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

Richard Pyle deepreef at bishopmuseum.org
Thu May 12 21:03:41 CDT 2016


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
>  > >
>  > >
>  >
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