As Chazal say, Hashem said to His world “dai” – stop! – at which point the laws of nature became fixed and stable. Those who attempt to explain creation as an ongoing natural process empty our cessation from work on Shabbos of all meaning. They cannot help but stumble in the fundamentals of Torah. They thereby undermine the very essence of Shabbos which is fundamental to our awareness of the Creator (see Rashi to Chulin 5a, as quoted by Rav Shlomo Zalman Auerbach in Mevakshei Torah).
It is the post-creation stable order that scientists legitimately study today. Contra Rabbi Slifkin, the pseudo-scientific naturalistic account of origins is at loggerheads with the principle God presented to us in the Torah – the principle of a purposeful meta-natural creation by a transcendent Creator.
There is no way to reconcile or eliminate this conflict in worldview. Nor is it a question for concern because, on this issue, evolutionary naturalists have overstepped the legitimate bounds of science. We refer the reader to toriah.com/wiki for further details.