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Sherborn: Pyle - Towards a Global Names Architecture: The future of indexing scientific names

by ICZN on Nov 04, 2011

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In 1758 it was feasible to create a catalog of life using ink on paper. Today, it would require the equivalent of nearly 264 volumes of Systema Naturae to achieve the same thing. Or, you could fit the whole thing on a tiny memory card.
In 1758 it was feasible to create a catalog of life using ink on paper. Today, it would require the equivalent of nearly 264 volumes of Systema Naturae to achieve the same thing. Or, you could fit the whole thing on a tiny memory card.
This is a typical species accumulation curve. Over time, the cumulative number of species approaches an asymptote, which is the predicted total number of species. But if we look at actual data over the past 250 years for fishes – a group that quite recently many believed was approaching that asymptote…
… we see a rather striking pattern. Not only is the accumulation curve not leveling off, it’s actually rising more steeply. This major spike during the last two decades is particularly interesting. But the point is, even within the vertebrates, there is no easy way yet to predict how many species are actually out there. And, of course, vertebrates represent only a tiny fraction of total biodiversity.
We used to see this graph a lot ten years ago, when the All-Species Foundation sought to document all species on Earth within 25 years. Even after 250 years of hard work, documenting what are almost by definition the easiest species to find, at best we’re only ten percent of the way there. The point is, we need a real paradigm shift if we want to have any hope of completing the Linnaean Enterprise. The problem is particularly pressing when you consider how little we know about what sort of extinction rates we may be encountering in the decades to come.
These two magnificent paintings by Isabella Kirkland remind us that we are in a race to document and understand declining biodiversity before it is gone forever. Global biodiversity is unquestionably Earth’s most valuable asset. It is an enormous library, where each species represents a unique book – the product of about 4 billion years of editing, re-editing, and fine-tuning. They are the survivors, and like the books in the world’s greatest libraries, they harbor priceless secrets. Today we are like kindergarteners running through the corridors of the Library of Congress. We take the books off the shelves, throw them at each other, build forts out of them, tear out pages and color them with our crayons, having only the vaguest notion of the true value of the information they contain. We’ve only barely begun to learn how to read “See spot run”, amid volumes that describe the equivalent of the inner workings of super-computers and nuclear reactors; and the words of the greatest philosophers, politicians, and historians. Whenever a species goes extinct, it’s like burning the last copy of a book; the information it contains lost forever. Eventually, perhaps fifty or a hundred years from now, our ability to decipher the information content of global biodiversity will be that of an educated adult. What tragedy it will be if we squandered this precious and irreplaceable resource before we understood its true value. We are the first generation to recognize the global biodiversity crisis. We may well be the last generation in a position to do anything about it. There is no time to waste.
We used to see this graph a lot ten years ago, when the All-Species Foundation sought to document all species on Earth within 25 years. Even after 250 years of hard work, documenting what are almost by definition the easiest species to find, at best we’re only ten percent of the way there. The point is, we need a real paradigm shift if we want to have any hope of completing the Linnaean Enterprise. The problem is particularly pressing when you consider how little we know about what sort of extinction rates we may be encountering in the decades to come.
Now I’ll describe a small example of this sort of integration, that began two years ago, nearly 400 feet deep, where a little fish with bright blue dots was captured on a coral reef in the western Pacific.
My colleagues and I described this and four other new species in an article in the journal Zootaxa last year. The electronic version of the article included nearly 200 embedded hyperlinks to external web-based resources, such as type specimens, high-resolution color images, DNA sequence data, scanned literature, and other online resources. Zootaxa published it on January 1 st , 2008 – exactly 250 years after the official start of all Zoological nomenclature – both to commemorate the publication of Linnaeus’ Systema Naturae, and to launch ZooBank, which is intended to become the official future online registry of zoological names. But make no mistake: While this was (and continues to be) an interesting and somewhat enlightening exercise, it does not represent the paradigm shift we so desperately need in our community. It really just represents little more than the digitization of our old habits.
It’s no surprise that the biodiversity community is going digital. Many Natural History Museums are databasing their collections. Historical literature is being digitized by the Biodiversity Heritage Library and others… … and many modern scientific journals are embracing the digital age directly. Authoritative Nomenclators have been built, and a variety of groups are working to distill the taxonomic concepts from the sea of names. Databases of observation records are growing at a fast rate, as are genomic databases. The internet has made feasible the cheap and easy dissemination of multimedia files related to biodiversity. And, of course there is biodiversity content spread across the billions of web pages indexed by Google. To make sense of it all, several organizations serve as aggregators of all this diverse content. And this is just a small sample of icons that I could fit on a slide. This massive effort to digitize biodiversity information is a great step in the right direction. But it is only one step. We must now focus our energies on integrating all of this information in a coordinated, cohesive way. The critical informatic piece to this puzzle is Taxonomy, because almost all of these data providers link their content to taxon names one way or another.

