Soak the beans in a large pot or bowl overnight, covered with at least 4 inches of water.

When ready to cook, heat 2 tablespoons of olive oil in a large saute pan over medium-high heat.

Saute the diced carrot, celery, onion, garlic, parsley stems, rosemary, thyme, lemon peel, chile flakes, coriander and fennel seeds until the vegetables just start to brown, 5 to 6 minutes.

Remove from heat and transfer to the center of a 12-inch-square piece of cheesecloth.

Gather the ends of the cheesecloth together to create an enclosed sachet, and tie with kitchen twine.

Drain water from the soaked beans, then place beans in large pot.

Add 4 quarts fresh water and the sachet.

Bring to a boil, skimming foam that rises to the top.

Reduce to a gentle simmer and cook until beans are soft and creamy, but not falling apart, about 18 to 20 minutes; older beans will take longer.

Remove from heat and add about 2 tablespoons salt.

Discard sachet and allow beans and their cooking liquid to cool.

Beans, like potatoes, absorb a lot of salt so re-taste after about 10 minutes and add more salt, if needed, and pepper to taste.

To finish: Heat the olive oil in a large pot over medium-high heat.

Add the carrots, a pinch of salt and black pepper, and cook until carrots soften and are slightly browned, about 2 to 3 minutes.

Add celery and leeks with a bit of salt and fresh pepper, and cook another 2 to 3 minutes.

Once tender, push vegetables to the side of the pot; add garlic, chile flakes and rosemary, and stir until aromatic, about 30 seconds.

Lower heat to medium and cook, stirring, until the flavors have combined, another minute or so.

Add tomatoes and cook another 3 to 5 minutes.

Add the beans and their cooking liquid.

Bring to a simmer and continue cooking, stirring occasionally, about 1 hour, until the vegetables are tender and flavors are balanced.

Stir in parsley before serving; adjust flavors with salt, pepper and olive oil.