Q: Why do my baked beans never seem to cook completely, no matter how long I leave them in the oven?

Beans cooked in water that contains a high level of calcium can take a very long time to cook, or may never soften at all.  The calcium combines with the pectins between cells in the beans.  The strengthened pectins reinforce the walls of the cells, making them more firm.  Also, acidic ingredients such as ketchup, tomatoes or vinegar used in the recipe can slow down dissolving of the cell walls, contributing to the sense that the beans haven't cooked completely.  Once the beans have softened, however, these ingredients can be added without affecting the final texture.

Some cooks may add a small amount of baking soda to encourage beans to soften, although in doing so they risk turning the beans to mush as well as affecting the flavor.

Sugar can act in the same way as calcium to prevent the beans from softening, so molasses is a triple threat to cooking beans, as it is acidic and contains both sugar and significant amounts of calcium.

Beans should be soaked prior to cooking.  Slow soaking is done by covering the beans in water and leaving them sit, covered,  at room temperature for eight or more hours.  Use about 3 times as much water, by volume, as you have beans.  To quick soak them, put the beans into a cooking pot, cover them with the three times the volume of water and bring them to a boil on the stove.  Boil for about two minutes and then leave them sit off heat for an hour.  In either case, drain off the soaking water before proceeding with the recipe.

What I like to do at this point is put the beans into a pot on the stove, add enough water to cover them by about an inch, and then simmer them for about an hour, until they are soft enough to bite into but not yet fully cooked.  Check the water and top it up if necessary.  This water is drained off again, but may be reserved to use in the final dish, if needed.

If you are making baked beans or some other dish that cooks for a long time, you may wish to cook them less at this point.  If the remaining cooking time for the recipe is shorter, you may want to cook the beans a bit longer at this stage.

This extra step takes a bit longer for the dish over all, but allows you to better control the texture of the end result.  I also find that beans done this way are more tolerant of the other ingredients in dishes like Brown Baked beans, where the molasses and ketchup might work against you.

If your tap water is particularly hard, you may need to use water from another source to cook your beans.   Softened or bottled water should work well.  And I don't mean some expensive bottled water.  Most grocery stores sell purified or distilled water in gallon jugs at a much more modest price than the fancy stuff, and it will do just as good a job.