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Breaking the patterns of habitual thinking is crucial in order to welcome a new revolution of science and technology (S&T) and to realize a new paradigm of scientific research. We are facing a new era for S&T, in which there are more opportunities than challenges. However, this new era calls for governments and scientific communities to recognize that the most important issue might be something other than discussions of investment and rewards. Contemporary science achieved remarkable progress in the 20th century, contributing to the expansion of knowledge and human capability in sustainable development. As science continues to expand in both temporal and spatial dimensions, it has given rise to many new technologies. In particular, the development of energy, materials, information, and biological technologies has fundamentally changed the production mode and lifestyle of human beings, and promoted civilization. On the other hand, people have gradually come to realize that, while new challenges in human sustainable development demand solutions, some problems in nature, engineering, social science, and humanity itself cannot be solved based on currently available knowledge. Reductionism focuses on details at smaller and smaller scales, while holism emphasizes global behaviors. Bridging these two perspectives is still not possible. As a result, it is difficult to establish correlations between different levels of a system or between different scales on the same level, severely limiting human capability in sustainable development and presenting challenges to both natural and social science. Meanwhile, the progress of information technology and the explosive expansion of knowledge are propelling the possible emergence of a new scientific research paradigm [1]. Transdisciplinarity [2–5] and the integration of different disciplines are believed to be the main path [3] to new breakthroughs. Contemporary science is becoming more and more open and globalized. At such a time, when opportunities are greater than challenges, all countries around the world have promulgated various key research programs, reconstructed their national innovation systems, and placed increasing expectations on contributions from S&T. A new S&T revolution is being widely anticipated. Scientific communities in all countries are appealing to their governments to increase S&T investment, and in turn, governments are more eager than ever to see rewards from their investment. Therefore, relationships among governments, industries, universities, and research institutions are drawing more and more attention from all levels of society, and seem even more complicated than the science itself. Increasing S&T investment and promoting coordination between governments, industries, universities, and research institutions are certainly important. However, has this single-minded focus detracted attention from other issues that may have a greater influence on the evolution of S&T? This author posits that the evolution of S&T itself is being widely overlooked and may play a more critical role in responding to global challenges, accelerating scientific progresses, and creating a new scientific research paradigm than is currently acknowledged. For example: • The knowledge system and its missing links: Can we sort out the logical relationship and architecture of scientific knowledge on the basis of current understandings, so as to optimize the layout of modern S&T and further identify the missing links in the knowledge system? • Actions driving a new paradigm: Facing the waves of big data, open access to knowledge, and globalization of scientific research, how do we rationally guide and drive the formation and development of a new scientific research paradigm, as opposed to passively waiting for its appearance? In addition, understanding the logic and structure of the knowledge system and the resulting shift in scientific research paradigms will pose a series of new requirements in the structure and management of innovation systems and education systems in all countries. This paper breaks away from habitual thinking and attempts to explore these questions.

Exploring the Logic and Landscape of the Knowledge System: Multilevel Structures, Each Multiscaled with Complexity at the Mesoscale