The main objective of this paper is to study the roots of secularism in methodology of science and also to discover some obstacles in the way of bringing about change in humanities. The postulates of this research are: 1. Inextricability of science and value; 2. Transfer of logic and values of natural sciences to humanities; 3. Valuational exchange between the society and science; 4. Necessity of following up the valuational developments of the Iranian society in humanities’ projects; and 5. Role of methodology in reproduction of philosophical principles of science. Descriptive-analytical method has been employed in this research. The findings indicate the followings: 1. There are correlations between secularism and reductionism. 2. Secularism perpetuates in science and with the assistance of science. 3. Some methodological principles, through supervision over scientific research intervene in formation of relations between science and religion. 4. Causal explanatory methods and referentiality of the system and concept of mechanism assist perpetuation of secularism in science. The research approaches and methods or techniques employed in humanities are among the factors behind promotion of secularism.
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