What's so bad about species extinction?

A couple of weeks ago, an article in BMC Biology argued that there may be six reproductively isolated species of giraffes: "By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them." Reproductive isolation is, of course, the primary feature of species as defined in a modern biological way. Let's grant, for the sake of the argument, that the geneticists did their job correct, and that there are six biological species of giraffes (if not, the following will be hypothetical, but the same conclusions will follow).

So far, then, so good. But the The BBC says:

Mr Brown [the first author of this study] also highlighted the conservation implications of this study: "Lumping all giraffes into one species obscures the reality that some kinds of giraffe are on the brink.
"Some of these populations number only a few hundred individuals and need immediate protection."

Here is one place where things get philosophically interesting. The idea is that once we find out that, e.g., the Nigerian giraffe, of whom the BBC says "[t]he last 160 individuals are found in West and Central Africa", is a species, we have strong reason to prevent the extinction of the Nigerian giraffe.

Let K be a kind, natural or not, of organism. For some kinds K, we do not think there is anything bad about the extinction of Ks. Granted, the deaths of the individual members of K may be bad, but whether a kind K goes extinct or not, each individual has exactly one death to die (the last point I got from a comment by Jeff Schloss at a workshop we both attended; he may not endorse the use I make of the remark). Suppose K is the kind Dalmatian with exactly one spot shaped like in the diagram on right. There really is nothing bad about K ceasing to have members, over and beyond the individual members' deaths (note that one way for K to go extinct would be for the descendants of Dalmatians that have exactly one such spot to have two such spots, and there never again be any Dalmatians with exactly one such spot). Or maybe for diversity reasons, we think that in the best of all possible worlds all non-bad kinds are realized, and so there is something bad about the Ks dying out over and beyond the individual deaths, but it is a very minor bad.

I suspect what is going on here is that there is an equivocation between two senses of species: an intuitive non-scientific one (at least in the post-Aristotelian sense of "scientific") that understands a species as a kind of organism distinguished in a significant way from other organisms (the normative term "significant" is what marks this as non-scientific in the modern sense), and the modern scientific one in terms of reproductive isolation. For while there is something bad about a species in the intuitive sense going extinct, it is not at all clear what is so bad about a species in the reproductive-isolation sense going extinct. In particular, it is not clear why one of the giraffe species going extinct would be worse than Dalmatians with exactly one spot of some precise shape going extinct.

All this suggests that there is a need for a notion of species going distinct from the biological one. I rather hope that the Aristotelian notion of species as defined by qualitative identity of essence will do the job here.

Let me end with a question: Suppose that some kind of subatomic particle were to cease to exist forever, with no way of bringing it back. Would there be any non-instrumental bad in that (there might be an instrumental bad, if there is some use for the particle, or if studying it empirically might help with the progress of science)? (I am inclined to say yes.)