[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 12:00:33 CET 2010


Laughing at the "splitter"

After I wrote this post last night, I remembered a funny story that I 
heard when I used to hang out with plant taxonomists as a grad student 
at Vanderbilt (that was when Vanderbilt actually still HAD 
taxonomists).  The story was told of a certain old taxonomist who was a 
"splitter".  He was always taking species and dividing them into 
subspecies or varieties that didn't seem to be clearly definable.  When 
others would question this, he always said that he could tell the 
difference.  One day his graduate student went to a tree of a species 
that he had "split" and cut a half dozen branches from it.  The student 
came in and asked his mentor to help him identify the specimens that 
he'd collected.  The mentor confidently placed the branches into piles 
representing the several subspecies that he had established.  Then the 
grad student revealed that they were all from the same tree.

Every time this story was told, it was greeted with snickering and 
laughter.  Why do people think this story is funny?  It's because we 
know from our background in biology that it is not possible for several 
pieces of the same tree to be different taxa.  That is why it is useful 
to anchor the concept of Individual at the level of the biological 
Individual.  If we call mixtures of biological individuals of different 
lower-level taxa Individuals, then we loose the certainty of that all 
instances of Occurrences arising from that Individual are the same 
taxa.  If we call pieces of biological individuals Individuals, then we 
set up the circumstance where we can assign those pieces differing 
Identifications.  We set ourselves up to be the butt of jokes like the 
one I told above.  In my original thinking about the proposed class 
Individual, I only grudgingly accepted the idea that several biological 
individuals could fall into the category Individual.  I did this because 
I acknowledged that sometimes I couldn't tell when one individual ended 
and another began (think individuals of moss) or because it wasn't worth 
the effort to separate biological individuals (try to take a photo of a 
single individual of grass; herbarium sheets of grass often have several 
biological individuals on them because it's clear they are the same 
species).  I have accepted the broadening of the definition to include 
"taxa" at any level, but I'm thinking that may have been a mistake.  
However, I don't know how to restate the definition to mean what I think 
it needs to mean without causing the taxonomists of the group to go for 
each other's jugular veins.

Steve

Steve Baskauf wrote:
> 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

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