Right after the election of Donald Trump, a man widely considered a fake and a fool by many of its writers, the New York Times issued an extraordinary statement promising to “strive always to understand and reflect all political perspectives”.

In April, amid criticism that the Times, along with others in the mainstream media, had ignored the concerns of the American masses, the paper appointed a conservative columnist known for controversial views on climate change, race and gender. Welcoming Bret Stephens, the opinion page editor said that Times’ subscribers “want their views to be challenged.”

Following the publication of Stephens’ inaugural column last week, it is the Times itself that is being challenged, as well as its reputation for fact-checking and balance.

The column, which compared the certainty of those predicting global warming to those predicting a Clinton presidency, prompted more than 1,000 direct complaints, more on social media, and several cancelled subscriptions. Several leading scientists also published an open letter that accused Stephens of peddling “alternative facts”.

The substance of the complaints – that Stephens misstated the level of global warming and sought to make a political point out of scientific fact – is of huge significance in the debate over climate change.

But in linking the issue to politics, as the Times has through the pronouncements of its internal ombudsman and public editor on Wednesday, the paper has waded into the biggest issue facing the media. Facts, truth and opinion, always at the heart of journalism, are now the cause of an existential crisis over why it exists.

In her column responding to the complaints, the New York Times’ public editor, Liz Spayd, recognised the depth of passion aroused by the column. “No subject since the election has come close to producing this kind of anger toward the Times,” she wrote.

In a difficult position, Spayd stoked this anger by suggesting that the complaints were a matter of politics, not science. “The goal wasn’t to resolve the finer points of atmospheric physics, but to get an answer to a simple question: ‘Do you actually want a diversity of views on the Opinion pages?’” she wrote.

Stephens’ provocative choice of “a subject of urgent concern to the left”, wrote Spayd, did little to assuage the concerns of scientists who believe that rising CO 2 levels are not a matter of political affiliation.

Even before this column, Prof Stefan Rahmstorf, of the Potsdam Institute for Climate Impacts Research in Germany, wrote: “The Times has denounced the critics of its decision as ‘left-leaning’. This is an insult to me and was the final straw to cancel my subscription. There is no left-leaning or right-leaning climate science, just as there is no Republican or Democrat theory of gravity.”

Leading scientists who launched a campaign urging the paper not to “publish climate science misinformation” reiterated the point that opinion needed to be based on fact. “There are opinions and there are facts. Stephens is entitled to share his opinions, but not ‘alternative facts’ … Facts are still facts, no matter where in the paper they appear.”

The appointment of Stephens, a Pulitzer prize-winning columnist, was laudable in some ways. Few would argue against a democratic, journalistic rationale for newspapers to offer a broad spectrum of views to challenge its readers. The desire to do so often lands news executives in trouble – witness this paper’s own publication of the thoughts of Osama bin Laden in 2004 – but this challenge is exacerbated by the current climate of falling revenues.

Despite the adage that all publicity is good publicity, the reaction to Stephens’ first column should worry Times executives. As Spayd herself has written: “The Times has proclaimed a public commitment to reflecting a broader range of perspectives in its pages. What its mostly liberal or left-leaning base of readers thinks about that strategy obviously matters. They represent the business model, after all.”

Let’s leave aside for one moment the impact on diversity of appointing “yet another white male” to the paper’s editorial roster, a point forcefully made online. James Bennet, the relatively new editorial page editor, has struggled, like his predecessors, to broaden the opinion base of a paper with a mostly liberal roster of columnists. This need to diversify from any hint of echo-chamber opinionating became more extreme in the post-Trump era, an age of polarised views.

In an email, Spayd recognised the difficult line between fact and opinion. “There is no requirement to be neutral on the Opinion pages,” she wrote. “You’re paid to have positions. The point that some readers make is that everyone needs to work off the same set of facts.”

Few newspapers reliant on advertising and subscribers want to be the representative of such a small elite that there are too few willing to pay for them. Despite this, publishing something that questions science-based facts must surely cross a red line, no matter how beautifully written.

Go too far down the line of controversy – not just publishing an op-ed by Marine Le Pen, but views that deny scientific consensus – and anything can be published in the name of neutrality. Even “alternative facts” – otherwise known as lies.