[Taxacom] I'm furious over article: On typeless species and the perils of fast taxonomy

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Thu May 12 21:28:10 CDT 2016


Rich,

A good diagnostic photo is only already disallowed to actually *be* a type, it is not disallowed to *be a proxy* for the type, which is exactly what Evenhuis & Marshall did. This rather subtle difference is likely to be a source of confusion.

"The question I would like to see addressed is whether the "preserved specimen" should be singled out as being required to exist at the time a new name is published (in some or all cases), and how a revised Code should be crafted to ultimately result in more good than harm"

Trying again to address that very question, but with another question: Why should a preserved specimen be required in all cases, when (1) the specimen may be diagnostically poor or even useless; and (2) in cases, say, where there is no specimen but only a photo, the photo may be diagnostically sufficient for a good description? That is the question! Something of a dilemma: do we make a requirement such that we miss out on some good opportunities just to avoid some bad possibilities?

Cheers,

Stephen

--------------------------------------------
On Fri, 13/5/16, Richard Pyle <deepreef at bishopmuseum.org> wrote:

 Subject: RE: [Taxacom] I'm furious over article: On typeless species and the	perils of fast taxonomy
 To: "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>, "'JF Mate'" <aphodiinaemate at gmail.com>, "'Taxacom'" <taxacom at mailman.nhm.ku.edu>
 Received: Friday, 13 May, 2016, 2:03 PM
 
 Hi Stephen,
 
 Thanks for that.  I need to clarify, again, that a good
 diagnostic photo is already disallowed, because photos
 cannot serve as type specimens (I know you know this, but
 others keep confusing the photo for the type; which is not
 the case).  That's part of why I'd like to see this
 discussion shift away from being about "Photos" vs. "DNA
 sequences" vs. "poorly preserved specimens" vs. "well
 preserved specimens", etc.  All of these things
 represent evidence of the properties of a name-bearing type
 specimen. The question I would like to see addressed is
 whether the "preserved specimen" should be singled out as
 being required to exist at the time a new name is published
 (in some or all cases), and how a revised Code should be
 crafted to ultimately result in more good than harm.
 
 Aloha,
 Rich
 
 P.S. Doug made an excellent comparison with fossil material
 as well; presumably any rules associated with "extant
 specimens" would apply only to "extant species"?
 
