Since the ascension to power of Turkish Prime Minister Recep Tayyip Erdogan's AK Party  in 2002, there has been a rift between the government and Turkey's Higher Education Council (YOK) on various issues.
Prior to the 2002 election, the AKP promised its Islamic electorate that it would end the ban on Islamic headscarves in the universities, and that the graduates of Turkey's Imam Hatip religious schools would be accepted into the universities.
However, once in office, the ruling AKP could not deliver on these promises to its religious base, mainly because of the strong opposition on the part of Turkey's strictly secular Higher Education Council that governs the policies of Turkey's state universities. The conflict deepened with the recent arrest and incarceration of the president of Yuzuncu Yil University (YYU) in Van, Professor Yucel Askin, for alleged procedural misconduct.  The Turkish media is suggesting that Prof. Askin's incarceration was an attempt by the Islamic government to remove a secular republican president from a university that was known, until he took office in 1999, as a hotbed for Islamists.  During his tenure, Prof. Askin put an end to the activities of various Islamic extremists at the university.
All Turkey's university presidents, as well as the Higher Education Council and members of the Turkish Bar Associations, strongly protested Prof. Askin's arrest, and claimed that Turkey's judiciary system was being manipulated by the government. On October 22, 2005, 74 presidents and vice-presidents of Turkish universities flew to Van to visit Prof. Askin in prison, in a show of solidarity, and held a meeting at YYU. A declaration by the Board of Presidents of YOK read: "Defending President Askin means defending our Republic." Higher Education Council head Professor E. Tezic and the 74 presidents were met by a number of protesters in Van, who shouted "Allahu Akbar."
Soon after their visit to Van, President of the Turkish Republic Ahmet N. Sezer invited all the university presidents to his October 29 Republic Day Reception, further angering Prime Minister Erdogan, who earlier had said about the solidarity visit, "Those who go to Van [i.e. the university presidents] should mind their own businesses and not interfere with legal matters."
The case of the YYU in Van has once again brought into question academic freedom, the independence of the judiciary, and the rule of law in Turkey.
The following are excerpts of reactions to this matter from the mainstream Turkish media:
"The Goal of the AKP Government: To Turn the Republic's Universities Into Madrassas"
Columnist Tufan Turenc of the mainstream, high circulation, centrist Turkish daily Hurriyet wrote: 
"[…] From the first day [of their rule,] the AKP government wanted to take over the universities and change these institutions of knowledge to conform to their own view of the world.
"The goal was to turn the Republic's [state] universities into madrassas.
"This dream was almost realized in the case of the YYU in Van, but the appointment of Prof. Yucel Askin as president there spoiled the plan.
"Upon assuming his duties, the president [Prof. Askin] started a fierce struggle against the deeply rooted [Islamic] sects and their supporters. His battle became even more difficult when the AKP came to power. In the past three years, unimaginable libels and plots were organized against Prof. Askin and [some of] his colleagues. When those did not help […] they started a judicial investigation based on lies and went as far as incarcerating him. This decision of arrest outraged not only the university presidents but also the legal experts.
"[…] They are taking revenge on Prof. Askin on behalf of fanatical circles. […]
"Coming to the heart of the matter…:
"The universities know all too well that this [AKP] government is adamant in destroying the roots of all academic institutions.
"Their goals are to permit [Islamic] head coverings for women [on campuses], to accept into all faculties the graduates of the [Islamic] Imam Hatip schools, [and] to fill the academic positions with backward-thinking [religious] staff members. Their dream is to raise new generations with belief in and knowledge of their religion [Islam], and then to place them in all the key positions of the state. In Van, the religious had taken over almost all the places, except the university. There the obstacle was Prof. Yucel Askin. Hence the anger and the hostility against him.
"[…] this scandal in Van shakes our belief in the rule of law [in Turkey] and raises the suspicion that our judiciary may be under political pressure.
"Then the real question becomes: 'How will Turkey – with this mentality – become a member of the European Union?'"
"A War of Wills: Ataturk vs. The Islamists"
Columnist Can Dundar of the mainstream, centrist, high circulation Turkish daily Milliyet wrote: 
"The problem at YYU in Van is not new; it is 100 years old… At the end of the 19th century, Van was like a laboratory of modernization for the Ottomans. [In those days,] Van was a place where Turks and Kurds lived together, where Armenian revolutionary militias were active, where missionaries were at work, and where six imperialistic countries had opened consulates. Mullah Said  came to this cosmopolitan laboratory […] and thought that Islam had fallen behind the Western influence in the city. He saw a remedy – the building of a university in Van where Islamic studies would be taught [… which did not materialize].
"[…] Ataturk, in his last opening speech at the parliament [before his death in 1938] said that Van should be made into a modern city of culture, with its own university, on the shores of Van Lake. His wish took almost half a century to fulfill. This university, about which everyone had dreamed, came into being in 1981, on the 100th anniversary of Ataturk's birth.
"[…] One thing is certain: This is not about a case of corruption. This is about a 100-year-old case [of struggle for Kemalist secularism]. All the statements show the signs of a settling of accounts.
