Tannin wrote:

V-1 Flying Bomb: This is a *kind* of aircraft, but it is capitalised Labrador Retriever: This is a *kind* of dog, but it is capitalised Splendid Fairy- wren: This is a specific *kind* of fairy-wren, which is why it too is capitalised. (A non-specific kind is written as plain"fairy-wren".) ....

I've already explained why dog breeds can reasonably be considered to be proper nouns -- they are a specific product of selected breeding with pure-bred dogs having complete family histories. Aircraft are also specific products with specific histories. But the real reason why we capitalize dog breeds and aircraft is because they are almost always capitalized in nearly every context (specialist or otherwise).

Your hierarchy distinction does intrigue me but it has also been demonstrated that the common names of species are usually written in the lowercase outside of specialist publications (most notably in encyclopedias, dictionaries and textbooks):

Thus my ecology textbook writes "bald eagle" not "Bald Eagle," a generally-focused field guide on Yosemite of mine writes "peregine falcon" not "Peregine Falcon", Princeton University's Word Net writes "chinook salmon" not "Chinook Salmon", The Columbia Encyclopedia writes "yellow jacket" not "Yellow Jacket", Encyclopædia Britannica writes "sabre-toothed cat" not "Sabre-toothed Cat", Webster's Dictionary writes "mountian lion" not "Mountain Lion" and my intro-series biology textbook writes "sea otter" not "Sea Otter" etc, etc....

Given this, I'm part of the camp (that includes well-respected manual of styles) that says we should use down style for the common names of species.

-- Daniel Mayer (aka mav)