Who (or What) Deserves Protection?

At one point in my life, I wanted to study conservation genetics. Now, I just make fun of molecular ecologists and their flawed data. The most recent installment of Ask A ScienceBlogger takes me back to the days before I discovered the wonders of genomics:

Is every species of living thing on the planet equally deserving of protection?

Before I answer the question (or avoid answering the question) allow me to say a couple of things. First of all, this question would be much easier if it were rephrased, "Should we target any particular species for extinction?" If that were the question, my answered would be an emphatic, "NO!" Secondly, I'm assuming by protection they do not mean this or this.

On to my avoidance of answering the question. Designing a conservation program around a single species (or any taxon) is misguided. We should be conserving habitats and ecosystems, not species or populations. The question then becomes which habitats should we protect? My answer: those that are under the greatest threat from human disturbance. I'm not an ecologist or environmental scientist, so I'll differ to them to make the decision regarding the most threatened habitats.

Note: It is still useful to advertise a conservation program using some token species from the habit you are protecting. It's much easier for the public to rally around a cuddly mammal than an icky worm or a gross spider. A useful strategy is to choose a habitat to protect, and then identify a species which would be in danger of going extinct if that habitat were destroyed. You could then campaign to protect that token species, in turn protecting the habitat.