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

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Fri Nov 2 14:55:40 CDT 2018


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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