HELP!! Aggressive behavior

Question
We have a 4 yr old german shepherd - he is as sweet as he can be with us...although he was around others as a puppy - when he reached a certain age - he just barked and went in to protection mode. Lately he has become much more aggressive - banging in to the fence at the dog behind. Much more ferocious in barking and behavior.  He was "trained" when a pup by a gentleman with a phd in animal behavior - I halted that training when I saw him punch the dog in nose and also slam his neck in the fence gate.  Lately he has snarled at us when he has been in the kennel (i have placed him in the kennel when his behavior outside has been bad) in fear of him knocking down the fence - he is strong and extremely protective. He is not neutered.  We have a 2 yr old female who is spade - and is just the sweetest natured dog I have ever seen.  They adore each other and get along great.  Walks are a NIGHTMARE - people, dogs he is on constant "alert" or "protection" mode...I have read every thing I can - and am just at a loss.  He is much loved - and I just want the best for him. Thank you so much.-

Answer
Somebody with a PHD in animal behavior punched him?  I know I can't give good answer to some of the questions here, and should suggest for a professional to observe it and work with the owner.  Yet, I know many in the business are idiots, not professionals.  

I would start by neutering him.  It is no cure all, but should make a big difference.  You may or may not be able to salvage him if you do so, but likely not if you don't.  He certainly should never be allowed to pass on any genetic tendency toward aggression.

That will make it easier for you to take over as leader.  The key to most behavior problems is approaching things using the dog's natural instincts. Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at http://www.dogsbestfriend.com/ For more on being top dog, see http://www.dogbreedinfo.com./topdogrules.htm

If he sees you as leader, then he can rely on you to choose how you interact with others.  If you are positive and unstressed, then he should be.  

This could also be fear based aggression.  If when he shows aggression, his ears are back rather than up and forward, it is fear.  The best defense is a strong offense.  In that case, you need to work at building up his confidence.  Play tug of war with the dog and lose. However at the end of the game, take the rope or toy and put it up, less the dog becomes confused about who is top dog. Ropes from the pets' store quickly turn to hazardous shreds. Ones I made lasted much better. Go to a hardware or home center that sells rope by the foot. Buy 2' of 3/4" poly rope. Melt the ends, and tie knots in it. Get them as tight as possible, put it in a vise and pound it with a hammer. Watch carefully, and be ready to discard when it comes apart.

Finally, make sure it has a den to live in. If you are not using a crate, buy one. The dog may be happier in its den than loose in the house. It relaxes, it feels safe in its den. It rests, the body slows down reducing the need for water and relieving its self. Dogs that have been crated all along do very well. Many of them will rest in their crates even when the door is open. I think the plastic ones give the dog more of a safe, enclosed den feeling. Metal ones can be put in a corner or covered with something the dog can't pull in and chew. Select a crate just big enough for the full grown dog to stretch out in.

A dog that has not been crated since it was little, may take some work. Start out just putting its toys and treats in the crate. Praise it for going in. Feed it in the crate. This is also an easy way to maintain order at feeding time for more than one dog.