[Taxacom] Why stability? - Revisited
John Noyes
j.noyes at nhm.ac.uk
Tue May 5 03:46:22 CDT 2015
Even more disturbing is that in many institutions taxonomists are being told they are not required to do descriptive taxonomy because must give priority to obtaining funding for their continued existence. In this case even smaller articles are discouraged.
John
John Noyes
Scientific Associate
Department of Life Sciences
Natural History Museum
Cromwell Road
South Kensington
London SW7 5BD
UK
jsn at nhm.ac.uk
Tel.: +44 (0) 207 942 5594
Fax.: +44 (0) 207 942 5229
Universal Chalcidoidea Database (everything you wanted to know about chalcidoids and more):
www.nhm.ac.uk/chalcidoids
-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: 01 May 2015 23:07
To: AlanWeakley; TAXACOM; Roderic Page
Cc: Nico Franz
Subject: Re: [Taxacom] Why stability? - Revisited
One increasingly disturbing aspect, which is very apparent in this neck of the woods lately, is that instead of opting for large monographic revisions, taxonomists are now under "citation pressure" to split what could and should be one large work up into a number of smaller articles.
Stephen
--------------------------------------------
On Sat, 2/5/15, Roderic Page <Roderic.Page at glasgow.ac.uk> wrote:
Subject: Re: [Taxacom] Why stability? - Revisited
To: "Weakley, Alan" <weakley at bio.unc.edu>, "TAXACOM" <taxacom at mailman.nhm.ku.edu>
Cc: "Nico Franz" <nico.franz at asu.edu>
Received: Saturday, 2 May, 2015, 6:14 AM
Hi Alan,
The comment about
"munging" (not even sure if that's a word, I'm a Kiwi by the way) was specific to Avibase, where it takes multiple checklists (each may have several versions, so there is a lot of self similarity) and synthesising them.
I'm not denying
that this is valuable, but it frustrates me that there is minimal connection to the underlying literature. What I see missing from many checklists, and aggregators as well, is the ability to drill down to the underlying science.
Rod
Sent from my
iPhone
On Fri, May 1, 2015 at 10:55 AM -0700,
"Weakley, Alan" <weakley at bio.unc.edu<mailto:weakley at bio.unc.edu>>
wrote:
While I will have a
more detailed and lengthy response later (when I have time), here's a quicky:
One
has to love the brilliant ;-) pejorative Britishism "it's just munging together checklists".
;-)
All taxonomy work
should be based on the most thorough, careful, and expert science possible (monographs and their like). Most taxonomic work is then translated to a broader set of scientific users via (in the vascular plant world) Floras and other, more practical "field guides" -- for at least the more conspicuous organism groups; admittedly it helps if you are a vertebrate animal, a charismatic invertebrate (like Lepidoptera, Odonata, Hymenoptera), or a vascular plant. The set of users of a monograph is in the 10s (maybe the 100s for EVEN a bird or mammal monograph). The set of users of a Flora or regional Field Guide to an animal group is in the 10,000s. The set of users of a website is in the 1,000,000s. It is only by dealing effectively with ambiguities between taxonomy and nomenclature that we go from 10's to 1,000,000s with accuracy and real meaning. Don't you want the best information used (for ongoing scientific work, for conservation, for ecological studies, for citizen science, for ____)?
So, let me offer
a provocative translation here: "it's just munging together checklists" --> "it's just making the best, current, taxonomically accurate information accessible to the broad set of users who need it".
-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
On Behalf Of Roderic Page
Sent: Friday, May
01, 2015 1:10 PM
To: TAXACOM
Cc: Nico Franz
Subject: Re:
[Taxacom] Why stability? - Revisited
Hi Nico,
Just
to play devils advocate, as much as Avibase is an impressive achievement (I’m playing with some data from it right now), at the end of the day it’s basically munging together checklists. There’s no evidence base that we can access, we are essentially combining opinions on what species or subspecies go where. Some of these checklists are literally just lists of names, representing somebody’s - no doubt considered - opinion, whereas I’d really like to see why someone thinks two taxa are synonyms, or one species should be split into two, etc. What is the, you know, actual evidence?
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.
…
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.
I find the notion that monographs are
monolithic entities with boundaries to be respected to be a little last century ;) I would like traceability of evidence, but this doesn’t require a monograph as such. We could have single, citable assertions (say, equivalent to a single paper that shows what was thought to be a new species was actually simply the male of a known species), or we could have a set of assertions, each individually identifiable but all clustered as coming from the same monograph. In other words, nano publications, which may be aggregated into larger sets if desired. I suspect this is the way a lot of data curation subjects, such as taxonomy, are going to be heading in.
As always there seems to be a tension between doing things the way we always have, albeit using new technology, or using new technology to rethink they way we do things. I don’t mean it as pejoratively as that sounds
- new isn’t always necessarily better, but I think we are missing opportunities to rethink the way we do things.
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<mailto:Roderic.Page at glasgow.ac.uk>
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Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
ResearchGate https://www.researchgate.net/profile/Roderic_Page
On 1 May
2015, at 16:22, Nico Franz <nico.franz at asu.edu<mailto:nico.franz at asu.edu>>
wrote:
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<mailto: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<http://biostor.org/> and http://bionames.org<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<mailto:Roderic.Page at glasgow.ac.uk>
Tel: +44 141 330
4778<tel:%2B44%20141%20330%204778>
Skype: rdmpage
Facebook: http://www.facebook.com/rdmpage
LinkedIn: http://uk.linkedin.com/in/rdmpage
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com<http://iphylo.blogspot.com/>
ORCID: http://orcid.org/0000-0002-7101-9767
Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
ResearchGate https://www.researchgate.net/profile/Roderic_Page
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