remember the saying ...stop running around like a chook without its head on.. ever seen a chook run around without its head on?... so is the chook still alive or dead, if you have never seen an animal instantly killed, head chopped off or shot in the brain you probably have seen the movies of the subjects instant death where the animal (usually the good or bad guy gets shot in the head) becomes instantly motionless, real life doesn't work like that at all.. muscle memory , continual heart spasms and nerve systems all play their part in death, but not to disclose suffering and pain of the animals death but to disclose reflex actions.
i have shot many cows (mostly because they where ill) and the first thing i do is check there eyes for blinking reflex, its the best way to see if the animal is brain dead, i don't recommend standing behind a cow after its been shot dead, you may still get a kick in the shin.
i don't believe animals are intelligent as in they know they are about to die by being herded into a truck to the abattoirs. they are instinctive just as a pack of dogs will bring down a sick cow as instinctive hunting behavior so will a mob of cows find it uncomfortable to be placed on a truck in a confined space - although i can assure anyone , livestock transported in Australia are not packed as sardines ,crushed or ill treated this would not be in the interest of a farmer trying to sell prime beef without bruising discounts from the abattoir ..
where does instincts come from.. genetics and the environment both play a part , dogs are a great example as we have so many breeds and each selected through breeding programs for special traits , a golden retriever for example (my fav dogs btw) obviously love retrieving, in fact the genetic disposition of this requires very little reward training as a pup to perform such behavior, though the behavior of "letting go" needs to be positively reinforced. unfortunately dogs haven't been selectively breed not to crap on your shagpile, this too usually needs to be positively reinforced although negative reinforcement works also.
reward training can be constructed as intelligence and understanding but is that really so? coming back to the pack mentality of dogs in the wild, dogs naturally have a pack mentality no mater what breed.. its why we call dogs loyal and mans best friend. rewarding dogs for behavior is in my view further reinforcing that pack mentality for food by performing functions with the leader of the pack.
and one last thing about being confined and crapped on.. i have seen cows crap on their calves while the calf was feeding... so i don't think they mind all that much about poo poo's and wee wee's ...

not trying to convert vegetarians to meat eaters , i don't eat that much red meat either to be honest.. i love chicken, fish and usually at least have one night a week meatless. sometimes two nights , moderation is the main thing for my eating habits.
one more interesting point for the vegos , have you ever heard a chook lay an egg.. now that sounds painful for the chook... they carry on like... um... a chook without its head on!