Soak the beans in water overnight. Rinse and drain the soaked beans. Place in a large pot and cover with fresh water. Bring to a boil over medium-high heat and skim off any foam that rises to the surface. Simmer the beans just until tender, 1-1 1/2 hours.
While the beans are cooking, fy the bacon in a large pot or dutch oven over medium-high heat just until crisp. Remove with a slotted spoon and drain on paper towels. Add the onions, scallions, and garlic to the bacon fat; saute, stirring occasionally until soft and translucent, about 10 minutes. Stir in the jalapenos and cook 5 minutes more.
Place all the seasonings in a dry skillet and toast them over medium-low heat, swirling the mixture in the pan continuously and being careful not to burn, 2-3 minutes. When the mixture is quite fragrant, add it to the onions and cook 5 minutes.
Add the tomatoes and beer; simmer over medium heat about 30 minutes.
In the meantime, saute the beef in a large skillet over medium-high heat. Crumble the meat with the back of a wooden spoon and cook just until the meat is no longer pink. Drain the fat and add the meat to the tomato mixture in the pot.
Once the beans have cooked, drain them and add them to the chili. Season to taste with salt and stir in the reserved bacon. If the mixture seems too thick, thin with water or more dark beer. Serve now or simmer the chili up to 1 hour to blend the flavors a bit more. The chili may also be chilled and reheated.