[Taxacom] Taxacom Digest, Vol 51, Issue 28

[LKrishtalka]

Folks

At the risk of continuing tis thread, the GBIF press release concerning the
2010 GBIF EbbeNielsen Prize and BOLD did NOT mention systematics,
phylogenetics, taxonomy o any other specific field within or outside
biodiversity science.  The relevnt part of the pressrelease is repeated
verbatim below.   Please, let's quit whippin a straw man or kicking a
non-existent horse.

³In making this awad,² wrote Chair of the GBIFScience Committee, Dr.
Leonard Krishtalka when informing the winner of hi achievement, ³GBIF
recognises how you have applied your expertise in computer an information
science to advancing informatics across biodiversity science from genome to
ecosystems.²  

The impact and strategic significance of BOLD, accordng to Krishtalka,
promises to rival that of Genbank. ³BOLD enabls a growing number of
scientists to both register and access critical genomc data in a common way
for complex research and research applications for science and societ, both
inside and outside the domains of biodiversity science.² On BOLD¹
application to the GBIF network, Krishtalka continues, ³BOLD Sytems also
represents a new class of tools for potential collaboration with GBIF in the
shere of genomic biodiversity data.² 

Respectfully, 

LK

L. Krihtalka
Director, Biodiversity Institute
Professor, Dept. Ecology & Evolutionary Biolog
University of Kansas
Dyche Hall, 1345 Jayhawk Blvd
Lawrence, KS 6045-7561
phone: 785-864-4540
fax: 785-864-5335
krishtalka at ku.edu
-- 



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> Subject: Taacom Digest, Vol 51, Issue 28
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> Today' Topics:
> 
>    1. Re: barcode of life wins Ebbe Nielsen Prize (Dona Agosti)
>    2. Re: barcode of life wins Ebbe Nielsen Prize (Schindel,David)
>    3. New big oil pipeline across U.S. heartland? (Kennth Kinman)
>    4. Neotropical hymenoptera course (Sharkey, Michael J)
>    5. e: barcode of life wins Ebbe Nielsen Prize (Doug Yanega)
>    6. GBIF, wasRE:  barcode of life wins Ebbe Nielsen Prize
>       (Lyn.Craven at csiro.au)
>    7. Re: GBIF, was RE:  barcode of life wins Ebbe Nielsen Prize
>       (Tony.Rees at csiro.au)
>    8. Re: GBIF, was RE:  barcode of life wins Ebbe Nielsen Prize
>       (Lyn.Craven at csiro.au)
>    9. barcode of life (Kenneth Kinman)
>   10. Re: barcode of ife (Neal Evenhuis)
>   11. Re: barcode of life (Stephen Thorpe)
>   12. Re: barcode of life (Richard Pyle)
>   13. 3 jos @ RBG Melbourne Australia (Frank Udovicic)
>   14. Re: barcode of life (Stephen Thorpe)
>   15. Re: barcode of life (Schindel, David)
>   16. Re: Polygonum cespitosum or P. caespitosum?
>       (Dilrukshan Wijesinghe)
>   17. Re: barcode of life wins Ebbe Nielsen Prize (Richard Zander)
>   18. Re: barcodeof life wins Ebbe Nielsen Prize (Richard Zander)
> 
> 
> ---------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Jun 2010 21:51:23 +0430
> From: "Donat Agosti" <agosti at amnh.org>
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> To: <taxacom at mailman.nhm.ku.edu>
> Message-ID: <C4E19A144533492FB44EB6F6E23A10AC at bern>
> Content-Type: text/plain; charset="us-ascii"
> 
> Dea Dave
> 
> This is exactly the point
> " will have the kind of usage by taxonomists, systematists, and other
> ganismal 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 fantatic 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 barode records.  The BARCODE data standard
> is about requirements for barcode rcords submitted to GenBank, primarily
> from BOLD.  The Natural History Museum t the University of Kansas, home of
> the specimen database Specify, have both been involved in our development o
> the data standard and attempts to build linkages between GenBank and voucher
> pecimens in museum databases.
> 
> Sorry, Donat - there are long and postive interactions among GBIF, BOLD and
> GenBank.  We can't provide Taxacom wih 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 comon 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 
> 
>  
> 
>  
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>  
> 
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> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 29 Jun 2010 16:02:30 -0400
> From: "Schindel, David" <schindeld at si.edu>
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> To: Donat Agosti <agosti at amnh.org>, "taxacom at mailman.nhm.ku.edu"
> <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <DB179119972FE14E8A80A23C3425ED9D031C729082 at SI-MSEV02.US.SINET.SI.EDU>
> Content-Type: text/plain; charset="us-ascii"
> 
> Just a footnote to my earlier message.  There were many initiatives an
> projects involved in developing the BARCODE data standrd 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, ARCTS, EMu, GRIN, ZooBank, ZooRecord, IPNI and others were all
> involved - the whol e-Biosphere crowd.
> 
> As for Donat's second message, I won't attempt to untngle what people clamed
> for barcode data versus what others claim they claimed. CBOL regards barcode
> sequences as amazingly reliable data (not perfect, not fol-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 minimalim versus the robustness of whole genome data.
> Unfortunaely, there is still a eal-world trade-off between depth and breadth
> of taxonomic overage of sequencing and it will likely persist for a while.
> Should we realy conclude that despite elevated extinction rates, we should
> wait for whol genomes to registerspecies in GenBank?
> 
> David
> 
> 
> 
> -----Original Messge-----
> From: Donat Agosti [mailto:agosti at amnh.org]
> Sent: Tuesday, June 29, 210 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 i exactly the point
> " will have the kind of usage by taxonmists, systematists,and other
> organismal biologists that GenBank is having among molecularbiologists"
>  
> And in the press release Krishtalka's remark:
> " BOD 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 amongmolecular biologists are among the big users of GenBank
> because there are many differet kinds of sequences, not "just" the barcode
> sequences. I do ot believe that barcodes will ever have the same role in
> organismal biology, taxonomy and systematics because it is a very
> restricted, targeted tool whih is very good for particular usages that it
> was intended for To consider this "critical genomic data" and extrapolate
> this to cover theentire taxonomy, systematics and organismal biology is,
> what I think, is nt correct and oversttes the value of barcodes. The large
> amount of barcode sequencs, and money being generated for its research does
> not change ths. At the same time there ae increasingly whole genomes
> becoming available and large arrays of nonbarcode genes being sequenced
> which are the base for most of phylogenics right ow, as well as a lot of
> digital images generated that visualize what's behind a seqence, are online
> accessible, and opens them up to still the overwhelmin majority of
> biologists.
> Such an attitude that there is one barcode) solution in a world
> (taxonomists, systematists, and other organimal biologists) that is so
> complex I find rather pretentious and I find not acceptable of he chair of
> the science committee of such an eminent organization likeGBIF. This,
> despite all the data, collaboration with GenBank ad 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 reerences are
> there.
> 
> Donat
> 
> 
> Dear Donat,
> 
> I'm afraid you have misinterpeted Krishtalka's statement.  Kris said the
> impact of BOLD woul rival that of GenBank, which was his way of saying that
> BOLD will have the kind of sage by taxonomists, systematists, and other
> organismal biolgists that GenBank is having among molecular biologists.  He
> didn't saythat BOLD competes withGenBank because Kris knows that they
> cooperate, not compete.  BOLD recods are submitted to GenBank as the
> ultimate archival repository fr barcode records.  The BARCODE data standard
> is about requirments for barcode records submitted to GenBank, primarily
> from BOLD.  The Natural Histry Museum at the University of Kansas, home of
> the specimen dtabase Specify, have both been involved in our development of
> the data standard and attempts tobuild linkages between GenBank and voucher
> specimens in mseum databases.
> 
>Sorry, Donat - there are long and positive interactions among GBIF, BLD and
> GenBank.  We can't provide Taxacom with a flame that's worth fnning.
> 
> David
> 
> David Schindel, Executive Secretary
> Conortium for the Barcode of Life
> NMNH, Smithsonian Institution
> 
> -----Originl Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxaco-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 developmet of the
> Barcode of Life Data (BOLD) systems.  <http://tinyurl.com/248w6qu>
> http://tinyurl.com/248w6qu
> 
>  
> 
> Tis 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
> reister and access critical genomic data in a common way for complex
> research and research applications for sciece 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
> bacodes make some very important contributions to biology, they can not and
> will never replace the many gene seqences 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 
> 
>  
> 
>  
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.e/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be seached with either of these
> methods:
> 
> (1) http://taxacom.markmail.org
> 
>Or (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxcom  your search terms here
>  
> 
> __________ Information from ESET Smart Surity, version of virus signature
> database 5236 (20100629) __________
> 
> Themessage was checked by ESET Smart Security.
> 
> http://www.eset.com
>  
 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 29 Jn 2010 18:02:11 -0500
> From: kennethkinman at webtv.net (Kenneth Kinman)
 Subject: [Taxacom] New big oil pipeline across U.S. heartland?
