Last week, I wrote an article defending free speech for everyone – and in response there have been riots, death threats, and the arrest of an editor who published the article.

Here's how it happened. My column reported on a startling development at the United Nations. The UN Special Rapporteur on Human Rights has always had the job of investigating governments who forcibly take the fundamental human right to free speech from their citizens with violence. But in the past year, a coalition of religious fundamentalist states has successfully fought to change her job description. Now, she has to report on "abuses of free expression" including "defamation of religions and prophets." Instead of defending free speech, she must now oppose it.

I argued this was a symbol of how religious fundamentalists – of all stripes – have been progressively stripping away the right to freely discuss their faiths. They claim religious ideas are unique and cannot be discussed freely; instead, they must be "respected" – by which they mean unchallenged. So now, whenever anyone on the UN Human Rights Council tries to discuss the stoning of "adulterous" women, the hanging of gay people, or the marrying off of ten year old girls to grandfathers, they are silenced by the chair on the grounds these are "religious" issues, and it is "offensive" to talk about them.

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This trend is not confined to the UN. It has spread deep into democratic countries. Whenever I have reported on immoral acts by religious fanatics – Catholic, Jewish, Hindu or Muslim – I am accused of "prejudice", and I am not alone. But my only "prejudice" is in favour of individuals being able to choose to live their lives, their way, without intimidation. That means choosing religion, or rejecting it, as they wish, after hearing an honest, open argument.

A religious idea is just an idea somebody had a long time ago, and claimed to have received from God. It does not have a different status to other ideas; it is not surrounded by an electric fence none of us can pass.

That's why I wrote: "All people deserve respect, but not all ideas do. I don't respect the idea that a man was born of a virgin, walked on water and rose from the dead. I don't respect the idea that we should follow a "Prophet" who at the age of 53 had sex with a nine-year old girl, and ordered the murder of whole villages of Jews because they wouldn't follow him. I don't respect the idea that the West Bank was handed to Jews by God and the Palestinians should be bombed or bullied into surrendering it. I don't respect the idea that we may have lived before as goats, and could live again as woodlice. When you demand "respect", you are demanding we lie to you. I have too much real respect for you as a human being to engage in that charade."

An Indian newspaper called The Statesman – one of the oldest and most venerable dailies in the country – thought this accorded with the rich Indian tradition of secularism, and reprinted the article. That night, four thousand Islamic fundamentalists began to riot outside their offices, calling for me, the editor, and the publisher to be arrested – or worse. They brought Central Calcutta to a standstill. A typical supporter of the riots, Abdus Subhan, said he was "prepared to lay down his life, if necessary, to protect the honour of the Prophet" and I should be sent "to hell if he chooses not to respect any religion or religious symbol… He has no liberty to vilify or blaspheme any religion or its icons on grounds of freedom of speech."

Then, two days ago, the editor and publisher were indeed arrested. They have been charged – in the world's largest democracy, with a constitution supposedly guaranteeing a right to free speech – with "deliberately acting with malicious intent to outrage religious feelings". I am told I too will be arrested if I go to Calcutta.

What should an honest defender of free speech say in this position? Every word I wrote was true. I believe the right to openly discuss religion, and follow the facts wherever they lead us, is one of the most precious on earth – especially in a democracy of a billion people riven with streaks of fanaticism from a minority of Muslims, Hindus and Sikhs. So I cannot and will not apologize.

I did not write a sectarian attack on any particular religion of the kind that could lead to a rerun of India's hellish anti-Muslim or anti-Sikh pogroms, but rather a principled critique of all religions who try to forcibly silence their critics. The right to free speech I am defending protects Muslims as much as everyone else. I passionately support their right to say anything they want – as long as I too have the right to respond.

It's worth going through the arguments put forward by the rioting fundamentalists, because they will keep recurring in the twenty-first century as secularism is assaulted again and again. They said I had upset "the harmony" of India, and it could only be restored by my arrest. But this is a lop-sided vision of "harmony". It would mean that religious fundamentalists are free to say whatever they want – and the rest of us have to shut up and agree.

The protestors said I deliberately set out to "offend" them, and I am supposed to say that, no, no offence was intended. But the honest truth is more complicated. Offending fundamentalists isn't my goal – but if it is an inevitable side-effect of defending human rights, so be it. If fanatics who believe Muslim women should be imprisoned in their homes and gay people should be killed are insulted by my arguments, I don't resile from it. Nothing worth saying is inoffensive to everyone.

You do not have a right to be ring-fenced from offence. Every day, I am offended – not least by ancient religious texts filled with hate-speech. But I am glad, because I know that the price of taking offence is that I can give it too, if that is where the facts lead me. But again, the protestors propose a lop-sided world. They do not propose to stop voicing their own heinously offensive views about women's rights or homosexuality, but we have to shut up and take it – or we are the ones being "insulting".

