Hello all: I have a few inserted comments, hopefully with some
clarifying effect:
On 5/4/2011 10:54 AM, Peter DeVries wrote:
Hi Steve,
I may have overloaded the term specimen to make
the explanation easier to follow.
A specimen could be an individual or it could be
part of an individual.
To some extent you need to think about how these
models will be used.
If you subscribe to the model that a species is
whatever a taxonomists says it is then it is difficult to make
statements like.
X% of the world's species will be extinct by 2050.
If you mean a species as defined by the concept
documented at this URI which is supported by these specimens,
images, and DNA then you are on firmer ground.
Species in the natural world do a pretty good job
recognizing those individuals that are appropriate mates. In
other words members of their own species.
Are we modeling species or variations in human
conceptualizations of species?
Assuming that there was
only one individual organism identified there is
really one one species (or hybrid).
Aaaaaaaaaaaaaah! Please Nico C., don't
take this one up!
I stick with this. Assuming you don't have a
hybrid individual. That individual is one species. The
fact that human may disagree on what species it is a
human issue.
Again, Are we modeling species or variations
in human conceptualizations of species?
NMF: I believe there is a history of biodiversity database
engineering that actually led some people, initially in Australia
(Greg Whitbread?) and Europe (Berendsohn's group) to place more
emphasis on modeling human conceptualizations of taxa. I understand
this happened in the late 80s / early 90s. The motivation was,
apparently, that no long-term consensus seemed available to model a
single and sufficiently widely accepted taxonomy of, say, Central
European vascular plant species or mosses. I believe that projects
such as the Euro + Med PlantBase (
http://www.emplantbase.org/home.html)
are examples of the persistence (success?) of this 20+ year old
practice. I think this is the kind of background that Steve is
referring to.
Which of these is of primary importance to
decision makers and non-taxonomist biologists?
Part of the problem with various
publications relating to ontologies and taxonomy is that
their species models entail a specific phylogenetic
hypothesis.
In the real world taxa are not as clean as
some would like to make them out to be.
Each individual is a unique combination of
thousands of separate gene lineages which often do not
follow clean monophyletic paths.
I would argue that most of those who work
with species related data see them as useful typological
constructs which in general follow the biological
species model.
NMF: The solution of how to properly model things such as species in
RDF, OWL (etc.) should ideally accommodate all "species concepts"
(BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral
towards this issue. The examples below are too simple, ignoring for
example cases such as pro parte synonymy, or a concept ("species")
that appears unique and monophyletic to one author but (vastly)
polyphyletic to another. To do an accurate mapping in that latter
case (which is not super-common but it's real), I think one would
have to come down on saying we're modeling human conceptualizations.
They are not just that, so really it's not a strict dichotomy,
meaning that by modeling conceptualizations we do not have to say
"the species only exist on our heads", or "well, then anything
goes". I agree (sheepishly) that it does come down to what the input
data look like, and what the expectations are towards just
accommodating the user community versus pushing them in a particular
direction.
Some of this also on p. 47 of this PDF:
https://journals.ku.edu/index.php/jbi/article/view/3927/3852
Aedes triseriatus owl:sameAs Ochlerotatus
triseriatus
Others seem to see them as phylogenetic end
nodes which entail a specific phylogenetic history.
Aedes triseriatus distinctFrom Ochlerotatus
triseriatus
If you are primarily interested in
understanding issues of ecology, disease, diversity and
conservation the former model is more appropriate than
the later.
Respectfully,
- Pete
Regards,
Nico
Nico M. Franz, Ph.D.
Assistant Professor
Director, UPRM Invertebrate Collection
Department of Biology
University of Puerto Rico
Call Box 9000
Mayagüez, PR 00681-9000
Phone:
(787) 832-4040, ext. 3005
Fax:
(787) 834-3673
E-mail:
nico.franz@upr.edu
Laboratory website:
http://academic.uprm.edu/~franz/
UPRM-INVCOL:
http://uprm-invcol-project.tumblr.com/