Newton's conception of the physical world provided a stable model of the natural world that would reinforce stability and harmony in the civic world. Newton saw a monotheistic God as the masterful creator whose existence could not be denied in the face of the grandeur of all creation. "In the absence of any other proof, the thumb alone would convince me of God's existence."
Newton embarked on an investigative study of the early history of the Church, during the 1680s succeeding into inquiries of the origins of religion instead, at about the same time as having developed a scientific view on motion and matter. Of Philosophiæ Naturalis Principia Mathematica he stated: When I wrote my treatise about our Systeme I had an eye upon such Principles as might work with considering men for the beliefe of a Deity and nothing can rejoyce me more then to find it usefull for that purpose. Newton's religious views developed as a result of participation in an investigative discourse with Nature (the nature of the world) and developed from the apparent dichotomy of biblical reality from the increasing revealing of the structure of reality from investigation, and the subsequent challenges these truths of nature posed toward established religion for Newton, especially in light of Christian scriptural belief.
According to most scholars, Newton was Arian, not holding to Trinitarianism. A manuscript he sent to John Locke in which he disputed the existence of the Trinity was never published. S. D. Snobelen has argued that manuscripts produced late in Newton's life demonstrated Newton rejected the view of the Trinity.
Newton saw God as the masterful creator whose existence could not be denied in the face of the grandeur of all creation. Nevertheless he rejected Leibniz' thesis that God would necessarily make a perfect world which requires no intervention from the creator. In Query 31 of the Opticks, Newton simultaneously made an argument from design and for the necessity of intervention: "For while comets move in very eccentric orbs in all manner of positions, blind fate could never make all the planets move one and the same way in orbs concentric, some inconsiderable irregularities excepted which may have arisen from the mutual actions of comets and planets on one another, and which will be apt to increase, till this system wants a reformation."
In addition to stepping in to re-form the solar system, Newton invoked God's active intervention to prevent the stars falling in on each other, and perhaps in preventing the amount of motion in the universe from decaying due to viscosity and friction.
In private correspondence Newton sometimes hinted that the force of Gravity was due to an immaterial influence: Tis inconceivable that inanimate brute matter should (without the mediation of something else which is not material) operate upon & affect other matter without mutual contact. "This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent Being. [...] This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called "Lord God" παντοκρατωρ [pantokratōr], or "Universal Ruler". [...] The Supreme God is a Being eternal, infinite, [and] absolutely perfect."
"Opposition to godliness is atheism in profession and idolatry in practice. Atheism is so senseless and odious to mankind that it never had many professors."
In a manuscript he wrote in 1704 in which he describes his attempts to extract scientific information from the Bible, he estimated that the world could end on 2060.
In predicting this he said, "This I mention not to assert when the time of the end shall be, but to put a stop to the rash conjectures of fanciful men who are frequently predicting the time of the end, and by doing so bring the sacred prophesies into discredit as often as their predictions fail."
Newton's conception of the physical world provided a stable model of the natural world that would reinforce stability and harmony in the civic world Though he would never write a cohesive body of work on Prophecy, Newton's beliefs would lead him to write several treatises on the subject, including an unpublished guide for prophetic interpretation entitled Rules for interpreting the words & language in Scripture. In this manuscript he details the necessary requirements for what he considered to be the proper interpretation of the Bible.
In his posthumously-published Observations upon the Prophecies of Daniel, and the Apocalypse of St. John, Newton expressed his belief that Bible prophecy would not be understood "until the time of the end", and that even then "none of the wicked shall understand". Referring to that as a future time ("the last age, the age of opening these things, be now approaching"), Newton also anticipated "the general preaching of the Gospel be approaching" and "the Gospel must first be preached in all nations before the great tribulation, and end of the world"
To understand the reasoning behind the 2060 prediction an understanding of Newton's theological beliefs should be taken into account, particularly his nontrinitarian beliefs and those negative views he held about the Papacy. Both of these lay essential to his calculations, which are themselves based upon specific chronological dates which he believed had already transpired and had been prophesied in Revelation and Daniel.
Despite the dramatic nature of a prediction of the end of the world, Newton may not have been referring to the 2060 date as a destructive act resulting in the annihilation of the earth and its inhabitants, but rather one in which he believed the world was to be replaced with a new one based upon a transition to an era of divinely inspired peace.
In Christian theology, this concept is often referred to as The Second Coming of Jesus Christ and the establishment of Paradise by The Kingdom of God on Earth.
Though he lived before Darwin, Newton was not unacquainted with the atheistic evolutionary theory on origins. He was convinced against it and wrote: Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being, necessarily existing It is the perfection of God's works that they are all done with the greatest simplicity. He is the God of order and not of confusion.
Newton, commenting on the complexity of the human eye, also said: “Did blind chance know that there was light and what was its refraction and fit the eyes of all creatures after the most curious manner to make use of it? These and such like considerations always have and ever will prevail with mankind to believe that there is a Being who made all things and has all things in His power and who is therefore to be feared.”