"The only question is where in the Constitution is this non-existent ‘separation of church and state’ to be found?”
The standard argument made by Christian Nationalists is that the specific words “separation of church and state” are not located in the Constitution, but rather in a letter written by Thomas Jefferson to the Danbury Baptist Church. They further contend that therefore there is no separation found in the Constitution, and that this “wall of separation” idea, is a myth fabricated by revisionist historians, and radical left-wing Supreme Court justices such as Hugo Black who first invoked Jefferson’s phrase in the 1947 Everson v. Board of Education of Ewing Township decision. This Christian Nationalist’s argument is constructed upon the most superficial and rudimentary word games imaginable. Just because the explicit words "separation of church and state" do not appear in the Constitution does not equate to there being no law separating church and state. We will not find the words “right to a fair trial” or the “right to privacy” in the Constitution either, but these terms do serve to describe the spirit of specific points of Constitutional law.
Far from being “non-existent,” the wall of separation was an essential element of the Constitution with clear meaning and intent. The development of the necessity for a clear separation between the church and state can be traced; it is not some unknowable mystery or some article that must be taken upon faith. There is no doubt that prior to the ratification of our U.S. Constitution, there was no separation between church and state, and religion permeated every aspect of public and private life. There is also no doubt that America has a deep religious tradition, and that this tradition has been overwhelmingly Christian in nature. But let us not fall victim to a common categorical error; confusing historical tradition with Constitutional law.
Indeed, it was this exact historic and traditional adulterous relationship between church and state, as well as the destructive nature of religion itself, which led the framers of the Constitution, after much debate and political struggle, to place for the first time in history, a clear wall of separation between “ecclesiastical and civil powers.”
How can we know this? First, we have the Constitution itself. We also have resources to help further understand the meaning and intention behind the Constitution concerning religion. The Federalist Papers are one essential source for understanding the Constitution. Personal letters, essays, and books written by the men themselves are another fantastic resource for gaining a glimpse into the minds of the formulators of our system of governance. The notes on the Federal Convention by James Madison, as well as David Robertson’s notes of the Virginia Ratification Convention, serve as essential guides in navigating the metaphysical waters of the Constitution. The Commentaries on the Constitution by Justice Joseph Story, which served as the earliest cornerstone for American jurisprudence, will also be of tremendous value in our quest for meaning and intention.
Where is the separation of church and state mentioned in the Constitution? In two places that serve as a sort of front and back door of the Constitution. The first is found in Article VI, where a ban was placed on religious tests being a requirement to hold public office. The second door is located in the establishment clause of the First Amendment. We’ll take each in order, starting with the evolution of the religious oath controversy of Article VI:
“The Senators and Representatives before mentioned, and the Members of the several State Legislatures, and all executive and judicial Officers, both of the United States and of the several States, shall be bound by Oath or Affirmation, to support this Constitution; but no religious Test shall ever be required as a qualification to any Office or public Trust under the United States.”
According to Christian Nationalists like David Barton, the intention behind Article VI was to insure that no person would be required to affirm an oath to any particular sect of Christianity, but that the founders fully intended public office holders to affirm their belief in the general tenets of Christianity. In support of this theory, Barton uses pre-Constitutional documents; quotes wretched from context, and even quotes that are unverified or outright fraudulent - combined with a skillful use of historical omission - to weave together a narrative so contorted from actual history, as to be truly Orwellian.
Let’s take a little walk down memory lane and follow the development of what came to be Article VI of the Constitution, and see if we can find the meaning and purpose of this article. We could begin our walk starting with the long struggle that Jefferson and Madison had in passing the Virginia Statute of Religious Tolerance Act, that drove the church out of Virginia’s government. We could begin with a detailed recantation of the old-world Puritan-style theocracy, with its often brutal penal codes, stifling and oppressive social structures, and magical epistemology. But rather than going through all of that, as fascinating and telling as it would be, we’ll pick up the story starting at the Federal Convention of 1787.
On Tuesday May 29, 1787, Edmund Randolph opened business by putting before the delegates what is known as the Virginia Plan. This set the agenda for the remainder of the convention, and was a radical move, for it did not simply set out to improve the Articles of Confederation, but put forth the outlines for a totally new system of government. The main figure behind the Virginia Plan was James Madison, who included the following concerning oaths of office:
“Res. That the legislative Executive & Judiciary powers within the several states ought to be bound by oath to support the articles of union.” 
Nothing specific about religion at this point and as we shall see, it’s not Madison who puts to the floor of the Convention that religious tests should be excluded from all oaths of office. That’s not to say that religion, and more broadly the “nature of faction” in general, was not front and center in Madison’s mind. To get a glimpse into the mind of Madison leading up to the convention, we shall visit his Vices of Political Systems of the United States, written just one month prior to the Federal Convention, and would serve as the foundation for much of his later writings in the Federalists; particularly his Federalist X, where Madison deals with both the problem and the cure for the nature of faction and political liberty.