 > -----Original Message-----
 > From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
 > Sent: Thursday, May 12, 2016 3:50 PM
 > To: 'JF Mate'; 'Taxacom'; deepreef at bishopmuseum.org
 > Subject: Re: [Taxacom] I'm furious over article: On
 typeless species and the
 > perils of fast taxonomy
 > 
 > Rich,
 > One point that I have been trying to make, but which
 may be lost in the
 > discussion is that I don't think it is worthwhile for
 the Code to get too fussy
 > about deposition of types, since there is no practical
 way that the Code can
 > ensure that any deposited type is actually diagnostic
 enough to be useful, so
 > why require the deposition of something which may be
 entirely useless? It
 > would be unfortunate if a good diagnostic photo was
 disallowed, but a
 > completely nondiagnostic type specimen was allowed!
 There is of course a
 > continnum between diagnostic and nondiagnostic.
 > Stephen
 > 
 > --------------------------------------------
 > On Fri, 13/5/16, Richard Pyle <deepreef at bishopmuseum.org>
 wrote:
 > 
 >  Subject: Re: [Taxacom] I'm furious over article:
 On typeless species and the
 >     perils of fast taxonomy
 >  To: "'JF Mate'" <aphodiinaemate at gmail.com>,
 "'Taxacom'"
 > <taxacom at mailman.nhm.ku.edu>
 >  Received: Friday, 13 May, 2016, 1:25 PM
 > 
 >  Hi Jason,
 > 
 >  My point wasn't that all
 >  holotypes will eventually be lost or
 destroyed.  My point  is that too much
 > emphasis is being placed on  "photo", and not
 enough is being placed on what
 > we're really talking about:  which is the scope
 of  acceptable evidence
 > regarding the properties and taxonomic  identity
 of a type specimen.  It's being
 > presented as a  "black and white", "Photo vs.
 Specimen"
 >  issue, but it's not.  There is a complete
 spectrum of  circumstances, which can
 > vary among different taxa,  different preservation
 techniques, and different
 > kinds of  characters that we use to define species
 boundaries.
 > 
 >  Specimens begin to deteriorate
 >  the moment they die.  Preservation
 techniques mitigate this  to varying
 > degrees, but almost without exception, 
 potentially diagnostic characters fade
 > or vanish from the  specimen over time. Most
 fishes are fixed in formalin,
 > rendering subsequent gathering of DNA sequences
 extremely  difficult. Many
 > species begin to lose their life color after 
 death, and such color characteristics
 > can not only be  diagnostic, but might even play a
 role in maintaining  species
 > boundaries (and, hence, are of fundamental 
 importance).  Of course, we
 > always do what we can to  circumvent these
 problems.  We extract tissue
 > samples and  store them in conditions that are
 conducive to subsequent  DNA
 > sequencing. We take high-quality color images of live
 or  freshly dead
 > specimens to preserve evidence of their life 
 color.  In an ideal world, the
 > holotype would be  flash-frozen while still alive
 and preserved cryogenically,
 > after high-resolution CT scans are made of its 
 three-dimensional internal
 > structure, ultra-high-resolution  images are taken
 from every conceivable
 > angle, scanning  electron microscopy is made of
 the most diagnostic tiny
 > structures, etc., etc.  Rarely do we achieve this
 ideal in  the real world.
 > 
 >  I have yet
 >  to meet ANYONE who doesn't agree that, in the
 vast  majority of cases, the
 > preserved specimen is the MOST  important evidence
 to maintain for
 > representing the  properties of a type specimen
 (and, hence, the biological
 > basis for a taxon name).  In some cases,
 high-quality  images of life color are
 > also extremely important.  Increasingly, the same
 might be said for tissue
 > samples for  DNA sequencing. I would wager that
 pretty-much everyone
 > agrees with all this.  NO ONE contends that "the
 type  specimen ... is not
 > valuable" -- suggestions to the  contrary are
 unhelpful and somewhat
 > hyperbolic.
 > 
 >  From my perspective, the issue
 >  that is at hand is about the question: "Should we
 alter  the Code to restrict or
 > disallow for the establishment of a  new
 species-group taxon name in cases
 > where the type  specimen is lost or destroyed
 prior to the publication of  the
 > name?" Obviously, the Code currently does allow
 for  it, and the Code does not
 > currently attempt to distinguish  circumstances
 when it is or is not appropriate.
 > 
 >  While everyone keeps focusing
 >  on the relative merits of images vs. preserved
 specimens  (I'm surprised there
 > hasn't been more talk on names  based on DNA
 sequences absent preserved
 > specimens), what I  see as the real (and
 addressable) issues are being largely
