The purpose of the paper is to examine philosophical aspects of the conflict relationship between religion and science within the development of Modernity as a civilization project that claims universality. Both this claim and the universality of scientific knowledge were put under question in contemporary culture. The notions of “transculturation” and “transcultural contact zone” are applied to the investigation of the global expansion of Modernity. The existing approaches to the understanding of the influence of Gnosticism and nominalism on the ideology of Modernity are compared and assessed. The so-called “nominalistic revolution” that was of great importance to the formation of early European science was also connected with the emergence of the contact points between religion and science thus creating zone of their future confrontation. The paper additionally draws upon specific Russian context.