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I think the boxes within boxes model comes closest to what I've learned so far to modeling behavior. The stimulus response model explains many basic behaviors but does not allow for any wiggle room. As the Harvard Law of Animal Behavior states, behavior is not so easily predicted. I think the boxes within boxes and multiple inputs/outputs will allow us to model more of the diversity in animal behavior, as aybala50 also stated. 

If we believe that brain=behavior then we should theoretically be able to model all animal behavior. However, I'm not sure that scientists will ever be able to do this, which leads me to think that there may be some other better model or maybe, just that the human brain isn't smart enough to fully understand the human brain.