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[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 20:50:17 CDT 2016 

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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 > The Taxacom Archive back to 1992 may be
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 > http://taxacom.markmail.org
 > 
 > Channeling
 Intellectual Exuberance for 29 years in 2016.
 
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