In this paper we will consider the logical structure of the theory of natural selection and adaptation. First we will make clear what the theory was and what it is now. Through this half historical analysis we will show that a clue of the success of Darwin was based on the concept-shift of the adaptive variation from explanandum to explanans (variation) and the result (adaptation) in the theoretical level. And this was inherited by the modern Synthetic Theory with slight modification. Like Darwin's theory, favorable variation or variation with higher fitness is the premiss of the explanation by natural selection. Next we will treat two logical criticisms against the theory. And then we will conclude that the principle of natural selection neither is tautological nor commit petitio principii. However we must compensate these favorable answers with indefinability of fitness in the theory. Finally, using above results, we will try to answer how we should think favorable variations and what the future theory of natural selection should be. Our tentative answer is as follows: we should separate variation, fitness and adaptation from the principle of natural selection and study them independently, and then we might have an explanation by the theory.