A recent New Scientist article http://www.newscientist.com/channel/mech-tech/mg18925416.300 points to research being undertaken to put implants into the brains of animals to direct their movements. It is hoped that such implants will improve understanding of how animals interact with their environment, as well as boosting research into tackling human paralysis. Of course you might say that the end justifies the means given the possibilities of giving human beings the ability to walk again.
There are (not surprisingly) ethical issues with this. We have been manipulating plants and animals for a very long time. Harvesting grain with bigger heads, breeding the biggest lumps of meat (cows), and so on. Sometimes selection has been unconscious, and sometimes very conscious. Genetic engineering greatly accelerates this process (maybe without understanding the consequences?) But direct neural interference seems to smack a little too much of Descartes automaton view of non-human creatures. Now I don't wish to anthropomorphise, but which creatures deserve a respect of their personal autonomy? The creatures suggested range from sharks and tuna to rats (poor Pinky and the Brain!) and monkeys.
The other lurking spectre is that of military usage. The Pentagon in its greediness for absolute dominance is suggesting using sharks as spies, employing their ability to smell and (what is the verb for detecting electric fields?) their way about to follow ships undetected. It reminds me of Soviet research into turning dolphins into bombs. Whatever we can pevert in nature, we do so militarily in the endless war on everything.
The radio signals used to direct dogfish (a small shark) in the tank will not penetrate water, so engineers plan to communicate with the sharks using sonar. Great, fill the water with more noise to confuse ceteans (dolphins, whales).
One wonders if it isn't possible to do direct research involving humans who are willing to see what they can do to regain mobility, or at least with rats (but perhaps rodent lovers will also disagree). The fact that all of this can so easily be turned to war reminds us that the pursuit of knowledge does not equal the pursuit of wisdom. Even sharks, which we hunt to extinction, kill for their tails, kill in revenge for the few human deaths (at least in part because we are so arrogant to think the entire planet exists soley for us) and now puppets on our strings.