Step 1 Sort through the beans; discard the funky ones and any small pebbles. Rinse well. Place the beans in a large pot and add enough water to cover them by several inches. Cover and bring to a boil.
Step 2 Reduce the heat and cook for about 1 3/4 hours, or until tender. Water should always cover the beans, so add more if the beans start to peek through. When the beans are cooked, strain, reserving 1 cup of the cooking water. Add the reserved cooking water back to the beans.
Step 3Heat the oven to 325 degrees. Toast the cumin seeds and oregano in a small pan until the fragrance is toasty, about 10 minutes.
Step 4Saute the onions, bell peppers and garlic in the oil over medium-high heat with the toasted cumin seeds and herbs, cayenne pepper, paprika and salt until the onions are soft, about 10 minutes. Add the tomatoes and chiles. Add this mixture to the beans and stir well. Add additional seasoning to taste.
Step 5To serve, place about one-quarter cup grated cheese in a warmed bowl, add a generous cup of beans, and dollop with a spoonful of sour cream. Sprinkle with 1 tablespoon green onions and cilantro.