[Taxacom] Two million molecular synonyms on the way

Tue Feb 16 02:21:30 CST 2021

Dear Jason,

It was not taken personally, not at all! Rather, I read very carefully all
comments and agree with some criticism towards the implementation of the
method (including most of your own), and believe it or not, also towards
the paper in question! On the other side, extreme opinions such as calling
"garbage" a work that has been supported by several leading braconid
taxonomists and quite many other scientists (as Rich said, "those people
are probably not stupid") in one way or another, are something I simply
couldn't refrain from commenting. Our reaction to the criticism and all
these discussions, which actually started years ago but have been forced up
by Sharkey at al. paper and other similar projects, is summarised in the
new ZooKeys guidelines, you kindly provided with comments and suggestions.
Thanks!

Most of your comments  are indeed reasonable and straight for
implementation. I still struggle with the term "DNA-only" descriptions
which perhaps should be replaced with "DNA-based". Actually, these are
rarely and purely "DNA-only". What kind of best practices they should
follow in our opinion and at the current stage of development of the method
is described in the guidelines, which will be refined with the time of
course. The BDJ paper you mentioned is an excellent example, no doubt,
however it is one thing to describe one species in a generally well-studied
group this way and another in megadiverse, poorly studied taxa. There
should be а reasonable and community-agreed "gold mean" in the room, though!

