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This essay intends to show that science, especially the natural sciences, operate on presuppositions. In a nutshell view of aspects of the history of science the presuppositions, as part of the relevant historical context, operate within the scientific enterprise. Science used to be views as positivist and final; yet, the logic of methodology, from E.A. Burtt to T.S. Kuhn and Karl Popper show that presuppositions are part of the scientific research. Particularly the pioneering work of the archeologist and philosopher R.G. Collingwood and the seminal thinker S.N. Nasr, who opened the doors for the inquiry of the role of science within Islamic Civilization, are highlighted. We show that the tension between the humanities (human sciences) and the natural sciences still exist and need to be explored on a global level, especially as to their cultural presuppositions involved.