Modern science developed its methodology through the Scientific Revolution in 17th century and established its social institution through the second Scientific Revolution in 19th century. In the latter period, science was specialized from science to sciences, and lost its unity as “natural philosophy.” The mainstream of scientific thought consists of atomism, analytic method and local optimization. To overcome the specialization of science and to realize the integration of knowledge, it may be stimulating to consult the intellectual heritage of Japanese thought which includes the unique concepts of “place (basho),” “scene (bamen)” and “between-ness (aida).”