I have a 6 month old border collie/lab cross who also whines when left alone. Dogs are very social creatures and generally need a good walk and a job to do. Even if that job is following simple commands for 5 minutes every hour.. sit, stay, come.
His whining may indicate a need. he may need attention or to go to the bathroom or he may need a game to play. There is also the possibility that he is in pain or discomfort. Dogs will show you when they are in pain, unlike cats, because dogs are pack animals and if he considers you to be the pack leader, the alpha dog, he will whine to let you know he hurts.