[tdwg-content] New terms need resolution: "Individual"

Chuck Miller Chuck.Miller at mobot.org
Sun Jul 17 18:21:59 CEST 2011

But Hilmar recommended a companion list of things not in the class. What are some of those?


On Jul 17, 2011, at 1:46 AM, "Richard Pyle" <deepreef at bishopmuseum.org> wrote:

>> Perhaps it's better to take one step back further, and enumerate a variety
> of
>> example instances of biological entities that we all agree should be in
> the
>> class, and a contrary enumeration of example biological entities that we
> all
>> agree should not be in the class. If you include less obvious and possibly
>> controversial ones in these lists, it may help to narrow down what the
>> differentiating criteria really are. And while this exercise may sound
> trivial, it
>> hasn't been done yet as far as I'm aware, and from a number of the posts
> in
>> this thread I sense that there is actually not consensus on which side of
> the
>> divider the border-cases go. And you can't hope for consensus on the label
>> (or the definition) if there isn't first consensus on how we want the
> instances
>> classified.
> I agree with Hilmar on this approach.
>> Just to throw in an example, I might argue that at least some organelles
>> should actually be among the biological entities included in the class.
> Some
>> organelles have their own genome and evolutionary history, and were once
>> independent organisms. If we accept this, then we might say that
> biological
>> entities to be included have a genome or a pool of genomes with a (shared
> in
>> the case of a pool) evolutionary history, and those to be excluded do not.
>> This would exclude vacuoles from the class, but include plastids, viruses,
>> cows, and buffalo herds.
> This *might* be close to what my own vision of how to establish the criteria
> for things to include within this class. But following Himar's suggestion, I
> will try to list some things that I think may be useful to represent as
> instances of this class.
> I'll start with the entities that most of us probably agree with:
> - A single whole-organism specimen curated and preserved at a Museum
> - A single whole organism (whale, wolf, buffalo, tree, insect, etc.)
> documented in nature
> - A single, cohesive colonial organism (e.g., coral head), either preserved
> in a Museum, or documented in nature
> Now some well-enumerated aggregates:
> - A single "lot" of multiple whole-organism specimens of the same taxon
> curated and preserved at a Museum
> - A well-defined and enumerated set of whole organisms (pod of whales, pack
> of wolves, etc.) documented in nature
> Now some non-enumerated, but still reasonably definable aggregates:
> - A colony of ants (or termites, or bees, etc.) in nature
> - A living culture of bacteria
> - A flock of birds in nature
> Now some parts of a single whole organism:
> - A preserved herbarium specimen
> - A preserved skeleton of a mammal
> - A preserved skin of a mammal
> - A preserved head of a fish
> - A tissue sample extracted from a whale in nature
> The preceding set requires some elaboration.  For example, a herbarium
> specimen is usually a clipping or other small part of a larger whole plant.
> Often multiple clippings from the same individual plant are taken and
> preserved as separate herbarium specimens.  Should there only be one
> instance of this class representing the whole plant?  Or should there be
> multiple distinct instances of this class, one for each herbarium specimen?
> If the former, would the herbarium specimens represent instances of the
> "Evidence" class, linked to the one instance of this class (whole plant)? If
> the latter, should there be a separate instance of this class to represent
> the whole plant, and then each of the instances of herbarium specimens be
> linked via a "derivedFrom" relationship to the whole-plant instance?
> Similarly, suppose the mammal skeleton and skin in the above list are from
> the same individual mammal.  Would there be one instance of this class (for
> the whole organism), and the Skeleton and Skin be treated as instances of
> the Evidence class?  Or, should there be two instances (one for the skin,
> one for the skeleton)?  Or should there be three instances (one for the
> whole mammal organism, one for the preserved skin derived from it, and one
> for the preserved skeleton derived from it)?
> Take the example of the whale.  Suppose there is a pod of 7 whales that is
> well-defined, cohesive, tagged, and studied in nature.  Would there be one
> instance of this class for the pod, and then 7 additional instances (one for
> each individual whale) that are linked as "memberOf" the pod instance?  What
> to do with the tissue sample?  Is it an instance of the Evidence Class?  Is
> it another instance of this class, "derivedFrom" the instance of this class
> representing the specific whale from which the sample was taken?
> Now some border-line and controversial cases:
> - A non-enumerated but otherwise well-defined population of a single species
> in nature. [How do we distinguish this from a well-defined taxonomic unit?]
> - A single rock in a Museum collection that has multiple fossils
> (representing multiple phyla of animals) embedded in it
> - A single rock preserved in alcohol containing multiple invertebrate
> specimens from different phyla
> I'm sure we can come up with other examples.  I do not have web access (only
> email), so I was unable to look at Peter DeVries' links to examples of what
> he felt belonged in this class.  Pete -- maybe you can summarize them in
> text form?
> I would like to believe that all instances of Occurrence can be rooted into
> one instance of this proposed new class.  So, maybe it would be useful to
> think about all the different ways that an Occurrence is currently
> represented in actual instances, and see if we can scope this new class to
> be the generalized "basis of record" for all Occurrences.
> Aloha,
> Rich
> P.S. I have BCC'd the BiSciCol list on this email, because of it's strong
> relevance to that project.
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