[tdwg-content] Request for vote on proposals to add Individual as a Darwin Core class and to add the term individualRemarks as a term within that class
Richard Pyle
deepreef at bishopmuseum.org
Thu Nov 4 03:49:07 CET 2010
Just a quick comment:
I think Bob's points are insightful and very much relevant to this
discussion overall. We should visit this point with some care and scrutiny,
to see if we need more terms and/or controlled vocabularies to be able to
make the sort of reasoning assumptions that Bob is touching on.
Having said that, I think the argument-of-the-moment is to what extent we
limit the scope of an aggregated Individual based on how narrowly or broadly
circumscribed the taxon assigned to the aggregate may be. I saw, but
haven't yet read, Steve's most recent post. Gotta run now, but I'll be
back...
Rich
_____
From: Bob Morris [mailto:morris.bob at gmail.com]
Sent: Wednesday, November 03, 2010 4:12 PM
To: Steve Baskauf
Cc: tuco at berkeley.edu; tdwg-content at lists.tdwg.org; Richard Pyle;
RichardsK at landcareresearch.co.nz
Subject: Re: [tdwg-content] Request for vote on proposals to add Individual
as a Darwin Core class and to add the term individualRemarks as a term
within that class
An remark about aggregations, but with no insight as to its value:
As a biologically naive lurker, it strikes me that the struggle here may be
an artifact of mixing all the reasons for aggregating organisms in an
observation, whereas there plenty of use cases that suit some sets of those
reasons but not others. For example some aggregates are artifacts of
collecting or observation methodology, e.g. lots of stuff in a vial. Some,
such as on paleo specimens are a consequence of a bunch of critters being at
the same watering spot when the mud came roaring down the river. Some are
ecosystem entanglements. The reason underlying the aggregation might itself
participate in some kinds of scientific inference but not in other kinds.
For example, if a bunch of species are all in the same paleo specimen, that
helps a lot with establishing the era for each of the species' presence on
earth and I suppose has implications for evolutionary history. Lichens, I
gather, are treated as a single individual and given a taxon name, even
though for much about lichen biology it's important that there are two
individuals, from different taxa, in a specimen. Etc., etc. So to me, it
looks like the problem might be less in whether there are disagreements
about what constitutes an individual, so much as that there are several
different kinds of aggregation based on \why/ the aggregation arose. It
might be \that/ is why defining 'individual' just in terms of an unadorned
notion of 'aggregation' seems to lead to debates about the fitness-for-use
of such a definition.
Bob Morris
On Wed, Nov 3, 2010 at 10:24 AM, Steve Baskauf
<steve.baskauf at vanderbilt.edu> wrote:
John,
I'm not sure that I agree with your analysis that the definition prevents
the possibility of making an Identification at a rank less specific than a
species. My revised definition says that the Individual should only include
groups of organisms that are reliably known to be of a single species - it
doesn't say that we need to know what that species is (i.e. an
identification to genus or family can be made with the hope that someone
down the line would be able to refine the identification to species).
Clarification on this point could be added to the comment or the Google Code
page, but I don't think there is a problem with the definition per se.
However, if there is a consensus that the definition is too restrictive, I
would not object to changing the wording of the definition from "species (or
lower taxonomic rank if it exists)" to "taxon" if there were clarification
added to the comments or Google Code page that Individual was not intended
to include aggregations of multiple species.
I agree that there is a need for a term that represents "collections",
"bags", "aggregations", or whatever you want to call an aggregation that
includes multiple species. But I have never intended that Individual should
be that term. If we expand Individual to include aggregates, then it
becomes unusable for its original intended purpose. I would prefer for
someone to propose a different term for aggregates of individuals instead of
adding that function to Individual. Then define the relationship of this
new thing to Individual as a one:many relationship (one aggregation:many
Individuals).
Steve
John Wieczorek wrote:
Most of you probably do not receive postings from the Google Code site for
Darwin Core. Steve B. updated the proposal for the new term Individual, and
then commentary ensued on the Issue tracker. Since there remains an
unresolved issue, I'm bringing the discussion back here by adding the
commentary stream below. The unresolved issue is Steve's amendment is the
restriction in the definition to "a single species (or lower taxonomic rank
if it exists)."
Rich argues that we should not obviate the capability of applying an
Identification to an aggregate (e.g., fossil), where the aggregate consists
of multiple taxa.
Steve argues that Identifications should be applied only to aggregates of a
single taxon.
Steve, aside from the aggregate issue (which should be solved
satisfactorily), your suggestion is too restrictive, because it would
obviate the possibility of making an Identification (even for a single
organism) to any rank less specific than a species. That is a loss of
capability, and therefore unreasonable.
Comment 7
<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2
0Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7> by
baskaufs <http://code.google.com/u/baskaufs/> , Today (8 hours ago)
As a result of the discussion that has taken place on the tdwg-content email
list during 2010 October and November, I am updating the term recommendation
for Individual as follows:
Definition: The category of information pertaining to an individual organism
or
a group of individual organisms that can reliably be known to represent a
single species (or lower taxonomic rank if it exists).
Comment: Instances of this class can serve the purpose of connecting one or
more instances of the Darwin Core class Occurrence to one or more instances
of the Darwin Core class Identification.
Refines: N/A
Please note that as a precautionary measure, I have removed the statement
that Individual refines http://purl.org/dc/dcmitype/PhysicalObject because
the definition of PhysicalObject specifically mentions that the object is
inanimate. I am not currently aware of any well-known term that defines
living things.
Steve Baskauf
Delete comment
<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2
0Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#>
Comment 8
<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2
0Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8> by
deepreef at hawaii.rr.com <http://code.google.com/u/deepreef@hawaii.rr.com/> ,
Today (8 hours ago)
I think the definition should be "...represent a single taxon". We
shouldn't restrict it to members of the same species (or lower), because
then we technically can't include things that may represent more than one
species, yet would best be treated within the scope of an Individual.
Also, I'm slightly partial to the term "Organism" for this class, rather
than "Individual", because it's more clearly tied to the biology domain, and
less likely to collide with the word "Individual" in other domains. I know
such collision is not a technical problem, but it might lead to some
confusion.
Delete comment
<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2
0Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#>
Comment 9
<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%2
0Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9> by
baskaufs <http://code.google.com/u/baskaufs/> , Today (8 hours ago)
Well, the reason that I defined it to be members of the same species is to
ensure that the term Individual can serve the primary function that I
perceived was needed: to make the connection from occurrences to
identifications. When I said one or more identifications, I meant one or
more opinions about what that single species (or lower) was, not that there
could be multiple identifications of several different species that happened
to be in the same "bag" such as the contents of a pitfall trap containing
multiple species, an image that contained several species, or a specimen
that contained parasites of a different species. I think that there is a
need for a term for this other kind of thing, (a heterogeneous "lot",
"batch", or something), but I think that including this in definition of
Individual defeats the purpose for which I proposed it. If there were
several different species in the "Individual", then
one would have to specify which identification went with which biological
individual within the "lot", which would result in actually breaking down
the "lot" into single species "Individuals" anyway.
--
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
http://bioimages.vanderbilt.edu
--
Robert A. Morris
Emeritus Professor of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390
Associate, Harvard University Herbaria
email: morris.bob at gmail.com
web: http://bdei.cs.umb.edu/
web: http://etaxonomy.org/mw/FilteredPush
http://www.cs.umb.edu/~ram <http://www.cs.umb.edu/%7Eram>
phone (+1) 857 222 7992 (mobile)
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