If Kent is the garden of England, this corner of West Sussex is its abundant greenhouse. As my train rumbles past Ford and Eastergate and on to Barnham, all I can see is acre upon acre of glass glinting in the blinding sunlight. To my left, a grand Victorian edifice soars like a miniature Crystal Palace; to my right, a hi-tech hangar is packed to the ceiling with leafy green tomato plants. On the taxi ride to Runcton Nursery (plum and vine tomatoes), we drive past Nature's Way (bagged salad), Tangmere Airfield Nursery (peppers) and Langmead Farms (iceberg lettuce). All are supplying the Big Five supermarkets, turning out flawless, high-yield crops as fast as Mother Nature - and a battery of smart technology - can manage it.

This is the horticultural equivalent of Silicon Valley, the geographical heart of a modern industry that touches all our lives. Wander the aisles of Tesco, Sainsbury's or Safeway and the fruits of this cosmetic endeavour are everywhere. There are flow-wrapped trays of identical tomatoes called Baby Plum, Sugar Plum or Pomodorino (depending on where you shop), a uniform red in colour and lightly ribbed like a gourd. All are the same thick-walled variety known as Santa, promoted vigorously by the seed companies, adored by the supermarkets for their extended shelf life and supplied by Runcton Nursery. On the next shelf, trusses of vine tomatoes (Flavorino, Elegance) are arranged in packs with exactly eight fruits on each. What happened to the other two or three that would complete the bunch in nature? The truss, or piece of vine, is cut to just the right length so that it fits the packaging perfectly.

Then there are the polystyrene trays of shrink-wrapped red, green and yellow peppers, free of blemishes and looking almost manufactured in their plasticky perfection; the bags of pre-washed oak-leaf lettuce, curly endive and lamb's lettuce, inflated with gas-like helium balloons from a funfair; and the paper-lined boxes of glassy, symmetrical orbs labelled 'apples'. Has fruit and veg ever been this perfect? Why do we demand our produce so thoroughly scientific and squeaky clean? In a world where salad is a convenience food and 'easy peelers' (berries, bananas, grapes) are the biggest boom sector in the fruit market, the consumer is so detached from the business of growing that the horticulturists could be selling us anything. GM hybrids, flavourless varieties laced with chemicals, super-chilled apples smothered in plant hormones and sprayed with wax to preserve their looks. I've heard about the methods used by the fruit beauticians, but are the rumours true? At Runcton, the flagship nursery of Humber VHB - formerly Van Heyningen Brothers - I begin to discover the truth about perfect fruit and the people and technology that make it possible.

'This is what we call the top site,' says Paul Challinor, operations director at Runcton, 'which has 23 acres of glass'. We enter a humid greenhouse the size of 10 football pitches, packed from floor to ceiling with dense foliage and smelling like a rainforest. From March to November, this site will produce 8.1 million trusses of tomatoes, harvested by 'operatives' who move along on rail-mounted trolleys, deftly snapping off trusses with their fingers. As we walk along the rows of vines, cooled by giant ceiling fans, piped music drifts from the PA speakers - 'It's for the workers, not the plants,' quips Challinor - and I notice with satisfaction that it is Sting's Fields of Gold (doesn't Pomodorino mean little apple of gold?) The ribbed plum tomatoes look like plastic replicas: shiny, symmetrical and perfectly clean, with not a trace of grit or mud.

'As you can see, there is no soil,' says Challinor, squatting down. 'All commercially produced tomatoes in Britain, apart from the organic ones, are grown hydroponically.' Tearing open its polythene covering, he digs his fingers into a slab of Rockwool in which the vines appear to thrive. 'It's a by-product of the loft insulation industry,' he explains, 'a mineral block drip-fed by water and enriched with fertilisers. There's potassium for fruit quality; calcium for strong healthy walls; nitrogen for growth.' When the water is drained of goodness, it is recycled - drawn by gravity along corrugated pipes to a unit where it is filtered and disinfected with UV light. A computer measures the sunlight, prompting the system only to provide water when the atmosphere is hot and the plants are thirsty. 'Over-watering can waterlog the slab,' says Challinor, 'which could damage the fruit. If it sucks up a lot of water, it can split.' As the clouds part, filling the greenhouse with dazzling sunlight, ventilation flaps open automatically in the roof like something out of a 007 movie; in some greenhouses, sunshades slide into place like roller blinds and a water spray cools the atmosphere and cleans the glass. Every few minutes, plastic sleeves running between the rows of vines pop open like inflated party whistles, discharging CO ² gas (essential for a plant's survival) into the atmosphere through pinholes. 'The computer will tell us that East Phase Two needs CO ² ,' Challinor says, 'and the system will oblige.'

