When the Beis Hamikdash was built, Shlomo Hamelech used the shamir worm in order to cut through the stone, just like the shamir was used in the mishkan to engrave the stones on the ephod. In this way, the stones were not cut through; rather, they remained whole and just split open in order to fit the proper dimensions. This is not breaking teva (nature), like the miracles of Yetzias Mitzrayim. The purpose of the mishkan and mikdash are to bring Hashem's presence into this world. The shamir worm does not break through the rock in order to carve it; but instead keeps the teva whole in order to welcome the presence of Hashem into even the hardest forms of physicality.