Qatar, a small Sunni Gulf state with a long history of Islamist associations, has emerged as the epicenter of the Middle East conflict. On one side are Iran, Turkey, Hamas and the Muslim Brotherhood aligned with Qatar, and on the other side the Saudis, UAE, Kuwait and Egypt.For American national security interests, management of this divide is crucial to stabilize the region. Despite Qatar’s anti-American, antisemitic and pro-Iranian views, it hosts an important but not indispensable American air base that targets Islamic State (ISIS) in Syria and Iraq, and the Taliban in Afghanistan.Yet Qatar has been playing a deceitful double game for years, supporting the worst Islamists on the Sunni side while simultaneously acting as ally and banker for the theocratic Iranian regime.Who said the Middle East is easy to decipher? So as America tries to navigate the five-dimensional chessboards of conflicting interests in the Middle East, a serious divide in messaging and leadership has emerged between the president and his state and defense departments.A Washington Post headline read: “State Department distances itself from Trump, creating an alternate U.S. foreign policy.”So who actually is in charge of American foreign policy?According to Josh Rogin in the Washington Post, the new State Department spokesperson Heather Nauert “fell back on a prepared line, quoting [Secretary of State Rex] Tillerson saying that the State Department would just not weigh in on what Trump is saying about U.S. foreign policy... the State Department’s plan is to push forward with its own policies and pretend they don’t contradict Trump.” Regardless of your political affiliation, any American citizen should be profoundly troubled if our State Department has its own independent foreign policy, as it is an unelected institution unresponsive to the American electorate.Isn’t the State Department supposed to follow the elected president’s Middle East foreign policy? This is a recipe for a disastrous US Middle East foreign policy, undermining the interests and trust of American allies, in particular Israel.This is especially true after the last American administration steered the US away from its traditional allies Israel, Egypt and the Sunni Gulf states toward closer relations with Iran, Qatar, the Muslim Brotherhood and Turkey, while creating vacuums filled by American enemies.While the president accurately tweeted an accusation that Qatar funds terrorist groups with radical ideologies, Defense Department spokesman Jeff Davis said he was not qualified to answer a question about whether Qatar supported terrorism.For context on Qatar’s nefarious funding, some of the groups that have benefited from Qatari support include: Islamic State; the Muslim Brotherhood; Hamas; the Khorasan Group; al Nusra Front; al-Qaida in the Arabian Peninsula; al-Shabaab; the Taliban; and Lashkar-e-Taiba, to name a few.Qatari-controlled Al Jazeera influences tens of millions of Muslims in the Middle East and Europe with a profoundly anti-American message, undermining US interests at least since 9/11, and often gives voice to known Islamist terrorists. A fuller picture of Qatar, which portrays itself as a pro-democracy forum supporting the Arab Spring, is Freedom House’s analysis of Qatar as a place where “Women face legal discrimination that pervades every aspect of life.” Sharia law is the source of the Qatari Constitution, with flogging and stoning advocated.So much for democracy.The executive branch’s contradictory and confused messaging extends to northern Iraq and the upcoming vote for Kurdish independence. The Kurdistan Democratic Party and Patriotic Union of Kurdistan have announced a referendum on Kurdish independence for September.The State Department is still married to the discredited idea that Iraq needs to be reconstituted, as if it had existed from time immemorial and was not an artificial nation created by Western powers after World War I.The Iraqi Kurds have been America’s true friend and ally in the region, while the Shi’ite Iraqi central government is controlled by Iran with an Iranian-controlled Shi’ite army of over 100,000 foot soldiers called the Popular Mobilization Front. Their mission is to create two Iranian corridors from Tehran to the Mediterranean, directly undermining American interests.During the American presidential campaign President Trump’s Middle East adviser Walid Phares said that a Trump administration would not stand in the way of Kurdish independence.But now State says the US has more urgent priorities in defeating ISIS, so while it acknowledged the “legitimate aspirations” of the Kurds, it supports a “unified, federal, stable and democratic Iraq.”So the question to ask is, is this President Trump’s policy on Kurdish independence, or is it the State Department acting on its own? Will America abandon the Kurdish people, who truly deserve and need a state of their own? One would think that Secretary of State Tillerson would be more sympathetic to the Kurdish interest as he ignored the Iraqi Shi’ite government in the past, selling Kurdish oil without Iraq’s permission when he was the head of Exxon.So where do he, the president and the State Department stand on Kurdish independence? “Iran’s principal position is to support the territorial integrity of Iraq” according to Iran’s Foreign Ministry spokesman Bahram Ghasemi.When America’s foreign policy aligns with Iran, on Iraq and Kurdistan, nine times out of 10 you are on the wrong side of history.To advance American interests I suggest the Trump administration follow its most clear-headed diplomat, Ambassador Nicki Haley, to guide American foreign policy. Her words at Yad Vashem should be a guiding principle for American foreign policy in the Middle East and beyond: “Leadership is not about power. Leadership is the acknowledgment and value of human dignity. We must always choose a side.”Regarding Qatar and Kurdistan, it is time for America to choose the right side.The author is director of MEPIN™, the Middle East Political and Information Network™. He regularly briefs members of Congress and think tanks on the Middle East. He is a regular contributor to The Jerusalem Post.