The development of quantum physics and formulation of complementarity and uncertainty principles gave rise to numerous interpretational problems. For the first time microworld laws were formulated in probabilistic rather than deterministic language. In the philosophy of nature there was a need for revision of views on realism, determinism, reductionism and the role of the observer in the conduct of research. However the question whether the perceived boundaries of knowledge are the result of the nature essence or of actual cognitive abilities remains open. In the social sciences, after years of dispute about the research methodology, the need for a complementary use of quantitative and qualitative approaches has been accepted. Qualitative researchers, however, continue to criticize legitimacy of quantitative research. At the same time the assumptions of qualitative approach build on neo-positivist interpretation already outdated in the light of naturalists new discoveries. The article aims to demonstrate that the changes that have taken place in the theory of knowledge as a result of naturalists discoveries lead to convergence between the two research approaches. Taking into account these changes will end the polemic with assumptions already outdated in the natural sciences.