The term "discipline" means primarily teaching or training. However, the Japanese, who tried to import sciences as an established system as efficiently as possible in the late 19th century, tend to understand the word in a derivative sense of specialty. As a result, the Japanese academic circle has acquired a habit to extend existing science rather than creating new principles on the basis of reality. The author, who has been engaged in the system science from its beginning in this country, has been opposed to make a "discipline" in this sense out of it, because it would prevent self-innovation of science stimulated by reality. The paper describes the development of the system science in Japan and discusses the principle of the research organization that allows such self-innovation.