I was perhaps unclear. I don't mean to suggest a superclass that has some other notion of taxonomic organization. I meant to suggest one that simply has \some/ notion of organization. That wouldn't change the offered definition of Organism, but rather give people who feel they need some notion of an organized set of biological stuff a way to define other subclasses with different organizations. It would, for example, let people use DwC to describe some aspects of ecosystems able to do so without having to pretend that an ecosystem is always a special kind of Organism, or vice-versa.
It doesn't look to me like you envision that http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity would be suitable for describing ecosystems, possibly even for those ecologists that think a hierarchy of ecosystem types is as fundamental to what the study as are classical taxonomic hierarchies to classical taxonomists.
Bob
On Thu, Sep 8, 2011 at 10:40 AM, Steve Baskauf steve.baskauf@vanderbilt.edu wrote:
Well, I think we've plowed this ground before (actually several times before). In the first attempt to come up with a consensus definition for "Individual" (previous name for what we are now calling "Organism"), we had allowed that an Individual be identified to a single Taxon, but with no restriction on the level of the taxon. In other words, the Individual could be taxonomically heterogenous at a lower taxonomic level as long as its components were part of the same higher-level taxon (e.g. the infamous marine trawl sample and various jars of samples taken from it; each jar an "Individual" identified to some higher taxonomic level that was common to all organisms in the jar). However, there was a point more recently when someone (I think it was actually you) requested competency questions for the proposed class. I provided three, one of which was the ability to track "duplicates" and to infer that any Identification which applies to one duplicate also applies to all others. I will say no more here, but simply refer to the email where I discussed this: http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002690.html Rich agreed that the ability to draw this kind of inference was valuable and agreed that requiring that Individuals (now called Organisms) to be taxonomically heterogeneous was a benefit that outweighted the benefits that would accrue from allowing them to be taxonomically heterogeneous. Rich can correct this if I've misrepresented anything he said.
Your suggestion that an Organism be a subclass of something more general is what Cam and I suggested in an alternate version of darwin-sw. I will not comment further on this because this approach has already been outlined in text and diagrams at http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity I don't have any objection to having a superclass of Organism that allows taxonomic heterogeneity, but one of the principles of Darwin Core is that in order for a term to become a part of the vocabulary, at least several people have to indicate that they want the term and there should be some reasonable explanation of how people would use the term. That has happened for Organism. It has NOT happened for TaxonomicallyHeterogeneousEntity or whatever you want to call it. As I discuss on the page reference above, allowing taxonomic heterogeneity introduces some significant complexities in modeling and I for one have no clue how to deal with them.
Steve
Bob Morris wrote:
What exactly is accomplished by requiring "taxonomically homogenous?" Perhaps the problem is that Organism is a subclass of something slightly more general, some more general "biologically organized" object that has a context dependent organizing principle. For example, biologists seem willing to talk about ecosystem instances in this way. Also, for some purposes, people seem willing to have discourse about an organism in which they include microbes that must survive not only on or in the organism, but even a tiny bit away from it. So, if one had a slightly more general class, and Organism is required to have some enumerated set of specific kinds of organizing principles, e.g. those presently on the table, several things happen: (a)those who need to have a different organizing principle than the current consensus of what organizes an Organism have a place to hang their organizing principle, (b) scientific advances about the organizing principles of life don't require massive ontological disruption(*)...you just move a principle into the appropriate subclass.
Bob Morris aka Recovering Algebraist
(*)well, I suppose the important ones do for the biologists, but I suspect they needn't for the formal ontologies, if the upper level organizing principle is "organizing principle".
On Thu, Sep 8, 2011 at 3:56 AM, Gregor Hagedorn g.m.hagedorn@gmail.com wrote:
Term Name: Organism Identifier: http://rs.tdwg.org/dwc/terms/Organism Namespace: http://rs.tdwg.org/dwc/terms/ Label: Organism Definition: The category of information pertaining to a specific instance of an organism (virus, symbiont, individual, colony, group of individuals, population) reliably be known to taxonomically homogeneous.
I see a problem with the "taxonomically homogeneous" since many taxa are not. All obligatory mutualistically symbiontic organisms are excluded (you mention symbiont, but the symbiont is the part of a symbiontic relation, e.g. both the algae taxon and fungus taxon each are a symbiont in a lichen.
Contradict if my German biology is at odds with English.
The problem is, that individual and set are mixed, so that the "homogeneous" appears to apply also to the individual. Proposal:
Definition: The information class pertaining to a specific instance or set of instances of a life form or organism (virus, bacteria, symbiontic life forms, individual, colony, group, population). Sets must reliably be known to taxonomically homogeneous (including obligatory symbiontic associations).
Gregor _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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