In a large pot over MEDIUM heat, heat 3 tablespoons of the oil. Add the onions, celery, carrots, and ½ teaspoon of salt, and saute for 5 minutes. Add the minced garlic, oregano, and red pepper flakes and continue to cook for another minute. Add the tomatoes and tomato paste and continue stirring the pot until the paste has browned about 2 minutes. Add the beans, 6 cups of water and bay leaves. Bring the pot to a boil, then reduce heat to simmer, partially covered, for 1-2 hours, or until the beans have become tender. Stir occasionally to prevent the beans from sticking to the bottom of the pot.
Remove about 1 cup of beans from the pot and mash until the beans become a paste. Return the mashed beans to the pot and stir in - this will help make the soup creamy. Continue to simmer the pot until the beans for an additional 30 minutes.
Before serving, remove the bay leaves and discard them. Stir in the vinegar and ½ cup of olive oil and season with salt and pepper, if needed.