Melt 4 tablespoons (1/2 stick) of the butter in a large heavy-bottomed stockpot. Add the onions and cook over medium-low heat for 10 minutes, or until translucent. Add the celery, carrots, potatoes, thyme, salt, and pepper and saute for 10 more minutes. Add the clam juice, bring to a boil, and simmer, uncovered, until the vegetables are tender, about 20 minutes.