[Taxacom] barcode of life wins Ebbe Nielsen Prize

Wed Jun 30 08:13:44 CDT 2010

The background to the barcode "debate" is, I think:

1. molecular barcodes cab be useful,
2. they are used in situations they shouldn't be,
3. even whole genome analysis does not reflect the course and
actualities of evolution, unless, of course, you redefine evolution.

*****************************
Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm
*****************************

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Schindel, David
Sent: Tuesday, June 29, 2010 3:03 PM
To: Donat Agosti; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize

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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