of a buffet of daily environmental news. And this buffet is already a choice of offerings hardly representing what's happening out there. Why else have all the large environmental NGOs, and in fact any larger organization, such a strong, professional media department? What is at the end more important, yet another high level meeting of politicians and high level conservationists talking about Africa, or a high caliber meeting of the biologists and conservationists studying Madagagascar at Duke university, talking specifics about Madagascar - a prerequisite of well-informed, and thus hopefully sustainable development. One is in the news, the other completely missed.

In a more general term, one could argue that it is not obvious that the more established a source is, the better it is. The most blatant case being our news reporting uncritically the lies of the Bush administration leading up to the war in Iraq and its early phase. This could also be argued for science itself: see the debate on climate change or GMOs, and the willingness of some scientists to work for particular interests, such as the extracting industy.

The solution I envision is rather that we must be lucky that we do have blogs. We are certainly in a nascent stage in its development, as opposed to a well established stage of our current sources of information. But then, individual meanings are not the final truth, and it is indeed a question, whether the politicians, the economy or the civil society ought to have the last word. With other words, an ever complex information highway most likely reflects much better a complex world.

What we need though, and that is certainly the challenge for the future, are tools to mine all the different bits of information and to visualize the results: What is the issue? What are the points? Where is it? What interests do the sources represent? This goes along the line, that there has been never before a greater responsibility on individuals to be more discriminating news consumer.

2006-06-26T05:36:00.000-07:00

TEAM initiative at Conservation International

Conservation International's TEAM (Tropical Ecology, Assessment & Monitoring) Initiative has the potential to be an initiative to integrate observation data and systematics into a cutting edge conservation project. Furthermore, it is organized from one of the most successful international NGOs (Conservation International), and thus might have the necessary resources.

When I recently visited its Web site and looked at the list of the participants at their recent TEAM meeting in Brazil, read through their manual (exaclty those on ants, a domain in which I have some knowledge), and went through my disussions I had in Brazil last November at the Simposio de Mirmecologia, some fundamental questions came up. Obviously, there must be a lot of money available to fly so many people, including top journalists, to such a meeting.

At the same time, there seems to be by far not enough money to process, identify and store the specimen. The two liner attached to the section on specimen processing and identification for ants represents almost prefectly, what will be a serious flaw endangering the entire ant part of this project, and I to some extent the future of the inclusion of invertebrates into global surveys and monitoring programs.

"Specimen processing and identification
Samples should be identified by an expert taxonomist, or under the supervision of one. Details regarding this process will be specified in later versions of this document."

In all the current leaf litter projects around the world, the identification of specimens is the bottle neck. And this in projects, where there is over ten years of experience (Fisher in Madgascar, Delabie in Bahia, Brandao in Sao Paulo, Longino in Costa Rica). If at least all those few specialists would have been involved in TEAM (and appropriately paid, so they can spend prime time on the project) then this could lead to synergisms - but this seems not to happen.

Synergisms would also arise if more thought would be given to sharing knowledge on ants. Working on ants has one advantage, that the IT infrastructure is one of the most elaborate for any taxon world wide:
- The entire catalogue of all the 11906 species of ants is online available at the Hymenoptera Name Server;
- almost the entire body of descriptions of ants is online (ca 80,000 pages, linked to the catalogue );
- specimen databases using digir, and thus linked for example through GBIF exist (eg antweb.org);
- species pages including cutting edge imagery exist (e.g. antweb, which allow to go back to the single specimen, literature, bibliography (antweb.org) or even including other relevant information such as gen sequences, but always based on the original specimen (ispecies.org). This is far beyond lists of species per region or simple images of specimens.
- Effords are on its way to extract all the information from the original literature (dig lib), leading in the development of specific xml mark up schemas for literature.
- Character matrix manipulation tools exist, including a large data set of morphological characters and thousands of SEMs are available, which are soon being released.
- There are even tools to up- and download leaf litter sample matrices, linked to specimen, and specifically designed to complement the Ants: Measuring and Monitoring Biodiversity book used as baseline for the TEAM ant monitoring protocol.
- CEPLAC in Brazil has itself establisehd as a fine resources for identification of Neotropical (especially Amazon Basin and Mata Atlantic) ants, similarily to the Zoological Museum in Sao Paulo, similarily the Bibikely Biodiversity Research Institute in Madadgascar, or the ANeT organisation in Asia.

