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When he was a teacher at a medical college in Islamabad, Shaikh was an active member of the South Asia Peace Movement and of the International Humanist and Ethical Union (IHEU). He took part in the Pakistan-India Forum for Peace and Democracy, and was a member of the Human Rights Commission of Pakistan. A free-thinker, he founded Enlightenment, an organization associated with the IHEU.
In October 2000, Pakistani authorities charged Shaikh with blasphemy. A judge ordered that he pay a fine of 100,000 rupees, and sentenced him to death by hanging. On appeal, on 20 November 2003, a court acquitted Shaikh, who fled Pakistan for Europe soon thereafter.
Shaikh studied Journalism and attained a diploma in Journalism from Islamabad; he was active in intellectual, literary and social circles and he regularly attended the meetings of the Halqa Arbab i Zoaq in Lahore and later in Rawalpindi and Islamabad. Shaikh attracted the attention of Islamic fundamentalists because as protest against the extremist Islamic Mullah and their atrocities, he gave up Islam, and as a member of the Human Rights Commission of Pakistan, he wrote letters to President Musharraf and different newspapers about Islamic attacks on peace-loving Ahmadis-a minority group, a former Muslim sect expelled from Islam, as well as he campaigned about the human rights of women, of Hindus, Christians and liberal, secular Muslims. He also took part in the Pakistan-India Forum for Peace and Democracy, and was a member of the South Asian Fraternity, South Asian Union. He also expressed disquiet and exposed the horrors of the Pakistan Army atrocities in Bengal in 1971. He founded Enlightenment, an organization associated with the International Humanist and Ethical Union, in 1990.
Shaikh's blasphemy was alleged to have occurred at a lecture he allegedly gave on 2 October 2000 at Capital Medical College. The accusation was that, during the lecture, Shaikh said that Prophet Muhammad did not become a Muslim until the age of 40 (the age at which he received the first message from God), and also that his parents were non-Muslims because they died before Islam existed, and furthermore that he wed, at 25, without an Islamic marriage contract, and that he was unlikely to have been circumcised or to have shaved under his armpits or to have shaved his pubic hair, because those practices were unknown to his tribe.
Shaikh denied that this lecture even took place, and denied that he had said what was alleged. In a letter to Babu Gogineni of the IHEU, Shaikh offered an explanation of why a charge was made against him; he claimed (albeit without corroborating evidence against the people he accused):
- 1. On 1 October 2000 I attended a meeting of South Asian Union addressed by an (alleged) ISI (Inter Services Intelligence) Brig. Shaukat Qadir (retd.) also (allegedly) running a religious-political association of Jamait – I – Islami. I asked a couple of questions about South Asian peace and Kashmir which offended him and he returned a threat ("Rebuttal", archived[dead link]). There were foreign office policy makers and newsmen sitting there.
- 2. Within 48 hours, a foreign office employee who was also my student at the medical college where I used to lecture at the morning time, prepared an application against me, alleging blasphemous remarks in their class and gave it to a cleric, who improving upon the complaint, accused me of a specific instance of 2-10-2000 in the class of IInd year male students and registered the case with the Police.
According to press reports, eleven students, all the students in Shaikh's class, signed a letter attesting to Shaikh's blasphemy. The cleric who received the letter was a member of an organisation known to harass and to attack non-orthodox Muslims. The reports call the organisation Aalmi Majlis Tahaffuz Khatm-e-Nubuwwat, which the press translates as the Committee for the Protection of the Finality of the Prophethood, or the Movement for the Finality of the Prophet, or the Organisation of the Finality of the Prophet. Pakistan said that Shaikh's accuser was the head of Majlis-e-Khatam-e-Nabuwwat. That organisation dispatched a mob to the medical school and to the police station, and threatened to burn them down if action was not urgently taken against Shaikh. Capital Homeopathic College, without explanation, suspended Shaikh on 3 October 2000.
Section 295C of Pakistan's Penal Code says "whoever by the words, either spoken or written, or by visible representation, or by any imputation, innuendo, or insinuation, directly or indirectly, defiles the sacred name of the Holy Prophet Muhammad shall be punished with the death sentence or imprisonment for life and shall be liable to fine." A charge under Section 295C requires that the accused be kept in custody. Pursuant to Section 295C, the police arrested Shaikh on 4 October 2000. He was held in Adyala Gaol, Rawalpindi.
In August 2001, defended by a lawyer, Shaikh went to trial. The judgement was rendered at Adyala Jail, which was under vigil by armed Islamic zealots. On 18 August, the trial judge, Safdar Hussain, ordered the death penalty as well as a 100,000 rupee fine. The judge declared, “He deserves to be hanged for making derogatory remarks against the Prophet." Shaikh is the third Muslim to be sentenced to death under Pakistan's blasphemy laws.
The International Humanist and Ethical Union, Amnesty International, Mukto-Mona and Sea of Faith launched a campaign to win Shaikh's release. Demonstrations on his behalf occurred outside the Pakistani Embassies in London, Washington, and several other western capitals.
Shaikh appealed to the High Court. There the two presiding judges differed on whether the judgement should stand. On 15 July 2002, the case went to a senior judge. On 9 October 2003, the senior judge announced that the original judgement was unsound. He ordered a retrial.
The retrial was held over three sessions in November 2003. Shaikh did not use a lawyer to defend him because of threats to his lawyers by the extremist Mullah and Pakistani Taliban; he defended himself on points of law as he had secretly studied law books during his 3 years incarceration in the Death cell. On 21 November 2003, the trial judge acquitted Shaikh on legal grounds, and ordered that he be released. Commenting on the judgement, Shaikh explained: “The judge accepted my legal arguments and found the charges against me to be baseless. My accusers, two Mullahs and some Islamist students, had lied while under the oath on the Holy Koran.” He described his ordeal as: “Islamic terrorism through the abuse of law and of the state apparatus”. Shaikh tried to sue his accusers, the mullahs and the Taliban. However, a fatwa was issued against him and he had to leave his family, friends and country.
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