Whilst almost all of the regions' minorities suffered from a 'democratic-deficit' and undermining of rule of law and human rights principles, the situation of religious minorities within Pakistan was particularly unfortunate. The year 2004–5 witnessed the strengthening of military rule, and, although some progress was made by the military ruler General Pervez Musharraf to inject a sense of moderation and pluralism in the societal fabric, marginalized communities (particularly the religious minorities and women) were targeted and victimized. Madrasas (Islamic religious schools) continued to flourish, and as the tragic events of London on 7 July 2005 have confirmed, several of these madrasas persist in disseminating fanatical and intolerant ideologies; it is now confirmed through media reports that three of the four men involved in the London bombings had visited madrasas in Pakistan. Notwithstanding the political rhetoric on the part of the government, discriminatory laws such as the Blasphemy Laws and the Hudood Ordinances continue to be deployed against religious minorities and women. Women in Pakistan suffer huge discrimination as a consequence of the arbitrary application of the Hudood laws. President Musharraf's efforts to introduce a minor amendment in the procedural application of the Blasphemy Laws – a measure approved by the national parliament in October 2004 – failed to reduce the number of arrests and detentions on blasphemy charges. According to the statistics provided by the Human Rights Commission of Pakistan, during the period January 2004-August 2005 more than 150 persons were detained for offences under the Blasphemy Laws. The abuse of blasphemy legislation was exemplified through the cases of Javed Anjum and Samuel Massih. Both were accused of blaspheming under s.295(c) of the Pakistan Penal Code 1860 (as amended). Samuel Massih was bludgeoned to death by his police guard while receiving treatment for tuberculosis in a Lahore Hospital, while the 19 year old Javed Anjum was tortured to death by students from a local madrasa. No action has been taken by the police or security forces against those involved in these murders. Furthermore, there was a substantial increase in sectarian violence across the country, with the Shia minority community being the principal target of victimization and killings.

Religious minorities also claim to have been excluded from the limited avenues of Pakistan's fragile democracy. The present military government had in 2002 agreed to abandon the much-despised separate electorate system – a system whereby separate electoral colleges were established for Muslims and Non-Muslims. Despite the promise of abolition, the system was deployed in the local elections held in August and September 2005. These local elections, seen as the precursor to the national parliamentary elections due for 2007, were marred by considerable bloodshed. There were also substantial accusations of widespread fraud and vote rigging and intimidation of minorities (particularly Christians) at the behest of the government. Minority groups have criticized the Pakistan Election Commission for retaining separate lists for such communities as the Ahmadiyas, and for reserving four seats for male Muslims and two for female Muslims in each of the 13-member local councils.

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