The book contains in-depth discussions in a rigorous manner of a host of interconnected issues and problems concerning the foundations of science. Some issues concern the substance of scientific subjects, such as the nature of spacetime and the problems in quantum mechanics, while other issues concern the methodology of science, such as the nature of theorization, idealization, as well as modeling. These discussions aim at clarifying the issues and problems, reviewing the proposed views and solutions, mapping out their logical spaces, and arguing for preferred views or solutions.