> To: taxacom at malman.nhm.ku.edu
> Message-ID: <10364-4C2A7B73-7539 at storefull-3252bay.webtv.net>
> Content-Type: Text/Plain; Charset=US-ASCII
> 
> Dear All,        
>        Only two days are left for anyone wanting to give feedback to
> the government concerning the proposed Keystone XL pipeline (for
> transporting "tar sands" oil from Canada to Texas).  Opposition comes
> from ranchers and farmers along the proposed route, environmentalists
>National Wildlife Federation, etc.), and others concerned with possible
> groundwater and air contamination, not to mention continued resistance
> to the tar sands industry in Alberta.
>       What is perhaps most shocking is that they are requesting waivers
> so that they can use thinner pipe over much of this pipeline.  Sounds
> like they want to sacrifice safety to save on construction costs (I
> guess they need to ask BP Oil if cutting corners is such a good
> idea---perhaps penny wise, but pound foolish).  Anyway, the following
> news story tells how one can comment, either online or by fax):
> 
> http://www.chron.com/disp/story.mpl/business/7085313.html
> 
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Tue, 29 Jun 2010 19:08:35 -0400
> From: "Sharkey, Michael J" <msharkey at uky.edu>
> Subject: [Taxacom] Neotropical hymenoptera course
> To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <BF3CDBFD7E9B2146BE3CEE83F049BC532A8A82BA66 at EX7FM01.ad.uky.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Dear all, 
>     We are offering a course on the biology, taxonomy and phylogeny of the
> Hymenoptera in the Amazon region of  Peru in January of 2011. If you or one of
> your students might be interested please see the announcement at the link
> below. Lectures will be given in English and Spanish (both translated).
> http://cebioperu.org/neotropicalhymenoptera/home.html
> PS. still looking for fresh Megarhyssa specimens.
> Mike
> Michael Sharkey
> Department o Entomology
> University of Kentucky
> Lexington KY 40546-001
> (859) 257-9364
> msharkey at uky.edu
> www.sharkeylab.org
> _
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Tue, 29 Jun 2010 16:17:26 -0700
> From: Doug Yanega <dyanega at ucr.edu>
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> To: TAXACOM at MAILMAN.NHM.KU.EDU
> Message-ID: <f05100302c85003a764e3@[138.23.68.6]>
> Content-Type: text/plain; charset="us-ascii" ; format="flowed"
> 
> David Schindel wrote:
> 
>> Taxacomers may (and alas, probably will) argue over the merits of
>> minimalism versus the robustness of whole genome data.
> 
> Tht's not the argument here. I think for many of us it's moe a
> matter of people using a mitochondrial marker - with all of the
> associated non-Mendelian pitfalls - as an arbitrary delimiter of the
> biological entities we know as species. Othe people seem to be using
> COI to work out higher-level phylogeny, as well, wher a very
> fast-evolving gene like COI is not really appropriate. If there are
 merits to be argued it's COI's merits versus non-mitochondrial genes
> in the forer case, and versus slow-evolving genes in the latter
> case. Both cases offer ood arguments against COI, too.
> 
>>   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 wile.  Should we really conclude that despite
>> elevated xtinction rates, we shuld wait for whole genomes to
>> register species in GenBank?> 
> I don't think that is what Donat was saying, nor have I heard any
> otherfolks raise such an objection; the objections are usually along
> the lines f overemphasis on a INGLE organismal character - the COI
> sequence - as if it, nd it alone, could and *should* tell us what
> was or was not a species.
> 
> It eems not very long ago when people who discovered differences
> between geographically islated populations of one species were often
> quite happy to use "sbspecies" to describe this variation. Now it's
> as if an etire generation of txonomists have completely forgotten
> that this taxonomic category ever xisted, and almost act as if it is
> *impossible* for geographically iolated populations to have genetic
> differences between them and still belong to the same species. Did
> the rest of us all miss the memo tellng us that subspecies don't
> exist any more? When one person cn conclude that we are dealing
> with, say, a single species that has 30 identifiable geetic
> variants, and another can conclude (from the exact same vidence)
> that this organism is actually 30 cryptic species, then we have a
> fundamenal difference in opinion on what a "species" is. If those
> two peopl then have to make their case to the public and political
> comunity regarding, say, the conservation of species, the first -
> and possiblythe ONLY - thing that any non-scientist is going to
> notice is that these to scientists do not gree, and if the
> scientists don't agree, then it's unlikely *ether* side will be
> taken seriously. Or, given human nature, if te two opinions a
> politicin hears is "This is a common, widespread species, and it is
> not threateed by this planned solar power array" versus "This is a
> complex of 30 species, ach of which occurs in such a small area that
> any one of them could go extinct at ay time, and 3 of them will
> probably go extinct if this solar power arra is built", then the
> latter scenario is not very likely to be hat anyone wants to hear.
> Just look at the "debate" over climate change. t's no longer just a
> purely academic exercise at that point.
> 
> Ultimately, the claim tht:
> 
> "CBOL regards barcode sequences as amazingly reliable data (not
 perfect, not fool-proof, just amazing) for species identificatin -
> more reliable than any other character of similar dimension."
> 
> is *entirely* dpendent on the associated belief that species limits
> can be deined arbitrarily (e.g., as 4% sequence divergence, rather
> than 5%, or 3%, or some oter number). Where is the published
> evidence that organisms witha 3% sequence divergence can interbreed,
> but those with a 4% divergence *can't* intebreed? How can one prove
> or disprove, say, that a COI haplotpe moved from one species to
> another via hybrid introgression? It's as f people believe that CI
> just *happens* to evolve at EXACTLY the same rate that speciation
> ocurs - *never* faster (because then one species could have many
> dfferent COI haplotypes, including variants exceeding 4%
> diverence), and *never* slower or laterally (because then more than
> one species could sharethe same COI haplotype, or haplotypes with
> divergence below 4). How realistic is that??
> 
> If one does not share that belief, then the claim that COI is a
>reliable species-level marker looks like a massive tautolog. What,
> after all,is the *independent test* that can be used to support or
> refute thehypothesis that any given "species" has a distinct *and*
> unique COI pofile? Building a tree of haplotypes is not a test of
> species oundaries. Isn't science supposed to be based on testable
> hypotheses??
> 
> Sncerely,
> -- 
> 
> Doug Yanega        Dept. of Entomology         Entomolgy Research Museum
> Univ. of California, Riverside, CA 92521-0314        skype: dyanega
> phone: (951) 827-4315 (standard disclaimer: opinions are mine, not UCR's)
>               http://cache.ucr.edu/~heraty/yanega.html
>    "There are some enterprises in which a careful disorderliness
>          is the true method" - Herman Melille, Moby Dick, Chap. 82
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Wed, 30 Jun 2010 09:21:04 +100
> From: <Lyn.Craven at csiro.au>
> Subject: [Taxacom] GBIF, was RE:  barcode of life wins Ebbe Nielsen
> Prize
> To: <kipwill at berkeley.edu>, <agosti at amnh.org>
> Cc: taxacom at mailman.nhm.ku.edu
> Message-ID:
> <3E532DB76CE28140A184F767FC624591010269633A85 at exvic-mbx04.nexus.csiro.au>
> 
> Content-Type: text/plin; charset="us-ascii"
> 
>  
> 
> Kip's posted URLs make for dispiriting reading, but I guess it all reflects
>our sorry times.
> 
> One should not be particularly surprised about GBIF's pouncing on bar-coding.
> When GBIF was announced to the world, it was patently obvious that the only
> benefit the organisation was going to provide would be realised by its office
> bearers and staff.    It clearly was only going to result in et another
> re-arrangement of the deck chairs on the Titanic.     The sooner its funding
> gets pulled, the beer off science will be.
> 
> GBIF, unfortunately, is merely smoke and mirrors.
> 
> 
> Lyn Craven
> 
>  
> ******************************
>  
> Lyn A. Craven
> Australian National Herbarium
> CSIRO Plant Industry
> GPO Box 1600
> Canberra.   ACT   2601
> Australia
>  
> Phone:  61 (0)2 6246 5122
> Fax:      61 (0)2 62465249
> Email:    lyn.craven at csiro.au
> Home page:    http://www.anbg.gov.au/people/craven.n.html
> 
> 
> 
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kipling (Kip) Will
> Sent: Tuesday, 29 June 2010 11:24 PM
> To: Donat Agosti
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> 
> To follow up on Donat's comments, I offer two important recent critiques of
> the Barcoding phenomenon:
> 
> One that shows how the "enterprise" is using taxonomy while eviscerating the
> sciene:
> 
> Ebache, M.C. and de Carvalho, M.R.. 2010. Anti-intellectualism in the DNA
> Barcoding Enterprise. Zoologia, Vol 27, No 2.
