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He said the Becket Fund will appeal the case to the 9th Circuit, which sided with Mr. Newdow in 2003. The Supreme Court struck down that ruling in June 2004, but did not rule on the merits of the case. Instead, the high court said Mr. Newdow, the divorced, noncustodial father of a fourth-grader in the Elk Grove district, did not have legal standing as a plaintiff.

Lee Strang, an assistant law professor at Ave Maria School of Law in Ann Arbor, Mich., said the public should not be surprised that the issue has resurfaced.

“The Supreme Court has been all over the map on this issue,” he said. “Their establishment clause case law has been such a muddle because you have these shifting coalitions of justices who come together to arrive at sometimes unprincipled results.”

Judge Karlton was “pushing the limits” of his job description, Mr. Strang said, “but judges have been known to guide litigants in subtle and not-so-subtle ways.”

“I think the judge made the right call,” said Rob Boston of Americans United for Separation of Church and State. “The whole question of patriotism and the religious content of the pledge hasn’t been explored like it should be. A student should be able to express patriotism and love of country without making a religious affirmation at the same time.”