Sherborn: Pyle - Towards a Global Names Architecture: The future of indexing scientific names — Presentation Transcript

Towards a Global Names Architecture The Future of Indexing Scientific Names Richard L. Pyle Bishop Museum, Honolulu / International Commission on Zoological Nomenclature Sherborn Symposium London, 28 October 2011
“ Hence, in determining whether a form should be ranked as a species or a variety, the opinion of naturalists having sound judgment and wide experience seems the only guide to follow.” “ We must, however, in many cases, decide by a majority of naturalists, for few well-marked and well-known varieties can be named which have not been ranked as species by at least some competent judges.” - Charles Darwin, The Origin of Species - Charles Darwin, The Origin of Species “ A species is what a community of taxonomists says it is.” - Richard Pyle, PhD “ A species is what a taxonomist says it is.” - Richard Pyle, Graduate Student, 1994
Biology Department, Indiana University
4,398 Species 429,829 “Names”
1,509,491 Names 1,370,276 Species
Cumulative Described Species Time Species Accumulation Curve – Theoretical Predicted Total Species
0 5000 10000 15000 20000 25000 30000 35000 1750s 1800s 1850s 1900s 1950s 2000s Cumulative Described Species Decade Data from Eschmeyer’s Catalog of Fishes, May 2009. Species Accumulation Curve – All Fishes Predicted Total Species? 0 500 1000 1500 2000 2500 3000 3500 4000 4500 New Species Described Per Decade
Year Number of Described Species (Millions) 0 5 10 15 20 1750 1800 1850 1900 1950 2000 2050 Total Global Biodiversity Something Needs To Happen Here
Year Number of Described Species (Millions) 0 5 10 15 20 1750 1800 1850 1900 1950 2000 2050 Total Global Biodiversity Something Needs To Happen Here ? ? ? ?
BPBM 40861, Chromis abyssus HOLOTYPE Belau; off Ngemelis Island (7.13791°N, 134.2218°E) -110 meters 27 April 2007
TAXONOMY A Global Names Architecture ToL GenBank Hymenoptera Name Server BDWB CalPhotos
WWSD? (What Would Sherborn Do?) From the Epilogue, Section 2, Part 29, pp. vi-vii: “ Now my work is finished, it may well be to glance at the difficulties met with during compilation.” “ This want of every book and every edition has been a serious hindrance and loss of time to me while working for over forty years in the British Museum (Natural History) and though I have acquired over a thousand volumes for the libraries, gaps still remain to be filled.” “ On the whole one has met with a generous response, but the amused smile, real apathy, or the remark ‘we have no money’ … have been encountered.”
WWSD? (What Would Sherborn Do?) From the Epilogue, Section 2, Part 29, pp. vi-vii: “ And now that rotography has superseded photography as regards cost, a rare tract can be reproduced in a few hours and placed on its proper shelf in any Library for a few shillings.”” “ In conclusion I may add that the whole of my papers, Books of Reference and apparatus will remain at the Museum for my continuator and I trust that arrangements will be made for the permanent indexing of even current literature as the only true method of economizing the time of the working zoologist.” - C. Davies Sherborn, London, March, 1932

Sherborn: Pyle - Towards a Global Names Architecture: The future of indexing scientific names

by ICZN on Nov 04, 2011

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Sherborn: Pyle - Towards a Global Names Architecture: The future of indexing scientific names — Presentation Transcript