Tom Donilon and Wendy Sherman, who had presided over Obama's State Department transition, were both proteges of the Clinton administration's Secretary of State, Warren Christopher, who was an ardent proponent of demonizing Iran. It should be of no surprise that Donilon said in 2011 that Iran had "a record of deceit and deception," and that Sherman declared in Congressional testimony in 2013 that Iran couldn't be trusted because "We know that deception is part of the DNA."
Secretary Kerry and other Obama administration officials may have moderated their views of the Iran's nuclear program over the course of negotiations, but the external and domestic pressures for an even tougher line toward Iran have clearly outweighed any such learning process on the issue. If it isn't changed dramatically from Kerry's testimony, the administration's choice of political strategy will certainly contribute to a domestic political atmosphere in which even the most limited steps toward greater cooperation with Iran are all but impossible for years to come.
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