It was night-time as my British Airways jumbo jet neared London’s Heathrow airport and through the window I could see the ominous glint of car headlights on the M25 motorway beyond the runway far below. I say ominous because I had been upgraded on this flight, not to Business or First class but to the captain’s seat in the cockpit, where the plane’s computerised voice system had started to announce a worrying amount of news.

“One thousand!” it barked, to warn of our rapidly falling altitude. “Five hundred!” Then, as the brightly lit runway hurtled closer: “Fifty above. Decide!” This meant we would soon be 50 feet above the height where I would have to decide if I could see enough of the runway to land safely or needed to abort.

Visibility seemed fine to me, though I would not have really known, never having flown a jumbo jet before. And, disturbingly, the plane had begun to bump loudly just as my co-pilot, BA’s Mark Vanhoenacker, started rabbiting on about something that sounded as if it could be important. “Remember, when we get to 50 we’re going to pull up,” he said, motioning to the control column in my grip.

This would all have been appalling if I really had been about to make my first landing, but in fact I was safely ensconced inside one of BA’s highly realistic £10m flight simulators at the airline’s Heathrow flight training centre. The simulator is a large, white, boxy contraption on legs that can buck and sway so much that, from the cockpit inside, with its convincing visual display (complete with motorway headlights), you really do feel as if you are airborne.

I went there in late February to see Mark Vanhoenacker because the American pilot had just written an oddly moving book about flying, an activity that, 112 years after the Wright brothers first took off beside a windswept beach in North Carolina, has become one of the great paradoxes of modern life.

For those of us fortunate enough to be one of the more than eight million people who fly each day, air travel has rarely been so cheap, routine or, statisticians keep assuring us, so safe. Yet it also provokes deep irritation in an age of tighter security measures; controversy over its environmental impact; and, after the events of the past 12 months, sheer dread. For one airline to lose 537 people in two accidents in less than five months would be shocking enough but, last year, one of Malaysia Airlines’ planes simply vanished into the skies and a second came down over a war zone.

And then, just four weeks after my meeting with Vanhoenacker, a plane from Germanwings, a budget airline in ultra-safe Europe, ploughed into the French mountainside, killing all 150 people on board. Its pilot was later found to have suffered from depression. The odds of any one of these profoundly disturbing incidents happening seem large, but to have three occurring within a year, and two at the same airline, seems extraordinary.

The disasters have cast an unsettling light on Vanhoenacker’s book, Skyfaring, which he wrote to chart his love of flight and the simple wonders he thinks it still offers, even in an age of 100ml liquid limits and mandatory shoe removal.

Could he have a point? Is there something about flying that transcends the tedium, and even the fear, that afflicts the modern traveller? To find out, he suggested we meet in the flight simulator, where he was eager for me to complete a jet “landing”.

Vanhoenacker is a gently spoken New Yorker, who looks much like the Boston business consultant he was before he decided to fulfil a lifelong wish to become a pilot 14 years ago. I had warned him that in a previous life, when I reported on aviation, I had had a few goes in a flight simulator and while take-offs were more or less fine, landing was another thing. “We’re going to do better today,” he said encouragingly, as we continued with what had become a very loud descent. “Fifty!” squawked the plane. And suddenly we were on the ground, roaring down the runway.

“OK, now brake,” said Vanhoenacker. I pushed down on the clunky pedals at my feet and we swerved to the left, then the right, then the left in what felt like a massive fishtail down the runway before finally, thank God, we stopped.

There was muffled laughter from the back seat, where a BA instructor had been monitoring the whole event. “That was great!” said Vanhoenacker. It clearly was not — but when it comes to flying, there appeared to be very little he did not like.

As the simulator’s noisy systems subsided he pointed out a vent in the cockpit roof. “On previous versions of the 747, that was a sextant port, to take star sights,” he said, a note of awe in his voice. “It’s like a legacy of a previous age of navigation.”

Vanhoenacker’s book is full of these details, revealing a world few of us contemplate in our mostly land-bound lives. Like having a job that means you spend the day flying to Africa and back, before going out to dinner with friends in London. Or thinking about countries in terms of the time it takes to fly over them (France is a one-hour country, while Belgium with a healthy tailwind is just 15 minutes and Russia a day-long land).

An illustration of Wright brothers' inaugural flight
The Wright brothers created, built and, in 1903, flew the world’s first airplane © Toby Leigh

Then there is the intriguing way airways are navigated, using radio beacons and “waypoints”, spots defined by geographic co-ordinates or their bearing and distance from a beacon. These waypoints are typically given five-letter capitalised names that are supposed to be simple enough for any controller or pilot to recognise them, regardless of their first language.

Europe’s sky-mappers turn out to have taken a fairly business-like approach to naming their waypoints, though there is a TULIP off the Dutch coast and England has a DRAKE, for Sir Francis. Australians have had a bit more fun, naming points off their west coast WONSA, JOLLY, SWAGY, CAMBS, BUIYA, BYLLA, BONGS, in honour of the opening lines of the country’s unofficial national anthem, “Waltzing Matilda”. The Americans have just gone mad. Detroit has MOTWN and WONDR (Stevie was born in Michigan). Houston has a ROKIT for its Space Center. There is a NIMOY in Boston (where Leonard was born) plus several local culinary references (CHWDH, LBSTA and CLAWW) and SSOXS, STRKK and OUTTT for the Red Sox baseball team.

“Let’s see if there is a Pilita,” says Vanhoenacker, grabbing the iPad BA pilots now use instead of bales of paper charts. It turns out there is a PILTA in my native Australia, as well as a CLARK, a coincidence obviously, but a childishly pleasing one.

