However, there were many questions about the universe and the solar system he could not answer. Why should one body emit light, while others that revolved around it did not? Where did it all come from? Newton did not know. He could not even imagine how it might be possible for it to happen naturally. Therefore he took the only other option open to him.
"I do not think [this arrangement] explicable by mere natural causes, but am forced to ascribe it to the counsel and contrivance of a voluntary Agent." Quoted in The Prophet and The Astronomer, Marcelo Gleisler, W. W. Norton, New York, 2002, p. 69, citing Isaac Newton, "Four Letters to Richard Bently," in Milton Munitz, ed. Theories of the Universe: From Babylonian Myth to Modern Science, Free Press, Glenco, IL, 1957, p. 212.
Newton had no idea about atoms and nuclear fusion, nor the elements made in the Big Bang and supernova, nor the development of the Solar Nebula into the Sun, planets, moons and comets. Current science now has answers for all these questions of his. Had he waited 300 years, he would not have had to ascribe these occurances to a voulntary Agent. Those who now ascribe certain unknowns in evolution to intelligent design may someday be able to see the natural processes by which new species are created.
Newton was also a profoundly religious man. His bringing the Solar System under his mathematical control, did not lessen his need for or faith in God. Science and religion can exist comfortably in the same person, without having to disparage each other's territory to prove their truth. Science is not a threat to religion. Religion is not a threat to science. Humans need both science and religion to live successfully in the global knowledge civilization, the First Flower of the Universe.