[tdwg-content] Why it matters what kind of things we include in the definition of Individual

Richard Pyle deepreef at bishopmuseum.org
Mon Nov 8 07:33:34 CET 2010


Thanks, Bob.  This is helpful.

> 1. Neglecting-if one can--issues about colonial organisms--is 
> a lichen one individual or two?

If my understanding of lichen is correct, I would answer two; one for each
taxon represented.

> 2. In a way consistent with your answer to 1,  counting the 
> human obligate symbionts such as gut bacteria, is a human one 
> individual or many?

This is a problem that is so fundamental that I don't think we can address
it through the DwC class individual (I thought about bringing it up at one
point during the thread, but decided not to go there...).  I would wager
that something on the order of 90% of the biological cells represented by
*any* Preserved Specimen are bacteria (some were there at the time of
capture, some came later). If we took this into account, then every
non-bacterial specimen we have in our collections could be identified only
to the level of "Life".  Not very practical.  Nor is it very practical to
take steps to remove all the bacterial cells from the non-bacteria specimens
in our collection.

I think the best way to characterize it is that the "Individual" is the
organism "of interest".  This is not to say that parasites are not
interesting.  But when they are encountered on living or preserved specimen
hosts, and are of interest to a parasitologist, then I would assume a new
Individual would be established (whether or not the parasite was physically
separated from the host).  We have this a lot, for example, in shark
specimens -- which have many internal (macro) parasites that are of interest
to the respective biologists.  Obviously, when a new Individual instance is
established for a parasite (or other commensal organism), thent he
appropriate semantic relationship would be establisshed between it and the
host Individual.

So....from my perspective, the answer to your question is that a human is
one individual, with a taxon Identification of "Homo sapiens Linnaeus sec.
Linnaeus", which is implied to exclude all of the organisms physically
associated with that human.  As those physically associated organisms are
recognized as something of interest, and Identified to a taxon other than
"Homo sapiens Linnaeus sec. Linnaeus", a new instance of Individual is
established for it/them.

Does that adequately address your question?

> 3. If you feel no compulsion to be consistent in answering 1 
> and 2, will the addition of class Individual to DwC require 
> further properties to determine which of your inconsistent 
> uses is in play, in order that semantic integration about 
> data on Individuals not become logically inconsistent?

If my answer above for #2 is satisfactory, you can count on me using it
consistently.

> 4. In the case of lichens or other(???) "compound" organisms 
> whose taxon name is conventionally given by the name of the 
> fungal component, are new DwC terms needed to distinguish 
> whether an Individual of that name is a lichen or a fungus?

Hmmm....isn't that a function of taxonomy?  If more than one taxon of
interest is involved, then I would think that a corresponding number of
Individuals would be established, with appropriate semantic relationship(s)
established between/among them.

> (As far as I can tell from a bit of browsing on the web, the 
> current answer to the conundrum of 4 seems to be that the 
> distinction is made mainly in the dataset metadata, declaring 
> in some way that the dataset is of fungi or is of lichens. 
> This doesn't seem very satisfactory in a world where 
> aggregators may isolate data from the datasets. It probably 
> imposes higher-than-record-level provenance requirements on 
> the integration.)

Maybe you could describe the situation better.  My understanding of lichens
is that we're dealing with composite organisms involving more than one
taxon, in which case our definition of "Individual" would require more than
one instance of such -- one for each discernable taxon (of interest) in the
aggregate.  The aggregate specimen can still be treated as a single
Individual (with either an appropriately broad taxonomic identification, or
no taxonomic identification at all).  I suppose the situation is analagous
with Corals, many of which include symbiotic photosynthetic zooxanthellae
(algae) in their tissues.  Many coral specimens in Museums are dried
skeletons (hence, sans zooxanthellae); but some are alcohol-preserved
(hence, taxonomic aggregate). I see no problem in establishing the coral as
an Individual, with an appropriate coral taxon identification, and leaving
it as that up until the point that someone has an interest in the
zooxanthellae cells also contained in the sample -- at which point a new
Individual instance is established.

I don't think the coral curators of the world will cry foul; but will the
lichen curators of the world be resistent to the idea of establishing two
individuals for each lichen specimen that consists of two taxa?

Aloha,
Rich




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