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When I was in the army I learned that assignment interviews with the commanders end in one of two ways. When you bend the system, they send you off with your assignment order with neither a blessing nor a hug; they just want you gone. When the system screws you the interview summary always concludes with the words, “I wished the soldier success on his chosen path.”

The prime minister’s farewell announcement for his national security adviser belongs to the second category. Benjamin Netanyahu blabbered on about the skills and capabilities of Uzi Arad, who resigned this week, and wished him well ‏(“I am certain he will continue to acquit himself superbly”‏) on his old-new path in academia. “Uzi is also a close and loyal friend,” Netanyahu said.

The prime minister is right: Arad was his most trusted aide. They met during Netanyahu’s first term as premier, when Arad was head of research for the Mossad. Netanyahu recruited him to the Prime Minister’s Office as a foreign policy adviser, and their ways never parted. Even in the leanest days, in the political desert, Arad rode alongside Netanyahu and helped him recapture his government seat. Their connection was intellectual, not political: Arad fulfilled Netanyahu’s need for a fascinating conversation partner, someone who read and understood history and philosophy and who shared his admiration for the United States. Netanyahu fulfilled Arad’s need for a commander who would read his recommendations and position papers.

When their mutual dream came true and Netanyahu became prime minister again, Arad slipped naturally into the role of national security adviser. He hoped and believed that his proximity to the boss would enable him to create a professional staff forum for the country’s political leadership. Fortified by the “National Security Council Law” passed after the Second Lebanon War, as well as augmented budgets and the personal charm needed to recruit staff, Arad set out on his mission. Using colored markers, he blocked out an organizational chart on a big newsprint pad, and felt that he was approaching the target: professional administrative work that would replace the “trust me” culture in Israeli defense and foreign policy administration.

But the loyalty was one-sided. Netanyahu is not analytical, as Arad is; his world is made up of people, not models and flow charts. Between his first and second terms Netanyahu cultivated a new genius, foreign-policy adviser Ron Dermer. Dermer had three pluses for Netanyahu: He is a native English speaker, he grew up with politics ‏(both his father and his brother served as mayor of Miami Beach‏) and his identification with Netanyahu was ideological rather than personal, as Arad’s was. As such, Dermer emerged as the main figure in the PMO, shaping policy on the most important issues − the peace process and relations with the United States − while Arad fell. The latter was relegated to bureaucratic battles and to issues that, while important, had no political value, such as arms control. The Turkel committee that investigated last year’s Gaza flotilla raid showed that the decisions on stopping the Turkish boats were made using the old “trust me” method, without input from the National Security Council.

His years in America, the land of rules and of orderly lines, did not turn Netanyahu into a devotee of organized work procedures. Like his predecessors he ruled by “compartmentalize and decentralize”: by dividing up a single task among five different envoys, each of whom reported to him separately, in order to maintain control by insuring that none of them became too strong.

The adviser closest to Netanyahu is his former commander, Defense Minister Ehud Barak. Netanyahu enjoys talking with him, but ignores his advice. The only figure who has influence over the prime minister is his political rival, Foreign Minister Avigdor Lieberman, who can boot him out of power at any given moment and in the meantime is neutralizing any peace initiative that would improve Netanyahu and his party’s popularity. The question “What will Lieberman do” concerns the prime minister about as much as the Iranian nuclear threat, and dictates his moves more than any other consideration.

When he returns to the lecture hall Prof. Arad can share with his students the lessons he learned in the PMO: Organizational structures, however sophisticated, do not make good decisions on their own. Political considerations will always beat out professional advice, and the leader will always reserve freedom of action for himself and postpone all decisions to the last moment. It’s the Israeli way, and it would be better to put energy into improving the content rather than pointless attempts to maintain the form.

Otherwise, you’re left with a farewell letter, good-luck wishes and a sense of missed opportunity.