The year 2008 marks the 60th anniversary of Japanese primatology. Kinji Imanishi (1902–1992) first visited Koshima island in 1948 to study wild Japanese monkeys, and to explore the evolutionary origins of human society. This year is also the 30th anniversary of the Ai project: the chimpanzee Ai first touched the keyboard connected to a computer system in 1978. This paper summarizes the historical background of the Ai project, whose principal aim is to understand the evolutionary origins of the human mind. The present paper also aims to present a theoretical framework for the discipline called comparative cognitive science (CCS). CCS is characterized by the collective efforts of researchers employing a variety of methods, together taking a holistic approach to understand the minds of nonhuman animals. While the researchers of animals usually carry out experiments in the laboratory and conduct observational studies in the natural habitat, a different permutation is also possible. Field experiments can be carried out in the natural habitat, and observational studies can be in the laboratory. Such a two-by-two contingency table based on location and research method thus provides the basis for a holistic approach. CCS provides a unique window on understanding the chimpanzee mind as a whole. The studies of the chimpanzee mind may also result in illuminating the evolutionary roots of the human mind.