It's also worth going through the arguments of the Western defenders of these protestors, because they too aren't going away. Already I have had e-mails and bloggers saying I was "asking for it" by writing a "needlessly provocative" article. When there is a disagreement and one side uses violence, it is a reassuring rhetorical stance to claim both sides are in the wrong, and you take a happy position somewhere in the middle. But is this true? I wrote an article defending human rights, and stating simple facts. Fanatics want to arrest or kill me for it. Is there equivalence here?

The argument that I was "asking for it" seems a little like saying a woman wearing a short skirt is "asking" to be raped. Or, as Salman Rushdie wrote when he received far, far worse threats simply for writing a novel (and a masterpiece at that): "When Osip Mandelstam wrote his poem against Stalin, did he ‘know what he was doing' and so deserve his death? When the students filled Tiananmen Square to ask for freedom, were they not also, and knowingly, asking for the murderous repression that resulted? When Terry Waite was taken hostage, hadn't he been ‘asking for it'?" When fanatics threaten violence against people who simply use words, you should not blame the victim.

These events are also a reminder of why it is so important to try to let the oxygen of rationality into religious debates – and introduce doubt. Voltaire – one of the great anti-clericalists – said: "Those who can make you believe absurdities can make you commit atrocities." If you can be made to believe the absurd notion that an invisible deity dictated The Eternal Unchanging Truth to a specific person at a specific time in history and anyone who questions this is Evil, then you can easily be made to demand the death of journalists and free women and homosexuals who question that Truth. But if they have a moment of doubt – if there is a single nagging question at the back of their minds – then they are more likely to hesitate. That's why these ideas must be challenged at their core, using words and reason.

But the fundamentalists are determined not to allow those rational ideas to be heard – because at some level they know they will persuade for many people, especially children and teenagers in the slow process of being indoctrinated.

If, after all the discussion and all the facts about how contradictory and periodically vile their ‘holy' texts are, religious people still choose fanatical faith, I passionately defend their right to articulate it. Free speech is for the stupid and the wicked and the wrong – whether it is fanatics or the racist Geert Wilders – just as much as for the rational and the right. All I say is that they do not have the right to force it on other people or silence the other side. In this respect, Wilders resembles the Islamists he professes to despise: he wants to ban the Koran. Fine. Let him make his argument. He discredits himself by speaking such ugly nonsense.

The solution to the problems of free speech – that sometimes people will say terrible things – is always and irreducibly more free speech. If you don't like what a person says, argue back. Make a better case. Persuade people. The best way to discredit a bad argument is to let people hear it. I recently interviewed the pseudo-historian David Irving, and simply quoting his crazy arguments did far more harm to him than any Austrian jail sentence for Holocaust Denial.

Please do not imagine that if you defend these rioters, you are defending ordinary Muslims. If we allow fanatics to silence all questioning voices, the primary victims today will be Muslim women, Muslim gay people, and the many good and honourable Muslim men who support them. Imagine what Britain would look like now if everybody who offered dissenting thoughts about Christianity in the seventeenth century and since was intimidated into silence by the mobs and tyrants who wanted to preserve the most literalist and fanatical readings of the Bible. Imagine how women and gay people would live.

You can see this if you compare my experience to that of journalists living under religious-Islamist regimes. Because generations of British people sought to create a secular space, when I went to the police, they offered total protection. When they go to the police, they are handed over to the fanatics – or charged for their "crimes." They are people like Sayed Pervez Kambaksh, the young Afghan journalism student who was sentenced to death for downloading a report on women's rights. They are people like the staff of Zanan, one of Iran's leading reform-minded women's magazines, who have been told they will be jailed if they carry on publishing. They are people like the 27-year old Muslim blogger Abdel Rahman who has been seized, jailed and tortured in Egypt for arguing for a reformed Islam that does not enforce shariah law.

It would be a betrayal of them – and the tens of thousands of journalists like them – to apologize for what I wrote. Yes, if we speak out now, there will be turbulence and threats, and some people may get hurt. But if we fall silent – if we leave the basic human values of free speech, feminism and gay rights undefended in the face of violent religious mobs – then many, many more people will be hurt in the long term. Today, we have to use our right to criticise religion – or lose it.

Postscript: If you are appalled by the erosion of secularism across the world and want to do something about it, there are a number of organizations you can join, volunteer for or donate to.

Some good places to start are the National Secular Society, the Richard Dawkins Foundation for Science and Reason, or – if you want the money to go specifically to work in India – the International Humanist and Ethical Union. (Mark your donation as for their India branch.)

Even donating a few hours or a few pounds can really make a difference to defending people subject to religious oppression – by providing them with legal help, education materials, and lobbying for changes in the law.

An essential source of news for secularists is the terrific website Butterflies and Wheels.