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

Richard Pyle deepreef at bishopmuseum.org
Sun Jul 17 08:43:19 CEST 2011

> Perhaps it's better to take one step back further, and enumerate a variety
> example instances of biological entities that we all agree should be in
> class, and a contrary enumeration of example biological entities that we
> 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
> this thread I sense that there is actually not consensus on which side of
> 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
> 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.
> organelles have their own genome and evolutionary history, and were once
> independent organisms. If we accept this, then we might say that
> entities to be included have a genome or a pool of genomes with a (shared
> 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.


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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