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The September 11, 2006 issue of Newsweek carried a news item in the “Beliefwatch” section on the candidacy of Katherine Harris and the topic of the “separation of church and state.” The article begins by stating “that Katherine Harris recently told a religious journal that separation of church and state was ‘a lie,’ . . . that the idea of separation of church and state was concocted by 20th-century courts, not the Founding Fathers. . . . Conservative activists point out that the words ‘separation of church and state’ appear nowhere in the Constitution—and they’re right. The phrase came from a letter Thomas Jefferson wrote to a group of Connecticut Baptists in which he praised the First Amendment's ‘wall of separation between Church & State.’” Can you believe it? The truth is finally out! What comes next in the article tells us why the people are finally getting informed on the subject:
A cottage industry has grown in recent years to push a more radical argument that the Founders intended virtually no separation. Books making the case include “The Myth of Separation Between Church and State,” by Dee Wampler, “What If America Were a Christian Nation Again?” by D. James Kennedy, and “America’s Christian Heritage,” by Gary Demar [sic].
That’s right. Yours truly is mentioned in Newsweek, although misspelling my name a bit. While Newsweek gets some things right in the article, it still misunderstands the nature of Church-State separation. It is a legitimate concept that did not start with Thomas Jefferson’s 1802 letter to the Danbury, Connecticut, Baptists. The phrase has a long history going back to the Reformation. The idea is a biblical one when properly understood.
In the simplest terms, separating Church and State means that the institution and the ecclesiastical jurisdiction of the Church is separate from the institution and the civil jurisdiction of the State. The Church as an institution cannot mingle in the institutional affairs of civil government. Neither can its officers. In the same way, civil government cannot disturb the ministry and operation of the Church by tampering with the Church's doctrines or courts.
Nowhere, however, does the First Amendment prohibit individuals from applying religious precepts to the legislative and judicial agenda of the State. For example, biblical laws against theft, murder, polygamy, abortion, homosexuality, rape, and perjury have been accepted by civil governments as having a civil application with no transgression of the First Amendment. At the same time, the State does not have the jurisdictional right to compel people to believe the gospel, confess the Christian religion, pay tithes, or attend church. Neither can the civil magistrate declare any single Christian denomination to be the nationally established Church, the real purpose of the first Amendment.
Many people incorrectly maintain that the First Amendment was designed to remove any and all religious precepts and considerations from civil affairs. For example, the Congressional Quarterly's Guide to the U.S. Supreme Court provides the following definition of the establishment clause of the First Amendment.
The two men most responsible for its inclusion in the Bill of Rights constructed the clause absolutely. Thomas Jefferson and James Madison thought that the prohibition of establishment meant that a presidential proclamation of Thanksgiving Day was just as improper as a tax exemption for churches.
The historical facts dispute this seemingly authoritative interpretation of the First Amendment. James Madison issued at least four Thanksgiving Day proclamations. If the Congressional Quarterly's Guide to the U.S. Supreme Court has accurately captured the meaning of the establishment clause of the First Amendment, then Madison “violated both his oath of office and the very instruments of government that he helped write and labored to have ratified.” In the same way, if Jefferson “construed the establishment clause absolutely, he also violated his oath of office, his principles, and the Constitution when, in 1802, he signed into federal law tax exemption for the churches in Alexandria County Virginia.” Of course, neither Madison nor Jefferson violated the First Amendment by these official State acts. It is the modern day secularist interpreter of Madison and Jefferson who has misread, misinterpreted, and misapplied the First Amendment. This misreading of the First Amendment has come about through “the change in the intellectual climate of the universities, and consequently in the media and the courts. It is these opinion-making centers that have influenced common thinking about law, morality, and religion. These centers have thrown the credibility of religious witness into doubt.”
Most of the misunderstanding surrounding Church-State issues arises from relying on secondary sources and misinformation. Most of this accepted misinformation is developed through the academic procedure which constitutional scholar Robert L. Cord calls “history by omission,” that is, the failure to deal with historical facts that run counter to a strict separationist interpretation of the First Amendment.
 Congressional Quarterly's Guide to the United States Supreme Court (Washington, DC: Congressional Quarterly, Inc., 1979, 461. Quoted in Robert L. Cord, “Church-State Separation and the Public Schools: A Re-evaluation,” Educational Leadership (May 1987), 28.
 The four proclamations in their entirely are published in Robert L. Cord, Separation of Church and State: Historical Fact and Current Fiction (Grand Rapids, MI: Baker Book House,  1988), 257–260.
 Cord, “Church-State Separation and the Public Schools,” 26.
 2 Statutes at Large 194, Seventh Congress, Sess. 1, Chap. 52. Quoted in Cord, “Church-State Separation and the Public Schools,” 28.
 Jude P. Dougherty, “"Separating Church and State,” The World & I (December 1987), 683.
 Cord, “Church-State Separation and the Public Schools,” Educational Leadership, 28.