[Taxacom] Why stability? - Revisited

Fri May 1 10:22:31 CDT 2015

Thanks, Rod (and Tony).

   Also for steering things back a bit.

   I believe that, if an individual produces a monograph that has well
defined reference boundaries - a domain of reference, so to speak (this
perceived taxon, at this time, in that region, given this nomenclatural and
taxonomic legacy, these sets of specimens, traits, inferred trees, etc.) -
and that monograph gets aggregated into a larger biodiversity information
environment, then in that environment the identity of the monographic
content should remain "relevantly recognizable". The aggregator environment
does in effect expand the monograph's original domain of reference in ways
that the monograph's author cannot readily or reliably predict.

   To me his puts the onus on the aggregator environment to provide
technical design solutions that are capable of supporting the communication
and social recognition models that human taxonomy making and revising
relies on.

   Where do taxonomic concepts fit in here? We have, at this point, some
individual efforts (two absolute stand-outs to me are Lepage's Avibase [
http://zookeys.pensoft.net/articles.php?id=3906] and Weakley's Flora [
http://www.herbarium.unc.edu/flora.htm]) that demonstrate at considerable
scales (thousands of currently recognized species concepts, > one century
taxonomy legacy depth, tens of thousands to millions of articulations) that
taxonomic concept individuation and integration based on semantics that
complement nomenclatural relationships is feasible. Avibase in particular
implements a database to sustain these reference services.

   I think a fair and contemporary assessment is, as we move to greater,
more integrative scales, there will be issues that we have not fully
grasped yet, and other issues that we can already identify and which will
be hard. For instance, I understand that Avibase uses taxonomic names at
the family level and above, while shifting to taxonomic concept resolution
at lower levels. But we also do have a small but growing body of theory and
practice that shows feasibility and value, to my mind. Worthy of praise
perhaps, and further exploration.

   The following is in my view a persistent challenge to the aggregators.
When we initially build these larger biodiversity data repositories with
successively more encompassing taxonomies whose intellectual authorship
origins are diverse, and then curate the taxonomies in the new environments
as we go along, we are in some sense generating new systematic theories
intended to reflect reference standards for a wide range of contributors
and users.

http://link.springer.com/article/10.1007%2Fs13752-012-0049-z

   But who owns the new theories, or identifiable parts of them? Who can
express their assessments of their validity, or perceived need for
correction or expansion? This will sound a bit dramatic, but many
aggregator systems are currently structurally designed in a way that the
graduate student, postdoc, or more senior scientist producing a monograph
is inadvertently disenfranchised when their taxonomic language contribution
migrates from the traditional to the integrative publication environment.

   So, yes, we do not have it all figured out. Maybe it won't work in the
end for very many important applications. We are also not alone in this.

http://link.springer.com/chapter/10.1007%2F978-1-84628-901-9_8

Cheers, Nico

On Fri, May 1, 2015 at 3:31 AM, Roderic Page <Roderic.Page at glasgow.ac.uk>
wrote:

>  Hi Nico,
>
>  To return to you’re original post and question, a couple of quick
> comments.
>
>  As Stephen Thorpe alluded to, once aspect of instability is IMHO a
> function of the burden taxonomic names carry. We would like:
>
>  1. human readable, globally unique names, that
>
>  2. also tell us something about relationships (e.g. the genus name
> matters), and
>
>  3. carry some link to provenance (e.g., taxonomic authority, author for
> new combinations, etc.)
>
>  There’s pretty much no way to satisfy these requirements without
> tradeoffs of one sort or another. For example, for reasons that I’ve now
> forgotten I thought it would be fun to try and track down the original
> species descriptions associated with a recent paper on the declining rate
> of descriptions of new bird species (
> http://dx.doi.org/10.1093/sysbio/syu069, see also
> http://eol.org/collections/116394 ). Cue much heartache as many of these
> names have changed, and often discovering the original name (and
> publication) is a world of hurt as people shuffle species between genera
> and up and down between species and subspecies rank (e.g.,
> http://bionames.org/names/cluster/642623 ).
>
>  We have a naming system that is hugely unstable because goals 1 and 2
> are incompatible (at least, they are in the absence of any system to track
> name changes, botanists do this quite well, zoologists don’t).
>
>  Regarding your bigger point about your “extreme” system, I think this is
> kind of where we are heading, especially when you think of things like DNA
> barcoding. However, I suspect that what people will focus on is not the
> long history of shuffling specimens between names and taxa, but what the
> latest snap shot is "right now". Databases that make this explicit (GBIF -
> taxa as sets of occurrences, NCBI and BOLD - taxa as sets of sequences)
> will be useful and underpin actual research. Databases that make this
> implicit (i.e., most taxonomic databases) will be a lot less useful.
>
>  I love the taxonomic legacy as much as anyone, indeed I spend most of my
> time trying to expose it as much as possible (hence http://biostor.org and
> http://bionames.org ), but I suspect a lot of discussion about the
> relationship between concepts will be of perhaps limited relevance except
> in some (possibly spectacular) edges cases.
>
>  Regards
>
>  Rod
>
>    ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email:  Roderic.Page at glasgow.ac.uk
> Tel:  +44 141 330 4778
> Skype:  rdmpage
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>  Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
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>