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I couldn’t believe it when a rock about the size of my hand flew past my face. I held out my arms, as did other academics, to try to stop these people from going towards the students

Inside the backpacks of many Turkish students, among the books and lecture notes, lie two items with a more unusual purpose: a scarf to hide the owner’s face from the police and a bottle of eye solution to��wash away tear gas.

The occupation of Gezi Park, the leafy Istanbul square threatened with demolition, may have been crushed, but the student-led protests that grabbed headlines across the world this summer are not over.

“The protests will continue, but they won’t happen again the same way,” predicts Bilal, a��third-year history student at Istanbul University, who is equipped for further confrontations with riot police.

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Like thousands of others, he is proud to have taken part in the 18-day anti-government demonstration, broken up in June by police using tear gas and water cannon.

“Each barricade in Gezi had its own name and ours was called ‘Paris to Istanbul’,” he says, evoking as inspiration the 1968 protests that rocked French society.

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What began as an occupation of the park in protest at plans to build a shopping centre on one of the city’s few green spaces grew into the biggest protest against the��Turkish state for more than a decade. Thousands of��protesters were injured and a report by Amnesty International accused authorities of a��“string of human rights violations”, including beatings and the use of live ammunition.

Bilal describes the violence he witnessed: “One of my friends was hit on the back by a��tear gas canister and others were clubbed with batons when the police came in.”

His prediction of further clashes turns out to be correct: later that day, news breaks of the death in southern Turkey of a student protesting against police brutality and government policies, drawing thousands of protesters on to Istanbul’s streets once more.

Unable to reach the heavily policed Gezi area, they battle with riot police in the narrow cafe-lined streets of the fashionable Ciangir district. Some smash up paving stones to hurl at officers, who return fire with tear��gas.

Student protests are not unusual in Turkey; violent clashes between leftist and conservative groups took place during much of the mid-20th century.

A statue of Turan Emeksiz, a student killed by the police during protests in 1960, stands outside Istanbul’s Faculty of Law – a reminder of troubled times amid the splendour of the converted Ottoman palace that is now home to an opulent campus.

But universities have found themselves heavily drawn into this year’s troubles, with students and academics taking a prominent role in the Gezi Park protests and the debate about the wider societal issues they represent.

“About 85 per cent of those in Gezi were students, but our teachers supported us: some��even visited us,” Bilal says. “One of my friends’ lecturers set him a statistics exam, where some of the questions were based on the protest, comparing things such as the numbers of police and protesters.”

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Other academics postponed exams – a��move seen by some as encouraging students to take part in the protests, which has led to a��number of investigations by the authorities.

Ipek Akpinar, associate professor of architecture at Istanbul Technical University, makes no apology for helping student protesters who struggled to submit work on time or whose exams were scheduled during the demonstrations.

“We had to evaluate student work done under extremely harsh conditions, so we could not expect as much as we normally do,” says Akpinar, whose architecture school near Gezi Park was turned into an infirmary to treat students injured during clashes with police.

“Students were saying they had to help their friends at the infirmary, resist police and represent our people,” she says, adding that some suffered after their halls of residence were tear-gassed the night before their exams.

According to Akpinar, four assistants at her architecture school have been investigated by police for organising the makeshift health centre.

Akpinar has featured prominently in discussions about Gezi Park and nearby Taksim Square, using her expertise in architecture to shape the debate over the use of public spaces and participatory planning policies.

“This is the symbolic centre of Istanbul and the entire country,” she says, gesturing towards the trees of Gezi Park that are scheduled for the axe. “We come here as a nation to protest and celebrate. People were angry that there was no transparent design process [for the mall] and it was not participatory. This is not acceptable in a democracy.”

Gezi Park has highlighted wider concerns about the lack of public space in Istanbul. Many believe that land is being sold off for development at an alarming pace under the business-friendly administration led by prime minister Recep Tayyip Erdoğan, chairman of the ruling Justice and Development Party, or AKP.

Academics such as Akpinar who took part in the protests felt the full brunt of police action during the storming of Gezi Park on 15��June. But trouble has followed them to campus, too.

About 100 AKP supporters, armed with clubs and stones and chanting Erdoğan’s name, attacked a graduation ceremony at Istanbul Technical University in July. Some believe this was retaliation for student and academic support for the anti-government Taksim Solidarity movement.

“I couldn’t believe it when a rock about the size of my hand flew past my face,” recalls Akpinar. “I held out my arms, as did other academics, to try to stop these people from going towards the students.”

Incidents like this also highlight a wider social rift in Turkish society: the educated, secular “elite” feel increasingly under attack from a resurgent Islamic middle class represented by the AKP. Bans on the sale of alcohol in bars near mosques and stricter birth control laws are just some of the changes introduced by the party recently. Many believe the country is sliding towards Sunni-style theocracy – something at odds with the fiercely secular state established by Kemal Atatürk, Turkey’s first president. There are concerns about academic freedom and a number of academics have been jailed for “dissident” views.