> 
> http://submission.scielo.br/index.php/zool/article/view/22823
> 
> and another that shows that the Social Scientists are not fooled by the
> hype:
> 
> Larson, M.H. 2007. DNA Barcoding: The Social Frontier. Frontiers in Ecology
> and the Environment, Vol. 5, No. 8 (Oct., 2007), pp. 437-442 # Stable URL:
> http://www.jstor.org/stable/20440731
> 
> Kip Will
> 
> 
> Donat Agosti wrote:
>> 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
>> "Th 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
>> 
>>  
>> 
>>  
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with either of these
>> methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>> 
> 
> 
> --
> Kipling W. Will
> Associate Professor/Insect Systematist
> Associate Director,Essig Museum of Entomology
> 
> mail to:
> 137 Mulford Hall
> ESPM Dept.- Organisms & Environment Div.
> University of California
> Berkeley, alifornia 94720
> 
> phone 510-642-4296
> fax 510-643-5438
> skype kipwill
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Wed, 30 Jun 2010 10:58:16 +1000
> From: <Tony.Rees at csiro.au>
> Subject: Re: [Taxacom] GBIF, was RE:  barcode of life wins Ebbe
> Nielsen Prize
> To: <Lyn.Craven at csiro.au>, <kipwill at berkeley.edu>, <agosti at amnh.org>
> Cc: taxacom at mailman.nhm.ku.edu
> Message-ID:
> <C2994967ABB5D54BB013821E4ABA60E103460A6BFA at exvic-mbx03.nexus.csiro.au>
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Lyn,
> 
> Just for information - GBIF as I understand it is a global scale biodiversity
> data aggregation initiative. There are also regional / local scale aggregation
> initiatives such as (e.g. in Australia) OZCAM (for faunal collections) and
> Australian Virtual Herbarium (for botany), of which your agency, the
> Australian National Herbarium is a prominent part, and which also - I presume
> happily - cooperate actively with GBIF. Is your problem with data aggregation
> activities in general, or just GBIF in particular?
> 
> Regards - Tony
> 
> Tony Rees
> Manager, Divisional Data Centre,
> CSIRO Marine and Atmospheric?Research,
> Hobart, Tasmania 7001, Australia
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Lyn.Craven at csiro.au
> Sent: Wednesday, 30 June 2010 9:21 AM
> To: kipwill at berkeley.edu; agosti at amnh.org
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: [ExternalEmail] [Taxacom] GBIF, was RE: barcode of life wins Ebbe
> Nielsen Prize
> 
>  
> 
> Kip's posted URLs make for dispiriting reading, but I guess it all reflects
> our sorry times.
> 
> One should not be particularly surprised about GBIF's pouncing on bar-coding.
> When GBIF was announced to the world, it was patently obvious that the only
> benefit the organisation was going to provide would be realised by its office
> bearers and staff.    It clearly was only going to result in yet another
> re-arrangement of the deck chairs on the Titanic.     The sooner its funding
> gets pulled, the better off science will be.
> 
> GBIF, unfortunately, is merely smoke and mirrors.
> 
> 
> Lyn Craven
> 
>  
> ******************************
>  
> Lyn A. Craven
> Australian National Herbarium
> CSIRO Plant Industry
> GPO Box 1600
> Canberra.   ACT   2601
> Australia
>  
> Phone:  61 (0)2 6246 5122
> Fax:      61 (0)2 6246 5249
> Email:    lyn.craven at csiro.au
> Home page:    http://www.anbg.gov.au/people/craven.lyn.html
> 
> 
> 
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kipling (Kip) Will
> Sent: Tuesday, 29 June 2010 11:24 PM
> To: Donat Agosti
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> 
> To follow up on Donat's comments, I offer two important recent critiques of 
> the Barcoding phenomenon:
> 
> One that shows how the "enterprise" is using taxonomy while eviscerating the 
> science:
> 
> Ebache, M.C. and de Carvalho, M.R.. 2010. Anti-intellectualism in the DNA 
> Barcoding Enterprise. Zoologia, Vol 27, No 2.
> 
> http://submission.scielo.br/index.php/zool/article/view/22823
> 
> and another that shows that the Social Scientists are not fooled by the
> hype:
> 
> Larson, M.H. 2007. DNA Barcoding: The Social Frontier. Frontiers in Ecology 
> and the Environment, Vol. 5, No. 8 (Oct., 2007), pp. 437-442 # Stable URL: 
> http://www.jstor.org/stable/20440731
> 
> Kip Will
> 
> 
> Donat Agosti wrote:
>> 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
>> 
>>  
>> 
>>  
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with either of these 
>> methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:  
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>> 
> 
> 
> --
> Kipling W. Will
> Associate Professor/Insect Systematist
> Associate Director,Essig Museum of Entomology
> 
> mail to:
> 137 Mulford Hall
> ESPM Dept.- Organisms & Environment Div.
> University of California
> Berkeley, California 94720
> 
> phone 510-642-4296
> fax 510-643-5438
> skype kipwill
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Wed, 30 Jun 2010 11:57:02 +1000
> From: <Lyn.Craven at csiro.au>
> Subject: Re: [Taxacom] GBIF, was RE:  barcode of life wins Ebbe
> Nielsen Prize
> To: <Tony.Rees at csiro.au>, <kipwill at berkeley.edu>, <agosti at amnh.org>
> Cc: taxacom at mailman.nhm.ku.edu
> Message-ID:
> <3E532DB76CE28140A184F767FC624591010269633A8E at exvic-mbx04.nexus.csiro.au>
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> 
> Hi Tony
> 
> Data aggregation activities are a good idea.     It depends on whether an 
> outfit exists for achieving its avowed ends or for itself.     And it is 
> sometimes good for a flea to ride on an elephant for it can then claim an 
> equal share of the mass.
> 
> Lyn
> 
> 
> -----Original Message-----
> From: Rees, Tony (CMAR, Hobart) 
> Sent: Wednesday, 30 June 2010 10:58 AM
> To: Craven, Lyn (PI, Black Mountain); kipwill at berkeley.edu; agosti at amnh.org
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: GBIF, was RE: barcode of life wins Ebbe Nielsen Prize
> 
> Dear Lyn,
> 
> Just for information - GBIF as I understand it is a global scale biodiversity 
> data aggregation initiative. There are also regional / local scale aggregation 
> initiatives such as (e.g. in Australia) OZCAM (for faunal collections) and 
> Australian Virtual Herbarium (for botany), of which your agency, the 
> Australian National Herbarium is a prominent part, and which also - I presume 
> happily - cooperate actively with GBIF. Is your problem with data aggregation 
> activities in general, or just GBIF in particular?
> 
> Regards - Tony
> 
> Tony Rees
> Manager, Divisional Data Centre,
> CSIRO Marine and Atmospheric?Research,
> Hobart, Tasmania 7001, Australia
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Lyn.Craven at csiro.au
> Sent: Wednesday, 30 June 2010 9:21 AM
> To: kipwill at berkeley.edu; agosti at amnh.org
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: [ExternalEmail] [Taxacom] GBIF, was RE: barcode of life wins Ebbe 
> Nielsen Prize
> 
>  
> 
> Kip's posted URLs make for dispiriting reading, but I guess it all reflects 
> our sorry times.
> 
> One should not be particularly surprised about GBIF's pouncing on bar-coding.   
> When GBIF was announced to the world, it was patently obvious that the only 
> benefit the organisation was going to provide would be realised by its office 
> bearers and staff.    It clearly was only going to result in yet another 
> re-arrangement of the deck chairs on the Titanic.     The sooner its funding 
> gets pulled, the better off science will be.
> 
> GBIF, unfortunately, is merely smoke and mirrors.
> 
> 
> Lyn Craven
> 
>  
> ******************************
>  
> Lyn A. Craven
> Australian National Herbarium
> CSIRO Plant Industry
> GPO Box 1600
> Canberra.   ACT   2601
> Australia
>  
> Phone:  61 (0)2 6246 5122
> Fax:      61 (0)2 6246 5249
> Email:    lyn.craven at csiro.au
> Home page:    http://www.anbg.gov.au/people/craven.lyn.html
> 
> 
> 
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kipling (Kip) Will
> Sent: Tuesday, 29 June 2010 11:24 PM
> To: Donat Agosti
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> 
> To follow up on Donat's comments, I offer two important recent critiques of 
> the Barcoding phenomenon:
> 
> One that shows how the "enterprise" is using taxonomy while eviscerating the 
> science:
> 
> Ebache, M.C. and de Carvalho, M.R.. 2010. Anti-intellectualism in the DNA 
> Barcoding Enterprise. Zoologia, Vol 27, No 2.
> 
> http://submission.scielo.br/index.php/zool/article/view/22823
> 
> and another that shows that the Social Scientists are not fooled by the
> hype:
> 
> Larson, M.H. 2007. DNA Barcoding: The Social Frontier. Frontiers in Ecology 
> and the Environment, Vol. 5, No. 8 (Oct., 2007), pp. 437-442 # Stable URL: 
> http://www.jstor.org/stable/20440731
> 
> Kip Will
> 
> 
> Donat Agosti wrote:
>> 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
>> 
>>  
>> 
>>  
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with either of these 
>> methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:  
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>> 
> 
> 
> --
> Kipling W. Will
> Associate Professor/Insect Systematist
> Associate Director,Essig Museum of Entomology
> 
> mail to:
> 137 Mulford Hall
> ESPM Dept.- Organisms & Environment Div.
