By Peter Gould
BBC News website
The furore over the Pope's remarks about Islam has left many Catholics inside and outside the Vatican shaking their heads in disbelief.
The Pope has said he deeply regrets any offence caused
Aides of Benedict XVI are dismayed that a quotation used to illustrate a philosophical argument should have provoked such anger from Muslims.
But for others, the row has highlighted their concerns about the Pope's attitude towards the Church's relations with the Islamic world.
The first year of his papacy passed off without controversy. Yet he was quietly planning a number of key changes in the Vatican hierarchy.
When Joseph Ratzinger was elected pope in 2005, it was assumed that he would follow closely the policies of his predecessor, John Paul II.
On many Church issues, the two men were completely in sync. Like the Polish pope, Benedict XVI could be relied upon to uphold the traditional teachings of the Church.
But on one key issue, Vatican-watchers detected a divergence in the views of the two men: the Vatican's attitude towards Islam.
John Paul II wanted to reach out to other religions and in 2001, on a visit to Syria, he became the first pope to set foot in a mosque.
It was a gesture intended to help end centuries of hostility and suspicion between the two religions.
Benedict XVI undoubtedly wants to achieve better relations with Islam, but there is an important proviso.
It can be summed up in a single word: reciprocity. It means that if Muslims want to enjoy religious freedom in the West, then Christians should have an equal right to follow their faith in Islamic states, without fear of persecution.
One of the first signs of a toughening of the Vatican's stance came with the removal from office of Archbishop Michael Fitzgerald.
The British-born cleric ran a Vatican department that promoted dialogue with other religions. A distinguished scholar on Arab affairs, he was an acknowledged expert on the Islamic world.
Archbishop Fitzgerald: a highly-respected scholar
The decision by Benedict XVI to remove him from his post, and send him to Egypt as papal nuncio, was widely seen as a demotion.
Some wondered about the wisdom of the move.
Father Thomas Reese, a Jesuit scholar and an authority on the workings of the Vatican, told the BBC news website of his concerns: "The Pope's worst decision so far has been the exiling of Archbishop Fitzgerald," he said in an interview in April this year.
"He was the smartest guy in the Vatican on relations with Muslims. You don't exile someone like that, you listen to them.
"If the Vatican says something dumb about Muslims, people will die in parts of Africa and churches will be burned in Indonesia, let alone what happens in the Middle East.
"It would be better for Pope Benedict to have Fitzgerald close to him."
It is often argued that a real dialogue with Islam requires an open debate, even at the risk of sometimes causing offence
That warning now seems prophetic.
Did nobody at the Vatican anticipate the way the Pope's words might be taken out of context, and the likely reaction?
Since the 9/11 terror attacks on America, and the subsequent invasion of Iraq, nobody has been in any doubt about the importance of promoting a better understanding between Christianity and Islam.
The sensitivity of Muslims about their religion was made clear by the publication in a Danish newspaper of cartoons depicting the prophet Muhammad.
The caricatures, reprinted in a number of Western countries, caused outrage in Islamic nations, leading to riots and acts of violence in February this year.
Pope Benedict has spoken of the responsibility of religious leaders to "work for reconciliation through genuine dialogue".
His task now appears even more daunting, with real concern being voiced about the possibility of a violent backlash from extremists in the Islamic world.
The Pope has said he is sorry if his words caused offence, and that may go some way to satisfying Muslim opinion.
It is often argued that a real dialogue with Islam requires an open debate, even at the risk of sometimes causing offence.
But the Pope is now acutely aware that wherever he is speaking, his words will be heard around the world by an audience ready to analyse every nuance of meaning.
He may have another opportunity to explain himself to Muslims in November, when he is scheduled to visit Turkey.
In the meantime, the Vatican will be giving a lot more thought to the words and actions needed to promote better relations between the world's two major religions.