It has been common for several years now to assert that science shows the concept of race has no biological basis, and that we must see it instead as a social construct. That case was argued, for example, by Kenan Malik in his 2008 book Strange Fruit, and it is presented, too, in Angela Saini’s Superior (which I reviewed for the Guardian in July), a popular choice on many “books of the year” lists.

I used to be sceptical about this claim. I have all the liberal lefty’s revulsion at racism, but I couldn’t help thinking: “If we insist that race is not biologically determined, won’t that just confuse people, given that it is so blindingly obvious that characteristic markers of race are inherited?” The usual argument is that genomics has identified no clusters of gene variants specific to conventional racial groupings: there is more genetic variation within such groups than between them. But doesn’t that insist on a definition of race that most people simply won’t recognise? Isn’t it better to say that yes, race has a biological basis – but the relevant bodily features are a trivial part of what makes us us?

I confess that I was too nervous to make this suggestion in such an incendiary area. Fortunately, after reading Saini’s book I no longer need to, for Superior gave me the perspective I needed to see what is wrong with it. Our concept of race is not really about skin colour or eye shape, and never has been. It has baked into it beliefs that can’t be dispelled merely by reducing its biological correlates to trivialities. For in our assumptions about race, those features have always been rather irrelevant in themselves. Rather, they serve to activate prejudices stemming from deeply ingrained cognitive habits.

Saini shows that what we have understood by race encodes the belief that literally superficial aspects of our appearance act as markers for innate differences we can’t see. And here’s the problem: it does so for good reason. In times past, and sometimes still today, the strong correlation between your appearance and your culture meant that visual differences really could act as proxies for certain differences in attitudes, traditions and beliefs.

Our brains are exquisitely adapted to pick up on such correlations – and, unfortunately in this case, to conclude that they are causative. We instinctively assume that differences in behaviour that are in fact due to culture must be linked to – even caused by – characteristics of appearance. That is what the traditional notion of race is all about. But genetics has found no such innate origins of behavioural differences between “races” – and it is highly unlikely, given what we know about genetic variation, that it would.

‘Angela Saini shows that what we have understood by race inherently encodes the belief that literally superficial aspects of our appearance act as markers for innate differences we can’t see.’ Photograph: ✎ Gareth Phillips/The Observer

So the notion of race depends on cultural difference – yes, it is a social construct – yet our brains intuitively insist that biology must play a role. In short, we shouldn’t fool ourselves that it’s easy to realign our perceptions here. To confuse us further, while Saini points out that not all the medical correlations of disease and susceptibility with race are as robust as often assumed (not least because race can become entrained with socioeconomic status), some are undeniable. For example, people from Asia are much more likely to be lactose-intolerant than people of European heritage. But what our brains find so hard to process is that no one is lactose-intolerant because they are Chinese. We’re not cognitively well equipped to develop the right intuitions here.

It is probably showing white supremacists (from whom I heard a little after my review) more charity than they deserve to say that they’re caught up in the same confusion. There’s more to their delusions than that, however. Their brains are exercising another of its perilous adaptations: the tendency to find ways of rationalising what it suits us to believe.

This confusion persists, however, even among geneticists, biologists and doctors who we might expect to be better informed on such matters, for whom the use of “race” as a crude predictive tool can distort expectations and reinforce false assumptions about what it really means. We all have those corner-cutting brains.

I always knew at some level that race is an inference about traits based on appearance. But finding the right way to articulate it has made me appreciate that it is much harder to “see beyond” at the subconscious level. Rationalising and good intentions aren’t enough; this is about undoing a habit of mind. Still, my own experience in a multiracial family persuades me it can be done.

It’s a bit painful and embarrassing to admit my past misconception, not least because it could expose me to the understandably exasperated response: duh, white dude finally gets it. It also suggests that there is no tidy, comfortable story we can tell ourselves that dismisses the complexities and even the contradictions of race. Sure, this habit is not unique to white folks (as Saini illustrates) – but so what? My own task is to recognise how it manifests in myself and in a culture that confers privilege on me as a result. I’ll ignore sneers of “white guilt”; I see instead a duty to listen and learn, and a readiness to accept that I might still get it wrong.

• Philip Ball is a science writer