[Taxacom] Anolis classification (was: taxonomic impediment redux)

John Grehan calabar.john at gmail.com
Sun Nov 4 21:23:36 CST 2018


So I infer from your statement ken, that the definition of a "strict
cladist' is one who "abandons Linnaean categories altogether". Is this a
correct reading of you statement?

John Grehan

On Sun, Nov 4, 2018 at 9:29 PM Kenneth Kinman <kinman at hotmail.com> wrote:

> Hi Scott,
>       When it comes to the Anolis debate, I have to side with those who do
> not want to split Anolis into separate genera.  I think the compromise of
> recognizing the 8 subgroups as subgenera is optimal in that it recognizes
> the most recent molecular/cladistic splitting without too much disruption.
> I think the subgeneric splitting is a win/win solution.
>        As for recognizing the cladistic splitting of species groups within
> those subgenera, I would suggest that some sort of alpha-numeric coding
> would be just fine, especially since some of those lower-level
> relationships would be more likely to need adjustments in the future.  Or
> just a simple cladogram in the left margin would also work.  Trying to
> stretch the Linnaean system far beyond the normal categories is just an
> excuse of strict cladists for abandoning Linnaean categories altogether
> (and always has been).    There are solutions that would satisfy the needs
> of cladistics without abandoning Linnaean categories if we acted more like
> scientists and less like politicians.  Otherwise, the Phylocoders will lead
> us into total chaos.  They done enough damage already.
>
> ________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Scott
> Thomson <scott.thomson321 at gmail.com>
> Sent: Saturday, November 3, 2018 12:39 PM
> To: Richard.Zander at mobot.org
> Cc: taxacom
> Subject: Re: [Taxacom] taxonomic impediment redux (was Re: Earth BioGenome
> Project)
>
> Interesting discussion.
>
> A view I have held for a while and was in my mind with some of the things
> we said in the PLoS paper was that Universities have effectively wrenched
> the study of taxonomy in a direction that is good for funding agencies,
> good for Universities but bad for taxonomy. In other words the almost total
> reliance on molecular phylogenetics at most Universities and no funding to
> going to the broader science of taxonomy. I am not the first, wont be the
> last and am not unique in that view. At a conference I recently provided
> example after example of the downside of this, poor taxonomic and
> nomenclatural decision making with no reference to types, no way of pinning
> the decisions being made to existing nomenclature. Incorrect nomenclatural
> acts frequently made and being accepted. All my examples were vertebrates.
>
> So to me the standoff is that almost all funding for genuine taxonomic
> research has been funneled into quick and easy molecular analysis. To me
> this is one of the biggest issues facing taxonomy. As another example of
> this it was recently proposed, for about the third time, by taxonomists to
> split the genus Anolis (500 species) into about 8 genera. This has been
> rejected by the Anole community on the grounds that they do not like it and
> they do not see why their community should be beholden to a small group of
> taxonomists. I do not know how much merit of splitting the genus has, but
> some of those who worked on the group really wanted this, others who were
> more conservation, medical and other research oriented did not. So clearly
> proposals by taxonomists do not carry much weight these days.
>
> I think that some form of international taxonomic body as Doug described
> would be a good idea, however I also think it is unlikely to happen. I also
> agree we are basically out of time. I really do not see how this can be
> repaired easily. Perhaps the only real way is to clearly and publicly
> reject the mistakes being made by this type of research. In particular not
> examining types, using websites such as fossilworks to justify the position
> of fossils in molecular trees for dating exercises which borders on a joke.
> It is not impossible to bring types into molecular data, I have a paper
> submitted now that sequences 22 types (23 attempted so one failed). The
> funding agencies are complicit in the madness of this, and yes so are
> government agencies. Only way to change this is to show them how idiotic it
> is.
>
> Cheers Scott
>
> On Sat, Nov 3, 2018 at 11:24 AM Richard Zander <Richard.Zander at mobot.org>
> wrote:
>
> > In reply to Doug Yanega, who wrote in part:
> > "In an ideal world, there would be a Global Taxonomic Institute that
> would
> > have centers of research on every continent, staffed by thousands of
> > taxonomists worldwide, whose jobs would be to describe and identify
> > organisms (including confirmation of others' IDs), whose salaries would
> be
> > permanently supported, and without whose "seal of approval" nothing would
> > get into print that relied upon identification. That is certainly never
> > going to happen. A few of you may even recall the "All-Species
> Initiative",
> > which proposed to do something along those lines, and it died on the
> vine."
> >
> > This not so unreachable. Consider the following:
> > With climate change, say 3 or 4 degrees C, ecosystems and communities are
