Bring the water to a boil in a medium saucepan. Add the beans, reduce the heat to a simmer, cover and cook, skimming occasionally, approximately 1 1/2 hours. To test for doneness, taste 3 or 4 of the smaller beans. They should be cooked through and creamy inside. Mash, along with the liquid in the pot, with a potato masher or the back of a wooden spoon until creamy.
Heat the lard or other fat in a medium saucepan over medium high heat. Saute the onions with the salt and pepper until golden brown, about 10 minutes. Add the mashed beans and continue cooking, stirring occasionally, until the liquid evaporates and the beans form a mass that pulls away from the sides and bottom of the pan, about 10 minutes. Serve immediately. Refried beans can be kept in the refrigerator 3 or 4 days and reheated in a covered casserole in a 350 degree oven.