Spread the beans on a baking sheet and pick out any little stones or shriveled or discolored beans. Rinse the beans well in a colander, then place them in a heavy pot with a lid. Fill the pot with enough water to cover the beans by 2 inches (5 cm). Bring to a boil over medium-high heat and skim off any foam that has risen to the surface.

Lower the heat to keep the beans at a gentle simmer. Add the orange, skin side down, to the pot. Add the onion half, garlic, kombu (if using), salt, pepper, cumin, bay leaves, and red pepper flakes. Do not skim once you have added the spices, as they may rise to the surface.

Cover the pot, leaving the lid slightly ajar. Give the beans a stir every once in a while to help them cook evenly and to make sure they don't stick to the bottom. Add more water if needed during cooking to make sure the beans stay immersed. Continue simmering until they are tender. This should take 1 to 1 1/2 hours.

Remove the orange from the pot and set aside. Discard the onion half, garlic cloves, and bay leaves. When the orange is cool enough to handle, squeeze its juice into the pot. Drizzle with the oil and give it a final stir. Garnish with the cilantro, if desired. Cool and refrigerate in an airtight container for up to to five days or freeze for up to 6 months.