So why are there differences in the way academics, who signed the peace petition, are treated? We can put his down primarily to economic reasons. Turkey’s toxic blend of neoliberalism and fascism, means that they support the idea of free markets, while at the same time making sure that the state exercises control over all aspects of public life. This contributes to an academic environment, where private universities are often afraid to get on the wrong side of the regime. Staff are put on short term contracts, making them easy to get rid of if they step a foot out of line. Academics being treated as mere items in the budget at these universities, puts them on a precarious footing with authorities and employers, where they have to produce engaging work, without in any way challenging authority.
Why Are Academics Being Persecuted In Turkey?
Libsoc Blogs
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This toxic blend of fascism and neoliberalism is nothing new. In fact, authoritarianism works rather well with free-market ideologies. Look at what happened under Margaret Thatcher.

“Some observers claim to have found something paradoxical in the fact that the Thatcher regime combines liberal individualist rhetoric with authoritarian action. But there is no paradox at all. Even under the most repressive conditions . . . people seek to act collectively in order to improve things for themselves, and it requires an enormous exercise of brutal power to fragment these efforts at organisation and to force people to pursue their interests individually. . . left to themselves, people will inevitably tend to pursue their interests through collective action — in trade unions, tenants’ associations, community organisations and local government. Only the pretty ruthless exercise of central power can defeat these tendencies: hence the common association between individualism and authoritarianism, well exemplified in the fact that the countries held up as models by the free-marketers are, without exception, authoritarian regimes.” [“The Continuing Relevance of Socialism”, in Thatcherism, edited Robert Skidelsky, p. 146] — http://www.spunk.org/texts/otherpol/critique/sp001280.html