There is a "stirring myth", says John Polkinghorne, that "the heroic armies of science are driving back the obscurantist forces of theology".

He devotes much of his time to challenging this notion. His life journey, as the title of his 2007 autobiography says, has seen him move from physicist to priest.

A scientist for 25 years and professor of mathematical physics at the University of Cambridge for a decade, in 1979 Polkinghorne resigned his chair to study for the ministry at Anglican theological college Westcott House. He was ordained in 1982.

He is convinced that this journey has given him "binocular vision", allowing him to see that science and theology are parallel paths on the great human quest for truth. But he also knows that his position arouses "the kind of suspicion or curiosity that might follow the claim to be a vegetarian butcher".

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As someone who feels a "vocation" to write about science and religion, Polkinghorne has produced more than 20 books in the field, most aimed at a non-specialist audience. The most recent, Questions of Truth: Fifty-One Answers to Questions about God, Science, and Belief, co-authored with social philosopher and management consultant Nicholas Beale, is specifically designed to address the questions most often raised by visitors to his website.

Such books inevitably address topics that philosophers think of as their patch - and some of them bite back.

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Simon Blackburn, professor of philosophy at the University of Cambridge, has savaged some of Polkinghorne's earlier works for "their supreme contempt for philosophical reasoning and historical thinking ... Everything will be alright in the end, we are washed in the blood of the lamb, we are blessed, and above all God is on our side."

Nevertheless, Polkinghorne's "twists and turns ... have much to teach those who protect their belief in the deity mostly by not thinking the thing through," argues Blackburn.

Polkinghorne is also a source of puzzled irritation to atheists such as Richard Dawkins. Among religiously committed British scientists, Dawkins has written, "the same three names crop up with the likeable familiarity of senior partners in a firm of Dickensian lawyers: (Arthur) Peacocke, (Russell) Stannard and Polkinghorne ... After amicable discussions with all of them, both in public and private, I remain baffled, not so much by their belief in a cosmic lawgiver of some kind, as by their belief in the details of the Christian religion: resurrection, forgiveness of sins and all."

One can see why Polkinghorne annoys people who want to mount a scientific case against religion. He is a notably gracious, thoughtful man who seldom resorts to shrill polemic and who admits the difficulties in his own position. But he is also a genuine scientist who says he has acquired "a strong but essentially amateur concern with matters theological" and sees no need to choose between the two domains.

He even comes up with some startling parallels, describing the Bible as something like "a laboratory notebook, recording the unique events of divine self-disclosure".

Although Polkinghorne has said he has nothing against creationism if it means a belief that "the mind and purpose of a divine Creator lie behind the fruitful history and remarkable order of the universe which science explores", he is unequivocally dismissive of "creationism in that curious North American sense, which implies interpreting Genesis 1 in a flat-footed literal way, supposing that evolution is wrong".

"It grieves me that people who may genuinely be seeking to serve the God of truth are not prepared to accept truth," he explains. "Not all truth comes from science, but some does.

"It's a very brittle position. I always want to say to young creationists that if you come to change your views about the history of the world, don't think you have to lose your Christian faith by doing so. It doesn't all shatter if you reject that bit," Polkinghorne says.

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The prevalence of outspoken creationists, at least in the US, has had a terrible impact on common perceptions of religion, he continues. "It creates in the public mind the idea that you have to shut your mind to become a religious believer, which is not the case.

"A lot of my friends in the academic world are both wistful and wary about religion. Wistful because they see that science doesn't tell you all you need to know, but wary because they think religion is ultimately based on submission to authority and signing on the dotted line. They don't want to commit intellectual suicide - and neither do I."

Polkinghorne is the first to admit that there are no knock-down arguments for the truth of religion, although he sees his commitment not as blind faith but as "an existential commitment that goes beyond simple rational motivation, although it builds upon it".

And he argues that "theists explain more than atheists can". He appeals, for example, to "the rational beauty of the world" uncovered by physics: "A lot of physicists, including Einstein, have a sort of cosmic religiosity."

