[Taxacom] barcode of life

Schindel, David schindeld at si.edu
Wed Jun 30 06:25:16 CDT 2010 

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

More information about the Taxacom mailing list