If the scientific issue clearly contradicts a clear, decisive and explicit rule, hadith or Quranic verse, classical scholars would reject the scientific position because science in that sense is Dhanni (hypothetical), while the Islamic teaching in that sense is Qat'i (substantial).
For example, Ibn Hajar commented on Hadiths regarding the formation of the fetus in the womb from the water of man and women:
وَزَعَمَ كَثِيرٌ مِنْ أَهْلِ التَّشْرِيحِ أَنَّ مَنِيَّ الرَّجُلِ لَادَوْرَ لَهُ فِي الْوَلَدِ إلّا فِي عَقْدِهِ وَأَنَّهُ إِنَّمَا يَتَكَوَّنُ مِنْ دَمِ الْحَيْضِ ، وَأَحادِيثُ الْبَابِ تُبْطِلُ ذَلِكَ
"Many experimental scientists argue man's semen has no role in the formation of the fetus except for its beginning, and only women's menses is responsible for that. But the Hadiths in this chapter contradict." (Ibn Hajar, Fath al-Bari, Vol. 11, p. 480)
The victory was given later to religion over the scientific hypothesis.
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