[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
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
> > >
> > >
> >
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