As a species we need to get out more. Humans now spend so much time indoors that many of us are cultivating a variety of serious health complaints, and for some they could be fatal. It is not so much that outdoor time is inherently good; more that our bodies are built to anticipate it and the way we live now is confusing to our systems. Nearly two decades ago a study published in Nature magazine concluded that the average American spent 93% of their time indoors. And that was before tablets and smartphones.

In trying to cope with the shaded, sedentary world we have made, our bodies wage war on what should be harmless antigens; they fail to make bones strong enough to support our weight; even our eyes struggle to focus without the help of lenses. This incremental creep across the threshold to the great indoors began tens of thousands of years ago when the first settled communities emerged.

As our shelters have become larger and sturdier, the time that we spend in them has extended. And we are only just beginning to understand the number of health risks that are associated with living a permanently sheltered life. Take shortsightedness, which is a growing problem among the young, particularly in south-east Asia. Almost everyone believes that close work (reading, phone use, too much TV) plays a part. And, because the condition is more common in certain populations, coupled with the fact that parents seem likely to pass the condition on, many also believe that it is hereditary. While both assumptions are not wrong, they are a long way from telling the whole story.

In Singapore, for example, where I went with the BBC to make one of a series of programmes about how modern life is changing our bodies, myopia affects 85% of young people. The fact that only 30% of the older generation are shortsighted suggests that the current spike is not being driven by inherited genes.

To grow to its optimum shape, a developing eye needs exposure to good quality light, which can’t be found indoors. In Singapore, there are virtually no houses with gardens where children can play – only tower blocks. Even if they wanted to play outside, a hyper-competitive educational environment means that children are often buried under academic work. The city boasts miles of subterranean outlets that interconnect between main streets. All of which contribute to children’s exposure to artificial light.

Our indoor habits are so ingrained that many of us are also not getting enough vitamin D. To make bone, we need calcium and phosphorous, but calcium in particular is difficult for the body to absorb without vitamin D. Although we can get some vitamin D through our diet, most of it is made by our skin on exposure to sunlight. There have been a number of infant deaths caused by vitamin D deficiency in Britain in recent years.

Research is also showing that vitamin D deficiency is increasingly linked with the prevalence of allergies. An allergic reaction is an inappropriate immune response (itching, swelling, anaphylaxis) to an otherwise harmless substance. With every generation since the 19th century, the number of children with allergies has seemingly increased exponentially. Asthma, for example, was practically unheard of 200 years ago, but today it accounts for 1,200 deaths a year in the UK.

Studies contrasting rural and modern populations have shown that exposure to “natural environments” may reduce allergy risks by more than 90%. Historically, these figures make sense. Hay fever, when it began in the 19th century, was associated either with the bookish or the well-to-do, being two groups who spent little time working the fields. The second wave of allergic disease is food allergy. Research in Australia suggests that vitamin D deficiency is linked to an elevenfold increase in the likelihood of peanut allergy (and a tripling of the prevalence of egg allergy).

Around the world, various solutions are being sought with varying degrees of success. In China, there have been rather sketchy experiments with glass classrooms (they failed because everyone cooked in the heat). In Singapore, schools are introducing a variety of measures specifically to improve children’s exposure to sunlight. In some, playtimes are now of a greater length and frequency, lessons are deliberately timetabled so that students are required to walk longer distances between class. The experiments also have additional benefits such as curtailing children’s gadget time while building social engagement.

A smartwatch is being trialled for children in Singapore, which as well as tracking activity also calculates minutes of exposure to good quality light. The watches are collecting masses of data that in a few years’ time will prove invaluable in determining the ideal light diet for children throughout the world.

Our DNA does not expect us to be out hunting all day on the savannah. But what began with a few branches as an easy solution for settling in one place has since ballooned into a total shade-binge. If urban planning for the future is to succeed it needs to take into account everything that humans need: not just food, water and shelter, but sunlight, too.

The causes of our modern maladies are complex. But the uncomfortable truth is that too many of them are all finding their feet in the perennial shade afforded by our 21st-century lifestyles.

• Vybarr Cregan-Reid is the author of Primate Change: How the world we made is changing us