I felt like this draft paper by Anders Sandberg was a well-thought-out essay on the morality of experiments on brain emulations. Is there anything you disagree with here, or think he should handle differently?
http://www.aleph.se/papers/Ethics%20of%20brain%20emulations%20draft.pdf
The vast majority of animals being raised for food aren't in environments that try to minimize suffering even slightly.
See my other two comments.