Best regards,
Lyubo

-----
Prof. Dr. Lyubomir Penev
ORCID: http://orcid.org/0000-0002-2186-5033
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On Tue, Feb 16, 2021 at 5:31 AM JF Mate via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Lyubo, apologies if you interpret the discussion as a personal attack on
> Pensoft, it is not. In fact, in private discussions I have mentioned an
> article published by your journal as a good example of good integration (
> https://doi.org/10.3897/BDJ.9.e59892). Their written diagnoses could have
> been shorter but the combination of barcodes, rich imaging and written
> diagnosis should be the norm. Anybody who reads this article, regardless of
> their background, can use it.
>
>
> Now, it is good to see that there is an ongoing discussion within Pensoft
> and the recommendations you list are a useful springboard, on which I would
> like to make the following comments:
>
>
> “*Types and taxonomically important specimens. *
>
> …*.*
>
> *Strongly recommended: Type specimens should be deposited in a publicly
> accessible collection. “ *
>
> This should be mandatory for the holotype within a sensible timeframe, in
> particular if the intention is to streamline descriptions.
>
>
>
> “*Differential diagnosis. *
>
> *...*
>
> *Strongly recommended: Include all relevant congners [sic] and cite the
> reference taxonomy being followed, so that others can see which species
> have been considered.” *
>
> -I would make the reference taxonomy mandatory to reduce the ambiguity that
> is coming our way. We need to know which definitions other researchers are
> using.
>
>
> “*Strongly recommended: Consider presenting the differential diagnosis in a
> table, if long lists of differences and/or species are included.” *
>
> -I like this, this is a sensible recommendation, it simplifies descriptions
> and makes the information more accessible to all (also imaging already
> covers most of the morphologically descriptive part anyway) but it needs to
> apply to BC-species as well, at least to a rough species-group, but see
> below.
>
>
> “*Morphological description. To the extent accepted as a minimum standard
> in the respective taxon group, so that to provide the diagnostic evidence
> that the species is new. Rich illustrative material including images,
> drawings, and where possible microCT should be included.*
>
> ...
>
> *DNA-only descriptions. Given some controversies and criticism related to
> "DNA-only" descriptions, such descriptions could be considered only in
> special cases, e.g. in a necessity of streamlined descriptions of multiple
> new species in megadiverse, poorly studied taxa with strong record on the
> informativeness of DNA barcodes (deep divergences) and correlated external
> features shown on rich illustrative material.*
>
>
> *Mandatory: Rich illustrative material (photos, drawings) of the voucher
> (type) specimens and morphological details important for the identification
> of the taxon under study (microCT or others). “*
>
> ...
>
> *Strongly recommended: Morphological descriptions are to be included in
> "DNA-only" descriptions as well, whenever possible.”*
>
>
> A distinction is being made with DNA taxonomy, but I think it is
> unnecessary
> inasmuch as there is a broad overlap. Many have commented already that long
> worded descriptions are unnecessary and you already provide the option of
> tabulated diagnosis. This would have made a world of a difference to both
> papers. In addition, and in view of the articles, it is necessary to
> tighten the definition of “Rich illustrative material (photos, drawings) of
> the voucher (type) specimens and morphological details important…” because
> these articles did not meet the criteria for diagnosability nor
> illustrations. I understand that it is early days and this is all “learn as
> you go” but if you want to avoid breaking taxonomy there needs to be an
> entente. It is incumbent on the B-coders to integrate their descriptions
> with +250 years of taxonomic work and that the only way to do that and not
> clog the system is to provide the needed information in an easily
> digestible form.
>
> In light of this, the fact that the style of plates in figures 1 & 2 were
> not required for all 400+ species, as a minimum description, should be seen
> as an unfortunate oversight. The provided images are insufficient and if
> somebody has to slog through this in the future, it is the authors’
> obligation to make it at least possible. Also this article needs to be
> useful to the vast majority of researchers outside of the BOLD bubble who
> will not be barcoding their mounted material or unsorted samples. That is
> why emotions are running high. It is not that the work is “garbage”, it is
> that they make it very difficult for others to interpret/verify it, which
> damages the basic tenet of peer review. Do we want to go back to the time
> when species were described with minimal information or scrutiny simply
> because the authors were the experts and were assumed to know what they
> were doing? As John said, we shouldn’t judge the opinion based on the
> perceived authority of the person but on the quality of the arguments and
> that requires sufficient data.
>
>
> I am all for speeding descriptions, and it is obvious from examples such as
> the Freitag article I provided at the beginning, that in the very near
> future (10 years until the cost is similar to a good stereomicroscope) it
> will be possible to get barcodes as easily and affordably as present day
> microscopy, but if the difference between proper work and slapdash is
> fivefold
> versus tenfold current rates of descriptions, the latter is preferable.
> Otherwise Carlos’ and Jean’s comments, though harsh, will come to be and we
> will be faced (the rest) with the thankless task of cleaning a taxonomic
> mess, or worse, a taxonomic Tower of Babel.
>
>
> Best
>
>
> J
>
> On Tue, 16 Feb 2021 at 04:54, Lyubomir Penev via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> > John,
> >
> > Well, the meaning of my rhetoric question woudn't change if I used
> > "renown", "well experienced" or so. These are the people you would most
> > probably contact if you have a student who wants to get training in
> > braconid taxonomy, or if you need to identify braconids for the purpose
> of
> > your own studies. If they accepted to support the paper, this most
> probably
> > means they have a specific knowledge about the taxon gained during all or
> > most of their career. I do not want to speak for them, opinion my own.
> >
> > Otherwise, I agree of course that criticism coming from outside small
> > scientific communities is not just helpful or desirable but much needed!
> >
> > Best regards,
> > Lyubomir
> > ----
> > Prof. Dr. Lyubomir Penev
> > ORCID: http://orcid.org/0000-0002-2186-5033
> > WoS ResearcherID: O-9982-2019
> > <https://publons.com/researcher/324250/lyubomir-penev/>
> > Founder and CEO
> > Pensoft Publishers <http://pensoft.net>
> > ARPHA Journal Publishing Platform <http://arphahub.com>
> > 13a Geo Milev Street
> > 1111 Sofia, Bulgaria
> > Tel +359-2-8704281
> > Fax +359-2-8704282
> > Publishing services for journals <http://arphahub.com/about/services> I
> > Journals <http://journals.pensoft.net> I Books
> > <http://pensoft.net/books-published-by-Pensoft>
> > Services for scientific projects <http://pensoft.net/projects>
> > Find us on: Facebook
> > <http://www.facebook.com/pages/Pensoft-Publishers/170816832934216?ref=ts
> >,
> > Google+
> > <
> >
> https://plus.google.com/u/0/b/114819936210826038991/114819936210826038991/posts
> > >,
> > Twitter  <https://twitter.com/#%21/Pensoft>
> >
> >
> > On Mon, Feb 15, 2021 at 8:07 PM John Grehan <calabar.john at gmail.com>
> > wrote:
> >
> > > Lyubomir,
> > >
> > > With respect to your rhetorical question:
> > >
> > > "As taxonomy is concerned: the "garbage" has been supported by several
> > > top braconid taxonomists, some of them as co-authors, and some as
> > > reviewers. Perhaps they know what they are doing in their group of
> > > interest?"
> > >
> > > I would note that the ever present danger for any science involving a
> > > relatively small group of participants is that of a shared viewpoint
> that
> > > may not have any relation to "knowing what they are doing". I emphasize
> > > that this danger is applicable to taxonomy or any science in general,
> > > including my own (in fact some of the best and most critical feedback
> has
> > > come from outside the research program).
> > >
> > > Also, what makes a "top taxonomist" as opposed to a less than 'top'
> > > taxonomist? Prolific does not necessarily equate to quality.
> > >
> > > Cheers, John Grehan
> > >
> > >
> > >> .
> > >>
> > >
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