So, how can TEAM explain, that it is not tapping into these resources?

Collaboration with other ant teams world wide would also allow integration of ants into related initiatives, such as analysing CI's hotspots, countdown2010 (eg through the Sampled Red List Index).

But none of these resources seems being used, and thus, with all my optimism, I can not see, that this part of the TEAM project has a chance to florish, which would be a tragedy beyond CI-TEAM.

2006-06-26T03:26:00.000-07:00

The Fourth Force: Control

The Independent online reports on June 25, 2006 an interesting story along the line, that Blair recognizes, that an independent force is needed to police (in our case rather control) pledges made to Africa at Gleneagles last year at the G8 meeting (Geldof is called in by Blair to police G8 poverty deal). The group will most likely be financed by the Bill and Melinda Gates Foundation.

The reason being, that too many pledeges are being made at prime time time, but later, only few of them are kept.

It includes also a statement, that Bill Clinton is too old for such an active role.

We should look into this for biodiversity conservation. We too had a large conference with all the top brass in Paris (Biodiversity, Science and Governance, January 24-28, 2005) convened by the French president Jacques Chirac), inlcluding comments by various minister, that the biodiversity issue will be brought up at Gleneagles. It didn't happen. Conservation International just run one of their global symposiums, this time held in Madagascar "Defying Nature's End: The Africa Context" on June 20-24. What is going to happen? How can we make sure, that we do not forget, and that we actually measure the success of such a conference? The US just designated nearly 140,000 sqaure miles, the largest marine reserve in the World (Science, June 23, 2006). Is the reserve big enough and do we know enough to ask such a question, not to speak how to monitor? The authors of this editoral suggest, that we need much more resources at a scale, not now available, but need increased international cooperative efforts.

An obvious important element is that scientists and conservationists change their culture and share data, write this into their mission statements and deliver. But, it seems, that unless we too start to look into a similar policing practice proposed for Africa, and headed by Bob Geldof, this might not happen. Why not get a biodiversity police headed by Harrison Ford?

2006-06-26T01:09:00.000-07:00

Harnessing the Wisdom of the Crowds

Recently, Perry Peterson sent me a copy of a lecture by Peter Nicholson (President of the Canadian Council of Academies) title Harnessing the wisdom of the crowds: the new contours of intellectual authority. In this paper he is essentially arguing, “that what qualifies as intellectual authority in contemporary societies – who and what to believe – is changing fundamentally”. His thesis in a nutshell is this. “People today are much less prepared to defer to the experts. But at the same time, we are being swamped with data and information – a glut that cries out for analysis and summary. So there’s a dilemma. Who to turn to? Increasingly the answer is – Well, to ourselves of course, as individuals empowered by a world wide web that has rapidly evolved into a social medium. More specifically, it is a medium that today supports massively distributed collaboration on a global scale that – we can only hope – will help us make sense of it all.” His thoughts are highly influenced by James Surowiecki’s The Wisdom of the Crowds, and Mike Kapor’s notion of massively distributed collaboration.

This is exactly the dilemma where biological systematics and conservation is stuck. Traditionally, we all rely on expert opinions, some of it well documented with detail down to one single specimen, and thus single observation or collecting events. Others are very cursorily, and only a name of a species is available, because all the rest is kept off the crowd by copyright, and when you get finally the original publication, you find only a very rudimentary summary information, such as “Central America”.

Similarly, the important RedLists of threatened animals and plants is for believers, since it is not possible to get to the base line data, which in many cases is hidden in somebody’s brain or drawer, to be opened only for good friends or money. There is no way, a RedList, or even the more advanced global amphibian assessments would hold out against such a scrutinzation as current climate model do (see for example the debate in the New York Times, June 23, 2006 Panel Supports a Controversial Report on Global Warming”).

