National coverage of the Gov. Don Siegelman (D-AL) controversy has centered on Republican lawyer Dana Jill Simpson's affidavit, but today The New York Times raises questions about another aspect of the case: the independence of prosecutor Lois V. Franklin.

Franklin took over the case after US attorney Leura Canary recused herself because of her husband's ties to the Republican Party and Karl Rove. Franklin has claimed a startling degree of independence from the Department of Justice and Canary.

The New York Times points to some unresolved issues there:

Yet questions about the Siegelman case persist, including about whether Mr. Franklin played the decisive role he says he did, and not just among the former governor’s supporters.

For one thing, the prosecution of a high official like a governor is nearly always undertaken under the watchful eye of Justice Department officials in Washington, former government lawyers say.

One of Mr. Siegelman’s former lawyers, G. Douglas Jones, former United States attorney in Birmingham, says that at a crucial moment in 2004, when the Siegelman investigation seemed to be flagging, he was told by government prosecutors in Montgomery that the “folks in Washington said, ‘Take another look at everything.’ ”

Referring to a unit of the Justice Department, Mr. Jones said, “There is no question but that the Public Integrity Section was intimately involved.”