In the past, all sciences came within a single philosophical framework. It was this framework that defined the ruling principles of each science. It was so until the advent of new science. However, with the appearance of experimental schools, that believed in no value but the data based on the senses, philosophy – and especially metaphysics – was removed from the circle of science. Yet, with the appearance of different schools in the philosophy of science in the second half of twentieth century, it became clear that we do not face nature with an empty mind, and that scientists make their efforts and develop their theories while having in mind some general (metaphysical) assumptions. Furthermore, experimental sciences cannot answer some questions raised within those sciences themselves. In order for those questions to be answered, they need a higher reference.In this article, and through showing the possibility and how metaphysical viewpoint would affect physical theorizing, we will point out that ruling principles over sciences can be taken from different philosophical schools, or from religions. In this concern, monotheistic religions can provide these principles in the easiest and most comprehensive way.