In all the cases, it would be much better, if all the data would be open access, and anybody could have a look at the data. Google Earth just illustrates the limitation of the approach described above. Whereas we can now look at almost any place in the world at a 25 Meter pixel resolution (a single reflectance value on the ground at 25 x 25 meter square), we are made to believe that an animal or plant is living somewhere in Central America.

If I am a local naturalist, or working at San Diego Super Computer Center, I want to have the highest possible resolution of the data. As naturalist, because I want to rediscover this organism, and add more observation, especially, if this is an endangered and not well known species. As somebody with powerful computer support, I would like to model and understand the niche of this species. I do not want to go and ask first somebody to be so nice to give me the data.

Perry’s company Pyxis Innovation can play a very important role in the transition, if they (and GBIF who is paying to develop a data viewer) come up with a tool allowing to find and visualize specimen and ecological data. If they even provide, or integrate existing analytical tools, such as those offered at CRIA, then we’ll improve our science tremendously, leverage the support of the crowd, and at the same time, we could much better control, who actually is providing access to their data. And this is needed, if we do want to be able to create something like a global biodiversity monitoring systems.

Since there is no standard in peer review of systematics data, the simple access to all the raw data will probably the single most decisive factor to improve the knowledge of our species, since this allows at least to criticize any piece of scientific work.

If Rod Page get’s his way with ispecies, his mash-up approach, we actually would have also a way to bring together on one page all the relevant information on a particular species, such as its DNA, images, distribution records, literature, etc (see semant, and a ppt there on this issue).

2006-06-22T14:09:00.000-07:00

Access and Benefit Sharing - a Swiss view

The Swiss Academy of Sciences has just published a hard cover version and a Web version of a "Good practice for academic research" to ensure that Swiss academics act according to Access and Benefit Sharing as defined in the Convention on Biological Diversity and its follow-up.

Having done a lot of fieldwork in the tropics, participating in the follow-up of the Convention on Biological Diversity (CBD), and working in some of the world largest natural history museum's environment, I find this is not an adequate response of the Swiss Academy of Sciences. In fact, I find it rather patronizing rather than in support of science. It is not, that I disagree with ABS (see comments about open access), but sc-nat and official Swiss policy in this field.

CBD has three main objectives, the conservation of biological diversity, the sustainable use of its components and the fair and equitable sharing of the benefits (...). The North normally considers the first and second objectives as the relevant ones, but the South sees considers the last as the most important objective, to an extend that it can be looked at yet another tool to get money from the North to the South. It is the South' colonial history which makes them very sensitive about being exploited again, especially since in the late 80ties and early nineties the genetic resources in biodiversity rich areas have been used to argue for their protection. Bioprospecting has been, and still is an important word, but also one, that does hardly deliver (see Nature's Rex Dalton's story about bioprospecting and InBio in Costa Rica, Nature 441, 567-569) ). But the ghosts are out of the bottle.

Switzerland has a peculiar set up with its natural history collections. Due to the federal structure of Swiss museums, and the lack of Swiss Natural History Museum, there is no strong voice for systematics at national level, and indeed the Swiss Science Foundation has no track record for supporting the main contribution of natural history collections to biodiversity conservation and research, that is monographic work. Clearly, with its strong bias on 'hypothesis driven' research, SNF dismisses an entire field of research which is at the base of many of the ecological and conservation work. At least, the conservationists recognize that without such research, a substantial part of ecological and conservation studies are up in the air (see eg Maze, 2004)

Since the delegation at the COP (Conferences of the parties, or in more plain text, the so far eight follow up meetings of the governments of the Convention on Biological Diversity) are not scientists but led by diplomats and administrators, be it here in Switzerland or in Brazil, biodiversity is rather perceived as a commodity rather than what it is, a very complex, little known piece of our planet earth which needs protection. A recently raised issue by the governments of Brazil, India and others at the current Doha round of the World Trade Organization (WTO) is about the issue of Access and Benefit Sharing, that is the declaration of the origin or genetic material, which is heavily fought by the developed world.

Furthermore, the development of protocols for ABS does not live up to another goal of the CBD, monitoring (Art. 6 of CBD). This in fact demands surveys of relevant parts of biodiversity. If, like the Swiss Government, puts all its efforts into ABS, and doesn't contribute at the same time substantially to resolve this issue, than I see this Swiss brochure as very short sighted, if not contra productive to the idea of the CBD. It is to nobodies avail, if areas such as legal Amazonia is out of research, whereas at the same time huge logging concession are provided.

