"To feed or not to feed, that is the main question," says scientist Tomasz Kaminski, as we stand a few dozen metres from Europe's largest surviving animal. Through the trees, the huge chocolate-brown bison are nibbling at the first green shoots of spring, their breath steaming in the cool air.

Kaminski's question is also the question which underpins the arguments over the whole Bialowieza forest. Put frankly, this last significant fragment of the primeval forest that originally covered all of lowland Europe looks a mess. Dead wood litters the ground, offending the foresters who think nature needs a helping hand to thrive but delighting ecologists who say this alien beauty is in fact what nature truly looks like. (There's more on the Bialowieza forest itself in my longer piece.)

The bison, says Kaminski, are semi-natural but on the brink of being able to fend entirely for themselves. They live freely in summer. But in winter they are fed by rangers, taming the beasts to the extent that scientists have used CDs of tractor noise to attract them to an expected delivery of hay.

This support is understandable given the bison's extraordinary story - described as "a trick of history" by nature writer Adam Wajrak. For five centuries or so, up to the first world war, they thrived under the protection of Polish kings and latterly Russian csars, who protected the forest as a royal hunting ground. A herd of up to 1200 roamed and the rulers occasionally sent a bison or two to foreign capitals as gifts. This relict of prehistoric Europe amazed and enthralled, which was lucky.

Because as the devastation of the great war laid waste to Poland, the bison - up to 800kg of meat on the hoof - were driven to extinction in Bialowieza by those left starving by the conflict. It was only the zoo-kept gifts that allowed the population to be restored, and now 470 inhabit the ancient woods, the biggest free-living herd in the world.

Yet today's bison all descend from just six founders, and only two bulls, meaning a meagre genetic inheritance. And that is what makes the annual cull of up to 40 animals so controversial.

"By intensive supplementary feeding, [national park] managers increase bison survival and increase their reproduction," says Rafal Kowalczyk, a scientist who works with Kaminski at the mammal research centre of the Polish Academy of Sciences in Bialowieza. "Then they cull bison because there are too many individuals."

Over the two years 2009-2010, 48 bison were culled and 45 died of natural causes. About 30 animals are kept in special breeding centre as safety measure, should catastrophe befall the free-living herd. The scientists argue that the feeding should be phased out and the cull should stop, leaving death to claim its victims naturally, and for a simple reason: "Nature is a better selector than humans" in pruning weak animals out of the herd, says Kaminski. Genetic diversity is not visible to the riflemen.

Zdizlaw Szkiruc, director of the Bialowieza national park, defends the cull, pointing out that the bison have been fed in winter for centuries, and arguing that some ill or aggressive animals have to be killed. Rather prosaically, he adds: "It is easier to manage the herd and count them when they are fed." Marek Maslowski, director of the state forestry service in the region, says large bison herds damage the trees.

Janusz Korbel, a local ecologist, says the forest thrived for millennia without human interference, and that this rare spot simply needs to be left to alone. The culled bison are sold as meat and fur, but Korbel says, that like the dead wood that sustains the forest, the carcasses of the big beasts are also part of the natural rhythm of life and should not be removed. "A bison carcass will feed 20 species for 6 weeks in winter – it can be the key to existence for many species in the winter and spring time", when other food is scarce.

The bison, one of the few megafauna outside Africa to survive the migration of human hunters around the world, also plays an important role in seed spreading, through the dropping of its fertilising dung.

A last, mysterious facet to the question "what is natural?" is whether the bison are in fact native to the forest at all.

"I'm more and more convinced that the European bison is not a real forest specialist," says Kowalczyk. "Its ancestor - Bison priscus - evolved on the steppes of Asia, and its very close relative, the American bison, is a grazer using open areas. European bison also have many adaptations to grazing: their dentition, muzzle width and stomach." The suggestion is that our ancestors drove the last bison herds off the plains and into the forests.

As the animals roll their massive shoulders and step disdainfully away from us through the trees, the question remains: what is natural? The winter-fed bison, at least surviving? A herd not fed or culled, but perhaps living in a forest that was not their original home? Or, if it could be achieved, bison living on open plains? How far back in time do we need to go?