> University of California
> Berkeley, California 94720
> 
> phone 510-642-4296
> fax 510-643-5438
> skype kipwill
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> ------------------------------
> 
> Message: 9
> Date: Tue, 29 Jun 2010 22:09:22 -0500
> From: kennethkinman at webtv.net (Kenneth Kinman)
> Subject: [Taxacom] barcode of life
> To: taxacom at mailman.nhm.ku.edu
> Message-ID: <14763-4C2AB562-10728 at storefull-3251.bay.webtv.net>
> Content-Type: Text/Plain; Charset=ISO-8859-1
> 
>  Dear All, 
> ????????I agree that using COI alone, or any other gene
> sequence alone, as the single marker for species delimitation, is a bad
> idea. Until we have whole genome sequences for a very large number of
> species, perhaps a combination of two or three independent genes (of
> which COI is just one) would be a good compromise. What the other one or
> two genes that would best evolve at different rates (than COI), I can't
> say. 
> ??????????????In any case, I find it
> disturbing that COI gene sequences would too often be used to excuse
> naming new full species, as opposed to subspecies or populations, based
> on some arbitrary number of changes in that single gene. Barcoding for
> identification of populations is probably valuable, but whether those
> populations are subspecies or full species is a whole different matter
> that a single gene cannot possibly determine across the whole gamut of
> organismal evolutionary rates.  Bar Code of Life based on this single
> gene has its place at this time, and may even be useful as a species
> deliimitator in some taxa. However, extrapolating beyond those
> limitations (without corroboration from other lines of evidence) can be
> a risky proposition that will cast doubt upon the work of those who
> delve too quickly into that kind of speculation based solely on a single
> gene sequence.       
> ??????????????????????----------Ken
> Kinman                      
> P.S. I am still convinced that the earlier (and still common)
> fascination with the 16S ribosomal gene sequence (used for delimiting
> much broader taxa) was equally suspectible to overextrapolation.  To
> this day, such overextrapolation seems to continue to be a persistent
> impediment to a true understanding of the higher level evolution of
> prokaryotes, early eukaryotes, and even how various subgroups of
> metazoans are related to one another.  Once scientists get addicted to a
> particular gene sequence, it is an extremely difficult addiction (and
> point of view) to argue against.  Once a single gene sequence (COI or
> 16S RNA) becomes a favorite of federal funding, there is an INCREASING
> risk that a growing number of researchers will overextrpolate from and
> overinvest funding on those particular genes.  Unfrotunately but not
> surprising.              
>        It's similar to the media's current fascination with the Gulf Oil
> spill, but they will totally ignore other environmental threats until it
> is also too late.  They almost always try to close the barn door well
> after it is too late.  Reactivity continues to be the norm, and
> proactivity is unfortunately relatively uncommon and unprofitable.  I
> guess it is no surprise that big corporations are often tempted to cut
> corners (penny wise, but pound foolish).  Oil companies are the present
> targets of public and media scrutiny, but that only allows Wall Street
> to slip back into their old habits.  Letting the latter take advantage
> of the most recent events shows how the media can overreact to one
> problem and then be totally distracted from covering another major
> problem.  Not to excuse Wall Street greed, but perhaps it is at the root
> of Oil companies cutting corners to keep their stock prices up.  Either
> way, it is overpaid CEOs and their middle men that rake in the absurd
> salaries and stock options, and the real lower-level workers in their
> companies (a very few who become whistle-blowers to abuses) are far less
> well paid and likely to become fired, demoted, or scapegoats for their
> superiors.  Anyway, this is getting a little too far afield from
> taxonomy, but I guess these problems tend to trickle down from
> governmental funding at the top to those getting some benefit (large or
> small) from those spending decisions.  Suffice it to say that
> superificial PR too often prevails and superficial and repetitive media
> is more likely to repeat that PR than to dig deeper for the less
> exciting truth.  In the present scheme of things, anyone who still
> believes that the meek shall inherit the Earth are in for a long wait
> and further disappointment.  PR, money, and media access are still the
> major power brokers, and the meek have little influence whatsoever, and
> then only by rare accidents of very marginal media coverage.
> 
> 
> 
> 
> ------------------------------
> 
> Message: 10
> Date: Tue, 29 Jun 2010 17:17:35 -1000
> From: Neal Evenhuis <neale at bishopmuseum.org>
> Subject: Re: [Taxacom] barcode of life
> To: Kenneth Kinman <kennethkinman at webtv.net>
> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Message-ID: <p06240826c85067836617@[10.1.26.105]>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 
> It's not often that a P.S. is longer than the original text. This is 
> entering dangerous territory where you may be competing with Rich 
> Pyle. Be careful ....
> 
> ;-)
> 
> At 5:09 PM -1000 6/29/10, Kenneth Kinman wrote:
>>  Dear All,
>>         I agree that using COI alone, or any other gene
>> sequence alone, as the single marker for species delimitation, is a bad
>> idea. Until we have whole genome sequences for a very large number of
>> species, perhaps a combination of two or three independent genes (of
>> which COI is just one) would be a good compromise. What the other one or
>> two genes that would best evolve at different rates (than COI), I can't
>> say.
>>               In any case, I find it
>> disturbing that COI gene sequences would too often be used to excuse
>> naming new full species, as opposed to subspecies or populations, based
>> on some arbitrary number of changes in that single gene. Barcoding for
>> identification of populations is probably valuable, but whether those
>> populations are subspecies or full species is a whole different matter
>> that a single gene cannot possibly determine across the whole gamut of
>> organismal evolutionary rates.  Bar Code of Life based on this single
>> gene has its place at this time, and may even be useful as a species
>> deliimitator in some taxa. However, extrapolating beyond those
>> limitations (without corroboration from other lines of evidence) can be
>> a risky proposition that will cast doubt upon the work of those who
>> delve too quickly into that kind of speculation based solely on a single
>> gene sequence.      
>>                       ----------Ken
>> Kinman                     
>> P.S. I am still convinced that the earlier (and still common)
>> fascination with the 16S ribosomal gene sequence (used for delimiting
>> much broader taxa) was equally suspectible to overextrapolation.  To
>> this day, such overextrapolation seems to continue to be a persistent
>> impediment to a true understanding of the higher level evolution of
>> prokaryotes, early eukaryotes, and even how various subgroups of
>> metazoans are related to one another.  Once scientists get addicted to a
>> particular gene sequence, it is an extremely difficult addiction (and
>> point of view) to argue against.  Once a single gene sequence (COI or
>> 16S RNA) becomes a favorite of federal funding, there is an INCREASING
>> risk that a growing number of researchers will overextrpolate from and
>> overinvest funding on those particular genes.  Unfrotunately but not
>> surprising.             
>>        It's similar to the media's current fascination with the Gulf Oil
>> spill, but they will totally ignore other environmental threats until it
>> is also too late.  They almost always try to close the barn door well
>> after it is too late.  Reactivity continues to be the norm, and
>> proactivity is unfortunately relatively uncommon and unprofitable.  I
>> guess it is no surprise that big corporations are often tempted to cut
>> corners (penny wise, but pound foolish).  Oil companies are the present
>> targets of public and media scrutiny, but that only allows Wall Street
>> to slip back into their old habits.  Letting the latter take advantage
>> of the most recent events shows how the media can overreact to one
>> problem and then be totally distracted from covering another major
>> problem.  Not to excuse Wall Street greed, but perhaps it is at the root
>> of Oil companies cutting corners to keep their stock prices up.  Either
>> way, it is overpaid CEOs and their middle men that rake in the absurd
>> salaries and stock options, and the real lower-level workers in their
>> companies (a very few who become whistle-blowers to abuses) are far less
>> well paid and likely to become fired, demoted, or scapegoats for their
>> superiors.  Anyway, this is getting a little too far afield from
>> taxonomy, but I guess these problems tend to trickle down from
>> governmental funding at the top to those getting some benefit (large or
>> small) from those spending decisions.  Suffice it to say that
>> superificial PR too often prevails and superficial and repetitive media
>> is more likely to repeat that PR than to dig deeper for the less
>> exciting truth.  In the present scheme of things, anyone who still
>> believes that the meek shall inherit the Earth are in for a long wait
>> and further disappointment.  PR, money, and media access are still the
>> major power brokers, and the meek have little influence whatsoever, and
>> then only by rare accidents of very marginal media coverage.
