There was once a place called the University. I knew it well – in fact I grew up there. The son of a mathematician, I often spent time in my formative years hanging around campus. I enjoyed interacting with my father's colleagues. They were people who loved to argue. Even when I was a child they paid me the respect of challenging my thinking. They did so in a manner as generous and good-humoured as it was intelligent and robust. The idea that it might take courage to be a dissenting voice would, I think, have occurred to them as strange.

The people who inhabited that University knew what academic freedom was. They didn't talk about it, they simply lived it. They understood implicitly that academic freedom was both a privilege and a duty. They understood that the University was an institution at the heart of democracy, that the health of democracy is a contest of ideas and that, as academics, they had leading roles in that contest. Academic freedom – the freedom to say things that are controversial, unpopular, almost unthinkable – kept culture fresh and provided grist to the mill of politics.

The University I grew up in is fading fast. In the New University, academic freedom is all too often seen as an embarrassing relic of the past, or worse, as a tool of oppression. Recent research commissioned by the Free Speech Union (FSU) shows just how far it has fallen out of favour.

The FSU commissioned Curia Market Research to send a questionnaire to just about every academic in the country. Respondents were asked to rate, on a scale of one to 10, how able they feel to exercise academic freedom in various ways.

Most academics still feel free to engage in research of their choice and to criticise the Government. They also feel reasonably free to make choices about the subject matter in the courses they teach and to assess those courses in the ways they want.

Nearly half of the respondents though, rated their freedom to debate or discuss specific issues to do with the Treaty of Waitangi, or sex and gender, at five or lower. Even more concerningly, nearly half rated the broader freedoms to raise differing perspectives and to question and test received wisdom on the lower half of the scale. These results should disturb anyone who values a free society.

The Treaty, as well as sex and gender issues, have become sacred cows. There are doctrines about them that many academics feel scared to openly disagree with. And it's no wonder when we recall what happened to the seven Auckland professors who called into question the idea that science and mātauranga Māori are one and the same.

Those professors were subjected to scurrilous attacks. They were called "racist" and "shuffling zombies" by fellow professors. They were denounced in an open letter signed by thousands of university staff. Two of the group, Robert Nola and Garth Cooper, both Fellows of the Royal Society Te Apārangi, were investigated by the society and threatened with expulsion. When international heavyweights Richard Dawkins and Jerry Coyne weighed in in their defence, the society called off its attack dogs. Professors Nola and Cooper have since resigned from the society in disgust.

It's heartening that the leadership of the society has been called to account over the matter by a number of its own Fellows. Professor Gavin Martin has written a letter to the CEO of the society calling for apologies to Professors Nola and Cooper, and to the family of Professor Michael Corballis, a third Fellow who was to be investigated over the affair, but who died shortly after the investigation was announced. The letter also called for the society's code of conduct to be amended so that no such incident can happen again, and for a review of the structure and function of the organisation.

The letter was signed by 73 Fellows. Professor Martin noted that a number of other Fellows also expressed support but felt too intimidated to sign, either because they feared harassment or that their academic careers would be damaged.

Given all of this, it's hardly surprising that so many academics are reluctant to challenge dominant views or to speak their minds, especially when those orchestrating the struggle sessions are so often academics themselves. What was, perhaps, most disappointing of all in the whole Auckland seven affair, was the failure of most other academics to defend unequivocally the professors' right to speak their minds. That failure constitutes a mass abrogation of academic freedom.

In a recent column on his blog, left-wing commentator and free speech advocate Chris Trotter quoted one respondent to the survey who really doesn't like academic freedom. According to this respondent, academic freedom is "an archaic feudal principal (sic) employed by colonial capitalism to advance the upward mobility of the few and maintain the status quo".

Trotter did an excellent job of skewering this word salad for its historical illiteracy. I will add only that academic freedom is actually one of the principal mechanisms at our disposal for challenging the status quo. But I suspect that the academic who made that comment thinks that the status quo is simply whatever he or she disagrees with.

I encounter some of my dad's old colleagues around campus from time to time. It's always good to see them, but it makes me sad about what's been lost. They're in their 70s and 80s now, and they must wonder what's happened to their university. To dispel any doubt, when I say, "their university", I'm not speaking of a specific university, but of the spirit of open-minded scholarship they embodied. I hope that, in time, we'll find a way to rekindle that spirit in the bricks and mortar of our country's campuses.