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Well no,<br>
<br>
we don't have to grudgingly choose between artificial and
natural. One can allow for the obvious that species names and
definitions are formulated and written down by humans (though other
animals and machines are sometimes capable of this too), and vary
over time, but at the same time nature has a strong corrective word
in shaping these definitions, and only if they are close enough to
some real natural order are our inferences also reliable enough. By
modeling species as human conceptualizations, we are not necessarily
throwing out the baby with the bathwater, i.e. saying they are not
real. See pp. 66-67 here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://docs.google.com/a/richard-boyd.net/viewer?a=v&pid=sites&srcid=cmljaGFyZC1ib3lkLm5ldHxob21lfGd4OjcyOWIwYWMyY2Y5M2NmMzg">http://docs.google.com/a/richard-boyd.net/viewer?a=v&pid=sites&srcid=cmljaGFyZC1ib3lkLm5ldHxob21lfGd4OjcyOWIwYWMyY2Y5M2NmMzg</a><br>
<br>
Regards,<br>
<br>
Nico<br>
<br>
<br>
On 5/4/2011 12:58 PM, Nico Cellinese wrote:
<blockquote
cite="mid:C04509AE-59BC-4936-9201-A974B3A407B5@flmnh.ufl.edu"
type="cite">
<div>Hi Pete,</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<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">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">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">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">X%
of the world's species will be extinct by 2050.</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>
</blockquote>
<div><br>
</div>
I would have stopped here! If someone wants to point to a series
of objects to indicate his own concept of a "species", then
that's ok. That's a convention we can work with.</div>
<div><br>
</div>
<div>Everything else you talk about below seem to be a confused
mashup of "species" as a taxon and "species" as ranks.</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div><span class="Apple-style-span" style="font-family:
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.</span></div>
</div>
</blockquote>
<div><br>
</div>
Really? Maybe in animals but everywhere else I don't think so!
And what about asexual organisms? I guess they do not deserve
the status of "species". So, the biological species concept you
are referring to can't be universally applied = not a good
concept to use for ALL organisms, right?</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div><span class="Apple-style-span" style="font-family:
arial,helvetica,sans-serif;">Are
we modeling species or variations in human
conceptualizations of
species?</span></div>
</div>
</blockquote>
<div><br>
</div>
Is there anything else out there besides the human
conceptualization of species? Do we have an absolute concept of
what a species represent? Last time I checked we have been
arguing about this for the past century and more. Species
defined by the 25+ species concepts out there can't possibly be
real. They are defined by human conceptualization = artificial.
The only think we can clearly try to discern are clades and
often those clades may correspond with someone's concept of a
species. In other words, you can take the rank of species and
point it at a node that define a taxon. Or you can take the
rank of species and point it to an assemblage of lineages,
regardless if that assemblage represents a monophyletic group or
not. Traditionally recognized species are most likely
polyphyletic anyways.</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div>
<div>
<div class="gmail_quote">
<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>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
What do you really mean by individuals? Are species created by
the gods and we just can't figure out what they meant? Human
issue? We, humans came up with this impossible to define
concept. Individuals are just that: individuals. The individuals
= species hypothesis has been argued in the literature and is
not an accepted notion by far (note: I am not saying I agree or
disagree, this is just another non-absolute concept). But maybe
you don't mean it that way.</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div>
<div>
<div class="gmail_quote">
<div><span class="Apple-style-span"
style="font-family: arial,helvetica,sans-serif;">Again,
Are
we modeling <b><font class="Apple-style-span"
face="Arial" size="5"><span
class="Apple-style-span" style="font-size:
18px;">species</span></font></b> or
variations in human conceptualizations of
<b><font class="Apple-style-span" face="Arial"
size="5"><span class="Apple-style-span"
style="font-size: 18px;">species</span></font></b>?</span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
Your statement is recursive. You have an idea of species that is
above all of the other variations on the theme. I don't
understand what you mean and that's why I think there is a
confusion between the usage of "species" as a taxon and
"species" as an arbitrary rank.</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div>
<div>
<div class="gmail_quote">
<div><span class="Apple-style-span"
style="font-family: arial,helvetica,sans-serif;">Which
of
these is of primary importance to decision makers
and non-taxonomist
biologists? </span></div>
<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>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
Even in the lack of a phylogenetic framework, every species is a
hypothesis. When we lump and split we generate hypotheses. A new
name points to a new hypothesis. Adding a new <i>genus</i> to
a <i>family</i> or a new <i>species </i>to a <i>genus</i>
refines and modifies the original hypothesis.</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div>
<div>
<div class="gmail_quote">
<div><span class="Apple-style-span"
style="font-family: arial,helvetica,sans-serif;">In
the
real world taxa are not as clean as some would
like to make them
out to be. </span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
In fact, the only way we can discover a little more clarity is
through phylogenies. When it comes to low level taxa, population
studies help a lot too. </div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div>
<div>
<div class="gmail_quote">
<div><span class="Apple-style-span"
style="font-family: arial,helvetica,sans-serif;">Each
individual
is a unique combination of thousands of separate
gene
lineages which often do not follow clean
monophyletic paths.</span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
But as you stated above you equate individuals with species. if
that's correct, then you admit that individuals can be
polyphyletic, and as such do we really care about polyphyletic
entities? As such you admit that species as you define them are
artificial.</div>
<div><br>
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div>
<div>
<div class="gmail_quote">
<div><span class="Apple-style-span"
style="font-family: 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.</span></div>
</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
I actually don't and I can name many others who don't. The rank
of species may be useful to many as communication tool but the
way it is applied vary a lot. The biological species concept is
not widely accept and certainly not followed by the vast
majority as you indicate.</div>
<div><br>
</div>
<div>The only think we can really achieve from an informatics
standpoint is to reconcile objects (specimens, images,
sequences, descriptions, etc.etc.) with the many names that may
have been associated with those and leave the rest
(philosophical masturbation) to the users. Reconciling names
with concepts, given the nature of the concepts and the
idiosyncratic way that names have been historically used, is a
Quixoterian challenge.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Nico</div>
<div><br>
</div>
<div><br>
</div>
<br>
</blockquote>
<br>
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