Great article, according to this, Professor Jones' article was well received by his peers and he is submitting it for a second review. BYU does admit however, that they "distanced themselves" from Professor Jones' research.

http://www.newsnet.byu.edu/story.cfm/57724

Reports that BYU administration put a gag order on Physics Professor Steven E. Jones are exaggerated, Jones said in a phone interview Friday.

Jones seemed surprised to hear that he’d been censored. He too was unaware of an e-mail that was circulating claiming that “BYU Brass Discredit Physics Professor for Saying WTC Brought Down by Controlled Demolition.” The e-mail quoted a “non-traditional” news Web site.

Jones said the only conversation he’s been involved in, in regards to the articles, was one he’d had with the dean of the College of Physical and Mathematical Sciences. Earl Woolley. Jones said the dean gave him tips on how to cut back on the interviews, but was never told not to talk to the media.

“The dean explained to me how he handled requests for media interviews; how he managed to give so few,” said Jones, a full-tenured professor whose controversial research into the WTC collapse has sparked national media attention. “I’ve made the personal decision to stick with peer-reviewed papers and scholarly seminars as a means of expressing my views, as much as possible. No one at the university has told me not to talk about this subject.”

When asked about the college’s stance on Jones, Woolley said, “I respect the review process for manuscripts, and since that has not been finalized as far as I know, than it would be inappropriate for me to make a comment.”
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Nearly three weeks ago, Jones posted a scientific paper online calling for an investigation into his “explosive demolition hypothesis,” which posits that pre-planted explosives, not planes, may have brought down the two Twin Towers and another, 47-story building known as WTC 7.
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Not long after this spate of interviews, BYU’s College of Physical and Mathematical Sciences posted a statement on its Web site stressing Jones’ right to publish what he wished while distancing itself from Jones’ current research.

That statement has since been removed, but a similar one is still online at the College of Engineering and Technology’s Web site.
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Reached for comment, structural engineering professors Steven Benzley and Rick Balling both said they supported the statement as written.
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In a Nov. 11 interview, Physics Professor Harold Stokes, one of several faculty members who attended the seminar, said the explosive demolition hypothesis “certainly raises some interesting questions” and that Jones’ claims “certainly appear to be valid.”
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“My paper was peer-reviewed and accepted for publication before being made available on the Web with the editor’s approval,” Jones said. “The reviewers included a physicist and an engineer, I now understand. The review has not been shown to have been inappropriate and I believe it was appropriate.”

Still, Jones said he willingly submitted his paper to another publication, where he is confident it will pass peer review a second time.