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Jefferson's letter to Benjamin Rush shows that Jefferson was a non-preferentialist.

In his 1996 book Original Intent, Barton argues that Jefferson believed that the First Amendment prohibited only preferential establishments of religion. Part of the proof he adduces for this claim is a letter Jefferson wrote to Dr. Benjamin Rush on Sept. 23, 1800. Here is the relevant passage from Barton's book:

There is little to commend this argument. In particular, we note that Barton's conclusion is illogical; one cannot conclude from Jefferson's opposition to preferential establishment that he believed the effect of the First Amendment was limited to preferential establishment. This would be the same as arguing that, because Jefferson believed that the free speech clause prohibited the Sedition act of 1798, the free speech clause was limited to sedition! In fact, Jefferson indicated on numerous occasions that he believed the First Amendment was a total prohibition on the power of government to aid or hinder religion:

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