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Is the Qur'an refuted by modern science?

Surah 65:12 and 41:12: Did science confirm that the sky is made up of seven layers?

Surah 4:40: Does the Qur'an mention atoms?

Surah 86:5-7: Is the Qur'an scientifically correct about embryology?

Surah 21:30: A Big-Bang theory fulfillment?

Surah 57:25: A scientific miracle of iron?

Surah 25:53, 55:19-20: Barriers between seas in the Qur'an?

Surah 30:1-3: Does the Qur'an predict that the Dead Sea is the lowest part of the earth?

Surah 41:11: Prediction of early universe and star formation from smoke?

Surah 55:37: Is the Cat's Eye Nebula the rose colored like paint?

Qur’an 16:69: Do Bees make honey in their belly?

Qur’an 81:15-16: Prediction about black holes and moving stars?

Qur’an 34:3: prediction splitting of an atom?