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Well, I think we've plowed this ground before (actually several times
before). In the first attempt to come up with a consensus definition
for "Individual" (previous name for what we are now calling
"Organism"), we had allowed that an Individual be identified to a
single Taxon, but with no restriction on the level of the taxon. In
other words, the Individual could be taxonomically heterogenous at a
lower taxonomic level as long as its components were part of the same
higher-level taxon (e.g. the infamous marine trawl sample and various
jars of samples taken from it; each jar an "Individual" identified to
some higher taxonomic level that was common to all organisms in the
jar). However, there was a point more recently when someone (I think
it was actually you) requested competency questions for the proposed
class. I provided three, one of which was the ability to track
"duplicates" and to infer that any Identification which applies to one
duplicate also applies to all others. I will say no more here, but
simply refer to the email where I discussed this:<br>
<a class="moz-txt-link-freetext" href="http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002690.html">http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002690.html</a><br>
Rich agreed that the ability to draw this kind of inference was
valuable and agreed that requiring that Individuals (now called
Organisms) to be taxonomically heterogeneous was a benefit that
outweighted the benefits that would accrue from allowing them to be
taxonomically heterogeneous. Rich can correct this if I've
misrepresented anything he said.<br>
<br>
Your suggestion that an Organism be a subclass of something more
general is what Cam and I suggested in an alternate version of
darwin-sw. I will not comment further on this because this approach
has already been outlined in text and diagrams at<br>
<a class="moz-txt-link-freetext" href="http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity">http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity</a><br>
I don't have any objection to having a superclass of Organism that
allows taxonomic heterogeneity, but one of the principles of Darwin
Core is that in order for a term to become a part of the vocabulary, at
least several people have to indicate that they want the term and there
should be some reasonable explanation of how people would use the
term. That has happened for Organism. It has NOT happened for
TaxonomicallyHeterogeneousEntity or whatever you want to call it. As I
discuss on the page reference above, allowing taxonomic heterogeneity
introduces some significant complexities in modeling and I for one have
no clue how to deal with them.<br>
<br>
Steve<br>
<br>
Bob Morris wrote:
<blockquote
cite="mid:CADUi7O7WSQAdwU0Vsxi3Ea7N7FdUWQOht_fg5Ctufv=_n_nY4g@mail.gmail.com"
type="cite">
<pre wrap="">What exactly is accomplished by requiring "taxonomically homogenous?"
Perhaps the problem is that Organism is a subclass of something
slightly more general, some more general "biologically organized"
object that has a context dependent organizing principle. For
example, biologists seem willing to talk about ecosystem instances in
this way. Also, for some purposes, people seem willing to have
discourse about an organism in which they include microbes that must
survive not only on or in the organism, but even a tiny bit away from
it. So, if one had a slightly more general class, and Organism is
required to have some enumerated set of specific kinds of organizing
principles, e.g. those presently on the table, several things happen:
(a)those who need to have a different organizing principle than the
current consensus of what organizes an Organism have a place to hang
their organizing principle, (b) scientific advances about the
organizing principles of life don't require massive ontological
disruption(*)...you just move a principle into the appropriate
subclass.
Bob Morris
aka Recovering Algebraist
(*)well, I suppose the important ones do for the biologists, but I
suspect they needn't for the formal ontologies, if the upper level
organizing principle is "organizing principle".
On Thu, Sep 8, 2011 at 3:56 AM, Gregor Hagedorn <a class="moz-txt-link-rfc2396E" href="mailto:g.m.hagedorn@gmail.com"><g.m.hagedorn@gmail.com></a> wrote:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Term Name: Organism
Identifier: <a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/Organism">http://rs.tdwg.org/dwc/terms/Organism</a>
Namespace: <a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/">http://rs.tdwg.org/dwc/terms/</a>
Label: Organism
Definition: The category of information pertaining to a specific
instance of an organism (virus, symbiont, individual, colony, group of
individuals, population) reliably be known to taxonomically
homogeneous.
</pre>
</blockquote>
<pre wrap="">I see a problem with the "taxonomically homogeneous" since many taxa are not.
All obligatory mutualistically symbiontic organisms are excluded (you
mention symbiont, but the symbiont is the part of a symbiontic
relation, e.g. both the algae taxon and fungus taxon each are a
symbiont in a lichen.
Contradict if my German biology is at odds with English.
The problem is, that individual and set are mixed, so that the
"homogeneous" appears to apply also to the individual. Proposal:
Definition: The information class pertaining to a specific
instance or set of instances of a life form or organism (virus,
bacteria, symbiontic life forms, individual, colony, group,
population). Sets must reliably be known to taxonomically homogeneous
(including obligatory symbiontic associations).
Gregor
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</blockquote>
<pre wrap=""><!---->
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
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