Tuesday, June 29, 2010

Barcode of Life to rival GenBank? Really?

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.

Wednesday, June 09, 2010

Canadian Biodiversity Information: A review

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.

Tuesday, June 01, 2010

iPad and open access (to what we do)

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."