The purpose of the paper is development of a conceptual model for the representation of knowledge as an active intellectual substance and, on this basis, study of metaphysics of knowledge transformation process being produced both individually and collectively in the practice of organizations. The first principle of knowledge engineering, as Edward Albert Feigenbaum noted, says that the power in solving problems that an intellectual subject (person or machine) manifests in the process of activity depends primarily on its knowledge base, and only secondly on the methods of inference used. Strength is hidden in knowledge. The process of producing knowledge is permanent and does not depend on whether an individual is going to use this knowledge or not. Knowledge constantly produces new knowledge regardless of the owner's desire. Besides that, knowledge can’t arise from nothing, but always – from some knowledge obtained earlier. As well as the intelligence, knowledge is an emergent instance arising from the collective interaction of a lot of intellectual atomic elements of knowledge (knowledge quanta). Idiosyncrasy of this interaction is expressed precisely in the creation of new knowledge. Due to postulating the knowledge self-organizing, the hierarchical knowledge structures in memory and the process of thinking as a kind of syntax for the procedure of new knowledge generation are described. This is an effort towards understanding the memory mechanisms, the process of thinking, the sources of heuristic knowledge just through the inner nature of knowledge. Also, based on the knowledge self-organization principle, an archetype of the appropriate knowledge-based system architecture is presented too. As an implementation of the concept, the perceptual act model is described, and on its base, a possible scenario for the behavior of a robot meeting an obstacle in its path is considered. As the mutual transformation of tacit and explicit knowledge makes new knowledge, the impact of the self-organization of knowledge on the transformation process as well as conditions of self-organization of both individual knowledge and organizational knowledge are analyzed in detail. Finally, modification of the known model of knowledge dimensions by Nonaka and Takeuchi is proposed. Because of the native activity of knowledge, it is impossible to build a knowledge management system without considering the internal structure of knowledge and its emergent ability to self-organize. Ensuring the natural process of knowledge development at all ontological levels in an organization is an essential prerequisite for the evolution of values in this organization.