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Little backstory...

We have two puppies, an Australian Shepard (Stella) that is almost 6 months and a German Shorthaired Pointer (Bandit) that is almost 11 weeks.

We got Stella at 8 weeks and we introduced her to the crate and there was maybe 4 or 5 days of crying (and barking) and then maybe a week of just some cries. Within two weeks she was totally quiet and completely accepting of the crate (going in there to lay down on her own when tired)

Bandit, well Bandit is a different story. Bandit we also got at 8 weeks and we followed almost the exact same routine with the crate as Stella. We are going on 4 weeks of him still howling and going nuts in the crate. We have tried the blankets and all that. We give him treats, feeding in the crate and a peanut butter filled Kong every time he goes in. Its not like he's not getting his exercise (Stella and him get at least a couple hours running around the dog park as well as general wrestling around the house). I genuinely believe that he is not scared of it anymore, he just is being a brat and voicing his displeasure.

Normally in these situations people recommend letting him go crazy and learn that he won't get his way by being loud. The problem is we live in an apartment right now and we can't have him going crazy for extended periods of time. Last night after his 1 am pee break he went crazy for 30 mins before I had to go out and smack the side of the crate and tell him to be quiet. We did that twice before he finally laid down and was quiet. I really don't want to resort to smacking the crate (or "earthquakes" are apparently another form of punishment) every time because I feel like he is eventually going to start seeing that as reinforcement (albeit negative).

I know that you can't really compare breeds of dogs but it seems to me that there should not be this big of a difference between two intelligent breeds of dogs. Anyone have any advice or tips? They would be greatly appreciated.
 

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More exercise for the puppy. He isn't tired and, isn't ready to rest. He may also feel isolated and alone in the crate, wear an old shirt, get sweaty, make it reek of you then, put it in the crate with the puppy. See if that helps.
 

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That was suggested to us but this is after a (minimum) 3 mile walk, about 2 hours of running around the dog park (this is when I answer emails and setup meetings for the next day) and then just normal running around the house. He is usually the one that is trying to find somewhere to lay down to sleep and Stella is still trying to play with him.

We tried the t shirt, he would just pee on it. Doesn't normally pee on his puppy pads but would pee on the t shirt out of spite.
 

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Dogs do not do anything out of spite. Dogs pee on T shirts because they absorb and there is no splashing.

Can you put the crate in an isolated part of the house AWAY from the 8 week old dog and all activity? No excitement outside the crate can create calm inside the crate.

You have taken on a LOT. Two puppies is not for the faint of heart. Bandit is of a breed of dog that must work independently but under control (pointing birds and flushing and then retrieving the game).
I would keep the two puppies separated. I would have the crates separated and out of sight of each other. Each dog should be worked and trained separately. Thinking wears a dog out a lot more than mindless physical exercise (walks and dogs playing). Make him do a lot of thinking games and work on impulse control.

IMO three miles is too far to walk with dogs this age.
 

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Separation anxiety is really common in GSPs, so I wouldn't assume there's no anxiety element to his barking. And I agree, peeing on the shirt didn't have anything to do with spite, just a puppy who doesn't realize soft, absorbent things aren't for peeing on.

Look into resources on preventing separation anxiety - there's some free online, but also books like Patricia McConnell's "I'll Be Home Soon" will have really helpful advice. Just in case.

Otherwise, you'll probably need to work on teaching Bandit how to relax. It's not something that comes naturally to all dogs, but you can help train in an "off-switch". Karen Overall's Relaxation Protocol is free and a really good place to start - it's basically a down-stay program that you can go as quickly or slowly as the dog needs. But working on staying in one place in general, often with the help of a food toy like a stuffed kong, will help teach him that he can chill out indoors.
 

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Howling and crying in the crate is normal for a pup that age...he's just a baby. And yes, some dogs just "get it" faster than others, no matter the breed. You do have to ignore the noise, and I know that's hard in an apartment. You can try moving the crate near your bed so the pup can hear you at night, then slowly start moving it away to where you want it to be all of the time. You can try a "puppy pal" which is a little toy that looks like a dog and you can put a hot water bottle in it to simulate a littermate. Look up crate games and start playing that with him.

Dogs don't do anything out of spite. They simply don't have that emotion or any concept of 'revenge'. Puppies like to pee on things that are soft because its kind of like grass...doesn't splash or run onto their paws.

I also agree that 3 miles is far too long to walk with an 11 week old puppy. Too much exercise can damage their joints. I believe that calculation is 15 minutes of activity per month of age...and that exercise should not be forced (forced meaning they have to keep moving and don't get to stop and just free-play) and should be on a soft surface, like grass. You probably shouldn't take the young one to the dog park, either. Dog parks are just not a great place to "socialize" puppies because the dogs are unpredictable and unknown, and your pup could easily have a bad experience in this key socialization period that haunts him for the rest of his life. Socialization with dogs should take place with dogs you know.

Dog parks can also be rampant with disease, and at 11 weeks your pup might not have finished his vaccinations yet. You can't confirm that all dogs at the dog park have received vaccinations, so it's not a good idea to take a puppy that has not completed their vaccinations to an area so heavily trafficked by unknown dogs.
 

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More mental exercise, less physical exercise. You're conditioning him to go-go-go, and you can never really physically wear out a healthy active young dog when exercising at human pace. You can wear out their little brains with puzzles, training sessions, and the like, though.
 
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