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I am back in the land of Internet access again after several weeks of
glorious lack of it. <br>
<br>
There have been a number of posts regarding John
Wieczorek's
proposed resolution of the "class Individual" proposal
(<a class="moz-txt-link-freetext"
href="http://code.google.com/p/darwincore/issues/detail?id=69">http://code.google.com/p/darwincore/issues/detail?id=69</a>)
though the
creation of the "BiologicalEntity" class
(<a class="moz-txt-link-freetext"
href="http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002575.html">http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002575.html</a>).
In these posts two general issues raised:<br>
<br>
I. Competency questions, i.e. how will the creation of this class help
us do something useful?<br>
II. What sorts of resources should be instances of this class, i.e. how
should the class be defined?<br>
<br>
These general questions were previously discussed at length between
October 2009
and February 2011 concurrently with general questions about the meaning
of "Event", "Occurrence","Taxon" and other existing DwC classes. Since
it requires many hours to review the many tdwg-content posts during
that period, I will refer to a summary at
<a class="moz-txt-link-freetext"
href="http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary">http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary</a>
for
anyone who is interested in skimming the main points of that
discussion. <br>
<br>
When I proposed the Individual class, I wanted to explicitly recognize
a class of
resources that would facilitate three things,
which I suppose are "competency questions" of a sort:<br>
1. To allow for linking multiple Occurrence records that involved the
same organism at different times and/or places (i.e. the intended
purpose of the existing dwc:individualID term; i.e. to facilitate
resampling). Examples would be mark/recapture, radio tracking,
photo-identification of whales, tracking the status of a sessile
organism over time, etc.<br>
2. To allow for the linking or grouping of multiple forms of evidence
associated
with the same organism which may have been collected at the same time
and place (multiple forms of documentation for a single occurrence) or
during several Occurrences. Examples would be collections of several
images, several specimens, or both images and specimens from the same
organism. <br>
3. To link multiple Identifications of the same individual organism,
particularly when these Identifications were based one different pieces
of evidence arising from the same individual. For example, if
"duplicate" specimens from the same organism ended up in different
museums they might be assigned different Identifications. An
Identification asserted for one specimen would apply to other specimens
from the same individual organism even if that Identification wasn't
explicitly assigned to the other specimens. I have referred to this
function as "inferring duplicates" - it could also be called "tracking
duplicates" if the two samples were known to have arisen from the same
individual organism before they were identified rather than after.<br>
(Since I'm not really up on the technical definition of "competency
question" please excuse me if I'm misapplying the term to mean "what we
want something to be able to do".)<br>
<br>
As the discussion progressed, it became clear that others wanted the
proposed Individual class to do other
things as well. In particular, Rich Pyle articulated a desire to
provide a
mechanism for grouping in a hierarchical manner pieces of physical
evidence that were derived
from living organisms. These could include aggregates of organisms,
organisms, and pieces of organisms. After some rather heated
discussion, Kevin Richards put his finger on the critical distinction
between what I wanted the Individual class to do and what Rich wanted:
"it seems like Steve's idea for the Individual more closely resembles a
many-to-many joining table in a database (ie doesn't serve much use
other than connecting two tables/classes together - and doesn't
normally relate to a 'real world' type of object). Whereas it seems
Rich's idea is to relate it more to 'real-world' objects, such as
samples, re-samples, etc, to allow tracking and connectability of the
observed/collected/processed individuals..."
(<a class="moz-txt-link-freetext"
href="http://lists.tdwg.org/pipermail/tdwg-content/2010-November/001956.html">http://lists.tdwg.org/pipermail/tdwg-content/2010-November/001956.html</a>).