>> 
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with either 
>> of these methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as: 
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> 
> ------------------------------
> 
> Message: 11
> Date: Tue, 29 Jun 2010 20:22:07 -0700 (PDT)
> From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Subject: Re: [Taxacom] barcode of life
> To: Neal Evenhuis <neale at bishopmuseum.org>, Kenneth Kinman
> <kennethkinman at webtv.net>
> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Message-ID: <82727.5951.qm at web114207.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> otherwise known as "Pyling it on"! :)
> 
> 
> 
> 
> ________________________________
> From: Neal Evenhuis <neale at bishopmuseum.org>
> To: Kenneth Kinman <kennethkinman at webtv.net>
> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Sent: Wed, 30 June, 2010 3:17:35 PM
> Subject: Re: [Taxacom] barcode of life
> 
> It's not often that a P.S. is longer than the original text. This is 
> entering dangerous territory where you may be competing with Rich 
> Pyle. Be careful ....
> 
> ;-)
> 
> At 5:09 PM -1000 6/29/10, Kenneth Kinman wrote:
>> ? Dear All,
>> ? ? ? ? I agree that using COI alone, or any other gene
>> sequence alone, as the single marker for species delimitation, is a bad
>> idea. Until we have whole genome sequences for a very large number of
>> species, perhaps a combination of two or three independent genes (of
>> which COI is just one) would be a good compromise. What the other one or
>> two genes that would best evolve at different rates (than COI), I can't
>> say.
>> ? ? ? ? ? ? ? In any case, I find it
>> disturbing that COI gene sequences would too often be used to excuse
>> naming new full species, as opposed to subspecies or populations, based
>> on some arbitrary number of changes in that single gene. Barcoding for
>> identification of populations is probably valuable, but whether those
>> populations are subspecies or full species is a whole different matter
>> that a single gene cannot possibly determine across the whole gamut of
>> organismal evolutionary rates.? Bar Code of Life based on this single
>> gene has its place at this time, and may even be useful as a species
>> deliimitator in some taxa. However, extrapolating beyond those
>> limitations (without corroboration from other lines of evidence) can be
>> a risky proposition that will cast doubt upon the work of those who
>> delve too quickly into that kind of speculation based solely on a single
>> gene sequence.? ? ? 
>> ? ? ? ? ? ? ? ? ? ? ? ----------Ken
>> Kinman? ? ? ? ? ? ? ? ? ? 
>> P.S. I am still convinced that the earlier (and still common)
>> fascination with the 16S ribosomal gene sequence (used for delimiting
>> much broader taxa) was equally suspectible to overextrapolation.? To
>> this day, such overextrapolation seems to continue to be a persistent
>> impediment to a true understanding of the higher level evolution of
>> prokaryotes, early eukaryotes, and even how various subgroups of
>> metazoans are related to one another.? Once scientists get addicted to a
>> particular gene sequence, it is an extremely difficult addiction (and
>> point of view) to argue against.? Once a single gene sequence (COI or
>> 16S RNA) becomes a favorite of federal funding, there is an INCREASING
>> risk that a growing number of researchers will overextrpolate from and
>> overinvest funding on those particular genes.? Unfrotunately but not
>> surprising.? ? ? ? ? ? 
>> ? ? ? ? It's similar to the media's current fascination with the Gulf Oil
>> spill, but they will totally ignore other environmental threats until it
>> is also too late.? They almost always try to close the barn door well
>> after it is too late.? Reactivity continues to be the norm, and
>> proactivity is unfortunately relatively uncommon and unprofitable.? I
>> guess it is no surprise that big corporations are often tempted to cut
>> corners (penny wise, but pound foolish).? Oil companies are the present
>> targets of public and media scrutiny, but that only allows Wall Street
>> to slip back into their old habits.? Letting the latter take advantage
>> of the most recent events shows how the media can overreact to one
>> problem and then be totally distracted from covering another major
>> problem.? Not to excuse Wall Street greed, but perhaps it is at the root
>> of Oil companies cutting corners to keep their stock prices up.? Either
>> way, it is overpaid CEOs and their middle men that rake in the absurd
>> salaries and stock options, and the real lower-level workers in their
>> companies (a very few who become whistle-blowers to abuses) are far less
>> well paid and likely to become fired, demoted, or scapegoats for their
>> superiors.? Anyway, this is getting a little too far afield from
>> taxonomy, but I guess these problems tend to trickle down from
>> governmental funding at the top to those getting some benefit (large or
>> small) from those spending decisions.? Suffice it to say that
>> superificial PR too often prevails and superficial and repetitive media
>> is more likely to repeat that PR than to dig deeper for the less
>> exciting truth.? In the present scheme of things, anyone who still
>> believes that the meek shall inherit the Earth are in for a long wait
>> and further disappointment.? PR, money, and media access are still the
>> major power brokers, and the meek have little influence whatsoever, and
>> then only by rare accidents of very marginal media coverage.
>> 
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with either 
>> of these methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as: 
>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
> 
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:? 
> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
> 
> 
> 
>       
> 
> ------------------------------
> 
> Message: 12
> Date: Tue, 29 Jun 2010 18:25:57 -1000
> From: Richard Pyle <deepreef at bishopmuseum.org>
> Subject: Re: [Taxacom] barcode of life
> To: 'Stephen Thorpe' <stephen_thorpe at yahoo.co.nz>, 'Neal Evenhuis'
> <neale at bishopmuseum.org>, 'Kenneth Kinman' <kennethkinman at webtv.net>
> Cc: taxacom at mailman.nhm.ku.edu
> Message-ID: <526D96865150490D855248D9C854B69A at RLPLaptop>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Careful there, champ.....  
> 
> Lest ye cast too many stones, first review this:
> http://www.wordle.net/show/wrdl/1112089/Taxacom_2006-09
> 
> Now, by my reckoning, you started posting to Taxacom in July 2009, and hence
> are only represented in about 15% of the time period covered by the word
> cloud; yet you're clearly larger than I am (having myself posted throughout
> the entire period).
> 
> Not sure if Brian O'Meara can easily generate a revised version of this, but
> I bet the trend has continued.
> 
> Aloha,
> Rich
> 
> P.S. Haven't we settled the Barcode thing long ago?  It's a MAGNIFICENT tool
> for identifications (or at least narrowing down possible identifications).
> It also can point to possible (note my use of the word *possible*) cryptic
> species*. And not even the most ardent Barcode evangelists believe they
> should be used to *define* species boundaries (....right, David?)  It seems
> to me that this debate is mostly a consequence of (mercifully) slow Taxacom
> traffic in recent weeks.
> 
> *Definition of "Cryptic Species": populations for which assignment of
> distinct species-level taxon names best serves the communicative needs of
> biologists, but which are not immediately/obviously distinguishable on the
> basis of gross morphology.
> 
> P.P.S. It wasn't easy, but I think I did manage to pack more words into the
> "P.S." than the original text -- at least if you include this "P.P.S.".  It
> even has its own footnote. So there.
> 
> 
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu 
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of 
>> Stephen Thorpe
>> Sent: Tuesday, June 29, 2010 5:22 PM
>> To: Neal Evenhuis; Kenneth Kinman
>> Cc: taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] barcode of life
>> 
>> otherwise known as "Pyling it on"! :)
>> 
>> 
>> 
>> 
>> ________________________________
>> From: Neal Evenhuis <neale at bishopmuseum.org>
>> To: Kenneth Kinman <kennethkinman at webtv.net>
>> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
>> Sent: Wed, 30 June, 2010 3:17:35 PM
>> Subject: Re: [Taxacom] barcode of life
>> 
>> It's not often that a P.S. is longer than the original text. 
>> This is entering dangerous territory where you may be 
>> competing with Rich Pyle. Be careful ....
>> 
>> ;-)
>> 
>> At 5:09 PM -1000 6/29/10, Kenneth Kinman wrote:
>>> ? Dear All,
>>> ? ? ? ? I agree that using COI alone, or any other gene 
>> sequence alone, 
>>> as the single marker for species delimitation, is a bad 
>> idea. Until we 
>>> have whole genome sequences for a very large number of 
>> species, perhaps 
>>> a combination of two or three independent genes (of which 
>> COI is just 
>>> one) would be a good compromise. What the other one or two 
>> genes that 
>>> would best evolve at different rates (than COI), I can't say.
>>> ? ? ? ? ? ? ? In any case, I find it
>>> disturbing that COI gene sequences would too often be used to excuse 
>>> naming new full species, as opposed to subspecies or 
>> populations, based 
>>> on some arbitrary number of changes in that single gene. 
>> Barcoding for 
>>> identification of populations is probably valuable, but 
>> whether those 
>>> populations are subspecies or full species is a whole 
>> different matter 
>>> that a single gene cannot possibly determine across the 
>> whole gamut of 
>>> organismal evolutionary rates.? Bar Code of Life based on 
>> this single 
>>> gene has its place at this time, and may even be useful as a species 
>>> deliimitator in some taxa. However, extrapolating beyond those 
>>> limitations (without corroboration from other lines of 
>> evidence) can be 
>>> a risky proposition that will cast doubt upon the work of those who 
>>> delve too quickly into that kind of speculation based solely on a 
>>> single gene sequence.
