When Newton started his lectures on optics in 1669 as the follower of Isaac Barrow on the Lucasian chair at Cambridge he intended to develop the theory of colors as a mathematical theory of physical objects. It is in connection with this first attempt of mathematizing nature that we encounter most of the central questions with which Newton's subsequent interpreter were occupied. Why did Newton oppose to hypothetical physics? What did he mean when he contended that his principles of physics are "deduced from phenomena?" How is the relation between inductive and deductive inferences to be conceived within his methodological approach; What are Newton's sources of the methods of analysis and synthesis (or resolution and composition) that play an essential role in his investigations of colors and that also paved the way to the theory of universal gravitation. The paper attempts to discuss Newton's methodological presuppositions primarily from the perspective of his early optical studies.