Last year I did some work on a prototype system called speciesindex.org but have just taken it down and abandoned the idea. You may have reached this post via the speciesindex.org domain as it will probably resolve to here until I use it for something else.
Here is how speciesindex.org was described on its one and only page: Continue reading »
I am not sure how to say this. Either:
The distinction is a big one. Saying I had a paper published implies the blessings of my peers. This is more like vanity publishing or even ‘stupid’ vanity publishing as the whole thing is open to comments and voting. My inflated but fragile ego will likely get punctured by negative comments or worse (and more likely) by total apathy.
I did some work last year on merging occurrence status vocabularies for the PESI project and, as I really wanted to make use of OWL in some way, I attempted to do this by creating a set of related ontologies then using inference to produce a magical-semantic-merging of them all. As this was a new thing for me I wrote it up as I went along. Continue reading »
These are some figures I culled from Arthur Chapman’s excellent Numbers of Living Species in Australia and the World. The numbers speak for themselves really.
| Taxon | # Known | # Estimated | % known | # To Do | % of Problem |
| Chordates | 64,788 | 80,500 | 80.48 | 15,712 | 0.17 |
| Invertebrates | 1,359,365 | 6,755,830 | 20.12 | 5,396,465 | 57.16 |
| Plants (excl. Algae) | 297,857 | 390,800 | 76.22 | 92,943 | 0.98 |
| Algae | 12,272 | Unknown | Unknown | Unknown | Unknown |
| Fungi | 98,998 | 1,500,000 | 6.60 | 1,401,002 | 14.84 |
| Others (microbes) | 66,307 | 2,600,500 | 2.55 | 2,534,193 | 26.84 |
| Totals | 1,899,587 | 11,327,630 | 16.77 | 9,440,315 | 100.00 |
I have highlighted in blue the percentages for which DNA barcoding of some form is either a working tool already or likely to be the only practical solution i.e. more than 99% of unknown species. It is hard to imagine the micro algae yielding significant morphological characters ahead of some useful bar coding regions being developed.
Of course one could argue that this isn’t worth doing at all. There is no reason why we have to catalogue every species. Why would one want to create another ten million latin binomials?
I just completed my first weekend on the MSc in Mindfulness Based Approaches at Bangor University. It was a wonderful three days. I enjoyed communing with like minded people and learnt a great deal – notably some of the major differences between psychology research and taxonomy. In response to one of my questions the lecturer pointed out that most psychology research papers are out of date within two to five years and so there is no point in building a big bibliographic system. Taxonomists struggle to maintain their 250 year back catalogue.
Surprisingly I am once again the proud owner of a student card! I hadn’t thought I would be presented with one. It could be useful for a discount in the pubs in Edinburgh.
Being back at my desk and in the world of biodiversity informatics feels a little jarring. How on earth could I be motivated to pursue both the technicalities of biodiversity assessment and the therapeutic applications of mindfulness meditation? Fortunately I get enough email each day for an answer to be embedded in one of them.
Purity and Prejudice: Deluding Ourselves About Biodiversity Conservation by Douglas Sheil & Erik Meijaard (DOI: 10.1111/j.1744-7429.2010.00687.x) goes at least part of the way to making the link. My favourite quote is:
Legitimacy requires appreciation not only of biological diversity but of motivational diversity. Listening and engaging are essential in effective conservation and we should be willing to accept priorities that do not favor our own personal views and beliefs over others.
If the central tenet of this article – that we are unwittingly influenced by our notions of ‘tainted-nature’ – is true then it follows that we have a responsibility to look inward and work out what our real motivations actually are. I would argue that we can only understand this by putting discursive thought to one side for at least some of the time to live with our raw experience. How can we possibly hope to take our own motivations into account if we don’t have a systematised method for discovering them that goes beyond a sentimental response to our own likes and dislikes?
Just back from TDWG2010 where I gave a talk on the use of standards in PESI and the prospect for stable identifiers for taxa. The take home message was that if we bind the identifiers to nomenclature then the identifiers will not be stable. You can see the presentation as a PDF here: PESI Standards & GUIDs, Roger Hyam (Natural History Museum London) & Yde de Jong (University of Amsterdam)
In side conversations with the guys from Encyclopedia of Life and Barcode of Life I wondered whether we will eventually gravitate to using EoL page URIs as identifiers for taxa globally – combined with barcodes for normative identifiers for those taxa. It would be simple. It would remove the need for complex nomenclatural databases.
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