After thinking about this for a very long time, I've become convinced
that Kevin was on the right track. It seems to me that what we have
here is two
different sets of "competency questions" which define sets of entities
that overlap but which
are not congruent. An actual single, live organism can serve both as a
unit for resampling and "attachment" of Identifications, AND as an
organizational unit that is part of and which has parts that are
biological samples. Some other entities, such as cohesive pack/herds
and clonal organisms can also serve both purposes. Other entities
cannot: it doesn't make sense to resample dead organisms or pieces of
organisms, and an identification applied to part of a taxonomically
heterogeneous unit (e.g. a mixed flock of birds) cannot be reliably
inferred to apply to another part of the same unit. Neither intended
purpose/definition of "Individual" (the many to many database join or
the mechanism
for hierarchical grouping of physical evidence) is intrinsically
"wrong", they simply facilitate different competency questions.<br>
<br>
So I believe that the answer to question II (how do you define the
class?) is better answered by saying "instances of the class are
resources that facilitate the competency questions" than to base the
definition on a philosophical discussion of what people imagine an
"Individual" or "BiologicalEntity" to be (I think I'm agreeing with the
point Bob was trying to make). I think that at a minimum, functions 1
and 2 (defining an entity to which multiple occurrences can be linked
and to which multiple forms of evidence can be linked) must be
accommodated by the Individual/BiologicalEntity class; the utility of
those two functions is certainly implied by the already-existing term
dwc:individualID . <br>
<br>
Personally, I would like for the third function ("inferring
duplicates"; linking multiple Identifications to the same entity and
being assured that all Identifications of the same Individual would
apply to all artifacts associated with that Individual) to be
accommodated by the definition, but the current state of the discussion
is unclear on this point. The sticking point is related to the
definition of "taxonomic homogeneity". When I used that term, I
intended for it to mean that the entity is believed to be homogeneous
to the lowest possible level in the way that one knows that two
branches from the same tree or two parts of the same clonal organism
are guaranteed to have the same taxonomic identify at every level.
This is NOT the way Rich was using the term - he explained that he
intended that a "taxonomically homogeneous" biological entity could be
an aggregate of organisms that are known to be heterogeneous at a lower
taxonomic level but that for whatever reason were identified at a
higher taxonomic level common to all organisms (e.g. we know that the
five fish in this jar are different species of fish, but we are going
to identify the lot as class=Actinopterygii for the time being).
However, Cam and I have previously defined such entities as
"taxonomically heterogeneous" (see
<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
would prefer that "taxonomic homogeneity" be restricted to the
definition that I intended simply because I don't know of any other
thing to call something that is believed to be taxonomically
homogeneous to the lowest possible level. The reason why this is
important is that if an Individual/BiologicalEntity is allowed to be
taxonomically heterogeneous (sensu darwin-sw) then one cannot infer
that discovered "duplicates" share all Identifications given to any
duplicate pieces of evidence, whereas if an Individual/BiologicalEntity
is required to be taxonomcally homogeneous (sensu darwin-sw, NOT sensu
Pyle) then one can make that inference. This is a circumstance that
occurs fairly regularly when comparing specimens in different herbaria
- one discovers two "duplicate" specimens that have been assigned
different Identifications and one infers that both Identifications
apply to the source tree, clump of moss, small population of herbs,
etc. (i.e. Individual/BiologicalEntity). On the other hand, if a
taxonomically heterogeneous (sensu darwin-sw) marine trawl sample is
subdivided into two samples that are sent to two museums, one could not
safely infer that an Identification made based on one sample could be
applied to the other sample. The two subsamples may contain sets of
fish that can be identified to taxa that are at a lower level that the
initial Identification of the conglomerate sample and which are not the
same. <br>
<br>
So I'm not saying that the definition of Individual/BiologicalEntity
MUST facilitate my competency question 3. What I'm saying is that we
MUST make it clear whether or not we intend for the proposed class to
be restricted to taxonomically homogeneous entities (sensu darwin-sw)
because that will determine whether the class will facilitate
competency question 3 or not. It would be a bad thing for different
people to have different understandings about the restrictiveness of
the term. If there is a consensus that an Individual/BiologicalEntity
should be taxonomically homogeneous, then to some extent that provides
a practical functional definition of what kinds of things should
qualify as Individuals/BiologicalEntities. A herd of caribou, a clump
of moss, a tree, a small uniform patch of herbaceous plants, a coral
head, a tissue culture sample, and a network of slime mold would be
Individuals/BiologicalEntities because there is a reasonable
expectation that they are taxonomically homogeneous. If there is a
consensus that an Individual/BiologicalEntity need NOT be taxonomically
homogeneous, then pretty much any kind of thing involving life would
qualify: all of the animals in Yellowstone Park, all the jars sitting
on shelves in the Smithsonian Institution, the Great Barrier Reef, etc.
