The most fundamental origin of nature in the perspective of science and religion

What is the most fundamental origin of nature? What do natural phenomena fundamentally originate from? This question has always been attended to during all human scientific life; but nonetheless, it has been failed to be answered truly. Among ancient Greek theories, atomism lived a long life; Yet on quantum theory, atomic world beings do not follow the ordinary rules of nature any more and neither have they been replaced by some others. And if any, the differences are so much that no one can agree with them. Furthermore, scientific news of the existence of a fully strange and invisible matter, called dark matter, has made it more complicated.
The Holy Quran has referred to the matter in some verses; it has known something titled water to be the most fundamental principle for nature, calling it in some cases light facing darkness. In a deeper view , however, the most fundamental principle of nature (divine aspect of the heavens and earth) has been considered as something immaterial, given so, experimental methods of science never can solve the problem in a logically admitted way at all. It seems that Mulla Sadra, being influenced deeply by Quranic teachings and paying attention to the unity, fundamentality and analogicity of existence, has drawn a reasonable picture for unity of the first principle.