[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
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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> > Channeling
> Intellectual Exuberance for 29 years in 2016.
>
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