The present article analyzes and outlines significant changes in ideas about the object of scientific knowledge in modern science. Special attention is paid to the transition to the paradigm of complexity, within which the object of scientific knowledge acquires a complex systemic character and remains in the same complex connections with systems of different levels. It is marked that such changes entail a number of methodological requirements, which are especially clearly manifested in modern theories of bioethics and its real practices. A special role in this case is assigned to issues of transdisciplinary approach, complementary methodology, and values of the subject of bioethical cognition. The prospects for further research are related to the possibilities of deepening the methodology of the paradigm of complexity based on the application of a transdisciplinary approach.