The article shows methodological foundations of some natural science statements which demonstrate significant influence on modern linguistic conceptions of the relationship between the language and the knowledge. The topic under discussion is a developing linguistic theory of thesaurus offering a new view on the semiotic system of knowledge. The purpose of the work is to understand the transformation of the linguistic notion «thesaurus» under the impact of the actual natural science conceptions by critical review of the papers at issue. The article analyzes the relevant ideas of the general theory of systems, the theory of information, informatics, or the computer science, and synergetics. In particular, we discuss properties and functioning of complex developing systems, analyze the natural science vision of information, and study the thesaurus as the semiotic system necessary for reception of information from the environment and generation of new information. We compare natural science views on the semiotic system of knowledge and corresponding linguistic ideas as well as consider the proposed by natural science methods of its study. The main result of the work is the formulation of the departure statements of the linguistic theory of the thesaurus formed as the consequence of the discussed natural science conceptions.