For a community that is often portrayed as aggressive and pugitive, New Atheism has recently been on the backfoot, defending itself from claims dreamt up by those who should – and, surely, in many cases do – know better.

This time round, the scientific and intellectual elite of Sam Harris, Richard Dawkins and the late Christopher Hitchens have found themselves accused of Islamophobia. The whole sorry saga was conveniently summarised in last Friday’s Independent. In short, recent pieces at salon.com and on Al Jazeera’s website have argued, in the words of columnist Murtaza Hussain, that the likes of these prominent atheists are giving a veneer of scientific respectability to today’s Islamophobic bigotry.

Sam Harris is accused of advocating pre-emptive nuclear strikes on Muslims and the profiling of those who merely look like Muslims. Richard Dawkins has come under attack from calling Islam “the greatest force for evil today” and the late Christopher Hitchens has been described as having a bloodlust towards Muslims.

But, sadly, nuance and allegations of bigotry make strange bedfellows. Take Sam Harris. His 2003 book End of Faith catalogues the Qur’an’s long list of orders to murder and exhortations to avenge. He imagines a radical Islamist state acquiring long range nuclear weaponry, thus able to vent its rage against the west. Add in the possibility that it’s headed by an avowedly suicidal regime and nuclear deterrence becomes a worthless currency. Harris anticipates the possibility that in that situation the US may find itself having to press the button first. But it’s a scenario he hardly welcomes.