[Taxacom] barcode of life wins Ebbe Nielsen Prize

Tue Jun 29 15:02:30 CDT 2010

Just a footnote to my earlier message.  There were many initiatives and projects involved in developing the BARCODE data standard and promoting linkages among vouchers, taxonomic data and GenBank.  I mentioned Specify because of its connection to Kansas and Kris.  Other databases like ITIS, Species200, ARCTOS, EMu, GRIN, ZooBank, ZooRecord, IPNI and others were all involved - the whole e-Biosphere crowd.

As for Donat's second message, I won't attempt to untangle what people claimed for barcode data versus what others claim they claimed.  CBOL regards barcode sequences as amazingly reliable data (not perfect, not fool-proof, just amazing) for species identification - more reliable than any other character of similar dimension.  Taxacomers may (and alas, probably will) argue over the merits of minimalism versus the robustness of whole genome data.  Unfortunately, there is still a real-world trade-off between depth and breadth of taxonomic coverage of sequencing and it will likely persist for a while.  Should we really conclude that despite elevated extinction rates, we should wait for whole genomes to register species in GenBank?

David

-----Original Message-----
From: Donat Agosti [mailto:agosti at amnh.org] 
Sent: Tuesday, June 29, 2010 1:21 PM
To: taxacom at mailman.nhm.ku.edu
Cc: Schindel, David
Subject: RE: [Taxacom] barcode of life wins Ebbe Nielsen Prize

Dear Dave

This is exactly the point
" will have the kind of usage by taxonomists, systematists, and other
organismal biologists that GenBank is having among molecular biologists"

And in the press release Krishtalka's remark:
" 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 "

Systematists among molecular biologists are among the big users of GenBank
because there are many different kinds of sequences, not "just" the barcode
sequences. I do not believe that barcodes will ever have the same role in
organismal biology, taxonomy, and systematics because it is a very
restricted, targeted tool which is very good for particular usages that it
was intended for. To consider this "critical genomic data" and extrapolate
this to cover the entire taxonomy, systematics and organismal biology is,
what I think, is not correct and overstates the value of barcodes. The large
amount of barcode sequences, and money being generated for its research does
not change this. At the same time there are increasingly whole genomes
becoming available and large arrays of non-barcode genes being sequenced
which are the base for most of phylogenics right now, as well as a lot of
digital images generated that visualize what's behind a sequence, are online
accessible, and opens them up to still the overwhelming majority of
biologists.
Such an attitude that there is one (barcode) solution in a world
(taxonomists, systematists, and other organismal biologists) that is so
complex I find rather pretentious and I find not acceptable of the chair of
the science committee of such an eminent organization like GBIF. This,
despite all the data, collaboration with GenBank and vouchering standards
emerging that are a great and fantastic byproduct of barcoding.

May be I am reading this all the wrong way round but the references are
there.

Donat

Dear Donat,

I'm afraid you have misinterpreted Krishtalka's statement.  Kris said the
impact of BOLD would rival that of GenBank, which was his way of saying that
BOLD will have the kind of usage by taxonomists, systematists, and other
organismal biologists that GenBank is having among molecular biologists.  He
didn't say that BOLD competes with GenBank because Kris knows that they
cooperate, not compete.  BOLD records are submitted to GenBank as the
ultimate archival repository for barcode records.  The BARCODE data standard
is about requirements for barcode records submitted to GenBank, primarily
from BOLD.  The Natural History Museum at the University of Kansas, home of
the specimen database Specify, have both been involved in our development of
the data standard and attempts to build linkages between GenBank and voucher
specimens in museum databases.  

Sorry, Donat - there are long and positive interactions among GBIF, BOLD and
GenBank.  We can't provide Taxacom with a flame that's worth fanning.

David

David Schindel, Executive Secretary
Consortium for the Barcode of Life
NMNH, Smithsonian Institution

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Donat Agosti
Sent: Tuesday, June 29, 2010 8:41 AM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] barcode of life wins Ebbe Nielsen Prize

In today's GBIF news letter I discovered the announcement of the Ebbe
Nielsen Prize winner, Mr. Ratnasingham, credited with the development of the
Barcode of Life Data (BOLD) systems.  <http://tinyurl.com/248w6qu>
http://tinyurl.com/248w6qu

This in itself is fine, but what I find appalling is the statement of the
Krishtalka, the chair of the GBIF Science Committee, that states "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 comes that BOLD (Advancing species indentification and discovery through
the analysis of short, standardized gene regions" wants to compete with
GenBank? How does a short sequence compare with a whole genome? Though
barcodes make some very important contributions to biology, they can not and
will never replace the many gene sequences needed for phylogenetic analysis,
the increasing impact of entire genomes, nor all the other information
needed to define species, such as the rapidly increasing number of digital
online images of taxa in a very simple way.

May be I misunderstand this statement, but the very way it is written in the
press release, this shows a very questionable attitude of GBIF's Science
Committee chair, which has little to do with science but rather imperium
building of missing far sight.

Donat Agosti 

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