Switzerland ought to be much more pro-active. We have one of the six globally most important botanical gardens here in Switzerland (Geneva) with hundred thousands of types, desperately needed to chart and monitor global biodiversity (see Swiss Biodiversity Hotspot). By making these resources globally accessible, which is technically no problem any more, we could also gain a heavy weight in the discussion about collecting permits for scientific collections (and monitoring) and the separation of permits for bioprospecting. But siding with the industrialized countries in the WTO to avoid reference to the origin of genetic material, and a luke-warm position in the question abut terminator crops, we behave exactly the way the developing world is afraid of.

2006-06-21T02:41:00.000-07:00

Do we need a Forth Force?

Sometimes in the early 70ties, NGO's and grass-root movements have become a power, the Third Force, with impact on governmental and industrial actions, and thus could bring change. Today, NGOs are often a force listened to (e.g. Human Rights Watch or Amazonia), or at least on paper, have to be listened to. In many cases, large NGOs have more brainpower than many of the parties (governments) in international meetings on the environment such as the follow up meetings of the Convention of Biological Diversity, a topic I am interested in.

It seems to me though, that the step from a small grass-roots movement to a large international NGO, such as highly successful Conservation International, comes at a cost: More and more money needed to maintain their business is from large philanthropic foundations with their own agenda. Thus the independence of the NGOs operation is at least partially lost, even if its just because an emerging area is not yet on any of the funding agencies palate. Increasing the size needs more specialists. People doing properly fieldwork are often hard to find. Collecting data in the field was never high on the agenda because one cand get away with reliance on "experts". Finally budgets are very tight for this sort of work. At the same time, getting larger means more administrative personal, including a expensive counselors to avoid the cliffs of expensive legal battles, thus overheads have to be used respectively.

An article in yesterdays Independent on the number of giant pandas shows the difficulties to even get the figures right on the abundance of one of the most emblematic species in the world, the Giant Panda. How can a number of living organisms just double - a similar fluctuation being known in measuring the Tiger populations in

India

? In the case of the Giant Panda, the reason for this correction are inadequate methodologies to study the animals. Only the reliance on DNA collected in feces helped to figure out, that there are as many as double the number of the hitherto assumed specimens in the wild.

If this happens to one of the best studied organism, how can other figures be trusted? How can we document, how many species are disappearing, or that we actually have a successful program to decrease the rate of loss of species, as we ought to do according the Target2010?

What about the quality of the few numbers of global surveys, such as the global amphibian assessment, delivering a widely cited dismal outlook on the state of amphibians and our environment? To run a proper monitoring program, ‘hard’ figures ought to be out there and accessible to anyone, so that the analysis could be done independently, and that changes could be detected by comparing existing with a more recently assembled data set. But this is not the case, because the entire set up for the amphibian assessment relies on expert opinions, drawing circles to define the range of a particular species, discarding the original observations. The one single most significant advance in the amphibian assessment is, that it is an effort including up to 600 scientists world wide.

Supposedly, the original data is on the Global Amphibian Web site, but it is not there. This actually demonstrates a couple of other crucial impediments in conservation. It is one thing, to mention that data is accessible - something which ought to be done because donors such as the US National Science Foundation demand it, and then actually do it. Being one the interim steering committee of the Conservation Commons initiative, I (and some others) ponder for a while now how to deal with this problem. There are all these institutions signing up on the principles of the Conservation Commons, but then who actually provides access? May be it is the wrong approach that institutions as such can sign up, which gives weight to the initiative and in return allows them to use the CC label. May be, one should only be allowed to sign up products, like in the Creative Commons. This way, the Global Amphibian Assessment would have to make their data accessible and we could get access to the data of Conservation International and other signatories.

If we are really concerned about our environment, then we ought to do our best to fight against its decline. Certainly sharing data is one element which is, in my view, the most powerful new asset given to us by the digital revolution. See for example google Earth’ impact on innovation, or for a bit a more professional use, what the Global Land Cover Facility has to offer.

