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<<That's exactly what the original poster was pointing out.  "A species is
a kind of organism" does not mean that "What kind of organisms are
there" can be answered with "A species", but "A pig is a kind of
organism" does mean that you can answer that question with "A pig".  The
reason is that in the first, the "is" is an equative, it indicates that
"species = kind of organism", so species would answer the question "What
is a kind of organism?", but the second is categorical, indicates taht
"pig" is a member of the set "kinds of organisms".>>

Seems to me what you're dealing with here, then (now that I FINALLY get it; thanks very much, Nik :), is category membership versus category labels.  So, while you wouldn't answer "a species is a kind of organism" to the question "What kinds of organisms are there?", you would answer "species" to the question "Why types of classifications of organisms are there?"  So, I don't think the difference lies in the "is", but in the specification.  So, one asks for category members, the other for category, and, more specifically, scientific categories, not generic (you could answer "species" or "genus", etc., but why not "animals", "horses", "birds (i.e., things that fly)", "plants", "trees"?).

-David