The 50th anniversary of the assassination of John F Kennedy has been accompanied by a lot of soul-searching about the fact that a majority of Americans – and presumably millions of people elsewhere – believe we still don't know the whole story about the shooting. Demolishing conspiracy theories is, quite justifiably, a favourite pursuit of the self-styled "skeptic" movement, and psychological explanations of the phenomenon abound. There's evidence that people who feel socially powerless are prone to a conspiracist mindset; in an increasingly complex world, we're told, paranoid speculations are a way to reassert a feeling of agency and control; the echo-chambers of the modern media reinforce bizarre beliefs, protecting them from challenge. All true, no doubt, as underlined by conspiracists' embarrassing tendency to believe simultaneously in mutually contradictory conspiracies. People who believe Princess Diana was murdered, it turns out, are also more likely to believe she faked her own death.

But this kind of psychological explanation, however valid, always runs the risk of curdling into a kind of condescension, in which the critics of some social malaise imply that their grasp of reality must obviously be superior to the sufferers'. So if only as an exercise in humility, it's worth remembering that one of the many reasons people believe in conspiracies is because conspiracies actually happen.

This marks a crucial difference between conspiracy theorism and some of the psychological delusions with which it's frequently grouped. Disembodied voices don't ever occur outside a disordered mind; people who are convinced they were Napoleon in a previous life, or who believe they have telepathic powers, or that terrible accidents will befall those they think bad thoughts about, are all always wrong. (Or put it this way: if they're not, we'd have to radically overhaul our most basic assumptions about the world.) Whereas people who think government agencies or other shady groups are engaged in elaborate schemes to delude the general population for nefarious ends are only usually mistaken.

Just to be clear, I'm not suggesting there was any conspiracy to kill JFK. (Shall I say that again? I'm not suggesting there was any conspiracy to kill JFK.) But as Fred Kaplan pointed out recently in an excellent essay at Slate, devoted mainly to debunking the main Dallas conspiracy theories, it wasn't exactly insane to have a conspiracist mindset about politics in the 1960s:

Back in 1971, not long before he died, a retired Lyndon B Johnson told the journalist Leo Janos that the Kennedy administration had been “running a damn Murder Incorporated in the Caribbean.” Nobody knew what he was talking about at the time. A few years later, the Church Committee revealed the details of Operation Mongoose — an intense plot by the Kennedy White House and the CIA to assassinate Fidel Castro. Revelations also emerged of the mafia’s cooperation in Mongoose, of JFK’s affair with a mafia moll, and of his brother Robert Kennedy’s crusade against the same mafia kingpins. Could Dallas have been a revenge shooting, mounted by either Castro or the mafia? Even if Oswald had been the lone gunman, could he have been a recruit in some larger power’s plot?

There are many other examples. There's persuasive evidence that the US army really did test potentially damaging chemicals by spraying them around poor neighbourhoods of St Louis during the Cold War; the Tuskegee Syphilis Experiment really did take place; a group of wealthy American businessmen probably really did discuss a coup to unseat FDR; the CIA really did covertly fund modern American art in an effort to combat the menace of Soviet realism. None of this, it ought to go without saying, adds credibility to the chemtrail theory or the "global warming scam" or the vast labyrinths of 9/11 Truther lore. But they offer a partial explanation for conspiracy-mindedness that's not based on some deep psychological weakness.

Then there's the problem of how much gets encompassed by the phrase "conspiracy theorist". It refers sometimes to deeply unpleasant bigots, determined to find evidence for their anti-semitic or otherwise repugnant prejudices; to people who honestly seem to believe that the administration of George W Bush was able to stage an epic, multi-pronged cover-up over 9/11, yet was somehow unable to stop a twentysomething from upstate New York distributing a web documentary exposing the fact. (The most withering response to that idea can be found here.)

Then there are the sceptics who just think there are some "unanswered questions" about the JFK assassination, or 9/11, etcetera. Not only are these people not true-believer conspiracists; they're not even incorrect. Of course there'll always be unanswered questions, untied-up loose ends, about any momentary event that shifts the course of history – if only because we subject such moments to such relentless scrutiny. Combine that fact with the reality of at least a few alleged conspiracies, and it's not so strange or irrational to wonder if there's a story behind the story. In some sense or other – usually mundane, occasionally sinister – there often is.