Access to data, and ingenious users, would allow shifting power to a new, Forth Force of highly independent groups targeting environmental issues right on the spot with the most advanced tools, and at the same time allows assembling and addressing local issues within a global perspective, to mitigate the effects of the governments’ and increaslingly global industries’ action on the environment in places where they are listening, and in ways the now classical NGO can't do anymore.

2006-06-19T04:25:00.000-07:00

The EO Wilson Biodiversity Foundation

It is certainly good news, that on June 23, the EO Wilson Biodiversity Foundation is being launched in New York in a rather glamorous setting, the Tavern on the Green in New York’s Central Park. It’s especially good news, that in a time of great biodiversity loss, EO Wilson, a retired Harvard Professor rated by Time Magazine as one of the most influential US citizens, comes up with a foundation, with a board full of Nobel Laureates, entrepreneurs and other successful people.

It is the logic consequence of EO Wilson’s highly successful scientific and public career, and indeed modus operandi, to lend his name to a foundation created by highly successful businessmen in biotech. Wilson was an early advocate that we need to protect biodiversity, because, among others, of all its yet unknown genes and thus value for humankind. This was in 1987, and since then, we still struggle to produce even a simple list of organisms, not to speak of proper monitoring programs to assess the change of the world’s species. Despite a brief high-noon around 1992, the time of the Earth Summit in Rio, conservation of biodiversity has been dropped of the screen of politics and industry.

The Rio Earth Summit in 1992 led to the Convention on Biological Diversity ( – not signed by the US, but 150 governments worldwide) – has been hailed as a step towards the conservation of biodiversity, but not by all. The developing world, where most of the biodiversity is, was much more interested in Access and Benefit sharing of all the many valuable genes out in their backyards, who could lead to substantial revenue, as EO Wilson Foundation’s CEO Jay M Short point out. That this is still a main issue has recently been demonstrated under the lead of Brazil and India who asked for an amendment to the WTO’s intellectual property agreement to disclose the origin of inventions using biological resources or traditional knowledge, against the will of many of the industrialized nations (see), and which could be one reason of the current Doha round of negotiations failure.

Another reason of the dismal state of biodiversity knowledge and conservation is the failure to build adequate infrastructures to measure, monitor, access and communicate its state. There is on the one hand hardly any connection between the bio-systematics community (those able to discover and chart to worlds living creatures) and the conservation community. On the other hand, we systematists still struggle to change our culture from very introverted scientists to extroverted, from single project oriented, focusing on few taxa to an emphasis of being a member of the megascience project “Global Biodiversity”, as Sandy Knapp puts it. There are such structures being built (eg. Global Biodiversity Information Facility; the Biodiversity Heritage Library, and Zoobank and Ubio as name server. Conservation Commons (conservationcommons.org) and Science Commons both work towards a licencing system allowing building up a global semantic web, that is an open access based information network needed to link all the bits of information. These activities are not mentioned anywhere in the documents of the EO Wilson foundations currently available online.

Wilson himself has a dubious record in terms of practical achievements. He is clearly not a builder of organizations. There is no Wilson legacy in terms of a prolific institution, such Peter Raven's Missouri Botanical Garden and initiatives. The All Species foundation, under guidance of Wilson, disappeared, to a large degree because it's utterly unfocused strategy. His highly praised effort of building up an Encyclopedia of Live is undermined by siding with Harvard University Press to retain the copyright on his systematic work (see…"The last of its kind"). Searching new ways of funding and doing things is certainly laudable, but to “include academic experts on population genetics and evolutionary theory as well as business-school trained entrepreneurs”, questions whether the work can be done, since none of them has credentials nor experience in the complexity of assessing biodiversity and conservation, nor working with the respective scientific community.

It is great, that such a high-powered new initiative is on its way. Let’s be optimistic once more, and watch how they operate, and whether this will developed into a serious effort enhancing the megascience project “Global Biodiversity” and its conservation, or just another misinformed initiative to whitewash the hands of people generating their money and fame from biodiversity. Lets use the Internet watch this new foundation's actions unfold.