Newton did not consider his natural philosophy and his work in the supernatural as two separate endeavors.
We have Newton's translation of the Emerald Tablet:
Tis true without lying, certain and most true.
That which is below is like that which is above
and that which is above is like that which is below
to do the miracle of one only thing
For Newton the following is also true:
That which is beyond is like that which is within
that which is within is like that which is beyond
For Newton that which is natural is that which is supernatural
For Newton, natural (within) and supernatural (beyond) is the same thing.
This is why Newton does not hesitate to explain natural phenomena with a supernatural cause like his God.
This is why Newton has no scruples explaining natural phenomena like orbits with a supernatural cause he calls "force".
Explaining natural phenomena with supernatural causes is not an exception in Newton, on the contrary, this is Newton's main method. Newton should never be compared to rational and true scientists such as Huygens and Leibniz but to John Dee. Newton is an occultist like John Dee. The only difference is that Newton is a better mathematician than Dee.
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