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Hello all: I have a few inserted comments, hopefully with some
clarifying effect:<br>
<br>
On 5/4/2011 10:54 AM, Peter DeVries wrote:
<blockquote
cite="mid:BANLkTim_fyEHBdvE14rFT6C2Tmtxn_vEPw@mail.gmail.com"
type="cite"><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Hi Steve,</font>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">I may have overloaded the term specimen to make
the explanation easier to follow.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">A specimen could be an individual or it could be
part of an individual.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">To some extent you need to think about how these
models will be used.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">If you subscribe to the model that a species is
whatever a taxonomists says it is then it is difficult to make
statements like.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">X% of the world's species will be extinct by 2050.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">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.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">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.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Are we modeling species or variations in human
conceptualizations of species?</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div>
<meta charset="utf-8">
<div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
<div class="im">
<blockquote type="cite">
<div><font class="Apple-style-span" face="arial,
helvetica, sans-serif">Assuming that there was
only one individual organism identified there is
really one one species (or hybrid).</font></div>
</blockquote>
</div>
<font class="Apple-style-span" face="arial, helvetica,
sans-serif">Aaaaaaaaaaaaaah! Please Nico C., don't
take this one up!</font></div>
<div><font class="Apple-style-span" face="arial,
helvetica, sans-serif"><br>
</font></div>
</blockquote>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">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.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Again, Are we modeling species or variations
in human conceptualizations of species?</font></div>
</div>
</div>
</div>
</blockquote>
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 (<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.emplantbase.org/home.html">http://www.emplantbase.org/home.html</a>)
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.<br>
<br>
<blockquote
cite="mid:BANLkTim_fyEHBdvE14rFT6C2Tmtxn_vEPw@mail.gmail.com"
type="cite">
<div>
<div>
<div class="gmail_quote">
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Which of these is of primary importance to
decision makers and non-taxonomist biologists? <br>
</font></div>
</div>
</div>
</div>
</blockquote>
<blockquote
cite="mid:BANLkTim_fyEHBdvE14rFT6C2Tmtxn_vEPw@mail.gmail.com"
type="cite">
<div>
<div>
<div class="gmail_quote">
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Part of the problem with various
publications relating to ontologies and taxonomy is that
their species models entail a specific phylogenetic
hypothesis.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">In the real world taxa are not as clean as
some would like to make them out to be. </font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Each individual is a unique combination of
thousands of separate gene lineages which often do not
follow clean monophyletic paths.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">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.</font></div>
</div>
</div>
</div>
</blockquote>
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.<br>
<br>
Some of this also on p. 47 of this PDF: <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://journals.ku.edu/index.php/jbi/article/view/3927/3852">https://journals.ku.edu/index.php/jbi/article/view/3927/3852</a><br>
<br>
<blockquote
cite="mid:BANLkTim_fyEHBdvE14rFT6C2Tmtxn_vEPw@mail.gmail.com"
type="cite">
<div>
<div>
<div class="gmail_quote">
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><i>Aedes triseriatus</i> owl:sameAs <i>Ochlerotatus
triseriatus</i> </font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Others seem to see them as phylogenetic end
nodes which entail a specific phylogenetic history. </font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div>
<meta charset="utf-8">
<font class="Apple-style-span" face="arial, helvetica,
sans-serif"><i>Aedes triseriatus</i> distinctFrom <i>Ochlerotatus
triseriatus</i></font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><i><br>
</i></font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">If you are primarily interested in
understanding issues of ecology, disease, diversity and
conservation the former model is more appropriate than
the later.</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">Respectfully,</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif"><br>
</font></div>
<div><font class="Apple-style-span" face="arial, helvetica,
sans-serif">- Pete</font></div>
</div>
</div>
</div>
</blockquote>
<br>
Regards,<br>
<br>
Nico<br>
<br>
<br>
Nico M. Franz, Ph.D. <br>
Assistant Professor <br>
Director, UPRM Invertebrate Collection <br>
Department of Biology <br>
University of Puerto Rico <br>
Call Box 9000 <br>
Mayagüez, PR 00681-9000 <br>
<br>
Phone: (787) 832-4040, ext. 3005 <br>
Fax: (787) 834-3673 <br>
E-mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:nico.franz@upr.edu">nico.franz@upr.edu</a> <br>
Laboratory website: <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://academic.uprm.edu/%7Efranz/">http://academic.uprm.edu/~franz/</a>
<br>
UPRM-INVCOL: <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://uprm-invcol-project.tumblr.com/">http://uprm-invcol-project.tumblr.com/</a>
<br>
<br>
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