>>> ? ? ? ? ? ? ? ? ? ? ? ----------Ken
>>> Kinman
>>> P.S. I am still convinced that the earlier (and still common) 
>>> fascination with the 16S ribosomal gene sequence (used for 
>> delimiting 
>>> much broader taxa) was equally suspectible to overextrapolation.? To 
>>> this day, such overextrapolation seems to continue to be a 
>> persistent 
>>> impediment to a true understanding of the higher level evolution of 
>>> prokaryotes, early eukaryotes, and even how various subgroups of 
>>> metazoans are related to one another.? Once scientists get 
>> addicted to 
>>> a particular gene sequence, it is an extremely difficult 
>> addiction (and 
>>> point of view) to argue against.? Once a single gene 
>> sequence (COI or 
>>> 16S RNA) becomes a favorite of federal funding, there is an 
>> INCREASING 
>>> risk that a growing number of researchers will 
>> overextrpolate from and 
>>> overinvest funding on those particular genes.? Unfrotunately but not 
>>> surprising.
>>> ? ? ? ? It's similar to the media's current fascination with 
>> the Gulf 
>>> Oil spill, but they will totally ignore other environmental threats 
>>> until it is also too late.? They almost always try to close the barn 
>>> door well after it is too late.? Reactivity continues to be 
>> the norm, 
>>> and proactivity is unfortunately relatively uncommon and 
>> unprofitable.? 
>>> I guess it is no surprise that big corporations are often tempted to 
>>> cut corners (penny wise, but pound foolish).? Oil companies are the 
>>> present targets of public and media scrutiny, but that only 
>> allows Wall 
>>> Street to slip back into their old habits.? Letting the latter take 
>>> advantage of the most recent events shows how the media can 
>> overreact 
>>> to one problem and then be totally distracted from covering another 
>>> major problem.? Not to excuse Wall Street greed, but perhaps 
>> it is at 
>>> the root of Oil companies cutting corners to keep their stock prices 
>>> up.? Either way, it is overpaid CEOs and their middle men 
>> that rake in 
>>> the absurd salaries and stock options, and the real 
>> lower-level workers 
>>> in their companies (a very few who become whistle-blowers to abuses) 
>>> are far less well paid and likely to become fired, demoted, or 
>>> scapegoats for their superiors.? Anyway, this is getting a 
>> little too 
>>> far afield from taxonomy, but I guess these problems tend to trickle 
>>> down from governmental funding at the top to those getting 
>> some benefit 
>>> (large or
>>> small) from those spending decisions.? Suffice it to say that 
>>> superificial PR too often prevails and superficial and 
>> repetitive media 
>>> is more likely to repeat that PR than to dig deeper for the less 
>>> exciting truth.? In the present scheme of things, anyone who still 
>>> believes that the meek shall inherit the Earth are in for a 
>> long wait 
>>> and further disappointment.? PR, money, and media access are 
>> still the 
>>> major power brokers, and the meek have little influence 
>> whatsoever, and 
>>> then only by rare accidents of very marginal media coverage.
>>> 
>>> 
>>> _______________________________________________
>>> 
>>> Taxacom Mailing List
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>> 
>>> The Taxacom archive going back to 1992 may be searched with 
>> either of 
>>> these methods:
>>> 
>>> (1) http://taxacom.markmail.org
>>> 
>>> Or (2) a Google search specified as: 
>>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
>> 
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with 
>> either of these methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:? 
>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
>> 
>> 
>> 
>>       
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with 
>> either of these methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:  
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 13
> Date: Wed, 30 Jun 2010 14:38:19 +1000
> From: "Frank Udovicic" <Frank.Udovicic at rbg.vic.gov.au>
> Subject: [Taxacom] 3 jobs @ RBG Melbourne Australia
> To: <taxacom at mailman.nhm.ku.edu>
> Message-ID: <4C2B56DB02000004000F2F6A at arthur.rbg.vic.gov.au>
> Content-Type: text/plain; charset=UTF-8
> 
> 
> Vacancies - Molecular Systematist / Postdoctoral Fellow x2 (Plant
> Sciences and Biodiversity)
>  
> ?                      Rare Professional Opportunities
> ?                      Three fixed term 2 and 2 ? year contracts,
> starting July 2010
>  
> In these three important roles you will undertake research on the
> systematics of selected plant or fungal groups using molecular
> techniques. The Molecular Systematist will also manage a molecular
> laboratory, seek external funding for research, monitor expenditure, and
> contribute to the scientific curation of the collections held at the
> National Herbarium of Victoria.  One postdoctoral position will advance
> our understanding of the biodiversity and conservation of baobabs and
> Acacia farnesiana.   The other postdoctoral position will undertake
> phylogenetic research on Australian members of Cortinarius subgenus
> Dermocybe.
> The ideal candidates will have a PhD in systematics or equivalent
> experience, with extensive research experience in plant or fungi
> systematics using molecular techniques.  Excellent written and oral
> communication skills are also essential in order to communicate
> effectively with colleagues, the public, international and national
> researchers, and successfully prepare results of research for
> publication.
>  
> See website for position descriptions 
> http://www.rbg.vic.gov.au/about-us/job-opportunities
>  
> Please send applications to recruit at rbg.vic.gov.au by close of business
> Friday 9 July 2010. For further enquiries please call +613 9252 2313.
> All applications must address the key selection criteria as stated in
> the position descriptions, and provide an outline of their intended
> research program for the Molecular Systematist position.
>  
> Regards
> Dr Frank Udovicic
> Manager, Plant Sciences
> National Herbarium of Victoria
> Royal Botanic Gardens Melbourne
> Victoria, Australia. 
> 
> -- 
> This email and any attachments may contain information that is personal, 
> confidential, legally privileged and/or copyright. No part of it should be 
> reproduced, adapted or communicated without the prior written consent of the 
> sender and/or copyright owner.
> 
> It is the responsibility of the recipient to check for and remove viruses. 
> 
> If you have received this email in error, please notify the sender by return 
> email, delete it from your system and destroy any copies. You are not 
> authorised to use, communicate or rely on the information contained in this 
> email.
> 
> Please consider the environment before printing this email.
> 
> This email was Anti Virus checked by RBG Mail Gateway.
> 
> 
> ------------------------------
> 
> Message: 14
> Date: Tue, 29 Jun 2010 21:56:29 -0700 (PDT)
> From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Subject: Re: [Taxacom] barcode of life
> To: Richard Pyle <deepreef at bishopmuseum.org>, Neal Evenhuis
> <neale at bishopmuseum.org>, Kenneth Kinman <kennethkinman at webtv.net>
> Cc: taxacom at mailman.nhm.ku.edu
> Message-ID: <721466.11510.qm at web114211.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> I cast no Stones ... just the odd Beatle!
> 
> Cheers,
> 
> Noah Fents
> 
> 
> 
> 
> ________________________________
> From: Richard Pyle <deepreef at bishopmuseum.org>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Neal Evenhuis 
> <neale at bishopmuseum.org>; Kenneth Kinman <kennethkinman at webtv.net>
> Cc: taxacom at mailman.nhm.ku.edu
> Sent: Wed, 30 June, 2010 4:25:57 PM
> Subject: RE: [Taxacom] barcode of life
> 
> 
> Careful there, champ.....? 
> 
> Lest ye cast too many stones, first review this:
> http://www.wordle.net/show/wrdl/1112089/Taxacom_2006-09
> 
> Now, by my reckoning, you started posting to Taxacom in July 2009, and hence
> are only represented in about 15% of the time period covered by the word
> cloud; yet you're clearly larger than I am (having myself posted throughout
> the entire period).
> 
> Not sure if Brian O'Meara can easily generate a revised version of this, but
> I bet the trend has continued.
> 
> Aloha,
> Rich
> 
> P.S. Haven't we settled the Barcode thing long ago?? It's a MAGNIFICENT tool
> for identifications (or at least narrowing down possible identifications).
> It also can point to possible (note my use of the word *possible*) cryptic
> species*. And not even the most ardent Barcode evangelists believe they
> should be used to *define* species boundaries (....right, David?)? It seems
> to me that this debate is mostly a consequence of (mercifully) slow Taxacom
> traffic in recent weeks.
> 
> *Definition of "Cryptic Species": populations for which assignment of
> distinct species-level taxon names best serves the communicative needs of
> biologists, but which are not immediately/obviously distinguishable on the
> basis of gross morphology.
> 
> P.P.S. It wasn't easy, but I think I did manage to pack more words into the
> "P.S." than the original text -- at least if you include this "P.P.S.".? It
> even has its own footnote. So there.
