Back channels during presidential transitions are not unprecedented, but they are always fraught, as President Donald Trump and his son-in-law, Jared Kushner, have discovered.

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WASHINGTON — There was Robert F. Kennedy’s mysterious phone call with an Izvestia correspondent, actually a Soviet spy, on Dec. 1, 1960, signaling that his brother, the president-elect, wanted to change the nature of the United States’ relationship with its Cold War adversary. It wasn’t exactly a success: first came the Bay of Pigs, then the Cuban missile crisis.

There was Richard M. Nixon’s secret channel to the South Vietnamese through Anna Chennault, a prominent Republican fundraiser, urging the South Vietnamese to deflect President Lyndon B. Johnson’s effort to join peace talks in Paris because Nixon, she said, would give them a better deal. Fifty years later, historians are still arguing over what Nixon’s direct role was, and whether, as Johnson railed, the action was “treasonous.”

Back channels during presidential transitions are not unprecedented, but they are always fraught, as President Donald Trump and his son-in-law, Jared Kushner, have discovered in recent weeks.

In the end, the trouble hinges entirely on the content. “Getting-to-know-you is fine,” said James Clapper, director of national intelligence under President Barack Obama who raised the alarm when he saw intercepts suggesting a series of contacts between the Trump transition team and Russians. The risk, Clapper said, comes when those doing the talking violate “the tradition of one president at a time.”

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Kennedy probably did not go over the line, the evidence suggests. Nixon probably did.

Whether Kushner and Michael T. Flynn, and perhaps others in the Trump transition team, crossed that line remains an open question. The answer may be different for each of them. Kushner has never talked, at least publicly, about the content of his meeting with the Russian ambassador, Sergey Kislyak, or a later session with a Russian banker. That session has been described in various ways, as everything from a business meeting to an effort to open a back channel to Russian President Vladimir Putin.

Flynn, who was later removed as Trump’s national-security adviser for misleading Vice President Mike Pence about discussions on U.S.-led sanctions against Russia, was clearly discussing the specifics of policy. Whether he was trying to undermine sanctions placed on the country by the Obama administration is a matter of judgment — and of continuing investigation.

A central question, reported by The Washington Post, is why there was talk of conducting future discussions through Russian communication lines, presumably channels that the parties hoped could not be intercepted by the National Security Agency (NSA) or the FBI. That would seem to suggest the back channel was meant to be hidden from the sitting government.

“What is not normal,” wrote Eliot Cohen, a historian and former State Department official who led opposition to Trump among Republican national-security officials last year, “is asking a hostile government to provide secure comms to avoid FBI/NSA surveillance.”

Whether the contacts were nefarious or a rookie error is what the investigations will have to determine. “In contrast to Mr. Kushner, most of the earlier efforts at using back channels were done by experienced diplomats,” Michael Beschloss, the presidential historian, said Wednesday.

Back channels themselves are as old as U.S. diplomacy. Thomas Jefferson was an early enthusiast; he often routed around his secretary of state, once sending a secret letter to the U.S. envoy in France, Robert Livingston, that contained a coded message.

It was part of the secret effort that led, the next year, to the Louisiana Purchase. “There may be matters merely personal to ourselves, and which require the cover of a cipher more than those of any other character,” Jefferson wrote at the time.

Almost every president since has similarly indulged, up to Obama’s decision to dispatch Jake Sullivan and William Burns to feel out an opening with Iran that laid the groundwork for the 2015 Iran nuclear deal.

But try the same trick during a presidential transition, and there is all kinds of room for mischief, misunderstanding and, by some lights, criminality.

What makes the current investigation different? The obvious answer is the Russian meddling in the election.

On Oct. 7 last year, intelligence officials reported that Russia was behind the cyberattack on the Democratic National Committee. By the time December rolled round, and Trump had been elected, intelligence agencies had concluded that Putin was seeking to harm Hillary Clinton, help Trump and delegitimize the U.S. electoral process. All of those warning flags were missing from past moments of presidential transition back-channeling.