[Taxacom] Why stability? - Revisited
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Fri May 1 17:07:22 CDT 2015
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>
Tel: +44 141 330 4778
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
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
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
_______________________________________________
Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
The Taxacom Archive back to 1992 may be
searched at: http://taxacom.markmail.org
Celebrating 28 years of
Taxacom in 2015.
_______________________________________________
Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
The Taxacom Archive back to 1992 may be
searched at: http://taxacom.markmail.org
Celebrating 28 years of
Taxacom in 2015.
More information about the Taxacom
mailing list