> 
> 
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu 
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of 
>> Stephen Thorpe
>> Sent: Tuesday, June 29, 2010 5:22 PM
>> To: Neal Evenhuis; Kenneth Kinman
>> Cc: taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] barcode of life
>> 
>> otherwise known as "Pyling it on"! :)
>> 
>> 
>> 
>> 
>> ________________________________
>> From: Neal Evenhuis <neale at bishopmuseum.org>
>> To: Kenneth Kinman <kennethkinman at webtv.net>
>> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
>> Sent: Wed, 30 June, 2010 3:17:35 PM
>> Subject: Re: [Taxacom] barcode of life
>> 
>> It's not often that a P.S. is longer than the original text. 
>> This is entering dangerous territory where you may be 
>> competing with Rich Pyle. Be careful ....
>> 
>> ;-)
>> 
>> At 5:09 PM -1000 6/29/10, Kenneth Kinman wrote:
>>> ? Dear All,
>>> ? ? ? ? I agree that using COI alone, or any other gene 
>> sequence alone, 
>>> as the single marker for species delimitation, is a bad 
>> idea. Until we 
>>> have whole genome sequences for a very large number of 
>> species, perhaps 
>>> a combination of two or three independent genes (of which 
>> COI is just 
>>> one) would be a good compromise. What the other one or two 
>> genes that 
>>> would best evolve at different rates (than COI), I can't say.
>>> ? ? ? ? ? ? ? In any case, I find it
>>> disturbing that COI gene sequences would too often be used to excuse 
>>> naming new full species, as opposed to subspecies or 
>> populations, based 
>>> on some arbitrary number of changes in that single gene. 
>> Barcoding for 
>>> identification of populations is probably valuable, but 
>> whether those 
>>> populations are subspecies or full species is a whole 
>> different matter 
>>> that a single gene cannot possibly determine across the 
>> whole gamut of 
>>> organismal evolutionary rates.? Bar Code of Life based on 
>> this single 
>>> gene has its place at this time, and may even be useful as a species 
>>> deliimitator in some taxa. However, extrapolating beyond those 
>>> limitations (without corroboration from other lines of 
>> evidence) can be 
>>> a risky proposition that will cast doubt upon the work of those who 
>>> delve too quickly into that kind of speculation based solely on a 
>>> single gene sequence.
>>> ? ? ? ? ? ? ? ? ? ? ? ----------Ken
>>> Kinman
>>> P.S. I am still convinced that the earlier (and still common) 
>>> fascination with the 16S ribosomal gene sequence (used for 
>> delimiting 
>>> much broader taxa) was equally suspectible to overextrapolation.? To 
>>> this day, such overextrapolation seems to continue to be a 
>> persistent 
>>> impediment to a true understanding of the higher level evolution of 
>>> prokaryotes, early eukaryotes, and even how various subgroups of 
>>> metazoans are related to one another.? Once scientists get 
>> addicted to 
>>> a particular gene sequence, it is an extremely difficult 
>> addiction (and 
>>> point of view) to argue against.? Once a single gene 
>> sequence (COI or 
>>> 16S RNA) becomes a favorite of federal funding, there is an 
>> INCREASING 
>>> risk that a growing number of researchers will 
>> overextrpolate from and 
>>> overinvest funding on those particular genes.? Unfrotunately but not 
>>> surprising.
>>> ? ? ? ? It's similar to the media's current fascination with 
>> the Gulf 
>>> Oil spill, but they will totally ignore other environmental threats 
>>> until it is also too late.? They almost always try to close the barn 
>>> door well after it is too late.? Reactivity continues to be 
>> the norm, 
>>> and proactivity is unfortunately relatively uncommon and 
>> unprofitable.? 
>>> I guess it is no surprise that big corporations are often tempted to 
>>> cut corners (penny wise, but pound foolish).? Oil companies are the 
>>> present targets of public and media scrutiny, but that only 
>> allows Wall 
>>> Street to slip back into their old habits.? Letting the latter take 
>>> advantage of the most recent events shows how the media can 
>> overreact 
>>> to one problem and then be totally distracted from covering another 
>>> major problem.? Not to excuse Wall Street greed, but perhaps 
>> it is at 
>>> the root of Oil companies cutting corners to keep their stock prices 
>>> up.? Either way, it is overpaid CEOs and their middle men 
>> that rake in 
>>> the absurd salaries and stock options, and the real 
>> lower-level workers 
>>> in their companies (a very few who become whistle-blowers to abuses) 
>>> are far less well paid and likely to become fired, demoted, or 
>>> scapegoats for their superiors.? Anyway, this is getting a 
>> little too 
>>> far afield from taxonomy, but I guess these problems tend to trickle 
>>> down from governmental funding at the top to those getting 
>> some benefit 
>>> (large or
>>> small) from those spending decisions.? Suffice it to say that 
>>> superificial PR too often prevails and superficial and 
>> repetitive media 
>>> is more likely to repeat that PR than to dig deeper for the less 
>>> exciting truth.? In the present scheme of things, anyone who still 
>>> believes that the meek shall inherit the Earth are in for a 
>> long wait 
>>> and further disappointment.? PR, money, and media access are 
>> still the 
>>> major power brokers, and the meek have little influence 
>> whatsoever, and 
>>> then only by rare accidents of very marginal media coverage.
>>> 
>>> 
>>> _______________________________________________
>>> 
>>> Taxacom Mailing List
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>> 
>>> The Taxacom archive going back to 1992 may be searched with 
>> either of 
>>> these methods:
>>> 
>>> (1) http://taxacom.markmail.org
>>> 
>>> Or (2) a Google search specified as: 
>>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
>> 
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with 
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>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:? 
>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
>> 
>> 
>> 
>> ? ? ? 
>> _______________________________________________
>> 
>> Taxacom Mailing List
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>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with 
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>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:? 
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>> 
> 
> 
>       
> 
> ------------------------------
> 
> Message: 15
> Date: Wed, 30 Jun 2010 07:25:16 -0400
> From: "Schindel, David" <schindeld at si.edu>
> Subject: Re: [Taxacom] barcode of life
> To: Richard Pyle <deepreef at bishopmuseum.org>, 'Stephen Thorpe'
> <stephen_thorpe at yahoo.co.nz>, 'Neal Evenhuis'
> <neale at bishopmuseum.org>,  'Kenneth Kinman' <kennethkinman at webtv.net>
> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <DB179119972FE14E8A80A23C3425ED9D031C7290C0 at SI-MSEV02.US.SINET.SI.EDU>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Absolutely right, Rich.  
> 
> As I feared, Taxacom is now arguing about their claims for what others may 
> have claimed for COI.  Can anyone site a single formal description of a new 
> species based only on COI differences and a standard 2% threshold with no 
> other delimiting features, or is this an imaginary boogyman under the bed?  
> 
> CBOL has always supported barcode data for (1) *identification* of species 
> delimited by and corroborated with an integrated approach (morphology, 
> ecology, biogeography) and (2) documenting variation to *help* the species 
> discovery process.  When it comes to microbes we may not have enough 
> independent features, but shouldn't we welcome any tool that provides insight 
> into very poorly known biotas on which few people are working? 
> 
> David
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Pyle
> Sent: Wednesday, June 30, 2010 12:26 AM
> To: 'Stephen Thorpe'; 'Neal Evenhuis'; 'Kenneth Kinman'
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] barcode of life
> 
> 
> Careful there, champ.....  
> 
> Lest ye cast too many stones, first review this:
> http://www.wordle.net/show/wrdl/1112089/Taxacom_2006-09
> 
> Now, by my reckoning, you started posting to Taxacom in July 2009, and hence
> are only represented in about 15% of the time period covered by the word
> cloud; yet you're clearly larger than I am (having myself posted throughout
> the entire period).
> 
> Not sure if Brian O'Meara can easily generate a revised version of this, but
> I bet the trend has continued.
> 
> Aloha,
> Rich
> 
> P.S. Haven't we settled the Barcode thing long ago?  It's a MAGNIFICENT tool
> for identifications (or at least narrowing down possible identifications).
> It also can point to possible (note my use of the word *possible*) cryptic
> species*. And not even the most ardent Barcode evangelists believe they
> should be used to *define* species boundaries (....right, David?)  It seems
> to me that this debate is mostly a consequence of (mercifully) slow Taxacom
> traffic in recent weeks.
> 
> *Definition of "Cryptic Species": populations for which assignment of
> distinct species-level taxon names best serves the communicative needs of
> biologists, but which are not immediately/obviously distinguishable on the
> basis of gross morphology.
> 
> P.P.S. It wasn't easy, but I think I did manage to pack more words into the
> "P.S." than the original text -- at least if you include this "P.P.S.".  It
> even has its own footnote. So there.
> 
> 
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu 
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of 
>> Stephen Thorpe
>> Sent: Tuesday, June 29, 2010 5:22 PM
>> To: Neal Evenhuis; Kenneth Kinman
>> Cc: taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] barcode of life
>> 
>> otherwise known as "Pyling it on"! :)
>> 
>> 
>> 
>> 
>> ________________________________
>> From: Neal Evenhuis <neale at bishopmuseum.org>
>> To: Kenneth Kinman <kennethkinman at webtv.net>
>> Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
>> Sent: Wed, 30 June, 2010 3:17:35 PM
>> Subject: Re: [Taxacom] barcode of life
>> 
>> It's not often that a P.S. is longer than the original text. 