Madison had been in correspondence with Thomas Jefferson, who was then serving as the United States Minister Plenipotentiary to France, requesting from Jefferson a rather large quantity of books covering the history and philosophy of democratic governance. Madison spent considerable time reviewing not only the experiments from antiquity, but the ten years of experiments in constitution making that had occurred since 1776 in the states themselves. It is in Madison’s 11th vice that we find both the foundation for Federalist #10 and Madison’s view on the nature of religious faction and political power. Madison writes:
“The conduct of every popular assembly acting on oath, the strongest of religious Ties, proves that individuals join without remorse in acts, against which their consciences would revolt if proposed to them under the sanction, separately in their closets.” Madison continues: “When Religion is kindled into enthusiasm, its force like that of other passions is increased by sympathy of a multitude.” Madison concludes: “But enthusiasm is only a temporary state of religion, and while it lasts will hardly be seen with pleasure at the helm of government.” And that religion even at its best and “coolest state, is not infallible,” and that “it [religion] may become a motive to oppression as well as a restraint from injustice.” 
Madison reiterates the same theme during the convention itself, when he offers insight into the nature and the cure for faction, during the June 6th discussion on representative elections and the balance between the national and state government. Mr. Pinkney opened with a motion to move on the issue that “the first branch of the National Legislature be elected by the State Legislature” rather than directly by the people, maintaining that “the people were less fit Judges in such cases.” Mr. Sherman, arguing for a weak federal government stated that the “objects of the Union” were national defense from foreign nations, the powers to make treaties, the regulation of foreign commerce, and taxation. Outside of these, and “perhaps a few lesser objects,” all other “matters civil & criminal “according to Sherman, “would be much better in the hands of the States.”
This prompted Madison to point to an even greater object of a national government. Madison claimed that Mr. Sherman was in error “in thinking the objects mentioned to be all the principle ones that require a National Government.” Madison stated that the “security of private rights, and the steady dispensation of Justice” and the “interferences with these were evils” that had brought the convention about perhaps more than the objects listed by Mr. Sherman. The problem was the nature of faction, in all its forms, had to be dealt with. In reviewing the historical landscape Madison maintained that “in all cases where a majority are united by a common interest or passions, the rights of the minority are in danger,” and that “Religion itself may become a motive to persecution & oppression,” as is “verified by the Histories of every Country ancient & modern.” 
The issue of oaths of office did not come up again until after Monday August 6th when the Gerry Committee returned with the first draft of the Constitution. This draft contained some 23 articles that included the following two oaths of office in Article X, and in Article XX:
“Article X on the Executive oath: ‘Before he shall enter on the duties of his department, he shall take the following oath or affirmation, ‘I____ solemnly swear, (or affirm) that I will faithfully execute the office of President of the United States of America.”
Then in Article XX it states:
“The members of Legislatures, and the Executive and Judicial officers of the United States, and the several States, shall be bound by oath to support this Constitution.”
Both of these oaths are distinctly different from many of the State constitutions of the time, in that there is no religious test affixed. In fact, to help clarify the intention, on Monday August 20, Mr. Pinkney moved to have added to the Article that “no religious tests or qualifications shall ever be annexed to any oath of office under the authority of the U.S.”  Then again on august 30, Mr. Pinkney moved to add the forbearance of religious tests; when Mr. Sherman put forth opposition to Pinkney’s recommendation, stating that he “thought it unnecessary” seeing that the “prevailing liberality [was] sufficient security against such tests.”  Sherman’s was the only opposition to forbidding religious tests recorded in Madison’s notes. The Constitution was adopted and sent off to the states for ratification with the ban on religious tests included in Article VI.
The issue of religious tests was brought up and debated repeatedly throughout the ratification process. Luther Martin, who also attended the Federal Convention, campaigned in Maryland against the Constitution for, among other things, the lack of a religious test required for office.  At the Pennsylvania Convention religion was a hot topic as well, when Benjamin Rush put forth the proposition that they hire a clergymen to open the daily business with prayer, which was shot down by men such as John Smilie. When Rush argued that failing to open with prayer served as the cause of much of the division amongst the delegates, Smilie replied that this was an “absurd superstition.”
Towns such as Townshed, Massachusetts sent off instructions that “Atheists Deists Papists or abettors of any false religion” should be excluded from holding public office.  According to a letter written by Benjamin Lincoln to Washington, there were also delegates that expressed discontent over the lack of any reference to God in the Preamble of the Constitution. 
There were also several showdowns at the Virginia convention over the same issue of religious tests and public office. Unfortunately, David Robertson, who had been taking notes of the debates, was not present on June 23, the day some of the harshest criticisms of Article VI were offered. Zachariah Johnston argued for the restriction of religious tests, and also argued against the other amendments proposed by Patrick Henry. The other unfortunate happenstance was that Robertson, unlike Madison who at the Federal Convention had a front row seat, was stuck high in a balcony where it was hard to hear. Madison, who also argued at the state convention, had a soft voice, making it even more difficult for Robertson to record what was said.
