For many parents, childhood vaccinations are this century's abortion debate – highly divisive and driving a wedge between friends and neighbours. In the red corner are those banging the 'vaccinate at any cost' drum, and in the blue corner a collection of concerned parents and carers who say they're dealing with the damage done.

For people in the pro-vaccination camp, the fact that there is even a debate to be had is vexing. "What's wrong with these irresponsible parents?" they say. "So educated and yet so stupid! Don't they know that MMR study was discredited? And how can you take a Playboy Bunny seriously?" But there are reasons why the case of the curious link between vaccinations and autism is not closed, and Andrew Wakefield and Jenny McCarthy are not necessarily two of them.

If the voices of those concerned parents and carers aren't enough, consider this: recently, in a case before the US Court of Federal Claims, the US government conceded vaccines had aggravated a young girl's mitochondrial disorder to the point where she developed autism. As a result, the National Vaccine Injury Compensation Program awarded her family an upfront payment of $1.5 million, and an additional ongoing payment of $500,000 per year to cover her care as well as the family's lost earnings, pain and suffering.

It has since emerged that dozens of other families have reached similar settlements, and the Centers for Disease Control in the US has announced new research into vaccine safety.

Consider this, too: while we still don't know exactly what causes autism, the latest research – including the study released by Dr Amaral of the University of California last week – is coalescing around the view that it's a combination of genetic, immune system and environmental factors. Earlier this year, Dr Amaral said that, "there is a small subset of children who may be particularly vulnerable to vaccines if the child had a precondition like a mitochondrial defect ... vaccinations, for those children, may be the environmental factor that tipped them over the edge."

So why hasn't this come up in vaccination studies to date? Dr Martha Herbert, professor of neurology at Harvard Medical School, says, "the problem with the population studies is they aren't necessarily designed to have the statistical power to find subgroups like that if the subgroups are small."

That means we're not studying the right kids. We don't even know where to find them, because most of the time we don't know they have those vulnerabilities until they're aggravated. Herein lies the great mystery.

So where do I stand on this? I'm not a parent. I haven't yet had to make the agonising decision about whether or not to vaccinate my child. But I do know this: I'm definitely pro-vaccines and understand all too well the benefits they bring, and I also know they're toxic for some kids. Because I saw what happened in the case of one of my nephews, for whom vaccination was one of several environmental factors and assaults to his immune system that, along with genetic predisposition and an underlying vulnerability, stressed his body and his mind so much that he slipped into autism. It's not a conclusion that his mother, a sober individual pushing 40 with an honours degree in science and a background in public health, wanted to reach, but in the end it was undeniable.

His two brothers were vaccinated too, and they were fine. He was not. And it sends a chill down my spine when people talk dismissively about the "acceptable risk" of vaccines in the context of a broader public good. If it were their child, the risk would not be acceptable. Particularly if something could be done to mitigate it without compromising the benefits – and clearly, there is.

We can change the ingredients (like we did when we removed mercury). We can change the way they're administered (using drops instead of injections, so the virus can be broken down by the immune system's natural defence mechanisms before it gets into the bloodstream, instead of being propelled straight into it at full strength). We can get better at identifying children with vulnerabilities and treating them accordingly. And we can persevere with research until we find out why this keeps happening.

These are things we can and must do. The trouble is, in today's polarised public square, the middle ground seems to have disappeared from beneath our feet. Conversations about vaccines typically descend into petty point-scoring and vilification, particularly on the troll-fertilising Internet. It discourages honest, respectful discussion. And to those who think giving oxygen to the debate will cause parents to stop vaccinating their kids, I say this: it's happening anyway. It's precisely the lack of information, the factual vacuum, that fuels anxiety and stifles life-saving progress.

Like any issue with a degree of complexity, there are more than two sides to this one. We must have the courage and maturity to listen to everyone, including the mothers and the fathers dealing with the unacceptable, potentially avoidable consequences. They're the canaries in the coalmine, and the real reason why this case is not closed. It's just that science, like the law, sometimes takes a while to catch up.

Marj Lefroy is a freelance writer with a special interest in autism.

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