It's an absurdly cosseted environment, an eerie place with no wind, no rain, no movement and no dirt. Suddenly, I remember that Paul Challinor's PhD project was growing carnations in mineral-rich lunar rocks for two years. 'They didn't look great,' he admits, 'but they survived.' Here, the tomatoes look and smell wonderful. They are almost without exception Class 1, grown to an improbably high cosmetic specification set by the supermarket buyers, who believe their customers are driven more by appearance than by taste. 'With these Flavorino vine tomatoes,' says Challinor, 'there would be 10 or 12 flowers on each truss - but the likes of Sainsbury's want exactly eight tomatoes, so we have to prune. If we left 10 on, the top ones would be too soft and the bottom ones too green - they always ripen from the top - so the supermarkets would reject them. They complain, they warn you, and if it doesn't improve, they reject the whole batch. Since we pay the disposal costs, it pays to get it right.'

What the multiples want is pristine specimens with no sign of mould or insect damage, prompting me to ask Paul Challinor about the use of fungicides and pesticides. 'There is absolutely no spraying in this greenhouse,' he insists. 'These days, because growers have developed resistant or tolerant varieties - not using GM, but through natural breeding programmes - there is less of a need for spraying.' To combat whitefly, Runcton uses biological pest control in the form of the tiny encarsia wasp. 'It comes on these cards,' says Challinor, showing me what look like Christmas gift tags hanging among the vines. Stuck to the cards are parasitised whitefly larvae - the creamy white 'scales' of whitefly familiar to gardeners, injected with the egg of an encarsia wasp which turns them black. 'The wasp hatches from these black dots,' Challinor explains, 'lays its egg in another larva, killing it, and that scale then hatches into a wasp. Since the Seventies, we've been putting in encarsia every single week.'

Meanwhile, further titanic struggles are occurring among the snaking tomato vines. 'Red spider mite is our second biggest pest,' says Challinor, 'and a predatory mite is used to control that. We shake the mites from a bottle, they all have a big scrap - and hopefully ours win.' As if this insect menagerie isn't enough, further help is elicited from the bumblebee. Every few metres at Runcton, cardboard hives are attached to pillars, releasing a steady procession of bees which pollinate the yellow tomato flowers pre-empting the fruit itself. Though free to escape the greenhouse through vents in the roof, they prefer the easy life of horticultural service. 'They get their carbohydrate from liquid sugar sealed permanently into the hive,' says Challinor, 'and their protein comes from the pollen. If they do escape, most die because they're not used to it - but if they do come back impregnated with rapeseed pollen, say, the other bees won't let them in because it's toxic to the hive.' To emphasise the point, he taps a box as we wander past. 'If you do that,' he says, 'a guard bee will appear to keep foreigners out.'

Used widely in commercial greenhouses, the bee is more than a cute novelty or a nod towards green horticulture. Before the days of bumblebee pollination, workers would walk around the greenhouse with a stick and knock the branches, shaking pollen into the open cones of flowers. 'With production on this scale,' Challinor points out, 'that would be a full-time job. Also, you would get a lot more inferior, Class 2 fruit that way. Unless the pollination is totally even, you get fruit with no seeds, or the seeds all on one side, which leads to a misshapen product. Bee pollination is a big step forward.'

It's a mark of just how bizarre food production has become, that bees are seen as a useful new development. They were here long before the beekeepers in their peculiar, netted headgear; and aeons before the specialist growers who are 'breeding out' viruses to produce resistant strains of fruit; or the biotechnologist (Professor David James at Horticulture Research International in East Malling, Kent) who has isolated the gene for fruit ripening and is learning to switch it off; or the white-coated graders who use smart cameras and electronic sensors to detect even the tiniest flaw or asymmetry in a kiwi fruit as it rumbles off the conveyor belt on its way to Tesco; or the ethylene store manager, pumping a sealed chamber full of gas to trigger the ripening of bananas which arrived from the West Indies as green as grass and are about to turn yellow.

