In a large Dutch oven or soup pot, combine the beans with water to cover by 2-3 inches; get ready for them to expand as they soak. Cover and soak for 6 hours or up to overnight. If needed, add more water to keep the beans covered. When you’re ready to cook, drain the beans in a colander and rinse out the Dutch oven.
Return the beans to the pot and nestle in the onion, pepper flakes, oregano, rosemary, bay leaves, garlic, Parmesan rind (if using). Pour over ½ cup of olive oil and 10 cups water. Bring to a soft boil, then add 1 tablespoon of salt.
Reduce the heat to a gentle simmer, cover, and simmer for 40 minutes. Check for doneness, give the broth a taste and add another 1 tablespoon salt, but scale up or down to your tastes.
Cover and cook until the beans are tender and creamy, without any shrively skin or tough bite, another 20 to 60 minutes, checking the bean’s doneness every now and then. Note that the less time they have to soak, the longer they will take to cook. Test a few beans before you determine a pot is done, sometimes they can vary!
Once the beans are cooked through, remove the pot from the heat. Scoop out the onion, oregano and rosemary sprigs (it's ok if the leaves stay behind), bay leaves, garlic skin (again, ok if the cloves stay behind!) and Parmesan rind (if using).
Now your beans are ready for use!
