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For the second time during Donald Trump’s brief tenure as president, Secretary of State Rex Tillerson and the State Department won in the inter-administration battle over the fate of the nuclear deal with Iran, formally known as the Joint Comprehensive Plan of Action (JCPOA). That victory, however, may end up being short lived given the trajectory of the administration’s overall developing policy toward the regime in Tehran and the process by which the reoccurring 90-day certification of Iran took place in April and again on July 17.The whole ordeal cast a light on the shrinking esteem in which the president seems to hold Secretary Tillerson and the crew of Obama-era holdovers upon whose guidance he relies.Washington was briefly abuzz on the afternoon of July 17 when rumors began to circulate that President Trump was eager to declare that Iran was in breach of the conditions laid out in the 2015 Iran Nuclear Agreement Review Act (INARA).Those receptive antennas were further heightened given the previous signals sent. After all, the State Department already released talking points to reporters on the decision to recertify Iran. The Treasury Department also had a package of fresh sanctions on over a dozen Iranian individuals and entities ready to announce to appease the hawks who were eager to cut loose from the deal.But Trump didn’t want to recertify Iran, nor did he want to the last time around in April. That evening, a longtime Middle East analyst close to senior White House officials involved in the discussions described the scene to me: “Tillerson essentially told the president, ‘we just aren’t ready with our allies to decertify.’ The president retorted, ‘Isn’t it your job to get our allies ready?’ to which Tillerson said, ‘Sorry sir, we’re just not ready.’” According to this source, Secretary Tillerson pulled the same maneuver when it came to recertification in April by waiting until the last minute before finally admitting the State Department wasn’t ready. On both occasions he simply offered something to the effect of, “We’ll get ‘em next time.”That for the second time, Team Tillerson forced the president to recertify Iran because they prepared no other options appears to have left a mark on Trump.According to a recent report, the president assigned a White House team to focus on the Iran deal and sideline the State Department so that he has more options when the issue comes to the fore again in three months.It’s not just Iran where the president sees a problem; the secretary has been actively tugging in the opposite direction when it comes to solving the Qatar crisis and on a host of issues related to Israel as well.In many ways, the different view at the State Department should be expected, not just due to institutional issues where diplomats usually prefer finesse to force but because of personnel considerations as well.Most pundits have pointed to the dwindling bench of the department’s roster. After all, many positions remain unfilled. When Tillerson chose Elliott Abrams to serve as deputy secretary, a well-known conservative who served under Ronald Reagan and George W. Bush, Trump even intervened to quash the appointment. The problem, however, is more about the people already in the department, rather than those yet to be appointed or hired.Barack Obama holdovers are driving the State Department’s Iran policy.They include Under Secretary of State for Political Affairs Thomas Shannon; Deputy Assistant Secretary for Iran in the State Department’s Bureau of Near Eastern Affairs Chris Backemeyer, who previously served as the director for Iran at the National Security Council (NSC) under Obama; and Deputy Assistant Secretary and former US special envoy for Syria Michael Ratney. The first two were directly involved in the recertification fiasco – twice. They, among others, made their careers selling the Iran deal and are dedicated to its preservation.In April, the first draft of the language “was full of Obama-era lines” including several falsehoods promoting the utility of the JCPOA, such as the deal verifiably puts Iran a year away from a nuclear weapon, this source explained.“There was a huge fight after they wrote it because some said it was too pro-deal and it used all kinds of Obama language.”“The White House went ballistic,” he said, “and they forced rewrites until they had a statement that was just a few lines.”The revised version praised neither the deal nor Iran’s actions and pointed to the NSC-led interagency review of the JCPOA – a White House victory on the language used but a State Department win on preserving the status quo in policy.“Backemeyer and Shannon wrote the certification,” the source confirmed, “and they were closely involved in the certification process this time around.”For an administration that otherwise sounds determined to curtail Iran’s expansionist ambitions, it’s a wonder that the same people who brought the deal across the finish line, made careers out of selling the deal and helped fill Tehran’s financial coffers are still running the show at the State Department.What’s more, Secretary Tillerson seems supportive of that decision or oblivious to its impact.In either case, the department is in open insubordination to the White House and neither scenario reflects well on the secretary or his team. Nevertheless, whether or not his days are numbered, the current policy of rubber stamping Iran’s certification certainly appears to be coming to an end.The author is a senior fellow at the Security Studies Group in Washington, DC, a senior Middle East analyst at Wikistrat and a former director of policy at the Jewish Policy Center. He can be followed on Twitter: @RJBrodsky.