 > ignored.  These include:
 >  - Should the Code
 >  require that the name-bearing type specimen of
 all new  species group names
 > be extant and preserved at the time of 
 publication?
 >  - What proof for such would be
 >  required within the published work itself (or,
 perhaps  within the ZooBank
 > registration record)?
 >  -
 >  Should there be specific exceptions?  If so,
 does the Code  need to enumerate
 > them specifically? Or, would exceptions  require
 evaluation by the Commission
 > on a case-by-case  basis?
 > 
 >  These are just the
 >  basic questions we need to address.  Once
 these are  answered, there is a long
 > list of nitty-gritty questions  about exact
 wording -- not only of relevant Articles,
 > but  also of glossary definitions as well.
 > 
 >  Personally, as a Taxonomist, I wait until a 
 specimen is in hand before naming
 > a new species.  In fact,  I have delayed
 naming a conspicuous new species of
 > butterflyfish here in Hawaii by more than a decade
 even  though I have some
 > excellent specimens with great color  photos,
 because I wanted to make sure I
 > had a good tissue  samples from the Holotype to
 allow for future molecular
 > comparisons.  So my contributions to this
 discussion are  not an effort to ensure
 > the ability to name new species when  the type is
 lost or destroyed prior to
 > publication. Rather,  my interest is in actually
 understanding exactly how
 > restrictions of that sort could be implemented within
 the  Code.  The
 > Commission discussed this issue in detail at a
 >  2005 meeting in Washington DC.  Thus far, I
 have neither  seen any evidence
 > that this is actually more of a  "problem" in
 real-world taxonomy than it has
 > been  for two and a half centuries, nor have I
 seen any new  compelling reason
 > why the system that has worked for so long  will
 somehow work less effectively
 > in the future because of  this particular
 issue.  Given that the Commission is
 > now  re-visiting this question, now would be a
 really, really  good time to
 > discuss these things.
 > 
 >  Aloha,
 >  Rich
 > 
 > 
 >  Richard L. Pyle, PhD
 >  Database Coordinator for Natural Sciences | 
 Associate Zoologist in Ichthyology
 > | Dive Safety Officer  Department of Natural
 Sciences, Bishop Museum,
 >  1525 Bernice St., Honolulu, HI 96817
 >  Ph:
 >  (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org
 > http://hbs.bishopmuseum.org/staff/pylerichard.html
 > 
 > 
 > 
 >  > -----Original Message-----
 >  > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 >  On Behalf Of
 >  > JF Mate
 >  > Sent: Thursday, May 12, 2016 1:06 PM
 >  > To: Taxacom
 >  > Subject:
 >  Re: [Taxacom] I'm furious over article: On
 typeless  species and the  > perils of
 > fast  taxonomy  >  > I was 
 going to leave this thread die but I will jump in
 > briefly.
 >  >
 >  > Rich, I
 >  understand what you are getting at but even if I
 accepted  your  > hypothesis
 > that specimens have a  finite life of decades or
 centuries, so what? In  > a few
 > decades we might all have a Mr  CT-Scan and a Mr
 DNA and we might be  >
 > digitizing our types down to the molecular level. We
 can´t  do that to a picture.
 > I  > just can´t  understand how the type
 specimen (which often times is the  only
 > > specimen of a species) is not  valuable.
 >  >
 >  >
 >  Stephen, what are you talking about now.
 Field  identification is common but it
 > > does  not apply to pictures in the way you
 want us to think.
 >  Bird-watchers
 >  > examine the bird through
 >  their binoculars, listen to their song and
 observe their  >
 > behaviour/movements before identifying the 
 animal. It is identifiable in the  >
 > field  but it is not a picture.
 >  > Ditto with
 >  plants. Your example only applies to countries
 with poor  biodiversity  > and on
 > small groups of  large taxa. Talk about framing
 your point in the best  >
 > possible angle.
 >  >
 >  > This kerfuffle is because of the
 bigger  picture.
 >  >
 >  > Jason
 >  >
 >  > On 13 May 2016 at
 >  07:12, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
 > wrote:
 >  > > Hi
 >  Daniel,
 >  > >
 >  > >
 >  You said to me: "you seem to be imagining some
 sort of  excellent best-case  >
 > dream  scenario..."
 >  > >
 >  > > My reply: Not at all! I am only
 >  imagining the sort of situation wherein a 
 > species is distinctive enough to be
 > recognisable in the field (and therefore  >
 recognisable by way of good photo).
 > Are  you suggesting that no species are 
 >  recognisable in the field? Tell that to
 > a field botanist!
 >  > >
 >  > > You also
 >  said: "I cannot see how having a specimen in
 addition  to a set of  > photos
