They are often described as “The Unholy Trinity” – a trio of ferociously bright and pugilistic academics who use science to decimate what they believe to be the world’s greatest folly: religion.

But now Richard Dawkins, Christopher Hitchens and Sam Harris are on the receiving end of stinging criticism from fellow liberal non-believers who say their particular brand of atheism has swung from being a scientifically rigorous attack on all religions to a populist and crude hatred of Islam.

In the last fortnight a series of columns have been written denouncing the so-called New Atheist movement for, in one writer’s words, lending a “veneer of scientific respectability to today's politically-useful bigotry.”

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The opening broadside began earlier this month with a polemic from Nathan Lean on the Salon.com website. Lean, a Washington DC native and Middle East specialist who has recently written a book about the Islamophobia industry, was prompted to pen his attack following a series of tweets last month by Professor Dawkins attacking Islam in snappy 140 character sound bites.

“Haven’t read Koran so couldn’t quote chapter & verse like I can for Bible. But often say Islam [is the] greatest force for evil today,” the Cambridge evolutionary biologist wrote on 1 March.

For a man who has made a career out of academic rigour the admission that the author of the God Delusion hadn’t studied Islam’s holy book surprised many and led to a flurry of responses from both fans and critics alike. Three weeks later – in an apt illustration of Godwins’ Law (the idea that as an online discussion grows longer the probability of a comparison involving Nazis or Hitler approaches one) – Dawkins added: “Of course you can have an opinion about Islam without having read Qur’an. You don’t have to read Mein Kampf to have an opinion about Nazism.”

Muslims, Lean wrote of Dawkins, are “ a group that have come to occupy a special place in his line of fire — and in the minds of a growing club of no-God naysayers who have fast rebranded atheism into a popular, cerebral and more bellicose version of its former self.”

Lean argues that few atheists in the western world historically paid much attention to Islam, concentrating instead on debunking Christianity and, to a lesser extent, Judaism. But after the September 11 attacks, the New Atheists “found their calling”. Criticism of all religion on an equal footing was one thing. But the New Atheists, he argued, have begun flirting with Islamophobes, using irrational hatred, as opposed to rational critique, to attack an already deeply misunderstood and much maligned faith.

“Conversations about the practical impossibility of God’s existence and the science-based irrationality of an afterlife slid seamlessly into xenophobia over Muslim immigration or the practice of veiling,” wrote Lean. “The New Atheists became the new Islamophobes, their invectives against Muslims resembling the rowdy, uneducated ramblings of backwoods racists rather than appraisals based on intellect, rationality and reason.”

Writing on Al Jazeera’s website a few days later, Murtaza Hussain, a Toronto based Middle East analyst, penned an even more scathing critique. What the New Atheists were doing, he argued, was similar to the kind of scientific racism that was dominant within western cultures in the eighteenth and nineteenth centuries as they tried to use eugenics to classify – and consequently legitimise – the subjugation of certain races.

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Hussain reserved particular ire for Sam Harris, a neuroscientist by trade whose atheist tracts “The End of Faith” and “Letter to a Christian Nation” have made him one of the leading anti-religious polemicists of his age.

Harris is an accomplished writer and public speaker with a solid background in academic rigour. But there are no shortages of statements from his over the years lumping all Muslims into one box. “The idea that Islam is a ‘peaceful religion hijacked by extremists’ is a fantasy, and is now a particularly dangerous fantasy for Muslims to indulge,” is just one he wrote in “Letter to a Christian Nation.” Wearing a palpable disdain for Islam on his sleeve he has also written in favour of torture, pre-emptive nuclear strikes and the profiling not just of Muslims but “anyone who looks like he or she could conceivably be a Muslim.”

In response, Hussain wrote: “[Harris’] sweeping generalisations about a constructed civilisation encompassing over a billion people are coupled with fevered warnings - parallel with the most noxious race propaganda of the past - about the purported demographic threat posed by immigrant Muslim birthrates to Western civilisation.”

He added: “Citing “Muslims” as a solid monolith of violent evil - whilst neglecting to include the countless Muslims who have lost their lives peacefully protesting the occupation and ongoing ethnic cleansing of their homeland - Harris engages in a nuanced version of the same racism which his predecessors in scientific racism practiced in their discussion of the blanket characteristics of “Negroes”.”

Dawkins has so far remained silent on the attacks whilst Hitchens, who passed away in December 2011 after a long battle with cancer, is unable to defend himself. But Harris has not been willing to let sleeping dogs lie.

When left-wing US columnist Glenn Greenwald retweeted Hussain’s original article Harris got in touch, describing the piece as “garbage”, “defamatory” and an exercise in “quote mining”. In a lengthy email exchange that Greenwald eventually posted online, Harris insisted that there was nothing remotely racist about his criticisms of Muslims: “I criticize white, western converts in precisely the same terms,” he said. “In fact, I am even more critical of them, because they weren't brainwashed into the faith from birth.”

He added: “There is no such thing as “Islamophobia.” This is a term of propaganda designed to protect Islam from the forces of secularism by conflating all criticism of it with racism and xenophobia. And it is doing its job, because people like you have been taken in by it.”

But the email exchange did little to convince Greenwald who has since responded on the Guardian website with a lengthy piece attacking Harris. Like Chomsky, who has also been a vocal critic of New Atheism, he blames writers like Harris for using their particularly anti-Islamic brand of rational non-belief to justify American foreign policies over the last decade.

“When criticism of religion morphs into an undue focus on Islam - particularly at the same time the western world has been engaged in a decade-long splurge of violence, aggression and human rights abuses against Muslims, justified by a sustained demonization campaign - then I find these objections to the New Atheists completely warranted,” Greenwald concludes. “In sum, [New Atheism] sprinkles intellectual atheism on top of the standard neocon, right-wing worldview of Muslims.”