[tdwg-content] Why it matters what kind of things we include in the definition of Individual
Steve Baskauf
steve.baskauf at vanderbilt.edu
Sat Nov 6 04:17:40 CET 2010
What I think is getting lost in this attempt to define what is and what
is not an Individual is that there is a clear and straightforward
functional definition of Individual based on what it is intended to do:
An Individual serves as a resource relationship node that connects
Occurrences to Identifications.
(This is stated explicitly in the comment I included with the term
definition.)
If you don't like the technical language, then look at the diagram:
http://bioimages.vanderbilt.edu/pages/token-explicit.gif
which shows that there is a many-to-one relationship between Occurrence
and Individual, and a one-to-many relationship between Individual and
Identification.
If you prefer it in layman's language: an Individual can connect many
Occurrences to many Identifications.
If something that you want to call an Individual can't or doesn't do
this, then it shouldn't be an Individual. The purpose why I have asked
for this class to be added to DwC is to be able to accomplish the
purpose listed above, not to see how many things we can think of for
which we have philosophical reasons to think that they should be called
an "individual".
We gain three clear benefits from being able to create instances of the
Individual class:
Benefit 1. We can group Occurrences that document the same Individual
over time (i.e. resampling). This is exactly the reason why the present
term dwc:individualID exists (read the definition at
http://rs.tdwg.org/dwc/terms/index.htm#individualID). That function is
represented by the triangle on the left side of Individual in the
diagram referenced above.
Benefit 2. If there are multiple Identifications of an Individual,
those identifications automatically are associated to all Occurrences
that are associated with the Individual. That function is represented
by the triangle on the right side of the diagram. If we connect several
tokens to an Individual, those multiple Identifications are
automatically associated with all of the tokens as well.
Benefit 3. Individuals allow us to do semantic reasoning of a very
primitive sort. If an Occurrence A and the token that acts as its
evidence are associated with Individual A having Identification A, and
if Occurrence B and the token that acts as its evidence are associated
with Individual B having Identification B, then if we discover that
Individual A is the same as Individual B then we know that
Identification B also applies to Occurrence A (and its documenting
token) and that Identification A applies to Occurrence B (and its
documenting token). Writing it in this abstract way is a bit hard to
follow, so I'll illustrate with two examples. In a previous post, I
mentioned a living individual (possibly the only one) of Crataegus
harbisonii. I have documented the Occurrence of this Individual on
2008-10-31T09:49:29 at 36.07° latitude, -86.88° longitude by the token
http://bioimages.vanderbilt.edu/baskauf/70915 (an image) and have
applied an Identification of Crataegus harbisonii to that Individual.
Ron Lance has also recorded the Occurrence of the same Individual at the
same location around 2000 and documented it by propagating it by a
cutting which is now a living specimen in the North Carolina Arboretum.
If someone examines that living specimen and and applies an
Identification of Crataegus somethingelse to the Individual from which
it was collected, then I can infer automatically that his/her
Identification of Crataegus somethingelse applies to my 2008 Occurrence
and its associated image. The person who looked at the living specimen
would not need to look at my image for me to know that. Another example
happened when a taxonomist was looking at several bark and leaf images
for a particular species I had photographed. He wanted to know which
flower images that I had taken came from the same tree as particular
bark and leaf images. He knew logically that if he could identify the
Individual by its flower that by inference that Identification would
also apply to the bark image even if he couldn't do the actual
identification based on the bark alone. A final application involves
Identifications of "duplicates" found in different herbaria. A
taxonomist is doing a revision of a genus and borrows specimens of that
genus from several herbaria. Specimen A from herbarium A was identified
as species A in the genus of interest. Specimen B from herbarium B was
identified as species B in the same genus. By careful examination of
the label records, the taxonomist is able to determine that the
specimens are "duplicates" (i.e. they are from the same Individual). By
inference, the taxonomist knows that the identifications of species A
and species B apply to both specimen A and specimen B because they are
both from the same Individual.
In my original thinking about what should constitute an instance of the
class Individual, I only allowed actual biological individuals, or small
localized populations that were so tightly linked that a taxonomist
collecting specimens from it would call them "duplicates". Under that
definition of Individual, all three of the benefits listed above would
apply. My qualms about applying the term Individual to the various
buckets of dead homogeneous and heterogeneous mixtures of organisms
stems from loss of benefit number 1 in those cases. Moving subsets of
those dead organisms around and putting them into different jars has no
aspect of resampling. Sorting and re-assigning individualIDs to the
various jars still only involves a single Occurrence, the one in which
the trawler collected the original bucket from the ocean. There are
clever things we can do with multiple Identifications, but we've
basically lost the triangle on the left side of Individual (no benefit
#1). My qualms about applying the term Individual to cut up pieces of
organisms involves the triangle on the right side of Individual
(connecting Individuals to Identifications). If you chop up a fish into
100 pieces of organs, tissues, DNA samples, etc. and call all of those
pieces Individuals, there is no point in assigning separate
Identifications to all of them. Unless the original fish has had some
kind of tricky human intervention like interspecific organ transplants,
grafting, or creation of a chimera, it is a foregone conclusion that all
of the parts of the individual fish have the same Identification.
Assigning them all separate identifications would be a waste of time -
no Benefit #2. Finally, applying the term Individual to containers that
we know to contain biological individuals that probably differ at lower
taxonomic levels causes problems with Benefit #3. Unless one has a way
to specify that the Individual he is talking about is the kind of
Individual that a taxonomist would take "duplicates" from (i.e. reliably
a single taxon at a low level), it becomes difficult to be sure of the
accuracy of the type of reasoning that I'd like us to be able to do
based on Occurrences and tokens documenting a common Individual.
So what I've tried to do here is to explain why I'm opposed to
broadening the definition of Individual to include all of the things
that people have suggested it should include. If the definition becomes
so broad that we loose the benefits that were the reason for
establishing the class Individual, then there is no point in having the
class at all. I think that if we stick to the definition that I
proposed, we can at least get Benefits #1 and #2. With the substitution
of "taxon" for "species or lower...", I think to get benefit #3 we are
going to need to also have the individualScope term that Rich proposed
and it would need to include a value that indicated that the group of
biological individuals were restricted to those that a taxonomist would
call "duplicates".
Steve
--
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:
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Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
http://bioimages.vanderbilt.edu
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