“In a sense, this government has taken on the whole of the educated classes,” says Norman Stone, professor of international relations at Bilkent University in Ankara, one of the country’s leading private universities.

A ban on serving alcohol on campus, introduced in January, is just one “childish” example of pandering to religious elements, argues Stone, a former adviser to Margaret Thatcher who has taught in Turkey since 1995 after a spell at the University of Oxford.

“Having some drinks at a faculty club is very useful for relations within a university,” he says. “If a couple of bottles of wine go down the hatch, so what? It’s a very silly ban. We now have to take guests off campus to a��restaurant to have a drink.”

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At the nearby Middle Eastern Technical University, the destruction of 3,000 trees to make way for an eight-lane highway through the campus has provoked anger. Environmentally minded students and academics have taken on��the authorities over the lack of democratic involvement in planning issues – a direct challenge to the big-budget infrastructure projects seen by some as job creation schemes catering for the AKP-supporting middle class.

Yet amid a growing backlash against Erdoğan’s regime, the government has plans to loosen its grip on higher education.

Under proposals announced at the end of 2012, Turkey’s ����Vlog Board – YOK – said it would amend its founding law to allow universities to become “free and autonomous institutions”.

The reform would be a radical step for YOK, an organisation formed as a by-product of the 1980 military coup. It is perhaps best known outside Turkey for its ban in 1997 on students wearing headscarves on campus.

While that rule was repealed in 2010 (for students at least: scholars still cannot wear them), academics have long complained about the body’s interference, from the introduction of compulsory courses on Turkish revolutionary history to new rules governing the content of theology courses.

Despite his annoyance with some of YOK’s edicts, Stone argues that the body was originally “set up for good reasons and laid down some good rules”.

“It wanted to get away from a system where Left was fighting Right, academics did not do anything and the government flapped its hands,” he adds.

Many argue that reform of Turkey’s higher education system is long overdue. In recent decades, university numbers have grown rapidly: in 1980 there were just , compared with 175 today. This includes the rise of private foundation universities, which are able to charge higher tuition fees. Bilkent, set up in 1984, was the first such institution: there are now 71.

“The number of universities in Turkey has increased sixfold in about 30 years,” says Taner Bilgiç, vice-provost (international relations) at Bo˘gaziçi University, one of Turkey’s most selective public institutions.

He explains that about 300,000 students enter public universities each year via the demanding national entrance exam, with another 500,000 enrolling in private institutions, vocational courses or distance learning programmes.

With capacity increased, “the issue now is��quality”, Bilgiç says. “The current higher education law controls all universities from the centre and they have a very low level of autonomy. Academics are public employees subject to that law, so I think we need more room for contract-based employment, with researchers employed on different contracts.

“Academics are calling for more autonomy at their universities – financial, academic, organisational – and we need diversity for our sector.”

The government has set a target to increase the number of researchers fourfold by 2023.

According to Bilgiç, the most controversial proposal is the plan to change the law to allow for-profit providers: “That would need a change in the Constitution, which would be difficult.”

Allowing for-profits may be unpalatable to some, but the change is necessary, argues Beril Dedeoğlu, a YOK board member.

“One can’t simply expect everything to go on as it is because there is a clear need to increase salaries and research funds,” she explains. She believes the existing “cake is too small” – in other words, there is not enough money to go round.

“We have to either reduce the number of people sharing it or convince everyone to take smaller slices,” she says. “Or we have to bake a bigger cake. The ‘new cake’ is private funds.”

There are also concerns about loosening state control over a relatively young academy. Although Istanbul can claim to be one of the oldest higher education institutions in the world – it was an ancient Byzantine seat of learning turned into a university in 1453 by Mehmed the Conqueror – it remained the country’s only one for almost 500 years.

Some academics in Turkey’s intellectual strongholds – Istanbul and Ankara – view the new universities established in 81 cities over the past decade with suspicion and are not sure whether they are ready to take control of their own destinies.

“Some of my students at Bilkent are as good as any I saw in Oxford – and they’re operating in a foreign language, English,” Stone says. “It is quite moving to see them doing so well and the good private universities [offer] scholarships for bright students who can’t afford the fees.”

But he worries about standards in far-flung corners of the country: some of the new wave institutions, he believes, consist of no more than “a mosque and a few libraries”.

Meanwhile, a number of recent scandals have exposed the lack of academic rigour at some institutions, he says.

“One university advertised four academic jobs on an email, but accidentally announced the four successful candidates at the same time,” Stone recalls. “But the system has come a long way. When I came here, there were wolves on campus. It is now an educational and business hub, where flats are trading for $400,000 [£250,000] – a lot of money in Turkey.”

With Turkey’s sustained economic growth – estimated at 3.5 per cent in 2013 – and youthful population (43 per cent of the population are under 24), demand for higher education seems certain to increase. However, whether policymakers can oversee an improvement in quality at a time of such political upheaval is far less assured.