The discourse between Islam and modern science is defined by several historical anomalies, the most important being the initial encounter. Modern science arrived in the Muslim world at a time when most of the traditional Muslim lands were under direct colonial occupation. This first encounter is also intimately connected with a much larger transformation of the traditional Muslim lands that defined, to a large extent, the nature of the relationship that developed between Islam and modern science during the nineteenth and first half of the twentieth centuries. The relationship was also defined by connections between modern science and the colonial designs for the people of the occupied lands. All of these factors transformed the discourse between Islam and science that had existed for eight hundred years prior to the arrival of modern science.