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@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 by 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
Comment 8 by 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.
Comment 9 by 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@gmail.com
web: http://bdei.cs.umb.edu/
web: http://etaxonomy.org/mw/FilteredPush
http://www.cs.umb.edu/~ram
phone (+1) 857 222 7992 (mobile)