As an argument against bestiality, it is often said that animals are not able to consent to sex. If this is the case, though, wouldn't that mean that every instance of two animals mating is an instance of rape, since presumably neither of them are able to consent?

Well, if someone is struck by lightning is it murder? A necessary condition for the commission of a crime is that the candidate criminal be an agent. Arguably, non-human animals are not. So, just as they can't consent to sex, they are incapable of rape or murder. Concepts of moral or criminal propriety just don't apply to non-human sex. One reason one is tempted to think otherwise is that non-human animals have moral standing. That is, they are the proper objects of moral consideration, and one can act morally or immorally towards them. But not everything with moral standing is a moral agent. Now, having said that, I do think there are other reasons for your justly wondering about this question. The sexual congress of plants and microbes doesn't raise this question. You aren't likely to wonder whether bees rape flowers. But the sexual activity of animals more closely related to humans seems strikingly similar to our own conduct, as do many non-human ways of eating. Moreover, non-humans close to us can be trained to behave in all sorts of ways in conformity with our own rules of conduct--e.g. dogs can be trained not to defecate in the house. Plus the sexual activity of other primates seems to involve something like rules of propriety as well as violations of those rules (e.g. deceptions and infidelities). And, perhaps most of all, as anyone who's spent a lot of time with non-humans will know, a good deal of sexual activity engaged by non-humans close to us resembles rape, as it commonly involves the violent subduing of females by males. But still the question must be asked whether non-humans can come to grasp and self-regulate using norms of sexual conduct that would include prohibitions against rape. Dogs can be trained not to hump the legs of humans. Can they be trained to gain consent before engaging in sexual conduct? My guess is that the concept of consent or anything approximating the concept of consent is beyond them. Non-humans that live among humans and possess a sufficient level of intelligence and tractability may be capable of acquiring less violent forms of sexual activity, but without consent (both given and understood) the concept of rape just won't apply.

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