Soak beans in a large pot of water, 8 hours to overnight.
Drain beans, and refill the pot with chicken stock and enough water to cover beans with 2 inches of liquid. Season with salt and pepper. Cover, and bring to a boil. Reduce heat to medium-low, cover, and cook for 1 1/2 hours. Stir beans occasionally throughout the entire cooking process to make sure they do not burn or stick to the bottom of the pot.
Stir tomatoes, beer, onion, cilantro, jalapeño peppers, garlic, oregano, and bay leaves into the beans. Continue to cook uncovered for 1 hour, or until beans are tender.
With a potato masher, crush the beans slightly to thicken the bean liquid. Adjust the seasonings with salt and pepper to taste.