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

Doug Yanega dyanega at ucr.edu
Fri Nov 2 13:10:03 CDT 2018


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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