Using the writings of the early Church Fathers, the Greek and Latin manuscripts and the testimony of the first versions of the Bible, Newton attempted to demonstrate that the words "in heaven, the Father, the Word, and the Holy Ghost: and these three are one," in support of the Trinity doctrine, did not appear in the original inspired Greek Scriptures. He then traced the way in which the spurious reading crept into the Latin versions, first as a marginal note, and later into the text itself. He argued that it was first taken into a Greek text in 1515 by Cardinal Ximenes on the strength of a late Greek manuscript corrected from the Latin. Finally, Newton considered the sense and context of the verse, concluding, "Thus is the sense plain and natural, and the argument full and strong; but if you insert the testimony of 'the Three in Heaven' you interrupt and spoil it."
Newton argued that, by a small alteration in the Greek text, the word "God" was substituted to make the phrase read "God was manifest in the flesh." instead of "He was manifest in the flesh." He demonstrated that early Church writers in referring to the verse knew nothing of such an alteration.
Summing up both passages, Newton said: "If the ancient churches in debating and deciding the greatest mysteries of religion, knew nothing of these two texts, I understand not, why we should be so fond of them now the debates are over." In the two hundred years and more since that treatise was compiled by Isaac Newton, only a few minor corrections have been necessary to the evidence he adduced. Yet it was only in the nineteenth century that Bible translations appeared correcting these passages. Modern versions of the Bible usually omit 1 John 5:7, but some place it in a footnote, with a comment indicating that it is not found in the earliest manuscripts. Modern translations of 1 Timothy 3:16 usually omit "God".
Newton did not publish these findings during his lifetime, likely due to the political climate. Those who wrote against the doctrine of the Trinity were subject to persecution in England. As late as 1698 the Act for the Suppression of Blasphemy and Profaneness made it an offense to deny one of the persons of the Trinity to be God, punishable with loss of office, employment and profit on the first occasion, and imprisonment for a repetition. Newton's friend William Whiston (translator of the works of Josephus) lost his professorship at Cambridge for this reason in 1711. In 1693 a pamphlet attacking the Trinity was burned by order of the House of Lords, and the next year its printer and author were prosecuted. In 1697 Thomas Aikenhead, an eighteen-year-old student charged with denying the Trinity, was hanged at Edinburgh, Scotland.