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I see your point here. There has been some previous discussion on this
list about classes for describing things like ecosystems and other
larger scale phenomena involving collections of living things. But I
don't think that discussion has been anything close to as extensive as
the discussion surrounding individuals/organisms and
tokens/evidence/collectionObjects. So I think the questions: "who
needs the superclass?" and "what do they want to do with it?" (i.e.
competency questions) need to be asked. Then somebody needs to create
a definition and a proposal. I don't think any of those things have
happened so far for larger-scale aggregates of living things. <br>
<br>
I think it is possible (actually likely) that other groups may already
have terms for some aggregates that we might adopt. Vegetation
classification schemes come to mind as well as several ecoregions
classification schemes.<br>
<br>
Steve<br>
<br>
Bob Morris wrote:
<blockquote
cite="mid:CADUi7O4qKiPBeiHarL3Mn5Li7pSFgLnDsxwsb-_se=k4Kgu1RA@mail.gmail.com"
type="cite">
<pre wrap="">I was perhaps unclear. I don't mean to suggest a superclass that has
some other notion of taxonomic organization. I meant to suggest one
that simply has \some/ notion of organization. That wouldn't change
the offered definition of Organism, but rather give people who feel
they need some notion of an organized set of biological stuff a way to
define other subclasses with different organizations. It would, for
example, let people use DwC to describe some aspects of ecosystems
able to do so without having to pretend that an ecosystem is always a
special kind of Organism, or vice-versa.
It doesn't look to me like you envision that
<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> would
be suitable for describing ecosystems, possibly even for those
ecologists that think a hierarchy of ecosystem types is as fundamental
to what the study as are classical taxonomic hierarchies to classical
taxonomists.
Bob
On Thu, Sep 8, 2011 at 10:40 AM, Steve Baskauf
<a class="moz-txt-link-rfc2396E" href="mailto:steve.baskauf@vanderbilt.edu"><steve.baskauf@vanderbilt.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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:
<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>
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.
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
<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>
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.
Steve
Bob Morris wrote:
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:
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.
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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--
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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</blockquote>
<pre wrap=""><!---->
</pre>
</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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