The article discusses a complex of methodological issues generated by the fragmentation of the subject of scientific research. These processes today capture various fields of science. First of all, they are found in interdisciplinary research programs implying the involvement of disciplines with various languages and methods and, moreover, oriented towards an applied result. In addition, the processes of fragmentation of subjectivity arise in research carried out by large scientific communities, i.e. the collective subject of knowledge, where the scientist has access only to certain parts (aspects) of the studied subject and, for a number of technical reasons, is deprived of access to the knowable reality as a whole. Meanwhile, the scientist, as suggested by the fundamental scientific attitude, should be critical of everything that cannot be tested in his/ her individual rational practices. In modern science, these practices themselves have changed, which is in the center of the attention of philosophers of science. All this stimulates the relativization of fundamental epistemological attitudes, eroding the very foundations of the cultural status of science. The article advocates the thesis that one can resist these trends by turning the methodological consciousness to the cultural and historical dimensions of scientific activity and emphasizing the importance of the idea of the continuity of scientific knowledge underlying these dimensions.