- Consciousness: Why is there anything at all that it feels like to be a person, or a dog, or a bat? Where does subjectivity fit into the naturalistic framework?
- Free Will: Naturalism commonly assumes a causally deterministic universe (or at best, a quantum undeterministic universe, which is hardly an improvement). How then can we freely choose to act?
- Morality: How can anything possess inherent value? What does it mean for something to be right or wrong if all that exists is the physical world?
This is all a bit tongue-in-cheek, although there's a serious point to it as well. Rather than just discarding these as "magic things" that naturalistic philosophy cannot investigate, it might be better to simply regard them as ill-formed questions. In fact, scientific progress is being made on the subject of consciousness, but only by breaking it up into a number of smaller, related questions about attention, perception, and so on. Similarly, questions about the cognitive implementation of agency are tractable, even if the fundamental nature of free will is not. And whilst we might not be able to determine why something is right or wrong, we can ask more practical questions about how ethical principles should be applied in the world.
So maybe we should just accept that, at least for the time being, some things appear to be magic, and get on with answering the questions that we can answer.
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