This paper discussed how philosophy of science categorizes sciences into the formal and empirical sciences. The formal sciences include logic and mathematics. The empirical sciences include the natural and social sciences. Next, the paper discussed how philosophy of science analyzes empirical knowledge in the empirical sciences into three types: (a) particulars, (b) laws, and (c) theories. This paper pointed out that three types of research questions (case questions, relationship between variables questions, and theoretical questions) could be generated corresponding to these three types of empirical knowledge. Finally, with the help of the “mechanistic viewpoint of the universe,” many more research questions could be further formulated. Many examples of research questions, both in the natural and social sciences, were presented. Key words : philosophy, science, empirical, research questions