we don't have to grudgingly choose between artificial and natural. 

I actually do. I am not interested in representing, trying to define, or even talking about artificial entities but do not stop others from doing so.

One can allow for the obvious that species names and definitions are formulated and written down by humans (though other animals and machines are sometimes capable of this too), and vary over time, but at the same time nature has a strong corrective word in shaping these definitions, and only if they are close enough to some real natural order are our inferences also reliable enough. By modeling species as human conceptualizations, we are not necessarily throwing out the baby with the bathwater, i.e. saying they are not real. See pp. 66-67 here:

In fact, what I meant to say is that they are hypotheses waiting to be tested, whether we use one concept over another. If they turn to be artificial, the only reason to keep those around is purely historical, if anyone cares about that. You may, many don't. I don't.

http://docs.google.com/a/richard-boyd.net/viewer?a=v&pid=sites&srcid...

Yet another opinion. I could present a long list of others that would completely differ but I don't think this is the right mailing list. Nico

On 5/4/2011 12:58 PM, Nico Cellinese wrote:

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Hi Pete,

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Hi Steve,

I may have overloaded the term specimen to make the explanation easier to follow. A specimen could be an individual or it could be part of an individual. To some extent you need to think about how these models will be used. If you subscribe to the model that a species is whatever a taxonomists says it is then it is difficult to make statements like. X% of the world's species will be extinct by 2050. If you mean a species as defined by the concept documented at this URI which is supported by these specimens, images, and DNA then you are on firmer ground.

I would have stopped here! If someone wants to point to a series of objects to indicate his own concept of a "species", then that's ok. That's a convention we can work with.

Everything else you talk about below seem to be a confused mashup of "species" as a taxon and "species" as ranks.

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Species in the natural world do a pretty good job recognizing those individuals that are appropriate mates. In other words members of their own species.

Really? Maybe in animals but everywhere else I don't think so! And what about asexual organisms? I guess they do not deserve the status of "species". So, the biological species concept you are referring to can't be universally applied = not a good concept to use for ALL organisms, right?

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Are we modeling species or variations in human conceptualizations of species?

Is there anything else out there besides the human conceptualization of species? Do we have an absolute concept of what a species represent? Last time I checked we have been arguing about this for the past century and more. Species defined by the 25+ species concepts out there can't possibly be real. They are defined by human conceptualization = artificial. The only think we can clearly try to discern are clades and often those clades may correspond with someone's concept of a species. In other words, you can take the rank of species and point it at a node that define a taxon. Or you can take the rank of species and point it to an assemblage of lineages, regardless if that assemblage represents a monophyletic group or not. Traditionally recognized species are most likely polyphyletic anyways.

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I stick with this. Assuming you don't have a hybrid individual. That individual is one species. The fact that human may disagree on what species it is a human issue.

What do you really mean by individuals? Are species created by the gods and we just can't figure out what they meant? Human issue? We, humans came up with this impossible to define concept. Individuals are just that: individuals. The individuals = species hypothesis has been argued in the literature and is not an accepted notion by far (note: I am not saying I agree or disagree, this is just another non-absolute concept). But maybe you don't mean it that way.

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Again, Are we modeling *species* or variations in human conceptualizations of *species*?

Your statement is recursive. You have an idea of species that is above all of the other variations on the theme. I don't understand what you mean and that's why I think there is a confusion between the usage of "species" as a taxon and "species" as an arbitrary rank.

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Which of these is of primary importance to decision makers and non-taxonomist biologists? Part of the problem with various publications relating to ontologies and taxonomy is that their species models entail a specific phylogenetic hypothesis.

Even in the lack of a phylogenetic framework, every species is a hypothesis. When we lump and split we generate hypotheses. A new name points to a new hypothesis. Adding a new /genus/ to a /family/ or a new /species /to a /genus/ refines and modifies the original hypothesis.

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In the real world taxa are not as clean as some would like to make them out to be.

In fact, the only way we can discover a little more clarity is through phylogenies. When it comes to low level taxa, population studies help a lot too.

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Each individual is a unique combination of thousands of separate gene lineages which often do not follow clean monophyletic paths.

But as you stated above you equate individuals with species. if that's correct, then you admit that individuals can be polyphyletic, and as such do we really care about polyphyletic entities? As such you admit that species as you define them are artificial.

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I would argue that most of those who work with species related data see them as useful typological constructs which in general follow the biological species model.

I actually don't and I can name many others who don't. The rank of species may be useful to many as communication tool but the way it is applied vary a lot. The biological species concept is not widely accept and certainly not followed by the vast majority as you indicate.

The only think we can really achieve from an informatics standpoint is to reconcile objects (specimens, images, sequences, descriptions, etc.etc.) with the many names that may have been associated with those and leave the rest (philosophical masturbation) to the users. Reconciling names with concepts, given the nature of the concepts and the idiosyncratic way that names have been historically used, is a Quixoterian challenge.

Cheers, Nico