Short history of how science went from being a 'path to God' to being a 'tool for Atheism'
In principle the universe is a 'sign' of God. The Quran almost on every page refers to this. Study of nature, is the study of the attributes (99 of which are manifested in our world) and habit of God (Sunnatullah). This was the underlying inspiration for the founders of the Scientific Method (Jabir bin Hayyan, Ibn al Haytham, Al Kindi), something which neither the Greeks or the Indians had. And the Scientific Method in reality has enormous power.
Just look around and the modern world with all of its technology could not have been possible without experimental science. Our FB posts are literally travelling at the speed of light, nothing trivial about this ! But since in Islam the purpose of knowledge was the proximity to the Divine, other sources of knowledge (much more sturdy and less prone to error) were recognized along with the Scientific Method- ie. The Quran (infallible source of knowledge) and Spiritual Insight ( a much faster way to attain knowledge but isn't infallible as the Quran of course, because spiritual vision can be clouded and mistaken for people other than Prophets).
This pursuit reached crucial crossroads with the Ibn Rushd Vs Imam Ghazzali debate- Natural causation VS Occasionalism. The Muslim world chose Occasionalism and the west adopted Natural Causation (even though both opinions were derived from the Quran). Since the dominant thought in Medieval Europe was shaped by the Church, this notion of things having 'natural causes' fit very well because God as viewed from the Bible is the Original cause for the universe and then becomes irrelevant once the creation is initiated. So what you have is a God at the beginning and then nature takes over.
In an environment when science progressed so rapidly and God is sitting idle at the Beginning, it was very easy to drop God and accept Naturalism. What must've made it easier was the 'God of the gaps' outlook of Christian thought and of course it's censure of science. Dropping God from the pursuit of science means dropping the spiritual. The argument hence was since you can't see/experience anything other than the physical world, hence this is all that exists.
And now the obsessive addiction to 'naturalism' can be seen in conundrums like interpretation of Quantum Physics, the hard problem of consciousness, the Fine Tuned Universe. These wouldn't be problems if other forms of knowledge were recognized.
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