In 2007, the year before he was elected president, Barack Obama told a biographer that his favourite writer was EL Doctorow.

To my mind, Obama's political opponents did not make as much of this as they could have. Taken together, Doctorow's body of work might easily be painted as a fictional analogue to Howard Zinn's People's History Of The United States - a liberal-secular rejection of America's sustaining narrative, a chronicle of the betrayal or disfigurement of the nation's original promise.

His imaginative sympathies would seem to lie with labour activists and street punks, immigrants and Communists, hoboes and poets. His best-known novel, Ragtime, presumed to cast real-world figures - Harry Houdini, Henry Ford, JP Morgan - alongside invented characters such as Coalhouse Walker, a dignified black jazz musician who takes up arms against the capital-industrial pharaohs of the Gilded Age.

When it was first published in 1976, one aghast conservative critic accused Doctorow of writing "in a spirit adversarial to the Republic". Some three decades later, it was far less likely that the prominent Republicans of the day had ever read that book or even heard of the author. What use had Bush, Cheney or Rumsfeld for leftist literary fiction when they were so busy creating "our own reality", as one aide to their administration so tellingly put it? But now that those three men have considerably more time on their hands, they might yet pick up a copy of Doctorow's new book, Andrew's Brain, and find themselves satirised within. Towards the end of this slim and slippery novel, the eponymous semi-narrator - a disaster-prone cognitive scientist - is appointed director of the White House Office of Neurological Research soon after the September 11, 2001 terror attacks.

It is a non-existent position created to buy his silence, as the unnamed but clearly identified President George W Bush does not want Andrew telling stories from their college years, when they shared a room at Yale. Officially, the job requires him to predict how foreign powers might respond to certain stimuli. Privately, he takes this opportunity to study Bush and his advisers - here referred to by their juvenile nicknames Chaingaing and Rumbum - for signs of a shared pathology within the "government brain".

Persuasive as he is in sketching out the playground mentality of the White House in that period, it is hard to know how seriously or literally to take Andrew's story, as he tells it to a vaguely-rendered interlocutor known only as "Doc".

The latter seems to be some kind of court-appointed psychotherapist, but the suspicion grows throughout the novel that he may be Doctorow himself, and that his conversations with Andrew are, in fact, some form of synaptic transcription - the rational left side of the author's own brain expressing constant disbelief at the creative sparks occurring on the right. "Are you making this up?" he asks repeatedly, as Andrew relates half a lifetime of tragic absurdity: a pet dachshund carried off by a hawk, a baby daughter killed by the wrong prescription medicine, a first wife who left him for an opera singer with a penchant for dressing up as Boris Godunov when drunk.

His second wife, the daughter of retired circus midgets, was lost in the World Trade Centre attacks, even as her stockbroker ex-boyfriend was berating Andrew by phone from the 95th floor of the North Tower. While the overall tone is uncharacteristically comic - Doctorow has never come so close to whimsy - this fictive proxy-memory of September 11 rings through the novel like a fire alarm. The last words and moments of Andrew's former love rival are recorded in his answering machine, along with the "voices of others … their cries the last organic traces of their enflamed bones".

Followers of Doctorow's half-century career may or may not be surprised to find him addressing such recent events from such an odd angle. In historical terms, he tends to take the long view, and his reputation as the great prose-poet of bygone New York was built on his gorgeous portraits of the city in the 19th century (The Waterworks), the early 20th (Ragtime), the prohibition era (Billy Bathgate). But just before the millennium, his universe suddenly expanded into a formally experimental novel called City Of God, where the theft of a cross from a Catholic church in present-day Manhattan opened a dual inquiry into human morality at cosmic and sub-atomic levels.

Andrew's Brain seems to continue that work, and light as it feels by comparison to his early novels, a spoonful weighs a tonne. "How can I think about my brain when it's my brain doing the thinking?" asks Andrew, who is nothing more or less than Doctorow's projection. "I am a mysteriously generated consciousness, and it's no comfort to me that it's one of billions." A brave thing for anyone to admit, let alone an 83-year-old novelist. In Bush and his ilk he sees the terrifying spectacle of power without a mind, and foretells of a microgenetic future where all our neural codes and circuits will be finally exposed, and all our illusions with them.

If Doctorow were to retire now, as Philip Roth has done (and Roth is two years younger) this novel would stand just fine as a last laugh, tempered with a sob. But here's hoping he keeps writing long enough to draw Barack Obama into his counter-mythology, and this new American era of digital surveillance and drone strikes. The current president is at least self-aware. In an interview published last week, Obama sounded almost like his favourite author, or perhaps one of his characters: "You're a swimmer in a river full of rapids," he said, "and that river is history."