This study is essentially intended to reveal more about the pattern of the right management to manage the interaction of science and Islam at the Islamic university, especially in the process of learning and studying of the natural sciences such as physics, chemistry, biology, and mathematics. This management model is important to find because there are some practices of the existing management types that offering dogmatic approach, being exclusive in the use of references, being normative, attributive and many other forms. The methodology that we use is the qualitative method, with interviews as data collection techniques with the principle of snowballing which in practice follow the advice of a previous interviewee about who is the most competent for the next interview. To add to the completeness of the study, the researchers also conducted an analysis document, especially for books or papers wrote about the integration of science, especially to explain how this concept implemented either at the level of department and universities, both at the conceptual level as well as at the curriculum formulation by faculty and students. Temporary findings show that there are complexities ontologically, epistemologically, and axiologically in determining the relationship pattern of science and Islam in the context of managing it at the Islamic university particularly in relation to the formulation of curriculum, research, teaching, and other aspects that interact with both. Ontologically, this discourse seems unfinished. Epistemologically is much less. In Axiological, or rather pragmatically, the pattern is well set. Pragmatically, there is an obvious tendency that there should be an appreciative mechanism for Muslim scientists in the past and in the present by giving priority to cite their works more than the works of non-Muslim scientists. Also there is a need for Muslim scientists now to be proportionally normative in their scientific works. These models usually require Muslim researchers to cite more Quran verses in their scientific publications, or even in their research proposals. From the flash of the above results, it appears that the urgency of this research is how the Islamic university can manage the harmony between science with its scientific method, and Islam with its dogmatic and pragmatic principles. With one goal, that any scientific discovery produced by the university can remain valid scientifically.
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