Mike Rowbottom_3There was a rich irony in Oscar Pistorius' outraged reaction after his defeat here in the T44 200 metres final to the Brazilian who passed him in the final 25m, Alan Fonteles Cardoso Oliveira. But it was also a reaction which begged a very large question which still hangs over the business of amputee athletes running with the assistance of prosthetic "blades".

The defending champion whose right to run against able-bodied opposition in the World Championships and Olympic Games was only won after extended legal wrangling over the degree of mechanical advantage afforded by his own twin prosthetic "blades" insisted that his opponent had run on blades that were too long, making him much taller and offering him an unfair advantage in terms of speed.

"We are not running a fair race here, absolutely ridiculous," Pistorius told Channel 4's Sonja McLaughlan immediately after his race. "I'm not taking away from Alan's performance but I can't compete with Alan's stride length. The IPC (International Paralympic Committee) have their regulations and their regulations mean that some athletes can make themselves unbelievable high...his knee-heights are four inches higher than they should be.

"We have spoken to the IPC about the length of these blades but it has fallen on deaf ears. Guys are coming from nowhere to run ridiculous times. I don't know how you pull that back. I run at 10 metres per second and I don't know how someone comes back from eight metres behind in the home straight. It's not right."

In reply, however, IPC spokesman Craig Spence commented: "All blades are measured and Oliveira's passed the test. There has been no infringement of the rules."

Under IPC rules, prosthetic limbs are measured in the call room to ensure they are of equal length to the other limb, or prosthetic.

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"Oscar has to choose – either he was beaten fair and square by a better athlete or blade design CAN radically affect your performance level," tweeted Sir Matthew Pinsent, whose own involvement with blades was thankfully confined to the means by which he propelled himself and others to four Olympic rowing golds.

Bizarrely, almost two hours after the race had been run, both the IPC and Pistorius appeared to have shifted their positions, as Spence said that a special meeting would be convened on the following day to discuss Pistorius' "concerns" without the "emotions" of the race being involved.

Pistorius, meanwhile, appeared to backtrack on his earlier comments about Oliveira as he congratulated the Brazilian on "a great performance", adding that he had shaken the victor's hand on the warm-down track after the final.

Pistorius is unique. No other athlete has transcended the barriers in the way he has by becoming the first amputee to compete in world and Olympic track and field competition.

The South African's battles off the track have been as onerous as those on it as he has had to fight for the right to party at the Olympics, overturning an initial ban in January 2008 from the International Association of Athletics Federations (IAAF), whose lawyers contended that the two prosthetic carbon fibre "blades" on which this double amputee runs gave him a "mechanical advantage" over able-bodied athletes – and perhaps also single amputees, several of whom have complained in the past about the fact that Pistorius had an effective advantage by having two prosthetics rather than one.

The scientific judgement which ruled Pistorius out of competing against able-bodied athletes was routed in May 2008 by the intervention of Professor Hugh Herr of the Massachusetts Institute of Technology Media Lab, whose evidence and argument persuaded the Court of Arbitration for Sport (CAS) to reverse the IAAF ruling and give Pistorius clearance to run in the world championships and Olympics.

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"Perhaps there is some level of negative bias that exists in today's society," said Herr, a double amputee himself after suffering exposure on a mountain climb when he was a teenager. "When people look at Oscar Pistorius they see he has an unusual body. That's fine when he's not competitive. But when he's being competitive, it becomes threatening. In the same way that, for some people, the colour of a person's skin is threatening. There are people out there who simply have a negative bias.

"My personal view is that we should architect a society where, if a person happens to be born without fully formed legs and if that person happens to be an extraordinary talent, he or she should be allowed to compete in a sports event such as the Olympic Games assuming qualifying time are satisfied. It's the dream of almost all top athletes to go to the Olympics.

"We should allow athletes that freedom, but we should also ensure fairness in sport."

Fairness, however, is a tricky thing to establish in Paralympic sport, as the recent spate of contention over classification at these Games has underlined. The IPC is doing its best to create a level playing field, but they are dealing with hugely complex factors.

Even Herr, Pistorius' impassioned champion, does not maintain that there is certainty about Pistorius running against able-bodied competitors, or about the full nature of how prosthetics assist performance.

"There are many aspects of this question that we are still to understand," he said. "Science can never prove anything. What science can do is provide overwhelming evidence to support a hypothesis.

"The conclusion of the CAS hearing was that there was insufficient evidence to support the hypothesis that Pistorius had an overall advantage in the 400 metres."

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One other factor became clear in the wake of Pistorius' successful appeal of 2008, which nullified comments suggesting he was benefiting from escalating technological innovations.

Herr pointed out last year that the Cheetah blades used by Pistorius have been available to athletes in their current form for 15 years, and that the South African has run on the same blades for the previous seven years.

He adds that it was made clear during the CAS hearing that the ruling was "only specific to that prosthesis", adding: "If there were any changes, we would have to undergo the same scientific testing all over again."

Less than a month after he had become the first amputee track and athlete to compete at the Olympics in this same stadium it seemed as if Pistorius was set to defend his 200m title for the second time after setting a world record of 21.30sec in the previous day's heats.

That mark had eclipsed the world record of 21.88 set by Oliveira – who won silver in the 4x400m relay at the Beijing Paralympics – earlier in the evening. In the final, however, Pistorius could only manage 21.52 as his rival, running three lanes outside him, swept past in the final 25 metres to record a personal best of 21.45.

For once, the "Blade Runner" had failed to cut a swathe through his Paralympic opposition, and the capacity crowd which had acclaimed Pistorius so loudly registered the shock victory with something close to a murmur of surprise.

Now the 25-year-old from Sandton, Johannesburg, finds himself in an awkward spot as he looks ahead to the defence of his individual 100m and 400m titles.

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Amidst all the arguments about Pistorius' advantages or disadvantages, what has never been in doubt is the quality of the athlete himself, and the extraordinary courage he has displayed in taking on every challenge that has presented itself to him.

Tonight, however, he faced a different question concerning whether he was as admirable in defeat as in victory. His considered statement about Oliveira was clearly designed to erase the impact of his initial comments. But the fact that there will be an official meeting to discuss the matter makes it clear that he is pressing ahead with his case.

And the fact that the IPC are taking the matter so seriously also makes it clear what a complex matter it continues to be to ensure fair competition within the Paralympic Games.

Mike Rowbottom, one of Britain's most talented sportswriters, has covered the past five Summer and four Winter Olympics for The Independent. Previously he has worked for the Daily Mail, The Times, The Observer, the Sunday Correspondent and The Guardian. He is now chief feature writer for insidethegames and insideworldparasport.