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This is the sort of thorny question scientists from the British Antarctic Survey (BAS) will be investigating in a three-year study of the interaction of aircraft and penguin colonies.

The research is part of a general effort by the agency, which operates Twin Otter and Dash-7 aircraft on the South Polar ice-cap, to minimise the impact of its operations on the environment, as required by the Antarctic Treaty.

It will begin this year by observing the effects of the two Lynx helicopters from the ice patrol ship HMS Endurance on colonies of gentoo penguins on the island of South Georgia. 

The helicopters are used to count the nests in the colony using aerial photography, but this year for the first time video cameras will be installed on the ground to record the birds' reaction to the choppers' presence above them. Next year it will be the turn of king penguins, and then either chinstrap or adelie penguins. 

"We want to be able to characterise what the impact of aircraft is, and we want to relate the impact to the particular species of bird and the type of aircraft," said Dr David Walton of BAS.

"There are various possible responses by the penguins, from adopting a defensive posture to actually leaving the nest and the eggs. If we decide we need to fly across areas where there are seals or birds we need to be able to take the risks associated with that into account when planning the operation. That's just good management." 

There are potential risks, Dr Walton says, citing stories of disastrous encounters between penguin and aircraft. At Macquarie Island in the Southern Ocean, he says, a large number of royal penguins are believed to have stampeded over a cliff in 1980 when buzzed by a low-flying Australian Hercules transport.

"It was hard to verify – there wasn't anybody in the rookery at the time – but they found a lot of penguins dead," he said. "There were thousands of mortalities." 

Even stranger is the long-standing rumour in the Falklands of what happened when a penguin colony was buzzed by a low-flying Hercules from the Royal Air Force. 

"The birds are supposed to have looked up, followed the aircraft across the sky, and all fallen over backwards," Dr Walton said. 

"Personally, I've got my doubts."