Thomas Huxley, the British biologist who so vociferously, and effectively, defended Darwin's theory of natural selection in the 19th century, had a basic view of science. "It is simply common sense at its best – rigidly accurate in observation and merciless to fallacy in logic."

It is as neat a description as you can get and well worth remembering when considering how science is treated by the UK media and by the BBC in particular. Last week, a study, written by geneticist Steve Jones, warned that far too often the corporation had failed to appreciate the nature of science and to make a distinction "between well-established fact and opinion". In doing so, the corporation had given free publicity to marginal belief, he said.

Jones was referring to climate change deniers, anti-MMR activists, GM crop opponents and other fringe groups who have benefited from wide coverage despite the paucity of evidence that supports their beliefs. By contrast, scientists, as purveyors of common sense, have found themselves sidelined because producers wanted to create controversy and so skewed discussions to hide researchers' near unanimity of views in these fields. In this way, the British public has been misled into thinking there is a basic division among scientists over global warming or MMR.

It is a problem that can be blamed on the media that believe, with some justification, that adversarial dispute is the best way to cover democracy in action. It serves us well with politics and legal affairs, but falls down badly when it comes to science because its basic processes, which rely heavily on internal criticism and disproof, are so widely misunderstood.

Yet there is nothing complicated about the business, says Robert May, the former UK government science adviser. "In the early stages of research, ideas are like hillocks on a landscape. So you design experiments to discriminate among them. Most hillocks shrink and disappear until, in the end, you are left with a single towering pinnacle of virtual certitude."

The case of manmade climate change is a good example, adds May. "A hundred years ago, scientists realised carbon dioxide emissions could affect climate. Twenty years ago, we thought they were now having an impact. Today, after taking more and more measurements, we can see there is no other explanation for the behaviour of the climate. Humans are changing it. Of course, deniers disagree, but that's because they hold fixed positions that have nothing to do with science."

It is the scientist, not the denier, who is the real sceptic, adds Paul Nurse, president of the Royal Society. "When you carry out research, you cannot afford to cherry-pick data or ignore inconvenient facts. You have to be brutal. You also have to be sceptical about your own ideas and attack them. If you don't, others will."

When an idea reaches the stage where it's almost ready to become a paper, it has therefore been subjected to savage scrutiny by its own authors and by their colleagues – and that is before writing has started. Afterwards, the paper goes to peer review where there is a further round of critical appraisal by a separate group of researchers. What emerges is a piece of work that has already been robustly tested – a point that is again lost in the media.

Over the centuries, this process has been honed to near perfection. By proposing and then attacking ideas and by making observations to test them, humanity has built up a remarkable understanding of the universe. The accuracy of Einstein's theories of relativity, Crick and Watson's double helix structure of DNA and plate tectonics were all revealed this way, though no scientist would admit these discoveries are the last word, as the palaeontologist Stephen Jay Gould once pointed out: "In science, 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional assent'," he admitted.

Certainly, things can go wrong, as Huxley acknowledged. Science may be organised common sense but all too often a beautiful theory created this way has been skewered by "a single ugly fact", as he put it. Think of Fred Hoyle's elegant concept of a steady state universe that is gently expanding and eternal. The idea was at one time considered to be philosophically superior to its rival, the big bang theory that proposed the cosmos erupted into existence billions of years ago. The latter idea explained the expansion of the universe by recourse to a vast explosion. The former accounted for this expansion in more delicate, intriguing terms.

The steady state theory continued to hold its own until, in 1964, radio-astronomers Arno Penzias and Robert Woodrow Wilson noted interference on their radio telescope at the Bell Labs in New Jersey and tried to eliminate it. The pair went as far as shovelling out the pigeon droppings in the telescope and had the guilty pigeons shot (each blamed the other for giving the order). Yet the noise persisted. Only later did the two scientists realise what they were observing. The static hiss they were picking up was caused by a microwave radiation echo that had been set off when the universe erupted into existence after its big bang birth.

That very ugly fact certainly ruined Hoyle's beautiful theory and, no doubt, his breakfast when he read about it in his newspaper. But then the pursuit of truth has always been a tricky and cruel business. "It is true that some things come along like that to throw scientists into a tizz but it doesn't happen very often," adds Jones. "The trouble is, the BBC thinks it happens every day."

And this takes us to the nub of the issue: how should science be reported and recorded? How can you take a topic such as climate change, about which there is virtual unanimity of views among scientists, and keep it in the public's eye. The dangers of rising greenhouse gas emissions have dramatic implications after all. But simply reporting every tiny shrinkage in polar ice sheets or rise in sea levels will only alienate readers or viewers, a point acknowledged by May. "Newspapers, radio and TV have a duty to engage and there is no point in doing a lot of excellent reporting on a scientific issue if it is boring or trivial. The alternative is to trivialise or distort, thus subordinating substance in the name of attraction. It is a paradox for which I can see no answer."

Jones agrees. "What we don't want to do is go back to the days when fawning reporters asked great figures to declaim on scientific issues – or political ones, for that matter. On the other hand, we cannot continue to distort views in the name balance," It is a tricky business, but as former Times editor Charlie Wilson once told a member of staff upset at a task's complexity: "Of course, it's hard. If it was easy we would get an orang-utan to do it."

Jones, in highlighting a specific problem for the BBC, has opened up a far wider, far more important issue – the need to find ways to understand how science works and to appreciate its insights and complexities. It certainly won't be easy.