 > could possibly give  you less data than just
 having the photo. How,  > exactly, is
 > the specimen reducing the  amount of information
 obtainable from  >  the
 > photo(s)?"
 >  > >
 >  > > My reply: I didn't say that! What
 >  I said was "having a specimen might
 actually  > give you no more data (and
 > possibly even  less data) than a good photo does,
 as  >  specimens tend to
 > degrade", meaning that a specimen can  tell you
 less than a  > photo. I  didn't
 > say that specimen + photo might tell you less 
 than the photo  > alone!
 >  > >
 >  > > You said:
 >  "In any case, my original point was that given
 how much  of an  > unnecessary
 > hassle it can be to  work with species where the
 type is known only  > from
 > photos and the specimen has  subsequently
 deliberately (or accidentally)  >
 > been destroyed, I cannot see any virtue in 
 essentially destroying the specimen
 > >  that could have been deposited as a holotype
 already before  the manuscript
 > > has been  published"
 >  > >
 >  > > My reply: Nobody is advocating the
 >  deliberate avaoidance of depositing a
 >  >
 >  type specimen. It is a question of what to do if
 you *only*  have a photo.
 >  > >
 >  >
 >  >
 >  > > Cheers,
 >  >
 >  >
 >  > > Stephen
 >  >
 >  >
 >  > >
 >  --------------------------------------------
 >  > > On Fri, 13/5/16, Daniel Leo
 >  Gustafsson <kotatsu.no.leo at gmail.com>
 >  wrote:
 >  > >
 >  > >
 >  Subject: Re: [Taxacom] I'm furious over article:
 On  typeless species  > > and
 > the perils of  fast taxonomy  > > 
 To: "Stephen  Thorpe"
 > <stephen_thorpe at yahoo.co.nz> 
 > >  Cc: "JF Mate"
 > <aphodiinaemate at gmail.com>, 
 "Taxacom"
 >  > > <taxacom at mailman.nhm.ku.edu>
 >  > >  Received: Friday, 13 May, 2016,
 >  4:20 AM
 >  > >
 >  >
 >  >  Hi,,
 >  > >
 >  >
 >  >  Conversely, you seem to be imagining
 some  sort of  excellent  > >
 best-case
 > dream  scenario, in which all  possible
 characters are  > > adequately
 > catalogued and  illustrated by the original
 photos,  >  > including
 > characters  that have not yet been 
 recognised as useful for  > > the taxon
 > in  question, and basing your argument on that. I
 find  that  > > to  be as
 > unhelpful an  approach as assuming the opposite.
 >  >
 >  >
 >  > >  Other than that, I agree
 >  with
 >  > >  Jason that photos plus
 >  specimens is potentially a greater  source
 of  > > information than just photos.
 > and I  cannot see how  having a
 specimen  > >  in addition to a set of
 photos
 > could  possibly give you  less data
 than  > > just having the  photo.
 > How,  exactly, is the specimen reducing the 
 > > amount of
 > information  obtainable  from the photo(s)?
 >  > >
 >  > >  In any case, my original point
 was  that  given how much of an  > >
 > unnecessary hassle it can be to work  with species
 where  the type is  > > known
 > only from photos  and  the specimen has
 subsequently deliberately  > > (or
 > accidentally)  been destroyed, I  cannot see
 any virtue in  > >
 > essentially  destroying the specimen that could
 have been  deposited as  > >
 > a  holotype already  before the manuscript
 has been published.
 >  > >  At the very least, it creates
 >  unnecessary extra work future
 >  > >
 >  taxonomists.
 >  > >
 >  >
 >  >  Cheers,
 >  > >  Daniel
 >  > >
 >  > >  On Tue,
 >  May 10, 2016 at
 >  > >  11:17 PM,
 >  Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
 > >  wrote:
 >  > >
 >  Hi again
 >  > >  Daniel,
 >  > >
 >  > >  I think I
 >  have just replied to Jason on some of these 
 points, but  > > again: nobody is
 > advocating the  deliberate  reduction of
 available  >  > data. If you only have a
 > photo, and  little or no  prospect of
 getting  > > additional  material,
 then  it is a
 > waste of existing data (i.e. the  > > photo)
 not to use  it. Also, having  a
 > specimen might actually give you  > > 
 no more  data (and possibly even less
 > data) than a good  photo does,  > > as
 specimens tend to  degrade. Anyway,
 > there is nothing, to  my mind  > >
 anyway, that precludes more data  turning up
 > after  description to help  >  >
 to confirm or refute the original  hypothesis (i.e.
 >  that it is a new
 >  > > species). I think
 >  that you  may be thinking of the worst
 case  > > scenario, and basing
 > your  argument  on that! By the way, I
 wasn't  > >  accusing *you* of 
 "bashing
 > amateurs", or of  misrepresenting the  >
 > Code! That  comment was directed
 > at the articles in  Systematic Ent.
 >  > > and BZN.
 >  > >
 >  > >  Cheers,
 >  >
 >  >
 >  > >  Stephen
 >  > >
 >  > >
 >  > >
 >  > >
 >  --------------------------------------------
 >  > >
