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

Stephen Thorpe stephen_thorpe at yahoo.co.nz
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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