"The incarceration of the [university's] president, the showdown in Van by all [the protesting] university presidents, and the remarks made by the prime minister reflect that same old 'settling of accounts'… The headline on the front page of [the center-left, secular Turkish daily] Cumhuriyet that read 'A War of Wills' [i.e. what Ataturk wanted versus what the Islamists want] is fitting. The desire to politicize the universities is also added into the mix of this old quarrel.
"The judiciary, that recently seems to be tainted by politics, is also suffering from this fighting. That is why we cannot agree with the prime minister's words, 'let everyone mind his own business.' We have come to such a point that from now on Van is 'everyone's business.'"
"The Arrest of the University President: A Political Decision"
Turkish columnist Emin Colasan of Hurriyet wrote: 
"[…] Van was one of the bastions of the [Islamic] fanatics. Van University was in the hands of Islamist sects. Then its president changed. Yucel Askin was appointed to the position. He liberated the university and took great steps towards its development.
"Yet the AKP government and the Islamic press were afraid of strong university presidents. They had captured all the bastions in Turkey, but could not break into the universities.
"Therefore, as a first step they had to destroy the [university] presidents and find ways to eliminate them.
"The first plot was in Van. They entered and searched Prof. Askin's residence while he was abroad.
"In the face of protests, the attorney general of Van organized a PRESS CONFERENCE [emphasis in original] to defend himself, even though by law this stage of an investigation must remain secret. Even journalists are banned from writing about an investigation [in this stage]. If they do, they get penalized. But [apparently] the law does not apply to this prosecutor in Van, since no legal action was taken against him.
"Finally the president of Van [University] was arrested. Clearly, the decision was political. They selected as 'expert witness' someone [from the university] whom the president had recently removed and replaced!
"Police officers held the president by the arm and took him to the detention center. The Islamic press and TV channels are jubilant, and wishing the same for other university presidents.
"Naturally, AKP's Van parliamentarian and the Minister of Education Huseyin Celik had 'nothing' to do with all of this! [After all,] he himself said, 'I swear by Allah with my fasting mouth [i.e. during Ramadan] that I had nothing to do with the situation about the [university] president. Those who say that I had anything to do with it are lying!'
"Every day some [other] universities' presidents are designated as targets. Bolu, Samsun, Malatya, and other [universities]… they are all in their sights.
"They [the AKP government] do all that they can to conquer all these bastions, to bring down the secular presidents who are the followers of Ataturk, in order to be able to do everything they wish at those campuses and to place their religious extremists in all the vacated key positions. […]"
"One Day You Wake Up and Find That the Nazis Have Invaded Turkey "
Turkish columnist Mehmet Y. Yilmaz wrote in Hurriyet: 
"The debate regarding the arrest of Van's YYU President Prof. Yucel Askin is becoming more interesting by the day. An AKP member of parliament recently said that the president [Prof. Askin] was in fact an 'Armenian' and was appointed to his position 'in order to divide Van, a city claimed by the Armenians.' Following his remarks, [the Islamist Turkish daily] Vakit wrote that President [Askin's] grandfather Mehmet Yakup Bey and his grandmother Ayse Huriye Hanim had notations in their registration documents showing them to be 'converts,' meaning they had changed their religion [from Christianity to Islam].
"I know nothing about the veracity of these allegations.
"But when I combined this 'news' with the remarks made by this AKP parliamentarian, I felt as if I was watching a 'Twilight Zone' film: One day you wake up and find that the Nazis have invaded Turkey! [People] with swastikas on their armbands are taking away all those who have in their pasts any relationship with Armenians, Greeks, Jews, Serbians, Georgians, Croatians, Albanians, Gypsies, Russians, Moldavians, Bulgarians, Arabs, Persians, [and others]!
"For centuries, we lived on the lands of an empire [i.e. the Ottoman Empire] that included many ethnic groups. We intermarried. We lived as neighbors and became also relatives.
"[…] In such a nation that lived in harmony, tolerance and peaceful relations, that can set an example for many other nations in the world, how can anybody go back, search, and find 'pure blood'?
"[…] Those who have recently gone searching with a magnifying glass for Armenian blood in all those they dislike remind me of […]Nazi Germany. Because what ended in concentration camps and gas chambers there started exactly in this manner.
"As a society, we must raise our voices against a new kind of fascism."
 AKP - Adalet ve Kalkinma Partisi (Justice and Development Party); the ruling party in Turkey since 2002.
 The alleged misconduct is related to the $25 million purchase of medical equipment for the university's Faculty of Medicine. The tender process for this purchase was underway before Prof. Askin took office as president.
 It was at this university in Van, which was nicknamed "the Hizbullah university," that a student by the name of Sirin Tekin was stabbed to death in May 1987 for not fasting during Ramadan.
 Hurriyet (Turkey), October 21, 2005.
 Milliyet (Turkey), October 22, 2005.
 Islamic leader Mullah Said (1880-1930) was the opponent of Mustafa Kemal Ataturk's leadership, of the Turkish nationalist movement, and of its War of Independence against the Allied forces who occupied the Ottoman Empire after WWI. Mullah Said collaborated with the occupying British forces against the nationalist struggle for independence because he perceived Mustafa Kemal to be an anti-Islamist who had put an end to Shari'a and the Caliphate.
 Hurriyet (Turkey), October 20, 2005.
 Hurriyet (Turkey), October 26, 2005.