The problem is that such beauty is only revealed to a privileged group of people with the right sort of training and mental ability; the rest of us have to take it on trust. If such "beautiful equations" are indeed pointers to God's existence, Polkinghorne agrees, "it does seem strange to say that's just a bit of luck for the chaps who happen to be good at mathematics".

Questions of Truth deals eloquently with many of the issues that keep coming up in the science-religion debate. But what about the "problem of suffering": how can a just God allow so much pain and cruelty in the world?

"The great American theologian Reinhold Niebuhr said the only empirically observable Christian doctrine was original sin," Polkinghorne points out. "Have a look at the world and within your heart and you see that something has gone wrong."

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This is a striking thought, but if Polkinghorne acquired a strong sense of his own sinfulness from "looking within", he doesn't reveal it in From Physicist to Priest.

In a strange moment, he admits to intense professional vanity in his ambition - realised in 1974 - to become a fellow of the Royal Society: "If you had put to me some curious scheme by which my election would have been assisted by the murder of my grandmother, I would certainly have declined, but there would have been a perceptible pause for mental struggle before I did so."

The other sins he mentions in the autobiography seem ludicrously mild. For example, when he worries that life in the British Army made his Christian observance "slacker", his shocking vices turn out to be "some bad language and occasionally a pint or two more of beer than would have been prudent".

Although he has experienced no "Damascus-road experience or heavenly voice", nor been granted "the gift of untroubled faith", his main concern is that "sometimes Christianity seems to be too good to be true". One can only imagine Blackburn's snort of derision.

Polkinghorne says he enjoyed his time as a physicist. Although not regarded as one of the discipline's true greats, he was a genuine contributor during "a very interesting period", who did his "bit for particle physics".

As the 1970s drew to a close, he was almost 50 and the subject was beginning to change. Although he was by no means disillusioned with physics, he felt it was time for him to try something else.

One option was to pursue a career in university administration and a position as vice-chancellor. Instead, in light of his faith, he opted for the priesthood.

He spent four years in parishes in Bristol and rural Kent before returning to Cambridge as dean of chapel at Trinity Hall.

His final appointment was as president of Queens' College, Cambridge from 1989 to 1996. His autobiography offers an amusing account of a preliminary getting-to-know-you dinner, where the most pressing question was whether he had a pet.

Since a recent predecessor had owned a widely disliked "small and somewhat snappy dog", the fellows had decided that "a pet-less president was high on the Queens' agenda". Long retired and now a widower, Polkinghorne still regularly lunches at his old college.

A decent man who has led a privileged life may not be best placed to solve the problem of suffering, and some of Polkinghorne's suggestions sound thin and unconvincing, if not callous.

"The existence of tectonic plates," he writes, "allows mineral resources to well up in the gaps between them, thereby replenishing the surface of the Earth, but it also allows earthquakes and tsunamis to occur. You cannot have one without the other."

It is hard to know who this is meant to console. And doesn't it imply that there's an optimal level of suffering in the world?

"The essence of the problem of suffering," Polkinghorne replies, "is not that it exists at all, but its scale. I certainly don't take the view that we live in the best of all possible worlds. I don't even think it's a coherent concept. What would be the best of all possible symphonies? It is perplexing and I don't have an answer.

"The idea of an optimal level of suffering is a funny sort of notion, but it's equally difficult to believe it's just an arbitrary level."

Asked about the hostility his work has engendered, he notes "a wave of rather polemical atheism lashing around at the moment ... Biologists are associated with it because (biology) is in a rather triumphalist phase. In the past 50 years, the great successes in science have been biological."

But physics, which once spearheaded arguments for a strictly mechanistic, anti-religious view of the world, has come out the other side, and Polkinghorne thinks that biology may, too.

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In the meantime, there are some things for which life is just too short. "Debating with Dawkins is hopeless, because there's no give and take. He doesn't give you an inch. He just says no when you say yes."