>> This is entering dangerous territory where you may be 
>> competing with Rich Pyle. Be careful ....
>> 
>> ;-)
>> 
>> At 5:09 PM -1000 6/29/10, Kenneth Kinman wrote:
>>> ? Dear All,
>>> ? ? ? ? I agree that using COI alone, or any other gene 
>> sequence alone, 
>>> as the single marker for species delimitation, is a bad 
>> idea. Until we 
>>> have whole genome sequences for a very large number of 
>> species, perhaps 
>>> a combination of two or three independent genes (of which 
>> COI is just 
>>> one) would be a good compromise. What the other one or two 
>> genes that 
>>> would best evolve at different rates (than COI), I can't say.
>>> ? ? ? ? ? ? ? In any case, I find it
>>> disturbing that COI gene sequences would too often be used to excuse 
>>> naming new full species, as opposed to subspecies or 
>> populations, based 
>>> on some arbitrary number of changes in that single gene. 
>> Barcoding for 
>>> identification of populations is probably valuable, but 
>> whether those 
>>> populations are subspecies or full species is a whole 
>> different matter 
>>> that a single gene cannot possibly determine across the 
>> whole gamut of 
>>> organismal evolutionary rates.? Bar Code of Life based on 
>> this single 
>>> gene has its place at this time, and may even be useful as a species 
>>> deliimitator in some taxa. However, extrapolating beyond those 
>>> limitations (without corroboration from other lines of 
>> evidence) can be 
>>> a risky proposition that will cast doubt upon the work of those who 
>>> delve too quickly into that kind of speculation based solely on a 
>>> single gene sequence.
>>> ? ? ? ? ? ? ? ? ? ? ? ----------Ken
>>> Kinman
>>> P.S. I am still convinced that the earlier (and still common) 
>>> fascination with the 16S ribosomal gene sequence (used for 
>> delimiting 
>>> much broader taxa) was equally suspectible to overextrapolation.? To 
>>> this day, such overextrapolation seems to continue to be a 
>> persistent 
>>> impediment to a true understanding of the higher level evolution of 
>>> prokaryotes, early eukaryotes, and even how various subgroups of 
>>> metazoans are related to one another.? Once scientists get 
>> addicted to 
>>> a particular gene sequence, it is an extremely difficult 
>> addiction (and 
>>> point of view) to argue against.? Once a single gene 
>> sequence (COI or 
>>> 16S RNA) becomes a favorite of federal funding, there is an 
>> INCREASING 
>>> risk that a growing number of researchers will 
>> overextrpolate from and 
>>> overinvest funding on those particular genes.? Unfrotunately but not 
>>> surprising.
>>> ? ? ? ? It's similar to the media's current fascination with 
>> the Gulf 
>>> Oil spill, but they will totally ignore other environmental threats 
>>> until it is also too late.? They almost always try to close the barn 
>>> door well after it is too late.? Reactivity continues to be 
>> the norm, 
>>> and proactivity is unfortunately relatively uncommon and 
>> unprofitable.? 
>>> I guess it is no surprise that big corporations are often tempted to 
>>> cut corners (penny wise, but pound foolish).? Oil companies are the 
>>> present targets of public and media scrutiny, but that only 
>> allows Wall 
>>> Street to slip back into their old habits.? Letting the latter take 
>>> advantage of the most recent events shows how the media can 
>> overreact 
>>> to one problem and then be totally distracted from covering another 
>>> major problem.? Not to excuse Wall Street greed, but perhaps 
>> it is at 
>>> the root of Oil companies cutting corners to keep their stock prices 
>>> up.? Either way, it is overpaid CEOs and their middle men 
>> that rake in 
>>> the absurd salaries and stock options, and the real 
>> lower-level workers 
>>> in their companies (a very few who become whistle-blowers to abuses) 
>>> are far less well paid and likely to become fired, demoted, or 
>>> scapegoats for their superiors.? Anyway, this is getting a 
>> little too 
>>> far afield from taxonomy, but I guess these problems tend to trickle 
>>> down from governmental funding at the top to those getting 
>> some benefit 
>>> (large or
>>> small) from those spending decisions.? Suffice it to say that 
>>> superificial PR too often prevails and superficial and 
>> repetitive media 
>>> is more likely to repeat that PR than to dig deeper for the less 
>>> exciting truth.? In the present scheme of things, anyone who still 
>>> believes that the meek shall inherit the Earth are in for a 
>> long wait 
>>> and further disappointment.? PR, money, and media access are 
>> still the 
>>> major power brokers, and the meek have little influence 
>> whatsoever, and 
>>> then only by rare accidents of very marginal media coverage.
>>> 
>>> 
>>> _______________________________________________
>>> 
>>> Taxacom Mailing List
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>> 
>>> The Taxacom archive going back to 1992 may be searched with 
>> either of 
>>> these methods:
>>> 
>>> (1) http://taxacom.markmail.org
>>> 
>>> Or (2) a Google search specified as: 
>>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
>> 
>> 
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with 
>> either of these methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:? 
>> site:mailman.nhm.ku.edu/pipermail/taxacom? your search terms here
>> 
>> 
>> 
>>       
>> _______________________________________________
>> 
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> 
>> The Taxacom archive going back to 1992 may be searched with 
>> either of these methods:
>> 
>> (1) http://taxacom.markmail.org
>> 
>> Or (2) a Google search specified as:  
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>> 
> 
> 
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these 
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> ------------------------------
> 
> Message: 16
> Date: Wed, 30 Jun 2010 06:00:46 -0700 (PDT)
> From: Dilrukshan Wijesinghe <dpwijesinghe at yahoo.com>
> Subject: Re: [Taxacom] Polygonum cespitosum or P. caespitosum?
> To: Taxacom <taxacom at mailman.nhm.ku.edu>
> Message-ID: <773958.59004.qm at web35405.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
> 
> Many thanks for all the responses. The consensus seems to be that cespitosum 
> is 
> the original spelling and therefore the correct form of the name.
> 
> Priyantha
> 
> D. P. Wijesinghe
> dpwijesinghe at yahoo.com
> 
> 
>       
> 
> ------------------------------
> 
> Message: 17
> Date: Wed, 30 Jun 2010 08:13:44 -0500
> From: "Richard Zander" <Richard.Zander at mobot.org>
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> To: "Schindel, David" <schindeld at si.edu>, "Donat Agosti"
> <agosti at amnh.org>, <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <471E2B0E09E14643942D99FC6AD54E6603BD9436 at MBGMail01.mobot.org>
> Content-Type: text/plain; charset="us-ascii"
> 
> 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 
> 
>  
> 
>  
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of
> these
> methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>  
> 
> __________ Information from ESET Smart Security, version of virus
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> 
> The message was checked by ESET Smart Security.
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> http://www.eset.com
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> 
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of
> these methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> 
> 
> ------------------------------
> 
> Message: 18
> Date: Wed, 30 Jun 2010 08:23:58 -0500
> From: "Richard Zander" <Richard.Zander at mobot.org>
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> To: "Doug Yanega" <dyanega at ucr.edu>, <TAXACOM at MAILMAN.NHM.KU.EDU>
> Message-ID:
> <471E2B0E09E14643942D99FC6AD54E6603BD9439 at MBGMail01.mobot.org>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Doug:
> 
> Testable hypotheses? I've recently discovered structuralism, the search for 
> hidden structures or patterns in nature or the human mind. It was started by 
> Saussure in linguistics, and is now found in many fields (check Wikipedia). 
> 
> Structuralism is intended as a replacement for empiricism. Structures are 
> pretty much engraved in the ground of being, and all theory and all 
> observation is just human-generated window dressing. Systematics has been a 
> structuralist stomping ground for the past 30 years, and "testable hypotheses" 
> are really quite pass?. 
> 
> *****************************
> 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 Doug Yanega
> Sent: Tuesday, June 29, 2010 6:17 PM
> To: TAXACOM at MAILMAN.NHM.KU.EDU
> Subject: Re: [Taxacom] barcode of life wins Ebbe Nielsen Prize
> 
> 
> If one does not share that belief, then the claim that COI is a reliable 
> species-level marker looks like a massive tautology. What, after all, is the 
> *independent test* that can be used to support or refute the hypothesis that 
> any given "species" has a distinct *and* unique COI profile? Building a tree 
> of haplotypes is not a test of species boundaries. Isn't science supposed to 
> be based on testable 
> hypotheses??
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> 
> Taxacom Mailing List
> 
> Taxacom at mailman.nhm.ku.edu
> 
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The entire Taxacom Archive back to 1992 can be searched with either of these 
> methods:
> 
> http://taxacom.markmail.org
> 
> Or use a Google search specified as:  
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> End of Taxacom Digest, Vol 51, Issue 28
> ***************************************