Rinse the dried beans. In a deep bowl, mix the 3 cups water and baking soda, stirring to dissolve the baking soda. Add the beans and let them soak, completely submerged, at room temperature for at least 8 hours or preferably 10 to 12 hours (if it is very warm in your kitchen, soak the beans in the refrigerator for 24 hours). As the beans soak, they will swell to several times their original size. To make sure they remain moist throughout the soaking, dampen sarashi or several layers of finely woven gauze or cheesecloth and place directly on the soaking beans.
Transfer the swollen beans and what remains of their soaking water to a deep 3-quart pot. If the beans are no longer covered with water, add water as needed to cover them. Place over medium-high heat and bring to a boil. Skim away any aku (froth, scum, or film) with a fine-mesh skimmer and add water as needed to cover the beans by about 1 inch. Adjust the heat to maintain a steady, not-too-vigorous simmer. Place the cloth you used when soaking the beans on top of the simmering beans. The cloth will become discolored, but if it is sarashi or other sturdy muslinlike cloth, it can be reused for the same purpose several times. If you have an otoshi-buta or other flat lid slightly smaller in diameter than the rim of the pot, place it on top of the cloth.
Cook the beans for 2 hours, checking the intensity of the heat and the water level every 15 to 20 minutes. Ideally, the beans will gently simmer in water that barely covers them. Throughout, keep the surface of the beans moist with the cloth (and otoshi-buta).