I am playing the Linux version of the game from Steam.
I have adopted Rationalism after fully completing Patronage and tradition. In rationalism I have adopted secularism and humanism. At this point Free thought should be available but it's not.
It says: "This policy may not be adopted yet because prerequisite Policies have not been acquired."
I look the web and found the wiki on social policies which also seems to have inversed secularism and humanism. It is writen here that Free Thought needs Humanism when in the game the tree clearly indicate that you need secularism. Inverselly, Sovereignty in the game tree indicate that you need Humanism but in the wiki, it says you need Secularism.
Since it doesn't work in the game, I wonder if the wiki is correct! Can anyone confirm this.
Here is a snap shot of what I see in the game. (note that you don't see that I had Humanism and Secularism because when I decided to go for Commerce since this tree wasn't working, I lost all my policies in the rationalism tree! Probably another bug...)