What is "academic freedom"?

It is curious that I should have come across an article by Andrew Bolt on that very topic in this morning's paper.  I spent part of yesterday reading a piece of research a colleague cannot get published.
In frustration he sent it to me and asked, "Am I missing something? Can you see the flaw in what I did? They keep saying I am wrong."
I read it and read it again. I asked someone else I know to look at the methodology. Then I went off to do some banking for the Senior Cat and I thought about it. The person I consulted on the methodology works in another area entirely but he has a reputation for meticulous work and his methodology has received accolades over the years. No, nothing there that he could see.
I have just sent an email saying that I can't see anything wrong and that I think the problem is that the results don't back up the previous research. There were questions raised about the methodology used in a previous paper but they were dismissed.
It is likely that he will just have to accept that the paper won't be published in a reputable academic journal. He can put it up on the internet in another way - if he dares.
And there is the problem. His colleagues in the field are not going to like his findings. He is going to be accused of going against the present theories.
It's not a politically sensitive area like climate change - the area that has Andrew Bolt's subject, Professor Ridd, in so much trouble he has lost his job over it. It is a potentially useful area in visual perception. 
I made one suggestion - that he sees if he can get someone else to replicate the results. The message came back, "Yes, on to that."
I thought he would be.
It is a problem I faced when I was doing my doctorate. There was absolutely no intention on my part to question the results of research done by people who were almost household names. It just happened. I couldn't get the results I was supposed to be getting in order to go on and do what I had planned. My chief supervisor was beside himself.
    "You must be doing something..."
No, I wasn't. We found three more potential subjects. He came and watched. Someone else came and watched. I got the same results. At the end of it I was told to go on with what I was doing. I realise now I should have been told to write it up - but mere students are not meant to question the results of their elders. I just did as I was told.  When I defended my thesis the only really searching questions were about the preliminary testing I had done.  The rest of what I had written was accepted with barely an interested squeak.  
I wonder now what would have happened if I had pursued a career in academia. What would have happened if I had insisted on writing up the work I did in the preliminary testing stage? Perhaps my supervisor was right. I simply would not have got anywhere. 
Research isn't about open and shut answers to questions. It is much more likely to be about questions which lead to more questions. 
The real problems start when people don't want to acknowledge that....when they want to stifle academic freedom to express doubts and new ideas.
Remember Galileo?