[tdwg-content] tdwg-content Digest, Vol 20, Issue 17

Wed Nov 3 21:59:09 CET 2010

I want to model things in a way that makes sense to me and everyone else who disagree with me too.  If we all disagree of what a species is, then let's not deal with species or even ranks.  Individuals = taxa.  As you said, species can be sets of individuals, so how's that differ from Steve's aggregates?

Nico

On Nov 3, 2010, at 4:42 PM, Peter DeVries wrote:

> Hi Nico,
> 
> Are you wanting to model things that you think are actually species within a larger clade or are these more like subspecies?
> 
> I think this gets at a bit of what these are to be used for. 
> 
> Are they for modeling classifications or occurrences and other data about individuals or sets of individuals which represent instances of species?
> 
> - Pete
> 
> On Wed, Nov 3, 2010 at 1:19 PM, Nico Cellinese <ncellinese at flmnh.ufl.edu> wrote:
> 
> Steve is using Species as ranks in his definition and I think this is the wrong approach.  Let's make all this rank agnostic please!  Use the word taxon!  What if I have a group of organisms that represents  a polyphyletic species and I want to name a lineage (group of organisms) within this traditionally recognized species that I am not recognizing as species per se (as in rank of species).  In other words, Identifications and ranks are two different things, so let's abandon ranks for a more objective discussion on taxa. Individuals are definitively not species.
> 
> Nico (the other one)
> 
>> 
>> On Wed, Nov 3, 2010 at 7:24 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 mult
>> 
>> iple 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.
>> 
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>> ------------------------------
>> 
>> Message: 2
>> Date: Wed, 3 Nov 2010 10:38:58 -0700
>> From: John Wieczorek <tuco at berkeley.edu>
>> Subject: Re: [tdwg-content] Request for vote on proposals to add
>> 	Individualas a Darwin Core class and to add the term individualRemarks
>> 	as a termwithin that class
>> To: "Blum, Stan" <SBlum at calacademy.org>
>> Cc: "tdwg-content at lists.tdwg.org" <tdwg-content at lists.tdwg.org>
>> Message-ID:
>> 	<AANLkTikBMK47LN0r7ppgb8MoQtGqzmseppYVKpTcj7FL at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>> 
>> This is what happened to Organism, from the thread?Re: [tdwg-content]
>> Treatise on Occurrence, tokens, and basisOfRecord [SEC=UNCLASSIFIED].
>> 
>> John said:
>> 
>> "I like Organism, but I don't like the inconsistency it would make
>> with individualID and individualCount on the one hand, or extra work
>> to change these to organismID and organismCount on the other.
>> Individual doesn't carry these extra burdens, and could be added
>> without breaking any existing applications."
>> 
>> Rich said "OK" so it must be OK. ;-)
>> 
>> On Wed, Nov 3, 2010 at 10:03 AM, Blum, Stan <SBlum at calacademy.org> wrote:
>>> 
>>> All:
>>> 
>>> What happened to changing the term to organism? ?I think the word organism, at least strictly speaking, is closer to our intention than individual.
>>> 
>>> Compare the definitions you get from:
>>> 
>>> http://www.google.com/search?hl=en&q=define:+individual&btnG=Search
>>> 
>>> And
>>> 
>>> http://www.google.com/search?hl=en&q=define:+organism&btnG=Search
>>> 
>>> 
>>> -Stan
>>> 
>>> 
>>> 
>>> On 11/3/10 9:02 AM, "John Wieczorek" <tuco at berkeley.edu> wrote:
>>> 
>>> I have no further objection if the wording is changed as you propose here. If no one else has any objections, this one seems ready to be prepared for the TAG following the voting mechanism proposed at TDWG this year. I'll take the responsibility to see that through as soon as I can.
>>> 
>>> On Wed, Nov 3, 2010 at 7:24 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 mu
>> 
>> ltiple 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.
>>> 
>>> 
>>> _______________________________________________
>>> tdwg-content mailing list
>>> tdwg-content at lists.tdwg.org
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>> 
>> 
>> 
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>> 
>> End of tdwg-content Digest, Vol 20, Issue 17
>> ********************************************
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> 
> 
> -- 
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> TaxonConcept Knowledge Base / GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
> ------------------------------------------------------------

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