Spread the beans out on a large surface, discarding any pebbles or debris.
SOAK THE BEANS: Place beans in a large bowl with plenty of cool water, about 8 cups/2 L water. Add 1 ½ tablespoons Diamond Crystal kosher salt and baking soda, if using. Stir well, cover, and soak for 8 to 12 hours on the countertop. If soaking for longer than 12 hours, transfer to the fridge. If cooking small beans, you can soak for 4 to 6 hours.
Drain the beans and rinse well.
PREP FLAVORINGS: Use kitchen twine to tie together the bay leaves and thyme; if you don’t have twine, use scissors to snip open a slit in the dried chile peppers.
COOK AROMATICS: Heat a Dutch oven or large soup pot over medium heat with 2 tablespoons olive oil. Once warm, add the shallots and cook until golden brown, stirring frequently, about 5 minutes. Add the garlic and cook until no longer raw and just starting to see some color, stirring frequently.
Pour in 6 cups water, soaked beans, herb bundle, dried chiles, a generous amount of black pepper, and 1 teaspoon kosher salt.
BOIL BEANS: Bring to a rapid boil. Once boiling, partially cover the pan and boil for 10 minutes.
SIMMER BEANS: Reduce the heat to low and gently simmer, uncovered, until the beans are tender, about 40 to 50 minutes for medium-sized beans.
CHECK BEANS FOR DONENESS: Test at least 5 different beans for doneness.
FINISHING: Once the beans are tender, turn off the heat and discard the chile peppers and bouquet garni. Season with salt to taste. Stir in some good-quality olive oil and vinegar or lemon juice. Adjust the seasonings until the beans taste perfect to you.
STORAGE: Store leftover beans with their liquid in the fridge for 5 days; or store in the freezer with their liquid for 3 to 6 months.