However, we do have Madison’s written remarks of June 24th, where he replied to Patrick Henry and the other critics of the religious restriction in Article VI, by stating “There is not a shadow of right in the general government to intermeddle with religion,” and that “Its least interference with it would be a most flagrant usurpation.” Madison’s general “remedy” for the nature of faction was pluralism, and to secure religious freedom, the government must take an indifferent position, holding to religious pluralism. Mr. Madison then expressed his gratitude that “fortunately… a majority of the people [were] decidedly against any exclusive establishment.” Clearly Madison and others were fighting for the separation of church and state. And while Henry’s moving oratory could stir men’s passions, Madison made men think, and the Constitution was ratified with the back door of the Constitution closed to the corrosive influence religion can have upon the body politic and good government.
This was a radical change, a true revolution in itself that was well debated and finely voted into law that “no religious Test shall ever be required as a qualification to any Office or public Trust under the United States,” thus for the first time in human history drawing a wall separation between church and state. 
To acquire further clarification as to the meaning and purpose behind Article VI, let us visit the Commentaries on the Constitution of the United States by Joseph Story. Story was nominated as an Associate Justice of the Supreme Court of the United States in 1811 by then President, James Madison. Story served on the Supreme Court until his death in 1845. Story is famous for the court case that was made into the 1997 movie, The Amistad. More important than his movie debut, is his Commentaries on the Constitution that was the first comprehensive treatises on the U.S. Constitution, and served as the authoritative cornerstone of American jurisprudence throughout the 19th century.
According to Story, “this clause [forbidding religious tests] is not introduced merely for the purpose of satisfying the scruples of many respectable persons, who feel an invincible repugnance to any religious test or affirmation,” but rather this clause “had a higher object; to cut off for ever every pretence of any alliance between church and state in the national government.”
Why would our founders wish to cut religion off from government? As Story says, “the framers of the constitution were fully sensible of the dangers from this source, marked out in the history of other ages and countries; and not wholly unknown to our own.” According to Story our founders knew that “bigotry was unceasingly vigilant in its stratagems, to secure to itself an exclusive ascendency over the human mind,” and that religious intolerance “was ever ready to arm itself with terrors of the civil powers to exterminate those, who doubted its dogmas, or resisted its infallibility.” 
Story makes note that this desire to end church-state alliances was not solely influenced by religious wars and persecution on the European side of the pond, but because of the religious oppression and persecution that had taken place in the colonies themselves. Jefferson expressed his concern over religious bigotry when he wrote that “the Presbyterian clergy are the loudest; the most intolerant of all sects, the most tyrannical and ambitious; ready at the word of the lawgiver, if such a word could be now obtained, to put the torch to the pile.” 
In other words, as soon as religion is able to get hold of political power, people suffer. Madison also noted that such a coalition threatens liberty so thoroughly, that the “danger cannot be too carefully guarded against,” and that a “perfect separation between ecclesiastical and civil matters, is of importance.” 
Regardless of personal religious beliefs and traditional alliances, the founders thoroughly debated the issue of religion’s relationship with civil government, and decided to try something truly revolutionary by erecting, for the first time in the history of government, a wall of separation between church and state. Let us therefore continue “the great examples of Greece and Rome,” and “set before us the conduct” of our founding ancestors “who have defended for us the inherent rights of mankind” from “foreign and domestic tyrants and usurpers, against arbitrary kings, and cruel priests,” against both “the gates of earth and hell.” 
 Madison, James, Notes of Debates in the Federal Convention of 1787 p. 33
 Madison, James, James Madison Writings, Literary Classics of the United States, (1999), p. 78
 Madison, James, Notes of Debates in the Federal Convention of 1787 p.75, 76
 Madison, James, Notes of Debates in the Federal Convention of 1787 p. 486
 Madison, James, Notes of Debates in the Federal Convention of 1787 p. 561
 Maier, Pauline, Ratification, Simon & Schuster, (2010), p. 91
 Maier, Pauline, Ratification, Simon & Schuster, (2010), p. 107
 Maier, Pauline, Ratification, Simon & Schuster, (2010), p. 170
 James, James Madison Writings, Literary Classics of the United States, (1999), p. 381-382
 Maier, Pauline, Ratification, Simon & Schuster, (2010 p. 303-304
 Story, Joseph, Commentaries on the Constitution, Harvard College Library, (1926) p. 690
 Padover, Saul, Thomas Jefferson on Democracy, Mentor Book, (1939), p.119
 James, James Madison Writings, Literary Classics of the United States, (1999), 788
 Adams, John, Adams His Political Writings, The liberal Arts Press, (1954), p. 19
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