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Did Supreme Court justice Joseph Story ever say that, at the time of the adoption of the Constitution, there was near universal consensus that "christianity ought to receive encouragement from the state?"

Yes, but this is a classic example of quoting a source out of context. In fact, Story's statement has nothing to do with the First Amendment or the powers of the federal government. On the contrary, a closer look at his writings suggests that he believed that the federal government had no ability whatsoever to aid religion.

Joseph Story was an Associate Justice of the Supreme Court from 1811-1845, and the most important legal commentator of his day. In 1851, while serving as the Dane Professor of Law at Harvard University, he published his Commentaries on the Constitution of the United States, which included a short section on religious liberty. In the opening pages of this section Story argued for the importance of religious faith for good government, and then proceeded to claim that:

Accomodationists sometimes use this statement as proof that the Constitution could not have been intended to prohibit federal support for religion. But this is to misread Story's claim. All Story is claiming here is that, at the time of the adoption of the Constitution, there was widespread sentiment for aiding Christianity. What Story does not claim here is that the Constitution empowered the federal government to give such aid. Indeed, only a few pages latter in his Commentaries he explicitly denies that the federal government had such power:

Story, in other words, believed, along with Madison, Jefferson, and a host of other framers, that the Constitution gave no power to the federal government over religion. With respect to the federal government, Story was a separationist. Accomodationists quote him out of context when they reproduce his general statements, but not his specific claim that the federal government has no authority over religion.

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