[Taxacom] taxonomic impediment redux (was Re: Earth BioGenome Project)

Fri Nov 2 20:07:10 CDT 2018

Ken,
Sounds like you may have missed the point of the "Creepy-crawlies" example. It isn't about funding cuts. It is about funding going to fake science projects designed (by the institutions claiming "overheads" from the funding) simply to maximise profits.
Stephen

--------------------------------------------
On Sat, 3/11/18, Kenneth Kinman <kinman at hotmail.com> wrote:

 Subject: Re: [Taxacom] taxonomic impediment redux (was Re: Earth BioGenome Project)
 To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>, "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
 Received: Saturday, 3 November, 2018, 1:43 PM

 Hi Stephen,

        It's not just the "creepy-crawlies"
 getting neglected.  Here in the U.S., seems like work on
 endangered vertebrates can even be on the budget cutting
 list.  Due to budget cuts,
  and after 51 years of valuable successes, the whooping
 crane breeding program at Patuxent, Maryland, is ending. 
 They will instead be bred elsewhere.  There seems to be a
 trend now to encourage private sector jobs, but government
 jobs not so much.  If whooping
  crane research is being cut, work on the creepy-crawling
 invertebrates is probably even more
 vulnerable.  

       https://www.wbaltv.com/article/whooping-cranes-leave-maryland-program-because-of-budget-cuts/12485927

      https://www.theadvocate.com/new_orleans/news/environment/article_32509bac-d3ef-11e8-8877-9312bd47dd56.html

 From: Taxacom
 <taxacom-bounces at mailman.nhm.ku.edu> on behalf of
 Stephen Thorpe <stephen_thorpe at yahoo.co.nz>

 Sent: Friday, November 2, 2018 2:55 PM

 To: taxacom at mailman.nhm.ku.edu; Doug Yanega

 Subject: Re: [Taxacom] taxonomic impediment redux
 (was Re: Earth BioGenome Project)

 What Doug
 says is the long version of what I said more succinctly,
 i.e. corporate funding driven BS! Note that about 50% of the
 $5 billion will disappear into institutional coffers as
 "overheads". The remainder will be spent as
 quickly
  and effortlessly as possible, so that they can quickly move
 on to new funding opportunities. They won't care one bit
 about quality control, or even if the entire enterprise is
 actually useful or not for any purpose. Are funders
 complicit, or do they really
  fall for this nonsense? I suspect that even governments are
 complicit, if it all serves to pump money through the
 economy in a "useful" way, keeping people employed
 and generating taxes. The bigger picture here is science
 being compromised by corporate profit
  seeking, all too often resulting in nonsense projects being
 funded just to maximise profits (by way of claiming
 "overheads" and spending the rest quickly and
 effortlessly on nonsense, for a small local example, see
 this charities funded "climate change" MSc:
 https://aucklandecology.com/2016/07/01/care-for-the-creepy-crawlies/
 )

 Stephen

 --------------------------------------------

 On Sat, 3/11/18, Doug Yanega <dyanega at ucr.edu>
 wrote:

  Subject: [Taxacom] taxonomic impediment redux (was Re:
 Earth BioGenome Project)

  To: "taxacom at mailman.nhm.ku.edu"
 <taxacom at mailman.nhm.ku.edu>

  Received: Saturday, 3 November, 2018, 7:10 AM

  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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