For a small country, Scotland punches well above its weight in science and technology.

So why is a group of people who make up half of the country's population chronically under-represented in it? Apparently, the shocking answer is that they do not have a penis. Women's lib has not translated into women's lab.

We know that the distribution of recognition and rewards in society continues to be skewed largely towards men but the figures in yesterday's report from the Royal Society of Edinburgh (RSE) are truly shocking. Forget for a moment that men continue to outnumber women considerably in choosing to study the STEM subjects (science, technology, engineering and maths) at university. This report shows that of young women who do plump for those subjects, only 27% take jobs in those fields, compared with nearly twice as many young men. Of Scotland's 56,000 female STEM grads, just 15,000 work in science and technology. A further 11,000 aren't working at all. That's a macro economic disaster as well as a micro economic one, especially in a country with a growing skills gap in these very sectors. The RSE compares the situation to a leaky pipe, spilling female talent along its route instead of tapping into it.

This subject interests me because three years ago my elder daughter Laura was awarded a good first-class science degree but headed for a career in advertising. "Compared with working at the centre of a dynamic team of creatives in London, the prospect of traipsing back and forth to the lab in Oxford to stare down a microscope at bits of fungus for the next three years seemed lonely and bleak," she told me, after refusing a research post.

Explanations for the lack of women in science fall into two broad categories: biological/psychological and historical/cultural. The former is a prickly subject because it borders on suggesting that women are somehow deficient. Men who venture there tend to get shouted down. Professor Larry Summers was pressured into quitting as president of Harvard after suggesting the paucity of women in science and maths might be down to innate differences between the sexes. It sounds less controversial coming from a 25-year-old female science grad. "I'm sure male and female brains are different. Men are into inanimate stuff and women prefer living things," ventures Laura, adding that there are certain subjects, such a 3-D visualisation, in which men consistently outperform women. That not only explains why we're weak on parking and map reading. It's pretty important in physics, chemistry and engineering too. In fact, she speculates that if we exclude biology – the science most popular with women – from the RSE figures, their stats would look even more diabolical.

There are some problems with Laura's thesis. It explains female subject choices better than why female science students fail to get science jobs. It ignores the fact that in medicine and veterinary science – not in the RSE figures – female students now form a majority and most go on to linked careers. Thirdly, it ignores the very wide international variations in the percentage of women in the STEM workforce. The former communist countries score significantly better than western democracies on women in science generally. Scandinavian countries produce far more women engineers than we do. All this suggests historical, cultural and sociological factors are at least as important as biology.

In Britain until the late 1960s women had to fight for acceptance in research and academic posts. Chair of the RSE working group behind yesterday's report, the distinguished astrophysicist Professor Dame Jocelyn Bell Burnell, the sole woman physicist in her year at Glasgow, has described her life as a wife and a scientist as "very difficult". Hypatia of Alexandria, Marie Curie, Dorothy Hodgkin, Anne Glover, Susan Greenfield, Heather Couper? How many female scientists or mathematicians can you name, off the cuff? In part their fame stems from the scarcity of women in such positions. So the first problem is a distinct shortage of role models for STEM-inclined young women.

In 35 years in Scottish journalism, I've seen numerous well-intentioned initiatives for getting more girls into science and engineering come and go without making any significant impact. Most featured photos of self-conscious women in hard hats.

It may seem blindingly obvious but that other biological factor –babymaking – remains the biggest barrier to women's participation in science and technology. Susan Greenfield makes the point that the profession doesn't easily allow time out to have children and there is a bottleneck in their late 20s when women tend to be at their most productive in terms of both babies and research. Re-entry is difficult. The RSE is right to say the STEM sector needs to take a leaf from the book of the NHS, which now makes serious efforts to retain female doctors and consultants, largely through offering part-time contracts. My friend Annabel, the only female engineer in her class in the 1970s, began a promising career in bridge design but ended up working as a classroom assistant on the minimum wage after two maternity leaves. Everyone talks about choosing employees on "merit" but it depends on your definition. If it includes a full-time uninterrupted career, mums can't win.

What's most worrying about this report is that even single childless women are leaking from the science and technology pipe and that implies the persistence of the sort of institutional sexism I remember from my father's generation. He used to say that female physicists were either beautiful and stupid or ugly and brilliant. He thought this funny. (A lesbian gas engineer I know says this sort of blatant misogyny persists, albeit less explicitly.) I rather doubt that bucketloads of Athena Swan awards for women-friendly policies, as the RSE recommends, will change much. But ultimately such antediluvianism will be replaced by a generation in business and academia who recognise that depriving ourselves of the creative and intellectual potential of half the population makes no sense.