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A group of charter schools in Phoenix is facing criticism for using teaching tools that have links to Scientology. These schools promote a study method called Applied Scholastics based on the work of L. Ron Hubbard. Hubbard is best known for founding the Church of Scientology.

From member station KJZZ, Peter O'Dowd reports.

PETER O'DOWD, BYLINE: Shortly after she was hired, teacher Katie Donahoe says she went to a memorable training session at the Applied Scholastics headquarters near St. Louis.

KATIE DONAHOE: They didn't start off talking about instruction. They started off talking about L. Ron Hubbard.

O'DOWD: It was 2010, and Donahoe was there at the urging of her new superintendent. Later that fall, she would start teaching English at Robert L. Duffy High School in Phoenix. But first, she was asked to get familiar with Hubbard's methods.

DONAHOE: The next stop was to watch a video talking about how great Applied Scholastics was. Well guess who was on the video. It was Isaac Hayes. It was Tom Cruise.

O'DOWD: And John Travolta.

DONAHOE: These are not education experts, these are Scientology spokespeople. It was very weird.

O'DOWD: Donahoe has since left the school. Applied Scholastics is a program based on something Hubbard called Study Technology. The idea is that some kids struggle because they can't overcome learning barriers. They misunderstand words or progress through the content too quickly. The Church of Scientology makes no secret of its support for the program. It even distributes highly produced videos like this one.

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UNIDENTIFIED ANNOUNCER: Since 1972, Scientologists have worked with and supported Applied Scholastics.

O'DOWD: Applied Scholastics would not comment on tape for this story. But in an email, a spokesperson says the materials are secular and their sole purpose is to help people learn.

However, in the past year, Applied Scholastics' presence in publicly funded schools has concerned parents and educators in places like Denver and Tampa. So here's the issue: does Applied Scholastics violate the Constitution when it shows up here?

(SOUNDBITE OF BABIES CRYING)

O'DOWD: Robert L. Duffy High School is home to mostly minority, low-income students who've struggled academically. The babies in this nursery belong to teenage parents taking classes down the hall. Robert Duffy, the man who runs the six-school charter district of about a thousand students, says Hubbard's work is effective here.

ROBERT DUFFY: You know, it's a tool. It's nothing that goes beyond this. Believe me.

O'DOWD: For example, if a student struggles with ratios, a teacher might ask the student to make a clay model to better visualize the concept. Duffy also makes available a booklet written by Hubbard that's described as a secular guide to moral living.

DUFFY: It's very basic stuff. I mean, it's nothing that has to do with the church or religion. Believe me, I'm not a Scientologist. I, you know, I hear things about them, and I don't support that at all.

CHARLES HAYNES: The materials, as I read them, are certainly not explicitly proselytizing.

O'DOWD: Charles Haynes is a First Amendment expert and director of the Religious Freedom Education Project.

HAYNES: The harder question is whether they implicitly promote the Church of Scientology.

O'DOWD: Haynes has reviewed Applied Scholastics on behalf of California public schools. He says there is no doubt these so-called secular materials share language with official Scientology teachings. A red flag, for sure.

HAYNES: And at some point you get enough of these red flags and it becomes a constitutional question that will be challenged.

O'DOWD: But Haynes says just because Hubbard wrote it doesn't make it inappropriate for public schools. Tell that to parent LeAnn Thomas.

LEANN THOMAS: They were literally trying to slide it in there without anybody supposedly knowing. No. That's not right.

O'DOWD: Her son graduated from Robert L. Duffy High School in 2011. Brandon Thomas was class president. And at times he really liked the school. But had his mom known the teachers were using L. Ron Hubbard's materials...

THOMAS: I definitely would pull him.

O'DOWD: Because, LeAnn Thomas says, not telling parents about something so potentially controversial just feels underhanded.

For NPR News, I'm Peter O'Dowd, in Phoenix.

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