These are the unknown faces of hi-tech fruit production - and another is coming towards me now in the form of Tim O'Neill, a plant pathologist with ADAS Consulting Ltd, who happens to be paying his routine visit to Runcton. Dressed in white overalls and carrying a protective mask, he has spent the morning checking plants for signs of disease, taking out suspicious roots, wilting or yellowing leaves for laboratory examination. Those are all signs of stress, and it is O'Neill's job to find the cause. 'The Dutch have problems right now with a fungus called verticillium wilt,' he reveals, 'which is why I'm testing for it. Since 1974, all tomato plants grown in the UK have been varieties with a built-in resistance to it - but now we are finding they can still get it even when a resistant VE gene is present.'

It's an impressive job, keeping one step ahead of wily old nature to match the supermarket specification sheets - but is there a price to pay for beauty? When Paul Challinor proudly offers me some Humber VHB tomatoes to taste, I can already predict the outcome. Though the green stems of the truss varieties smell overpoweringly of tomatoes, the same cannot be said of the flavour - even the Flavorino. Compared to the organic tomatoes I have delivered every week, they are watery and slightly chewy; they don't explode with sugary flavour, or exhibit the earthy, sunny complexity that can only be attributed to soil or - to borrow from the French winemaker's lexicon - terroir . When I sample the Santa mini plums, favoured by the supermarkets for their thick shells and extended shelf life (between five and seven days after picking, rather than the usual four), there is too much shell and not enough juice. They may be 'poppable' in the mouth and therefore popular with children, just as Paul Challinor said, and I can't dispute his claim that 'television chefs have used Santa for cooking because the skin stands up better to it' but it is still an average tomato.

That is the charge levelled at hydroponics - and, in particular, the high-volume, aseptic production methods perfected by the Dutch. Though safe and perfectly palatable for the average supermarket shopper, fruit and vegetables grown under laboratory conditions just don't get the gastronomic juices going. At New Covent Garden market in southwest London, wholesale supplier Charlie Hicks has plenty to say on the subject. 'Our company, Lenards, supplies the top end of the catering market, the restaurateurs,' he says, 'and if we show up with a box of Dutch gear, they want to know why. If you went to the River Café with Dutch gear, your feet wouldn't touch the ground. That would be it, wouldn't it? They'd laugh at you.'

As a passionate supporter of small, specialist suppliers and farmers' markets, Hicks has a host of stories to tell about the folly of supermarket buyers - and anyone else who shops with their eyes rather than their taste buds. 'The supermarkets don't want to know about scarred fruit,' he maintains, 'and I've heard of them rejecting Spanish oranges because they had marks on them. Now, the ripest, tastiest oranges are always on the outside of the tree because those are the ones that get most sun. They also get more wind damage, so they look a bit bashed and battered - so you will never find the best oranges in a supermarket.'

Apples, too, are routinely rejected (or downgraded for use in processing) for reasons that defy common sense; according to the survey Supermarkets and Great British Fruit conducted by Friends of the Earth in October last year, even cooking apples - which are almost always peeled - are often rejected because they have imperfect skin. Of the British fruit growers polled, 90 per cent said supermarkets had rejected fruit on the grounds of russeting or minor skin blemishes that had no effect on eating quality. Among the other cases cited were apples that were too red or not red enough, fruit that was too big or too small, and pears that were the wrong shape (ie, not sufficiently pear-shaped). The key finding, however, was that half the respondents were having to apply more pesticides to crops to satisfy the cosmetic demands of the supermarkets, literally endangering the planet for appearances' sake.

For consumers, it is a tough call. As subscribers to organic box schemes know, fruit and vegetables untouched by the fruit beauticians can be a ragged and unseemly bunch - torn and blackened outer leaves on lettuces, rocket and mizuna full of holes, the odd rotten orange or a cabbage riddled with caterpillars. Most people, if asked to choose between this and the more pristine version, would damn the planet and opt for cosmetic perfection. Such a choice not only puts growers out of business (they themselves bear the cost of rejected or downgraded fruit), but endorses the idea that appearance and symmetry are as important as nutritional value and flavour which they are not.

'I do think this quest for perfection has gone too far,' says David Johnson, a fruit specialist who works for Horticulture Research International. Though his job is to develop storage technology for apples - largely in a bid to satisfy the supermarkets, he recognises the pressure put on growers by the obsession with appearance. 'It drives some of our producers mad,' he concedes, 'and when you look at carrots, which have to be tapered with no cracks, and cucumbers that must be a certain shape and perfectly straight, you have to ask, "Do these things really matter?" If the product is wholesome and physically sound, how important is it? I think flavour is making a comeback and perhaps, in the fullness of time, people will accept a slightly different quality to get that flavour. But right now, appearance has a higher priority than it should.'