christina comments on Recommended reading on the ethics of Animal Cognitive Enhancement - Less Wrong
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It's also been said that ancient humans were more intelligent than modern ones. In fact, both the argument for human intelligence and the wolf-dog argument have put forward the idea that being domesticated lowers intelligence (in the case of humans, it can be said we domesticated ourselves). I don't really think this is a simple hypothesis to investigate at all given the complexity of investigating intelligence.
Some references:
News Article on Human Intelligence--News article discussing this hypothesis.
Gerald Crabtree--This is the researcher I've seen quoted a lot lately on the idea that ancient humans were more intelligent than modern ones. From the article above, and looking at his published work, it sounds like this is just a hypothesis he wants to test, rather than something that he has thoroughly investigated.
News Article on Dog-Wolf intelligence--This news article has some discussion of an experiment trying to determine differences between wolf-dog intelligence.