Elchonon, I think the Rambam in the Moreh Nevuchim, the Malbim quoted above, the Sefer Habris believe that it is a mitzva to reconcile if we can. The Ramban by orlah says that treifos are not healthy. We have a rule עולם כמנהגו נוהג. The gemora in Shabbos at story of the man nursing, one view is how ugly it is that nature had to change for him because he will lose his zechusim. Something like Darvin’s theory is against modern science as Newton said I am standing on great shoulders indicating that peiple before him were smarter. The Klei Yokor in Parashas Chukas uses the theory of Newton before him, opposites react by explaining the functioning of the parah aduma to a certain extent.
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