If the definition is broadened to that level, then I'm left wondering
what competency questions the proposed class could still serve.<br>
<br>
This email is now at or has exceeded the length of an email that many
people will take the time to read. So I will draw it to a close and
post a separate email on the topic of competency questions for John's
proposed class "CollectionObject" which I believe address Rich's desire
to track "real-world" objects (samples, re-samples, etc.). <br>
<br>
Steve<br>
<br>
Bob Morris wrote:
<blockquote
cite="mid:%20%3CCADUi7O6noyRZmZo2sZGTEaNK7pTqbfMQd1KLD_3YnMcAQ+Ax4A@mail.gmail.com"
type="cite">
<pre wrap="">There is a series of jokes, and an entire TV quiz show, essentially
starting from the meme "What is the question to which the answer is
<X>". Now, I am not a biologist (surprise!), so it is likely that
domain ignorance leaves me unable to understand whether all the
postings in the thread about new DwC term resolution are arguing from
the same set of questions their authors hope to have answered by a
resolution of the term "Individual". (It's even a little unclear to
me whether everybody has the same notion of "resolution of a term",
but that's a whole different discussion, which would contain a lot of
uses of "rdf:type" and the contentious "rdfs:domain").
I speculate that lengthy term definition debates would be shorter if
they started with agreement on competency questions for the term.
Competency questions are sort of usage scenarios cast as questions.
See <a class="moz-txt-link-freetext"
href="http://marinemetadata.org/references/competencyquestionsoverview">http://marinemetadata.org/references/competencyquestionsoverview</a> .
Bob Morris
On Thu, Jul 14, 2011 at 2:41 AM, Richard Pyle <a
class="moz-txt-link-rfc2396E" href="mailto:deepreef@bishopmuseum.org"><deepreef@bishopmuseum.org></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">My turn to disagree (strongly, in this case). It's not an instance of a
taxon, it's an instance of an Organism. A taxon is merely a non-factual
(i.e., opinion-based) attribute of an organism, secondarily associated via
an Identification instance.
I could probably be comfortable with "OrganismInstance"; but in that case,
why not just "Organism" as Paul suggested? Isn't "Instance" sort of implied
by all the classes?
I am certainly open to debate about where the "upper boundary" of an
instance of this class, and I agree that "population" could be interpreted
more as a low level of "taxon", rather than a high level of "organism". But
I certainly don't think that instances of this class should be limited to a
singular organism. Would a coral head then constitute thousands of
instances of this class? Surely such colonies could be collapsed into a
single instance of this class. And the same would likely also be useful for
colonies of insects (ants, termites, bees, etc.), as well as small groups
(pack of wolves, pod of whales, etc.); not to mention a specimen "lot" in a
Museum collection.
I agree it should have only *one* taxon, but that there should be no upper
limit on the rank of this taxon. If more than one taxon is identified, then
there needs to be a separate instance of this class for each identified
taxon. But this only applies when multiple taxa are acknowledged -- it does
NOT restrict multiple taxa being linked to the same instance via multiple
identifications when there is a difference of opinion about what the correct
taxon identity should be. In other words, an instance of this class may be
identified as "A" *or* "B", but could not legitimately be identified as "A"
*and* "B" simultaneously (except, perhaps in the case of hybrids, but that's
another situation altogether).
More later.
Aloha,
Rich
</pre>
<blockquote type="cite">
<pre wrap="">-----Original Message-----
From: <a class="moz-txt-link-abbreviated"
href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [<a
class="moz-txt-link-freetext" href="mailto:tdwg-content">mailto:tdwg-content</a>-
<a class="moz-txt-link-abbreviated" href="mailto:bounces@lists.tdwg.org">bounces@lists.tdwg.org</a>] On Behalf Of Gregor Hagedorn
Sent: Tuesday, July 12, 2011 10:09 AM
To: Steven J. Baskauf
Cc: <a class="moz-txt-link-abbreviated"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
Subject: Re: [tdwg-content] New terms need resolution: "Individual"
</pre>
<blockquote type="cite">
<pre wrap="">represent a single taxon. I think that Individual is probably not a
good name due to confusion with the technical use of that term
</pre>
</blockquote>
<pre wrap="">elsewhere.
TaxonInstance seems to me to be perhaps most precise.
Personally I have a problem merging individual with population, since
population -> metapopulation -> subspecies form a continuum in my
understanding. But I am quite willing to be pragmatical :-)
Gregor
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</pre>
</blockquote>
<pre wrap="">_______________________________________________
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</pre>
</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>
</pre>
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