In his long-awaited history of the 9-11 Commission due out February 5, New York Times reporter Philip Shenon calls into question the independence of the executive director who ran the investigation, according to an article published on the Internet this week by Max Holland. Shenon, who covered the Commission's proceedings for the Times, reportedly argues that Executive Director Philip Zelikow kept in "surreptitious" touch with Karl Rove during the investigation. In the book, The Commission: The Uncensored History of the 9/11 Investigation, Shenon also reportedly claims that when the Bush administration was being organized Zelikow played a key role in the transition that led to the demotion of Richard Clarke, the counter-terrorism "czar" who tried to warn the administration that Osama bin Laden was planning a deadly attack on the United States.

Zelikow, a professor of history at the University of Virginia, served as counselor to Secretary of State Condoleezza Rice after leaving the Commission. They were known to be close friends and had previously coauthored a book. But Shenon, according to Holland, states that the Commissioners were not aware that Zelikow had served on the transition team that led to the reorganization of the National Security Council when Rice was named NSC advisor.

Zelikow has had a difficult relationship with both Shenon and Holland. He and Shenon crossed swords during the 9-11 investigation and has had a long-simmering fight with Holland stemming from the time both served at the the University of Virginia's Miller Center of Public Affairs. The Zelikow/Holland dispute played out on the pages of HNN in 2005 when Holland criticized the Miller Center's transcription of the Kennedy tapes. (Zelikow served as director of the Miller Center; Holland was a research fellow with the Presidential Recordings Program.)

Zelikow declined to comment to HNN on Shenon's book at this time. In an interview with ABC News he denied ever talking with Rove about the work of the Commission and insisted he never asked his secretary to stop logging his calls, as Shenon claims.

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