[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

[Bob Morris]

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%20Status%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%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#>
> Comment 8<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%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%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#>
> Comment 9<http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%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) 343-6707http://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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