Last week, I argued that although science and religion clearly can be compatible, they often make for far less comfortable bedfellows than most believers sanguinely maintain. There is, however, another side to the story of science's relation to belief: the idea held by many atheists that science is not only on their side, but is their best buddy. The uncomfortable truth for believers and atheists alike is that science is a loner who never shies from revealing embarrassing truths about anyone who tries to claim ownership of it.

This is not the rather silly view that science is "just another myth", that the physics of Niels Bohr is no more "valid" than the poetry of Beowulf. Indeed, I'm not sure that anyone who gave this more than a second's thought really believes this. John Gray often sounds as though he does, but what he actually says is that science "has become a vehicle for myths", such as that of inevitable progress, not that science itself is no better way of understanding the world than folk beliefs about sun gods or earth spirits.

Talk about "myths" seems to me to be a cheap way of trying to equate secular problems with science with religious ones, when really they are quite different. While the religious merely need to find a way to co-exist with science, atheist humanism often claims too close a kinship with it. Science is portrayed as what underlies and vindicates the humanist outlook. In one very important senses this is right. Atheism may be defined negatively as opposed to theism, but atheists are first and foremost naturalists, committed to a positive view of the universe as containing only natural entities and forces. This view is not held as a matter of faith but because that is what the scientific evidence strongly suggests.

If this represents a marriage of science and atheism, then it has to be admitted that in every other respect, the two enjoy a non-exclusive relationship. Take the claim made a few years ago by the British Humanist Association that agreeing with the statement "scientific and other evidence provides the best way to understand the universe" is a distinguishing characteristic of the humanist outlook, or the international humanists' 2002 Amsterdam Declaration, which maintained "Humanism advocates the application of the methods of science and free inquiry to the problems of human welfare". Both statements are held with equal conviction by many religious believers. It is just that, for them, science leaves many questions open, and in such cases we are entitled to base our judgements on non-scientific grounds. Only the most fanatically scientistic would insist otherwise, demanding that, of which science cannot speak, we must remain silent. You might find the odd such person standing in front of a painting, only interested in knowing what their brain is doing in response to the visual stimulus, but such a person would be just that: odd.

Atheism does not own the scientific method, and nor does good, secular thinking reduce to scientific reasoning. What is too often forgotten is that modern atheism was born in a humanistic way of thinking that drew as much on arts and humanities as it did natural science, if not more so.

Most problematic of all, however, is the sometimes glib way in which science is supposed to vindicate, or even determine, the secular humanist approach to life. First of all, it seems very clear that science actually threatens to undermine many of the cherished beliefs traditionally held by secular humanists. Most obviously, secular humanism upholds the value of the autonomous, free, rational individual. If the science of humanity has shown anything at all over recent decades it is that human beings are far less autonomous, rational and free than we usually suppose. As a matter of fact, I don't think any of these challenges defeats what really matters about the humanist view of ourselves. But to argue this would be difficult and I'm not sure I could successfully do so as yet. What's more, it remains possible that progress in science really will shatter a few atheist shibboleths in time. These are reasons enough to think that by embracing science so closely, atheists are only making it easier for it to stab them in back.

What's worse, however, is when atheists talk of science as though it is the source of all the knowledge and wisdom we need to live. The most egregious recent example of this is Sam Harris's The Moral Landscape, with its subtitle "How science can determine human values". It's hard to imagine a more hyperbolic claim about the power of science, and when I interviewed Harris about his book, most of the time was spent trying – unsuccessfully on my part – to understand it in a way that was remotely plausible (you can listen to some of that interview in this podcast).

When Harris sounds convincing is when he is attacking the batty view that science has nothing to say about human values. Scientific evidence might indeed reveal morally important facts, such as that inequality as well as absolute levels of wealth affects wellbeing; that different "races" are not that different and not really races; that some animals do feel pain, and of what kind it is; and so on. Science can also reveal the physiological and neurological mechanisms that underlie the things we value in life, like achieving states of flow or avoiding pain. But science could never tell us what we should value, because when it tells us how things are, we are always left with the question, what ought we to do about it? It can, for instance, tell us that X produces more happiness than Y, but it cannot tell us that we ought to do whatever produces the greatest happiness.

The rapturous reception Harris's book received from many atheists – though thankfully far from all of them – is a symptom of an unhealthy desire to raise science to the level of our saviour. That is the kind of mythologising Gray is right to warn against. Science is indeed one of our highest human achievements and we should respect it, admire it and draw on its findings to inform our world view. But it cannot provide the entirety of such a view and nor can we blithely assume that it will always support our most fundamental beliefs. Atheists need to accept that they are not of one flesh with science, and that their love and admiration may not be requited as passionately as they suppose.

The upshot of this and last week's argument is that science is not such a large problem for religion as atheists suppose, but not such a small problem as the religious suppose, and not as much of an ally to humanists as they suppose. All of which means that science just isn't as central to the disputes between believers and atheists as almost everyone seems to suppose. It's time to move on.