 >  > >  On Wed,
 >  11/5/16, Daniel Leo Gustafsson <kotatsu.no.leo at gmail.com> 
 > >  wrote:
 >  > >
 >  > >
 >  > >
 >  > >   Subject: Re:
 [Taxacom]
 >  I'm furious over article: On  typeless
 >  > > species and the perils of fast
 >  taxonomy
 >  > >
 >  >
 >  >   To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz> 
 > >  >  >   Cc: "JF
 > Mate" <aphodiinaemate at gmail.com>, 
 "Taxacom"
 >  > > <taxacom at mailman.nhm.ku.edu>
 >  > >
 >  >
 >  >   Received: Wednesday, 11
 May, 2016, 5:05  PM  > >  >
 >  > >  > 
 >   We seem
 > to be talking past each  > > 
 >  >   other, as your post is
 largely a  reiteration of
 > my  post.
 >  > >
 >  > >   Even if the photos
 are
 >  the best photos since the dawn  of
 >  >
 >  >
 >  > >   photography, I
 >  still have "no way to get more data 
 than  > >  > 
 >   what was in the original
 > publication,  regardless of what  the 
 > >  > >   code
 actually  says". If the
 > holotype is lost --  whether  > > 
 >  >   it was released or
 destroyed in a fire or
 > deliberately  > >  > 
 >   thrown away -- this is still the
 case,  with the
 > caveat  that  > >  >
 >   if a deposited holotype  existed
 somewhere in
 > a  collection  >  >  >
 >   between the  description and the
 disappearance, there
 > is  a  > >  > 
 >   chance that some other taxonomist may
 have  had a look at  it
 > > >  > >   and added
 information.
 >  This is also still the case if  the
 >  >
 >  >
 >  > >   species was
 >  described by text only, or text and 
 drawings,  > >  > 
 >   regardless of the
 > quality of any of these  sets of  >
 >  >  >   information. I
 agree with all of these
 > points; the photo  as  > >  >
 >   such is a red  herring.
 >  > >
 >  >
 >  >
 >  > >
 >  >
 >  >   What remains, and what I
 sought to
 >  illustrate
 >  > >
 >  >
 >  >   with my first example, is
 that it is  tedious and  > > 
 >  >   time-consuming,
 > not to mention impossible,  to try to 
 guess  > >  > >   what
 characters a  species
 > possess when it is impossible  to  >
 >  >  >   study a
 specimen, regardless of the
 > reason  for this  > >  > 
 >   impossibility. Just as limiting
 the  sources of
 > nomina  dubia  > >  >
 >   is a valid way to try to  limit
 the number of (at least  >
 > >
 >  new)
 >  > >
 >  >
 >  >   nomina dubia, limiting the
 sources of  guesswork is a  valid  >
 >  > >   way to
 > limit the number  of species for which we have
 to  > >  > >   guess
 the
 > characters  because of idiosyncrasies of its 
 >  >  >
 >   author(s)  (including their
 > having released the specimens  for  >
 >  >  >   whatever
 reason).
 >  >
 >  >
 >  > >
 >  > >
 >  > >   For what it's worth,
 >  the same author
 >  > >
 >  > >   who presumably threw
 >  away the holotype of the species I
 >  >
 >  >
 >  > >   referred to
 >  previously also described virtually all his 
 > >  >  >   species and
 genera based
 > solely of host  relationships,  and 
 > >  > >   the
 descriptions  typically contain
 > more text about the  >  >  >
 >   person he is  naming the species
 after than
 > any  diagnostic  > >  > 
 >   characters. He's also an early
 version  of Hoser,  and
 > > >  > >   spent his
 early career  going through older publications 
 and  >  >  >
 > >   giving names to  any
 population of chewing lice the  original  >
 >  >
 > >   author claimed to be slightly
 different,  without every  > > 
 >  >   having seen
 > specimens. Nevertheless, he  was a 
 professional  > >  >
 >   in the sense of
 > getting  paid to do this. I have not yet 
 read  >  >  >
 >   the paper that  started
 > this whole conversation, so I am  not  >
 >  >  >   here to bash
 amateurs. I just
 > don't  see how  > >  > 
 >   "promoting good taxonomy" is 
 consistent with  > >  >
 > >   arbitrarily and 
 irreversibly limiting the amount of  data  >
 >  >  >   available
 > to future workers.
 >  > >
 >  > >
 >  > >
 >  >
 >  >   Cheers,
 >  > >
 >  > >   Daniel
 >  > >
 >  > >
 >  >
 >  _______________________________________________
 >  > Taxacom Mailing List
 >  >
 >  Taxacom at mailman.nhm.ku.edu
 >  > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 >  > The Taxacom Archive back to 1992 may
 be  searched at:
 >  > http://taxacom.markmail.org
 >  >
 >  > Channeling
 >  Intellectual Exuberance for 29 years in 2016.
 > 
 >  _______________________________________________
 >  Taxacom Mailing List
 >  Taxacom at mailman.nhm.ku.eduhttp://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 >  The Taxacom Archive back to 1992 may be 
 searched at:
 > http://taxacom.markmail.org
 > 
 >  Channeling Intellectual
 >  Exuberance for 29 years in 2016.



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