Differences between humanities and natural sciences and the problem of their integration are considered in the article in view of a naturalist#s humanitarian knowledge formation. The main contradictions in scientific knowledge are revealed. Permanently deepening demarcation between humanitarian and natural sciences, as well as within individual disciplines has been formed as a result of the historic development of science; it is caused by the difference in the methods and objects of investigation. The main ways of scientific knowledge integration which allow passing on to a new scientific paradigm are revealed. The methodology of transdisciplinarity is among them. It is being developed in the International Center for Transdisciplinary Research. Another methodology aimed at the integration of sciences is a synergetic one. It allows studying such super complex systems as science. The ideas and principles of heuristic significance for the advancement of new views on nature and society are based on the synergetic

methodology. The author comes to the conclusion that new methodologies will be able to solve the problem of sciences integration provided they are coupled with the process of humanitarisation aimed first of all at the consciousness of the subject of science, the scientist. Humanitarian component possesses an integrative force which allows combining information flows, evaluating its constituents, determining the development direction on the basis of morality and mind.