The last time I was in Australia, at the start of this year, I was struck by how many people asked for the first time about the safest way to fly to London. One couple told me they were planning to fly to Europe via Canada, in order to avoid war zones. This probably should not have been a surprise. There were 37 people from Australia on board Malaysia Airlines’ flight MH17 when it was downed over Ukraine last July. Another seven were on the same airline’s flight MH370 when it disappeared in March, in what has become the aviation industry’s greatest modern mystery. Australia is still leading a search in the southern Indian Ocean for any sign of the missing aircraft.

Being a serving British Airways pilot, Mark Vanhoenacker was reluctant to speculate openly about things like a disappearing aircraft. He said he had never had one close call in more than a decade of flying for BA and, like most pilots, was eager to talk of statistics showing how much safer it is to fly than drive. “To be honest, what startles me when I land and get on [a motorway] is, ‘Why isn’t this better controlled? Why isn’t somebody telling everybody where to go and why are we so close to those other objects?’” he said wryly.

He even managed to sound cheerful about all the security measures that came after hijackers crashed two jets into New York’s World Trade Center on September 11 2001, ending one of the great joys of flying: a visit to the cockpit. People forget it is still possible to ask to visit the cockpit once a plane is on the ground, he said. “We love to have visitors before take-off and after landing.”

And there is still a lot to marvel about in the sheer physics of flying, he added, recommending passengers get a window seat up the back so they can watch how a 747’s great wings bend in flight or how the flaps are deployed as the plane lands. Another tip he offered, for those flying anywhere near the Northern Lights, is that pilots rarely announce such things because they normally occur as passengers are trying to sleep. If you want to be alerted, you need to let the cabin crew know.

Still, I doubt any of this is enough to compensate for all the frustration that accompanies the average flight these days. The tedium of having to remember if toothpaste is banned or struggling to get your shoes off in a security line would not be so annoying if the rules were not so randomly applied.

Even pilots get fed up with such things, I discovered, after talking to Paul Mattson, a Boeing 777 captain on a major US international airline until his retirement last October. He said some pilots from his old airline deliberately avoid going to Heathrow because they find the security checks so irksome. “We have numerous pilots that do not fly to London simply because of the security measures. They go through absolutely everything. They single us out. With glee sometimes!” said Mattson.

An illustration of aviation security rules on 100ml limit on liquids
Bugbears include the random application of security rules such as the 100ml limit on liquids © Toby Leigh

Another thing that annoys him is the way the airline industry has changed. “Airlines are more and more run by business people rather than aviation people,” he says, which has led to a surfeit of regulations and procedures.

If there are more business people running airlines that is no doubt because the airline industry is such a difficult business. It is nearly 20 years since the billionaire investor Warren Buffett said capitalism would have been better off if Orville Wright had been shot down in 1903, because the industry has been a death trap for investors ever since. The only time the world’s airlines have made meaningful economic profits since 1947 was a four-year period in the 1960s, according to the sector’s main trade body, the International Air Transport Association (Iata). The recent fall in oil prices has helped drive down jet fuel costs, but profit margins remain woefully thin in an industry beset by a glut in capacity.

This year, Iata expects airlines to make profits of $25bn on revenues of $783bn, meaning they will only retain about $7 for every passenger carried. As a result, airlines subject passengers to an endless round of ruses to flog services once offered free of charge, from a seat reservation to a coffee.

An illustration of in-flight services that used to be free
So tight are today’s profit margins that airlines now often charge for services once offered free © Toby Leigh

Many in the industry counter that flying is cheaper than ever before. “Back in 1975 it would have taken a bit more than one week’s average UK earnings to have bought a typical return air fare. Today, one week’s earnings will buy almost two return air fares,” says Iata’s chief economist, Brian Pearce. It is also true that on the rare recent occasions when flights have suddenly been grounded, such as when millions of people were stranded after the eruption of Iceland’s Eyjafjallajökull volcano in 2010, passengers quickly realised how much they depend on flying.

Passenger numbers are only continuing to rise, especially in fast-growing emerging economies, where newly enriched middle classes are scurrying to board planes as eagerly as their predecessors in richer nations. But that points to one of the more contentious aspects of flying today: its environmental impact.

“The aviation sector faces a grave environmental challenge that is yet to be fully acknowledged,” says Bill Hemmings, an aviation policy specialist at the Brussels-based Transport & Environment research organisation, which estimates the industry’s emissions may be growing by as much as 3 to 5 per cent a year.

“Technical innovation can’t keep pace,” he said. “The answer has to be we all stop flying, certainly to the extent that we do today.”

Businesses need to look seriously at alternatives such as videoconferencing, he says. Governments need to start taxing aviation as much as road and rail transport, and stop building more airports to encourage more subsidised low-cost airlines.

Back in the flight simulator, Vanhoenacker was well aware of such criticism and eager to point out how the industry is working to improve its environmental footprint. Airlines are starting to warn pilots about delays at airports, which means they can slow down, burn less fuel and reduce circling time. The latest aircraft are far more fuel-efficient than their predecessors. And big efforts are made to reduce the weight of aircraft by, for example, ditching baby-changing tables that, incredibly, Vanhoenacker says were once widespread in cockpit toilets.

For all this, he knows that his message about the joys of flight is not easily heard in the modern industry. “I know not everybody loves flying as much as I do,” he said. But he insisted there is a fundamental fascination with flight, and I suspect he is probably right. “I don’t think it will ever go away,” he said. “It’s congenital really. We’re an aspiring species that doesn’t have wings. What else would we dream of?”

Pilita Clark is the FT’s environment correspondent and was previously its aerospace correspondent

Slideshow photographs: Greg Funnell

Illustrations by Toby Leigh

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