> > going to move or die (a metaevolution). Because of differential migration
> > rates, the species will smear out. Lots of competition and selection will
> > ensue. A paper I recently read predicted that the changes to ecosystems
> > after the most recent glaciation may well happen in the next 100 to 150
> > years, a catastrophic compression.
> >
> > This means that our keys to species will not work for a given geographic
> > area, nor will out floristic and faunistic checklists. One might say
> > taxonomy will be obsolescent. Is this true?
> >
> > I believe that it is time for the systematics community to repurpose its
> > collections and retool its expertise. Surely, our present collections can
> > be used as benchmarks for biodiversity change from preindustrial times to
> > say 1960 (beginning of exponential rise in population), then  to present,
> > to help infer possible composition of mostly novel ecosystems of the
> > future. Maximizing biodiversity of such future ecosystems should be an
> > activity fundable by government, with considerable oversight regarding
> > nonsensical, unhelpful, or bad science.
> >
> > I suggest a focus on maximizing evolutionary and ecological redundancy.
> > Some suggestions on how to do that are in the last two chapters of my
> book:
> >
> >
> https://www.researchgate.net/publication/324363615_Macroevolutionary_Systematics_of_Streptotrichaceae_of_the_Bryophyta_and_Application_to_Ecosystem_Thermodynamic_Stability_Edition_2
> > , which as an aside now has 1100 "views" on ResearchGate which might mean
> > downloads and perhaps interest on the part of some.
> >
> > The systematics community has the facilities, data, and expertise to
> > directly address coming massive change in fauna and flora (including
> crops
> > and livestock). A " Global Taxonomic Institute" is not a pipe dream. One
> > might rename such a thing an "Ecosystematics Institute" following Duke's
> > 1978 coining of word ecosystematics, as a combination of taxonomy,
> ecology
> > and evolution.
> >
> > Richard Zander
> >
> >
> > -------
> > Richard H. Zander
> > Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri –
> 63110
> > – USA
> > richard.zander at mobot.org Ofc: +1 314 577-0276
> > Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and
> > http://www.mobot.org/plantscience/resbot/
> >
> > -----Original Message-----
> > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> > Doug Yanega
> > Sent: Friday, November 02, 2018 1:10 PM
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: [Taxacom] taxonomic impediment redux (was Re: Earth BioGenome
> > Project)
> >
> > On 11/1/18 3:32 PM, KD Dijkstra wrote:
> >
> > Hi all,
> >
> > I was just pondering the announcement when Tony's message came in. The
> > Earth BioGenome Project states that "we desperately need to catalogue
> life
> > on our planet now". Their solution is to spend 5 billion dollars on
> reading
> > the genomes of 1.5 million (described?) species.
> >
> > I've lately developed the feeling that a new problem is arising on top of
> > the 'old' taxonomic impediment (i.e. the phenomenon that taxonomists
> can't
> > keep up with biodiversity's extent). We might call the new issue the
> > "taxonomic standoff": we can now generate so much data (specimen records
> on
> > GBIF, DNA-barcodes on BOLD, and now apparently millions of billions
> genomic
> > data) that there's a risk that remaining experts won't keep up with the
> > verification and eventually give up, making most of the effort redundant.
> > This occurs if investment in innovations that could (and indeed were
> > intended to) strengthen biodiversity expertise is so disproportionate
> that
> > it tips the balance between quantity and quality. The entire effort to
> > catalogue biodiversity would then effectively collapse under its own
> weight.
> >
> > So my questions to the taxonomic community are (1) whether such a
> > "taxonomic standoff" is indeed unfolding and (2) if taking a collective
> > stance relative to this latest initiative (which will make huge demands
> of
> > the community, but might benefit it too) would be a way to strengthen our
> > position.
> >
> >
> >
> > A colleague just this week showed me a paper he had been sent for review
> > by an established, peer-reviewed journal, that is instructive in this
> > regard.
> >
> > In it, a number of plant-feeding insects and their presumed parasites
> were
> > listed, all identified to species, but not a single one of which had been
> > identified by a taxonomist. They had all been IDed by simply looking for
> > the nearest match in GenBank. They were all in genera that contained
> dozens
> > to over a hundred species for which no GenBank sequences were available
> > (and, on top of that, a quick check revealed that a few of the taxa
> showing
> > on GenBank clearly have sequences from multiple species represented, and
> no
> > way to know which ones actually were the taxon named). Several of the
> > resulting IDs were therefore of species that didn't even occur in that
> > Hemisphere, and all but one or two of the rest were almost certainly
> wrong.
> > The authors saw nothing wrong with this, the editor that sent the
> > manuscript out for review saw nothing wrong with this, and the odds are
