In a large pot or Dutch oven, bring the beans and enough water to cover by 1 inch to a boil. Lower the heat and simmer for 2 minutes. Remove from the heat, cover and let stand for 1 hour. Drain and rinse the pinto beans, return to the pot and add water to cover by 1 inch. Add the onion, garlic, jalapeno and bay leaves and bring to a boil. Lower the heat and simmer, partially covered, for 1 hour, stirring occasionally.
Stir in the beer and simmer until the beans are tender and creamy, about 30 minutes. Discard the bay leaves and stir in the chipotle chiles, vinegar and cilantro; season with salt.