The imagery of a “wall of separation” was actually in use prior to Thomas Jefferson’s famous use of the phrase, and so it is wise to find out how it had been used in the context of religious freedom in America. This is particularly important in light of the fact that Jefferson used it while corresponding to Baptists, who had felt the brunt of government persecution in America. The phrase had a theological genesis as opposed to the modern supposed deistic, constitutional, or secular genesis.
Roger Williams, a clergyman, staunch advocate of religious freedom, and “founder of Rhode Island” used the phrase before Jefferson. For that reason, before looking at Jefferson’s use of the phrase, one needs to be familiar with how it was used by Williams. In order to understand the metaphor, one has to understand the man and the times. Williams was a Puritan who eventually separated from the Church of England, then became a Baptist in 1639 for a short time, and later became a seeker.
Unlike his Puritan brothers in Massachusetts, Williams adamantly rejected the idea that the civil authorities had any jurisdiction over the church or spiritual matters. He “declared that the state should not undertake to punish such purely religious offenses as idolatry, blasphemy, heresy, or Sabbath-breaking. No attempt should be made to maintain religious conformity by law; nor should civil penalties be imposed on sinful persons. The entire religious realm should be removed from the sphere of competence of the state.” These views kept him in constant conflict with the Puritan leaders, and Williams was finally banished in 1635 from the jurisdiction of the Bay colony.
The theological basis for a wall of separation grew out of Williams understanding of the church being based on the New Testament model instead of the Old Testament with theocratic Israel as the model. Stow Persons comments, “Drawing upon the analogy of Eden, he spoke of the church or community of the faithful as a garden. Beyond its bounds lay the wilderness of the sinful world from which the garden was preserved by a wall of separation. Should the wall be breached, weeds from the wilderness would invade the garden and choke off its flowers“ (italics added). Notice that a breach in the wall allowed the wilderness government into the garden church, and not the reverse. This is the same idea expressed in the First Amendment by the words, “Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.”
Williams basis for this grew out of his belief in the corruption of man. He did not believe in government coercion of the unregenerate in order to cause them to believe in the teachings of Christ, the declaration of an official state church, or taxation of citizens to pay ministers, as well as the use of civil power to assure religious conformity or preserve the church from doctrinal error. Williams said, “So far as the natural man was corrupt and sinful, the power of the magistrate must be the power of Satan. How could the protection of the church safely be entrusted to such a power?” Therefore, the wall of separation was a separation of institutions so that the government or world, wilderness, would not corrupt the church, garden. Persons sums up Williams influence. “In later times, when it became the fashion to extol Williams for his principles of liberty of conscience and the separation of church and state, his fame was celebrated by liberals who would break the remaining shackles of official religious power over the state. But it was precisely the opposite situation that had concerned Williams. It was the release of religion from the incubus of state control for which he contended. Why? Because the state was the instrument of natural men. It was the wilderness, evil, and the domain of the devil. It tended, therefore, in the nature of things to be corrupt. It was the corruption of the church by the world that stood out in Williams mind as the great fact of modern history” (italics added). Therefore, in Williams original figurative expression, the wall was not to protect the wilderness government and world from the garden church but the very opposite. A cursory reading of his book on the subject evidences this.
In Williams book, The Bloudy [Bloody] Tenent of Persecution for Cause of Conscience, he gives 12 theses that are developed in the book as he engages the Puritan John Cotton concerning the freedom of conscience. To summarize them, numbers 1-4 are against people being persecuted by the government because of their religious faith, or as he puts it, “persecution for conscience sake is not required nor accepted by Jesus Christ the Prince of Peace.” Numbers 5 and 8-11 specifically address the role of states, which is civil not spiritual, and in Williams words, over “bodies and goods, not souls and spirits.” Numbers 8-10 use the phrase “enforced uniformity of religion” to argue against the civil state forcing people to embrace a certain religion that “is the greatest occasion of. ravishing of conscience and destruction of millions of souls.” Number 11 argues that freedom of conscience to worship contrary to the state results in the good of the civil state through “uniformity of civil obedience”. Numbers 6 and 7 give the theological basis for his position, which is that the Old Testament state of Israel is not the pattern to be followed since the coming of Jesus Christ. The pattern is “permission of the most paganish, Jewish, Turkish, or anti-Christian consciences and worships be granted to all and they are only to be fought against with the sword of God’s Spirit, the Word of God.” Number 12 declares, “True civility and Christianity may both flourish in a state or kingdom, notwithstanding the permission of divers and contrary consciences, either of Jew or Gentile.”