> > good that my colleague may be the only one of the reviewers who DID see
> > anything wrong with this. That is, it may indeed get published, despite
> > being absolute rubbish.
> >
> > This is the old taxonomic impediment, but now it's just being ignored, by
> > removing taxonomy from the equation entirely.
> >
> > There is no way to prevent this from happening, that I can see, given
> > certain unavoidable realities. IN PRINCIPLE, every editor of every
> journal
> > would know that this is unacceptable, and reject every such submission.
> If
> > attempting to publish such a paper was 100% guaranteed to fail, then
> > researchers would be forced to incorporate support for taxonomy into
> their
> > research, or they would risk losing funding, and losing their jobs. But
> the
> > reality is that for every journal that rejects an unacceptable paper,
> there
> > are dozens of journals that will happily accept it and print it (and that
> > number keeps growing). So long as authors know that they can get things
> > published without involving taxonomists, they will have incentive to do
> > exactly that.
> >
> > So long as papers lacking taxonomic involvement are being published,
> > funding agencies won't cut off funding to the researchers publishing
> them -
> > they're just looking for "deliverables". They're effectively funding
> > homeopathic taxonomy; something that might look and smell like taxonomy
> but
> > is so hopelessly diluted as to be meaningless. We live in a world where
> > Wikipedia has higher standards of verifiability and accountability than
> > half the journals in print*, so expecting funding agencies to look for
> > verifiability and accountability seems like it's going to get harder and
> > harder, rather than the converse.
> >
> > If the funding agencies don't see or understand how their funding
> > priorities thereby undermine legitimate science, then who will explain
> this
> > to them, and convince them to stop supporting bad science? Unless I'm
> > missing something, the people at the top of the proverbial pyramid are
> NOT
> > listening to taxonomists, since we're the bearers of bad news, and I
> don't
> > see what options we have to get them to listen to us. We have no lobby,
> no
> > union, no advocacy group that can compel anyone to do anything on our
> > behalf (what leverage do we have?), and - perhaps just as bad - even if
> we
> > had their attention, we really don't have anything especially positive to
> > say to those funding agencies. There are an estimated 10 to 50 million
> > undescribed species out there (mostly arthropods), and what's the average
> > number of species that a fully-funded taxonomist can describe in a year?
> > What are the odds that any random organism will even have a living
> > taxonomist who can recognize it? It's hard to portray alpha taxonomy as a
> > cost-effective investment, when it moves at a relative snail's pace, and
> > it's a very hard sales pitch trying to tell someone that something that
> > isn't cost-effective is nonetheless an absolute necessity. If every
> dollar
> > spent on genome sequencing was matched by 100 dollars on taxonomy, could
> we
> > even hope to keep pace? In the face of this, what "collective stance" can
> > we possibly take that would be persuasive?
> >
> > In an ideal world, there would be a Global Taxonomic Institute that would
> > have centers of research on every continent, staffed by thousands of
> > taxonomists worldwide, whose jobs would be to describe and identify
> > organisms (including confirmation of others' IDs), whose salaries would
> be
> > permanently supported, and without whose "seal of approval" nothing would
> > get into print that relied upon identification. That is certainly never
> > going to happen. A few of you may even recall the "All-Species
> Initiative",
> > which proposed to do something along those lines, and it died on the
> vine.
> >
> > Again, this still comes back to the taxonomic impediment, but the gap
> > between the increasing pressure for "deliverables" and the capacity for
> > conventional taxonomy to deliver is getting worse. If anyone here sees a
> > practical solution, I think we'd all love to hear it.
> >
> > Sincerely,
> > --
> > * I was recently told, by an editor at Wikipedia, that Wikipedia policy
> > prohibits people from correcting misspellings in Wikipedia of scientific
> > names that appear in print, even if correcting those errors is mandated
> by
> > the ICZN, and even if the person making the corrections is an ICZN
> > Commissioner, because Wikipedia requires independent third-party
> > verification for any proposed edits (i.e., proof, in print, that there
> > really is an error at all).
> >
> > --
> > Doug Yanega      Dept. of Entomology       Entomology Research Museum
> > Univ. of California, Riverside, CA 92521-0314     skype: dyanega
> > phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
> >              http://cache.ucr.edu/~heraty/yanega.html
> >   "There are some enterprises in which a careful disorderliness
> >         is the true method" - Herman Melville, Moby Dick, Chap. 82
> > _______________________________________________
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>
> --
> Scott Thomson
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