Thanks, Dan. I changed the subject line because I think your comment:

tissue converted to DNA extract is still tissue (the tissue is still "material sample" after "destructive sampling", and still part of the event, just as is a photograph of the beast in the museum.

Relates to part of what Steve wrote:

We defined a class for evidence, but we also considered not having

evidence

being an explicit class. Not defining an explicit Token class would have

simplified

the diagram at the bottom of the page - one could just say that there

should be

evidence and it should be linked to the resource it documents. Token and THeE/IndividualOrganism are not disjoint classes - the physical

entity

can be the evidence if somebody "owns" it and makes it available for

people to examine.

However, in DSW, Token and THeE are not synonymous because we allow

evidence

to include things that are not physically derived from the entity (e.g.

images, sounds,

string data records) in addition to physical specimens.

This is an area that at first seems subtle, but once we actually started working with data, starts to became more and more intuitive (at least to me, anyway).

I first started thinking about this seriously during a 2007 meeting of ICZN Commissioners, when we were contemplating the question of what could/should, and what could/should not, fulfill the role of a type specimen under the ICZN Code.

Needless to say, we did not come up with a complete answer to the question, but the discussion did help frame in my mind the question in much better detail.

Under the ICZN Code (which differs in a few respects from the ICNafp Code in this area), the definition of a type specimen s fairly straight-forward:

1) It must be biological material. An image (e.g., illustration or photograph) cannot be a type specimen (I believe the ICNafp accommodates "iconotypes"). Rather, the organism depicted in an image is regarded as being the type specimen.

2) A type specimen consists of the entire organism. For example, in the case of a mammal that is captured and separated into its fur, skeleton, alcoholic-preserved tissues, and tissue samples for DNA analysis, all of these things together constitute the type specimen. In other words, the whole specimen is the type. This is in contrast to ICNafp, where a single specimen from a tree (for example) is the type, whereas other specimens taken from the same tree are isotypes, and the remainder of the tree is not a type at all.

3) It is understood that the community of organisms inhabiting a type specimen (e.g., parasites and commensals) do not form part of the type specimen.

There are other issues as well (especially for ichnotaxa, colonies, and other specific cases), but the general point is that under the ICZN Code, a type specimen consists of the sum of all cells that contain the same DNA material that were part of the same biological individual (i.e., identical twins, clones, and parthenogenic and other asexually reproducing organisms potentially contain the same DNA material, but are different "individuals").

Most of the above is pretty straight-forward. Where it gets a bit squishy is when you go down below the "tissue sample" level into smaller and smaller subunits.

Can a single cell containing intact DNA be a type specimen for a multicellular organism?

Can a single DNA molecule be a type specimen?

Can a single chromosome be a type specimen?

Can a PCR product be a type specimen?

...you can add as many hair-splitting examples as you wish.

Conversations like this let me to draw a distinction between matter that is actually from an organism, vs. stuff that is representative of the organism but lacks any material connection to the organism.

Coming back to Dan Janzen's comment; I would conclude that most things that would full under the term "materialSample" include actually matter from a biological organism. A PCR product is borderline, because it presumably does contain actual matter from the organism, but the vast majority of matter in the PCR product was not from the organism. Once you lose all the matter from the organism, you are no longer talking about the "individual", but instead are now talking about "Evidence of the Individual". This applies to images of the individual (whether taken in-situ, or in a lab), DNA "sequences" (rendered as text), images of the results of DNA sequencing analysis (in various forms), and various other non-biological derivatives.

So, this leads me to the comment from Steve about "Evidence" (which, if I understand correctly, is conceptually the same as the DSW "Token": https://code.google.com/p/darwin-sw/wiki/ClassToken). In our model, a specimen is *not* a Token or Evidence -- it is an individual. This has proven (in my mind at least -- Rob W. still has reservations) to be a MUCH more practical way to think of, and manage data for, specimens.

This email will be WAY too long if I try to explain all the subtleties of this, so I'll just leave it at that. But clearly there are some differences between our notion of "Evidence", and the DSW concept of "Token" -- although both seem to be intended to solve the same problem.

Enough for now....

Aloha, Rich