In summary, with regard to truly just civil laws, Williams said, “concerning only the bodies and goods of such and such religious persons, I confess are merely civil.” Whereas, state laws concerning religion that required obedience in areas such as worship, belief, and church governance are “far from reason.” Sometimes he referred to the domain of the church as the first tablet, and the government as the second tablet referring to the first four and the last six, respectively, of the Ten Commandments.
The real issue today concerning the wall of separation is obscured when it is forgotten that Williams argued against the government passing laws that required obedience in areas covered by the first tablet. It was not merely the government doing something like allowing prayers at school games, but rather that they would require everyone to pray or suffer due penalty. The loss of historical context is seen clearly in the words that are used.
Today, when religious symbols or words are used in public forums, people claim a violation of church and state because someone is embarrassed, does not agree, is potentially influenced, feels peer pressure, or is uncomfortable, inconvenienced, asked or called upon. In contrast, Williams used words like persecution, forced, violated, constrained, bloody act of violence, rape, commandeer, violent, imprisonment, banishment, compel, molest, kill, and devour. Note the words in the title of his book, Bloudy [Bloody] and Persecution, and he wrote another book, The Bloudy Tenent Yet More Bloudy.
He and the Baptists fought so that everyone could worship according to the dictates of their own conscience without being prosecuted by the government for violation of the law. They were not fighting to remove every vestige of religion from government or public life, regardless how inconvenient it is for citizens. They fought for freedom of conscience, not freedom of comfort. This fact is further demonstrated by Williams service as the President of Rhode Island for three years beginning in 1654, along with his public ridicule of the Quakers beliefs and practices, finding them unfit for certain public offices because of their religious beliefs like pacifism, which would, in his estimation, make them poor governors.
Despite William’s adamant disagreement with the Quakers teaching and his conviction that their beliefs made them unfit for certain public offices, consistent with his “wall of separation” he would not allow government to punish them for their beliefs. They were free to worship according to their conscience. “Williams himself linked religion to morals, and he expected magistrates in Rhode Island to enforce the second table of the Ten Commandments” because Williams believed that the second table of the Ten Commandments, Exodus 20:12-17, was appropriate for civil law, but the first table, Exodus 20:1-11, was not.  He clearly understood that the second table, the last six of the Ten Commandments, dealt with human relationships and interactions whereas the first four were personal. Even the first four could be expressed, valued, in public but not forced.
Williams referred to the second table as “the doctrine of the civil state” and the first table as “the spiritual doctrine of Christianity.” Therefore, the commandments dealing with men’s bodies, relationships, and things, e.g., adultery, lying, or stealing could become civil laws, but the first four commandments dealing with a person’s relationship and choice to worship God or not worship God or worship a different God than everyone else could not become civil law that citizens were required to obey or be punished.
This distinction between the first and second tablet was a belief that was shared by others like John Leland, a Baptist preacher, who “emerged a leader among the Commonwealth’s Baptists. He was instrumental in allying the Baptists with Jefferson and Madison in the bitter Virginia struggle to disestablish the Anglican Church and to secure freedom for religious dissenters“ (italics added). According to L.H. Butterfield, Leland “was as courageous and resourceful a champion of the rights of conscience as America has produced” (italics added). Leland, who allied with the Baptists, supported Jefferson because of his commitment to “the rights of conscience“(italics added).
The distinction between the two tables, or rights of conscience, did not refer to separating religious beliefs from politics, but rather allowed one to be able to believe according to one’s own conscience without governmental interference. Leland celebrated Jefferson’s election from his pulpit. He preached in a congressional church service January 1, 1802, and Jefferson attended. By conscience, Leland and others referred to the first tablet of the Ten Commandments as Williams did. Conscience refers to opinions referred to by Jefferson and the Danbury Baptists in their correspondence. Jefferson said, “The legitimate powers of government reach actions only and not opinions.” The Baptists said, “The legitimate power of civil government extends no further than to punish the man who works ill to his neighbor.” These refer to the same things as Williams did when he referred to the second tablet.
