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I’m one of the staunch critics of “scientific miracles in the Holy Koran” from epistemological and ontological points of view. But that doesn’t I believe Koran is against science! I mean the Book is not like Darwin’s “On the Origins of Species” that you can drive theories from.
There are also no “rulings” in science. We have theories and they are neither true nor false. Finding another theory doesn’t mean that other is false. It means more understanding from different source or another angle. This is why scientists “modify” theories not change them.
From the time Democritus said there is atom, no one demolished his assertion. When Rutherford and JJ Thompsons came they modified the theorems but the basic idea of atom is there untouched. Even with Quantum Mechanics the basic idea of atom is still there but with quarks.
Koran will never tell you there is no atom and science will never change its permutations on this because it is one of the basic scientific foundations upon which most theories stand. But the theories could be modified. So when Koran says :
وَقَالَ الَّذِينَ كَفَرُوا لَا تَأْتِينَا السَّاعَةُ قُلْ بَلَى وَرَبِّي لَتَأْتِيَنَّكُمْ عَالِمِ الْغَيْبِ لَا يَعْزُبُ عَنْهُ مِثْقَالُ ذَرَّةٍ فِي السَّمَاوَاتِ وَلَا فِي الْأَرْضِ وَلَا أَصْغَرُ مِنْ ذَلِكَ وَلَا أَكْبَرُ إِلَّا فِي كِتَابٍ مُبِينٍ
“The unbelievers say: "There is no coming of the Hour for us." Say: "Why not? By my Lord, the knower of the unknown, it will certainly come for you. Not even an atom's weight in the heavens and the earth, or something smaller or greater than it, is hidden from Him...”
Here God is not defining what atom is but he is giving us an insight that there could be a possibility of finding something smaller than atom (اصغر من ذالك). Today we found positrons, neutrinos and quarks. My view is we shouldn’t say these are the smallest. We should keep digging
This is what I mean from physical science points of view which I believe you are talking about. But when we go to social sciences there are many to talk about especially in sociology and psychology that Koran deals with in many verses. I hope you understand me.
When I say we should understand Koran with modern science, I don’t mean the metaphysical part of the Koran but the physical part of it that asks us to ponder over the heavens and cosmos. So when Allah asks us to study heaven we should not go back to superstition.
Any person that reads Koranic exegesis, from Dabariy to Ibn Kathir, would understand that they interpret some verses according to the available information in their time. Sometimes they add superstition and baseless claims to the interpretation. That’s their “ijtihad”.
Let me give you an example. We use to believe that “Thamuds” were giants. But Imam Zahabi used archeological evidences in debunking this claim. Is this not scientific approach? He then explained that people misunderstand the word of God when thinking about “Thamud”.
Saying there are no “scientific miracles in Koran” that people like Zakir Naik used to talk about doesn’t mean I will go to superstition and baseless exegesis in the name of “Tafsir”. Unfortunately this is what our clerics in Northern Nigeria do.
I watched the video of @DrIsaPantami and Muhammad Yusuf debating on “Theory of Evolution”. I was sad when I realised that Muhammad Yusuf was against the theory he didn’t understand but but based his whole anti-science theology on. The Pantami also didn’t understand it well.
Clerics in Northern Nigeria should understand science fully before embarking on refuting its theories. The theories also must be understood well before asking : “Why there are apes if we evolved from apes?” Or thinking that earth is flat and stars are closer to us than sun.
Thank you.

God knows best.
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