There are lots of ways one might bookend the New Labour years, if they are indeed coming to an end. One of the more obscure is the long and intractable argument about badgers. Not badgers as in cute, furry black-and-white creatures that we all love to glimpse pottering down rural roads at night, but badgers as evil, the reservoirs of a kind of tuberculosis that they give to cows, and that cows give to them. It illustrates all Labour's caution, the desire to appease every shade of opinion, the emphasis on fact and the capitulation to emotion – in fact all the stuff of daily politics. And after 13 years, a conclusion is no nearer than it was in 1997.

The badger debate brings head-on conflict between the economics of farming and the passionate defenders of the rights of animals, particularly wild animals. Both sides can marshall quantities of science to their support. They also tend to fall into rival political camps. To generalise more than a bit, farmers mostly aren't Labour and friends of the badgers mostly aren't Tory. Veterinary opinion leans to the farmers. The Independent Scientific Group on Cattle TB that was set up to try to make sense of the evidence leans towards the badger. For a wonderful example of the ding-dong that results, see the Defra website.

There are four important ways that bovine TB is spread. Badgers give it to badgers. Cows give it to cows. Badgers give it to cows. And cows give it to badgers. The rival positions might be caricatured like this: if you kill all the badgers and all the cows with TB, then you'll cure the problem. But if you kill all the badgers (because you can't tell which ones have TB) and left the cows, or if you kill all the cows with TB and all the cows that might have TB, then you won't. The disease will carry on spreading. Because for as long as there are badgers with TB, some cows that don't have TB will continue to catch it from them (don't ask how, you really don't want to know) and give it to other cows. And if you kill all the badgers but leave the cows, then cows with TB will spread it to the badgers that repopulate the area. Either way, off you go again.

One place that doesn't have a problem is Scotland. Stringent testing of cattle – and particularly of those that have just arrived from infected areas south of the border (the south-west of England and west Wales are hot spots) – has meant the country has achieved the EU's highly desirable TB-free status.

No one is suggesting kill the badgers and leave the cows. But the Welsh assembly is proposing killing the badgers in west Wales, and at the same time strictly monitoring and culling infected cattle. The rural affairs minister, Elin Jones, argues that this is, as far as it is understood, best practice: the area is bounded on three sides by water, reducing (but not eliminating) the impact of the most powerful argument against a cull – that the moment you clear an area of badgers, other, possibly infected, badgers move in from neighbouring areas, while others understandably scarper outwards, spreading the disease and triggering higher rather than lower infection rates in the immediate surrounding area. They propose continuing the cull for at least five years.

George Monbiot says this is daft. How can you test two propositions at once, especially when there is no controlled experiment taking place? And of course, scientifically speaking, he is quite right. But this is not an experiment in any scientific sense. It is a pilot.

Perfectly sane and lucid critics also argue that it is not a viable long-term solution. Only an effective vaccine against TB in badgers, combined with much more stringent cattle testing, will keep the disease under control. Elimination is not an option. Unfortunately, there is not yet (though there might be within the next five years) such a vaccine. As for stricter, and broader, monitoring of cattle, that is another political hurdle that neither Cardiff nor Westminster has managed to tackle: the more you test, and the more you cull, the more expensive it becomes.

For those engaged on both sides – such as Brian May, who clearly cares passionately about badgers – this is a defining moment, one that reveals our innermost souls. But maybe, if you strip away the furry black-and-white faces, and blot out the image of a cow's liquid brown eyes, and really, really, address the issues – well, it is a really hard call. But then, that's politics.