This is the way I learned to cook black beans when traveling in Brazil—the beans turn out perfectly. Wash and pick over the beans. Place them in a large nonreactive soup kettle and add enough water (about 3 quarts) to cover by 5 inches. Bring to a boil and cook for 2 minutes. Remove kettle from the heat, cover, and set aside for 6 hours or overnight.
Return the beans to a simmer and cook, partially covered, for 1 hour until the beans are almost, but not quite, tender.
In a small nonreactive sauce pan, heat the oil over medium heat. Add the onion and garlic and sauté for 5 minutes until the onion is translucent. Add the tomato and cook for 4 minutes. Stir in the parsley and thyme. Fold the tomato mixture into the beans and season with salt and pepper. Continue simmering the beans for another 30 minutes until the beans are tender.
Drain the beans, reserving the cooking liquid. Purée in a food processor fitted with the metal blade, adding some of the liquid to make a smooth soup. Transfer to a clean soup pot and stir in more liquid if the soup is too thick. Taste for seasoning. Serve in warm soup plates. (The soup can also be served chilled.)
Serving Suggestions: If serving hot, add a tablespoon of dry sherry to each portion; or float a thin lemon slice, a bit of chopped hard-boiled egg, and chopped chives or scallions on top. If serving cold, add a little cooked chopped shrimp or lobster, a thin slice of lime, and accompany with any New Orleans or Caribbean hot sauce.