Sorry, I think we're miscommunicating.
I agree that there is the *RISK* involved in the natural sciences, of
neglecting the supernatural,
then deciding that by Occam's razor the supernatural is not necessary for what you happen to be studying,
then being so successful at naturalistic predictions that you leave out the supernatural altogether,
then concluding that there is not, and never has been a supernatural,
and as an adjunct assuming that the supernatural is merely, and has only been, an abortive attempt at explanation of the world, rightly superceded by the scientific method.
Apparently some scientists, and some "camp followers" of the scientific endeavor, really DO feel this way.
But NOT ALL.
Leading with a strawman argument will not earn you respect or credence on these threads.
Cheers!
"Problems exist such as the Cambrian explosion"
It is not a problem. In recent years many more examples of precambrian fossils have been found. Calling the Cambrian an "explosion" is a bit of a stretch, anyway. It was over millions of years. We see the evolution of forms from the beginning of the Cambrian to the end. How does ID explain that? Does every little detail of anatomy change get separately designed?
Science doesn't waste its time investigating "systems" that are fantasies of misinterpreters of the Bible.