Article 156 of the Constitution provides for an independent judiciary. According to Articles 157 and 158, the highest judicial office is the High Council of Justice, which consists of five members who serve five-year, renewable terms. The High Council of Justice consists of the chief justice of the Supreme Court and the attorney general (also seen as State Prosecutor General), both of whom must be Shia mujtahids (members of the clergy whose demonstrated erudition in religious law has earned them the privilege of interpreting laws), and three other clergy chosen by religious jurists. The responsibilities of the High Council of Justice include establishing appropriate departments within the Ministry of Justice to deal with civil and criminal offenses, preparing draft bills related to the judiciary, and supervising the appointment of judges. Article 160 also stipulates that the minister of justice is to be chosen by the prime minister from among candidates who have been recommended by the High Council of Justice. The minister of justice is responsible for all courts throughout the country.
Article 161 provides for the Supreme Court, whose composition is based upon laws drafted by the High Council of Justice. The Supreme Court is an appellate court that reviews decisions of the lower courts to ensure their conformity with the laws of the country and to ensure uniformity in judicial policy. Article 162 stipulates that the chief justice of the Supreme Court must be a mujtahid with expertise in judicial matters. The faqih, in consultation with the justices of the Supreme Court, appoints the chief justice for a term of five years.
In 1980 Ayatollah Mohammad Beheshti was appointed by Khomeini as the first chief justice. Beheshti established judicial committees that were charged with drafting new civil and criminal codes derived from Shia Islamic laws. One of the most significant new codes was the Law of Qisas, which was submitted to and passed by the Majlis in 1982, one year after Beheshti's death in a bomb explosion. The Law of Qisas provided that in cases of victims of violent crime, families could demand retribution, up to and including death. Other laws established penalties for various moral offenses, such as consumption of alcohol, failure to observe hejab, adultery, prostitution, and illicit sexual relations. Punishments prescribed in these laws included public floggings, amputations, and execution by stoning for adulterers.
The entire judicial system of the country has been desecularized. The attorney general, like the chief justice, must be a mujtahid and is appointed to office for a five-year term by the faqih (Article 162). The judges of all the courts must be knowledgeable in Shia jurisprudence; they must meet other qualifications determined by rules established by the High Council of Justice. Since there were insufficient numbers of qualified senior clergy to fill the judicial positions in the country, some former civil court judges who demonstrated their expertise in Islamic law and were willing to undergo religious training were permitted to retain their posts. In practice, however, the Islamization of the judiciary forced half of the former civil court judges out of their positions. To emphasize the independence of judges from the government, Article 170 stipulates that they are "duty bound to refrain from executing governmental decisions that are contrary to Islamic laws."
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