[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.

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

The impact and strategic significance of BOLD, accordng to Krishtalka,
promises to rival that of Genbank. ?BOLD 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.? On BOLD?
application to the GBIF network, Krishtalka continues, ?BOLD Sytems also
represents a new class of tools for potential collaboration with GBIF in the
shere of genomic biodiversity data.??

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
-- 



> From: <taxaom-request at mailman.nhm.ku.edu>
> Reply-To: <taxacom at mailman.nh.ku.edu>
> Date: Wed, 30 Jun 2010 12:00:01 -0500
> To: <taxacom at mailman.nm.ku.edu>
> Subject: Taacom Digest, Vol 51, Issue 28
> 
> Send Taxacom mailing list submissions o
> taxacom at mailman.nhm.ku.edu
> 
> To subscribe or unsubscribe viathe World Wide Web, visit
> http://mailman.nhm.ku.edu/mailman/lstinfo/taxacom
> or, via email, send a message with subject or body 'help' to
> taxacom-equest at mailman.nhm.ku.edu
> 
> You can reach the person managin the list at
> taxacom-owner at mailman.nhm.ku.edu
> 
> When replying, please edit your Subject lineso it is more specific
> than "Re: Contents of Taxacom diget..."
> 
> 
> 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
>  
> 
> __________ Information from ESET Smart Security, version of virus signatur
> database 5236 (20100629) __________
> 
> The message was hecked by ESET Smart Security.
> 
> http://www.eset.com
>  
> 
> 
> 
> 
> ------------------------------
> 
> 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 
>> 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: 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
> signature
> database 5236 (20100629) __________
> 
> The message was checked by ESET Smart Security.
> 
> http://www.eset.com
>  
> 
> 
> _______________________________________________
> 
> 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
> ***************************************