The arrival of migrating greylags in search of winter feeding grounds is as much a harbinger of autumn as rowan berries and drifts of golden leaves. But this year, in Orkney at least, they will be as welcome as bird flu.

Yesterday it was reported that, in an attempt to reduce the impact of greylag geese on the islands' farming land, Scottish Natural Heritage will oversee the culling of 5500 birds as they land from Iceland and Greenland. Over the next few weeks, as snipers pick off birds as if they were as dangerous as drones, these normally peaceful islands will sound like a battle zone, the hungry birds as helpless as sitting ducks.

The barrage of gunshot in the north will soon be echoed in Gloucestershire, where the first English licence for a badger cull has just been awarded. Like the greylags, these creatures will be shot as they leave their setts at dusk. More such licences are to be issued in an attempt to reduce the transmission of tuberculosis from badgers to cattle, where the disease is rife and deadly. The badger cull is to last for four years, and expected to cut levels of bovine TB by around 16%.

Even as this historic licence was issued, however, experts were decrying the move. Lord Krebs, one of the Government's most respected scientific advisors, has called it a "crazy scheme that may deliver very small advantage, may deliver none". Nor does anyone in its favour appear to see the irony in killing an environmentally valuable, indigenous animal to protect a highly-bred, farmed beast that's destined, from the day it's born, for the slaughterhouse. In Wales, meanwhile, plans for a cull have been replaced by a programme of vaccination. In Scotland, thankfully, the problem is so negligible it need not disturb the sleep of farmers, vets or marksmen. On the evidence of the Orkney geese genocide, however, one fears that in the event of an outbreak, the first line of attack would be snipers rather than syringes.

One is not unsympathetic to farmers and their livelihoods. Any gardener who has waged war on slugs or greenfly or rabbits can appreciate the frustration and cost of damaged crops. And in fairness to Orkney's farmers, they have tried to scare off the birds with kites and gas cannon, to no avail. Training crosswires on the geese, which SNH must have known would be controversial, is clearly considered a last-ditch effort. But, as with the badger cull, the fact it's seen as a final solution does not make it right.

This is not to say that all controlled killing is wrong. There are situations where, whether it's a single animal or a herd, it is clearly the humane and best thing to do. And, so long as death is swift, shooting is the least painful method. But what is deeply disturbing is the growing sense one gets that as the countryside shrinks, and wildlife increasingly encroaches on human activities, the easiest answer is to eradicate the innocent offender rather than find a compromise that allows people and wildlife to live alongside each other.

It's understandable that in less enlightened and more economically straitened times it was easier to reach for a club or a noose than work out a strategic long-term plan for minimising conflict. But in previous generations mankind's genius for destroying the balance of the ecosystem had barely got into its stride. Consequently, nature alone kept wildlife – and human – populations in check. Its methods could be brutal: predators, climate, lack of food, and disease. Nevertheless, it is decidedly sinister that in an age when we've never been more scientifically inventive and skilled, nor more aware of our ethical responsibilities to other species, we are acting more primitively than our ancestors. The Orcadians who built Maes Howe and Skara Brae may have been uneducated by today's standards, but they knew one lesson we seem to have forgotten: treat nature badly, and one day it will wreak its revenge.