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There is a simple answer to the free will question,
Yes, humans and animals have free will
No, particles and fundamental physical laws don't have free will.
If you want to understand why something can be true at a large scale when it isn't true at small scales then you need to read up on emergence. For example 'wetness' or 'roughness' are properties that exist at a large scale but not a small scale.
Basically, you have free will because each person has a personal state of their brain that isn't knowable by any other person. Therefore when they make a decision it cannot be 100% predicted by another, therefore it is said to be made by that person.
Surely this over-studied question could be put to rest if someone developed a deterministic simulation in which 'animals' evolved and could be seen to make decisions of their own, for example for self-protection. This is certainly doable in Conway's game of life.