Jefferson said, “The legitimate powers of government extend to such acts only as are injurious to others. that the opinions of men are not the object of civil government nor under its jurisdiction.” Tablet one dealt with worship and opinions, and the second with relations toward other men, which was appropriate for civil law as distinguished by Williams. Leland said, “Government has no more to do with the religious opinions of men, than it has with the principles of mathematics. Let every man speak freely without fear, maintain the principles that he believes, worship according to this own faith, either one God, three Gods, no God or twenty Gods; and let government protect him in so doing, i.e., see that he meets with no personal abuse, or loss of property, for his religious opinions.” 
Other evidences that Williams did not intend to create a secular public square are: “In pursuit of his political aims, Williams spent much of his time lobbying members of Parliament.” Roger Williams religious views formed his political views and actions, like establishing Rhode Island “with the famous guarantee of religious liberty.” Williams named the place where he purchased the land from the Indians, Providence, “in a sense of God’s merciful Providence to me in my distress.” Of oaths he said, “An oath may be spiritual though taken about earthly business.” “Civil government is an ordinance of God, to conserve the civil peace of people so far as concerns their bodies and goods. and foundation of civil power lies in the people.” One cannot use the argument of separation of church and state to exclude or limit religious involvement in public life because the argument is based on a religious argument from Roger Williams, as demonstrated by Williams responses to John Cotton in The Bloudy Tenent.
Stow Persons, American Minds: A History of Ideas (New York: Holt, Rinehart and Winston, Inc., 1958), 53.
 Persons, American Minds, 53.
 Persons, American Minds, 52.
 Persons, American Minds, 52.
 Persons, American Minds, 54.
 Persons, American Minds, 57.
 Persons, American Minds, 59.
 Roger Williams, Richard Groves, ed., The Bloudy [Bloody] Tenent of Persecution for Cause of Conscience (Macon, Georgia: Mercer University Press, 2001), 3-4, originally printed in 1644 in London.
 Williams, Bloudy Tenent, 156.
 Williams, Bloudy Tenent, 156-57.
 Williams, Bloudy Tenent, the use of the words mentioned can be seen in context on the following pages. persecution, 11; forced, 146; violated, 6; constrained, 6; bloody act of violence, 7; rape, 7; commander, 14; violent, 14; imprisonment, 15; banishment, 15; compel, 15; molest, 14; kill, 17; devour, 17.
 Isaac Kramnick and R. Laurence Moore, The Godless Constitution: The Case Against Religious Correctness (New York: W.W. Norton & Company, 1996), 53.
 Kramnick and Moore, Godless Constitution, 58.
 Kramnick and Moore, Godless Constitution, 60.
 Williams, Bloudy Tenent, 146.
 Daniel L. Dreisbach, Thomas Jefferson and the Wall of Separation between Church and State (New York: New York University Press, 2002), 13.
 L.H. Butterfield, “Elder John Leland, Jeffersonian Itinerant,” Proceedings of the American Antiquarian Society 62 (1952): 157, as quoted by Dreisbach, Thomas Jefferson, 13.
 Herbert M. Morais, “Life and Words of Elder John Leland” (M.A. thesis, Columbia University, 1928), 44-50 as quoted by Dreisbach, Thomas Jefferson, 13.
 Dreisbach, Thomas Jefferson, 10.
 See the full text of these letters in Appendices B and C in my book, The Death of Man as Man: The Rise and Decline of Liberty.
 From Jefferson’s writings, as quoted by Dreisbach, Thomas Jefferson, 182; see also the complete bill for establishing religious freedom in Dreisbach, Thomas Jefferson, 133-135.
 John Leland, The Rights of Conscience Inalienable (New-London, Conn.: 1791) in The Writings of the Late Elder John Leland, 184 as quoted by Dreisbach, Thomas Jefferson, 167, note 47.
 Richard Groves, preface of Williams Bloudy Tenent, vii.
 Robert G. Torbet, A History of the Baptists, third ed. (Valley Forge: Judson Press, 1963), 202.
 Williams, Bloudy Tenent, xxiii.
 Williams, Bloudy Tenent, 157.
 Williams, Bloudy Tenent, 154.