It's not often that a science writer gets to say this, but the Pope is right. It's not as if he's always right: where scientific matters are concerned, Benedict XVI has displayed precious little infallibility. He has shown a disquieting sympathy for the rebranded creationism of intelligent design, and his views on embryonic stem cells, IVF and contraception are inimical to medical progress. But in attacking the notion that sex roles are invariably ordained by culture and not biology, the Holy Father has said something that needed saying.

As the Pope is finding out, anyone who criticises this “gender theory” invites vitriol from its liberal champions. Scientists such as Simon Baron-Cohen and Steven Pinker, who suggest that differences between typical male and female behaviour may be biologically influenced, have been accused of rationalising patriarchy and discrimination.

The work of these researchers and others shows that gender theory is built on sand. Anatomical variations between the sexes are not the only ones with natural roots. Women tend to be better at empathising, while men are more likely to excel at understanding systems from motorbike engines to offside laws, and there is growing evidence that these traits are influenced by testosterone exposure in the womb. They may also be linked to the recent discovery of hundreds of variations in the way that genes are switched on and off in male and female brains. If social factors are important in shaping gender roles, it is increasingly apparent that biology matters too, and recognising this in no way justifies sexism. Sex differences in behaviour apply only on average, across populations, and people should be considered as individuals.

It is refreshing to see the Pope taking the right side in this argument - not least as it bucks the Jesuit maxim of “give me the child and I'll show you the man”. This shouldn't be taken, though, as a sign of new-found pontifical respect for the latest science. It is better seen as fresh proof that even a stopped clock tells the right time twice a day. The reason is that while the Pope is willing to allow nature a role in shaping the sexes, and in requiring respect for the idiosyncracies of each, he has no time for its implications for sexual orientation.

Religious groups who object to homosexuality, including the Roman Catholic Church, like to present it as a moral choice that lies outside the norms of human behaviour. In October, a senior Vatican official described it as “a deviation, an irregularity, a wound”, and the Pope's remarks betray similar sentiments.

There was a time when mainstream science would have agreed. Homosexuality, after all, was removed from the American Psychiatric Association's list of disorders only in 1973. The Pope would be hard-pressed, though, to find a respected modern expert who thinks it is an irregularity, still less a wound. For evidence is mounting that it is at least as strongly guided by biology as gender roles are.

Homosexuality is natural, occurring across the animal kingdom. It is well documented in more than 450 species, from rams to swans and dolphins to giraffes. In humans, it is seen in every known culture.

Identical twins are more likely than fraternal sets to share a sexual orientation - a firm sign that genes are involved. The search for “gay genes” has so far drawn a blank, and there is certainly no gene that invariably makes people homosexual. But a consensus is building that genetic factors may predispose people to such preferences, in concert with environmental triggers. There are even good explanations for how such genes could have survived the obvious evolutionary drawbacks of gay sex. A genetic variation that promotes homosexuality in men, but makes their mothers and sisters more fertile, could easily thrive and spread.

The natural history of homosexuality, too, goes beyond genetics. Birth order, for example, is known to exert an effect. A man's chances of being gay grow with every older brother he has, probably because successive male pregnancies affect the hormonal balance in the womb. The effect does not apply to men with older adoptive or stepbrothers, which implicates biology and not family circumstance. It would be mischievous to suggest that this might have affected the historical practice of youngest sons making a career in the Church.

Homosexuality is not biologically determined - almost no human behaviours are. But it almost certainly begins with a delicate combination of genetic, gestational, environmental and social cues, which together forge a person's sexual orientation.

Few gay men and women feel they have chosen a way of life, and the science is with them. Their preferences are as much a part of normal human variation as traits such as height or intelligence, to which nature and nurture also both contribute.

In his address to Vatican staff, Benedict XVI declared the Church's belief in a natural order of men and women, and asked “that this order, set down by creation, be respected”. Science has made it clear that homosexuality is part of the rich diversity of that creation. That is something we should all respect - the Pope included.

Mark Henderson is science editor of The Times. His book, 50 Genetics Ideas You Really Need to Know, will be published in April by Quercus

Times Recommends

• Fundamentalist brew: faith and power
• Big guns wheeled out for the marginals
• Wanted: new merchants of light