We are caught in a battle between those who believe too much and those who believe too little – so Terry Eagleton was saying at St Paul's cathedral the other day. In the one corner are the fundamentalists for whom certainty can be pulled off the page of ancient scripture, and in the other are the "whatever" generation for whom the continual introduction of the word "like" is the perfect expression of anxiety about certainty per se. (Conversation with my daughter: she says "It is, like, raining." "No," I reply, "there's no like about it. It is raining.")

Sam Harris struck literary gold having a go at those with too much certainty in The End of Faith. Now he turns his attention to those with too little. His target is moral relativism. For too long religion has sheltered behind the popular idea that you can have your truth and I will have mine. Harris wants a more muscular form of God-denying liberalism, attained by tearing down the familiar idea that science does facts (where truth is possible) and religion does meaning and values (where relativistic respect is essential). With this fact/value distinction – inspired by no less a figure than David Hume – religion and science have announced the terms of their peace treaty, each claiming for themselves a non-competing jurisdiction. But Harris will have none of it. Science has sold itself cheap. The peace treaty must be torn up. Science can indeed tell us about morality. Indeed, science can determine morality.

First, the atheism. On that useful quadrant – interesting and right, interesting and wrong, uninteresting and right, uninteresting and wrong – Harris is mostly in the uninteresting and right category. Uninteresting because he is concerned only with the narrowest definition of religious belief, and right because the moral and intellectual crimes he pins on this form of belief – its ignorance and prejudice – are so obvious to the western secular imagination that they do not require argument, and certainly not a PhD in neuroscience. Given his definition of religion, his attack on it is the philosophical equivalent of taking sweets from a baby. These things are wrong: "female genital excision, blood feuds, infanticide, the torture of animals, scarification, foot binding, cannibalism, ceremonial rape, human sacrifice". The list goes on. With regard to the god Harris describes, I am a much more convinced atheist than he – even though I am a priest. For Harris asks constantly for evidence, with the implication that if he discovered some, he would change his mind. My own line would be that even if the god he described was proved to exist, I would see it as my moral duty to be an atheist. An all-powerful eternal despot is still a despot. Blake called this wicked villain "Nobodaddy".

Nonetheless, the attack on relativism leads Harris into much more interesting territory, but interesting and wrong. His astonishing lack of humility leads him to claim too much for what science can achieve in the realm of morality. The key concept is that of "wellbeing". It is, he suggests, both a fact word and a value word, like "health". So, for example, to suggest that a thing contributes to wellbeing is to make of it a positive evaluation as well as to claim something that can be measured scientifically. On this Harris has invoked the wrath of countless philosophers. But I'm with Harris here. As Mary Midgley argued years ago in her brilliant Beast and Man (a book with a comparable intention to Harris's, though more modestly expressed), an apparently neutral description – "natural" or "human" for example – relates to the empirical world and contains a moral charge. But to extend this point to the idea that wellbeing can shoulder all the work of morality is breathtakingly hubristic.

What is presented as Harris's big new idea is really just reheated utilitarianism with wellbeing in place of pleasure. Where this idea breaks down is where utilitarianism breaks down. Let me start with Harris's defence of torture. If the sum of general wellbeing (whatever that means) is increased by the torture of a terrorist suspect, then torture is not even a necessary evil – it becomes a moral duty. Worse still: discussing Robert Nozick's ingenious idea of a "utility monster", Harris asks "if it would be ethical for our species to be sacrificed for the unimaginably vast happiness of some superbeings". His answer is astonishing: "Provided we take time to really imagine the details (which is not easy), I think the answer is clearly 'yes'." For me this is back with the evil Nobodaddy. I will not worship superbeings nor sacrifice to them. Once again I am more atheist than he.

There are so many problems with utilitarianism, it's a pity Harris does so little to address them. How can one quantify the sum total of wellbeing produced by a single action when the potential consequences of any particular action are infinite? So keen is he to turn morality into science that Harris presses on regardless. His demand is that all morality be calibrated on a single scale. Yet if one observes what it is that people call good (and isn't observation a scientific golden rule?), instead of assuming what good ought to look like, one surely recognises very different sorts of moral value. Can the moral value of freedom and equality really be measured in the same way? Can a conflict between love and duty be resolved by some scientific calculation? No. As Isaiah Berlin rightly pointed out, moral values are often incommensurable. Not all things are good in the same way and for the same reasons. Thus they cannot be measured against each other, however attractive that seems to the scientific mind.

For all this, it is not so much that I disagree with Harris. Rather, I am scared of him. And not his atheism, which is standard scientific materialism with the volume turned up. But scared of his complete lack of ambiguity, his absolute clarity of vision, his refusal of humour or self-criticism, his unrelenting seriousness. Harris sees the great moral battle of our day as one between belief and unbelief. I see it as between those who insist that the world be captured by a single philosophy and those who don't. Which is why I fear Harris in just the same way I fear evangelical Christians, to whom he looks so similar. Like them, he is in no doubt about his faith. Like them, he has his devoted followers. Like them, he wants to convert the world. Well, I'm sorry. I am not a believer.

Giles Fraser is canon chancellor of St Paul's cathedral.