“This is your big chance. Just do your best.” Owen gazed down at 39-year-old Scott Routley, lying on a gurney. Scott had studied physics at the University of Waterloo, Ontario, but his promising career in robotics came to an end when, aged 26, he collided with a police vehicle. Since that accident, on 20 December 1999, Scott had been diagnosed as being in a vegetative state by a well-seasoned neurologist, Bryan Young, and in 2012 his diagnosis was confirmed by Owen’s team, again using traditional methods.

As Owen talked to him, Scott’s mouth remained wide open, apparently unaware, the same way that he’d been in the 12 years since the accident. This encounter was filmed by a crew from the BBC. Reporter Fergus Walsh was there to witness the moment that Owen attempted to reach inside Scott’s mind. Owen admits now that he was sceptical that the scans would reveal anything at all.

The team scanned Scott several times. To their surprise, the pattern of brain activity showed Scott knew exactly who he was, where he was and that he was actively choosing to answer the team’s questions. “My heart stopped when we asked if, after 12 years, Scott was in pain,’’ Owen recalls. “Thankfully, the answer was no.”

Although Owen’s colleague, Lorina Naci, recounts how the experience of telling the Routley family the news was “quite emotional”, the BBC crew were surprised at their relative lack of celebrations. Not Owen. Scott’s parents, Jim and Anne, and his brother, Ritch, had always been convinced that he was conscious. They insisted he could lift a thumb or move his eyes to indicate as much, even though standard tests had always reached the same gloomy conclusion: Scott was unresponsive.

Scott had the same neurologist — Young — for more than a decade and had appeared vegetative in every assessment, including more than a dozen separate assessments by Owen’s own team. Perhaps the family discerned subtle signs of consciousness that were almost undetectable, even to the trained eye. Or perhaps they had deceived themselves, as many families do for comfort. “Either way, it was the word of the family against that of my team, and their word against an army of specialists over many years,” says Owen. Where the family saw a sign of cognition, the doctors saw only wishful thinking. “The scans showed that they were right, perhaps for the wrong reasons — we will never know — but Scott’s story teaches us the value of objective measures. And the need for a little humility.”

There’s anecdotal evidence that when contact is re-established with the occupant of a living box they are understandably morose, even suicidal. They have been ground down by frustration at their utter powerlessness, over the months, even years, it can take to recognise their plight. Yet the human spirit is resilient, so much so that they can become accustomed to life in this twilight state. In a survey of patients with locked-in syndrome, Laureys has found that when a line of communication is set up, the majority become acclimatised to their situation, even content (again, these insights took some time to be accepted by the medical and scientific establishment — and even to be published in a scientific journal — reflecting the prevailing unease about the implications for hospitals and care homes).

The important question is detecting the extent to which such patients are conscious. Studies of large numbers of patients with brain injuries, and how they fare over the years, show that it makes a huge difference to the chance of recovery if a patient is minimally conscious rather than vegetative. The former have fragmentary understanding and awareness and may recover enough to return to work within a year or two. Yet there are still surprises, such as the case of New York fireman Don Herbert, who awoke after a decade from a minimally conscious state caused by a severe brain injury suffered while fighting a fire in 1995. In the past year, Schiff has recommended withdrawing care from a man who had lain in a coma for eight weeks after a cardiac arrest. “I was wrong,” he says. “This man is now back at work.” Schiff has used a technique called diffusion tensor imaging to show how a brain can rewire itself even decades after an injury.

It is important too not to lose sight of the impact on the families. Take Jamel, a 41-year-old construction worker left unconscious after a cardiac arrest. His family became convinced he had a glimmer of awareness and, fighting against the doctor’s stark diagnosis, spent almost 14,000 euros transporting him to Liège and Steven Laureys’s team for a detailed diagnosis. Sadly, their scans revealed no signs of consciousness. The family took the news badly. His sister Leila insists that Jamel can hear what they are saying. He was tired out by travel and surgery before he had his scan, she explains. The family has vowed to gather video evidence to show Laureys.

Parashkev Nachev has not changed his view since he first criticised Owen’s work and has spelt out the basis of his unease in a more detailed paper published in 2010. “For every relative of a living PVS [persistent vegetative state] patient given (probably false) hope, another is burdened with the guilt of having acquiesced in the withdrawal of treatment from someone who — he has been led to believe — may have been more alive than it seemed,” he says. “There are moral costs to false positives as well as to false negatives.”

“I find the whole media circus surrounding the issue rather distasteful,” he told me. “The relatives of these patients are distressed enough as it is.”

Laureys, Owen and Schiff spend a great deal of time with the families and understand these sensitivities only too well. Owen counters that, from his years of experience dealing with the families, they are grateful that doctors and scientists take an interest and are doing everything that they can. “These patients have been shortchanged over the years,” he insists. A recent study showed that many people would grant more ‘moral rights’ to a corpse than to someone in a vegetative state. This surprising finding emerged when a team from the University of Maryland and Harvard University asked 201 people to read accounts of a car accident in which the protagonist lived, died or sank into a persistent vegetative state. The latter was regarded as worse than death.

Owen is adamant that doctors have a moral duty to provide a correct diagnosis, even if the results do cause guilt, unease or distress. “We must give every patient the best chance of an accurate diagnosis, so we can give them the appropriate care that goes along with that diagnosis.”

Under the umbrella classification of ‘vegetative’ lies a vast array of different brain injuries and, as a result, even some of the most vocal critics accept that some vegetative patients are not as diminished as traditional measures suggest. Lynne Turner-Stokes chairs a group for the Royal College of Physicians that is revising UK guidelines on ‘Prolonged Disorders of Consciousness’. She remains unconvinced that the exceptional cases identified by Owen, Laureys and Schiff are particularly common or that enough has been done to establish brain scanners as a standard tool for routine diagnosis, particularly when the cost and convenience of these methods are taken into account. When it comes to extending these tests to all patients in a vegetative states as standard practice, “the evidence is just not there yet,” she says.

Despite all the hard work done since the pioneering research of Plum and Jennett, there’s still a need for basic spadework to harmonise standards, tools and timescales of assessment for these patients, says Turner-Stokes. More has to be done to ensure that a vegetative patient in, say, the UK is assessed in the same way as one in the USA, and to close gaps in understanding of this very complex group of patients, notably how their brains can change and heal over time. But she stresses that she is simply being cautious, not sceptical, describing the work of Owen, Laureys and Schiff as “important and exciting”.

“We are only just beginning to scratch the surface,” she says. “But I have no doubt [these techniques] will have a place, eventually, in the evaluation of patients.”