Nevertheless, some independent-minded observers think the Brotherhood should accept that provided the courts are independent, judges are entitled to put checks on the legislature, especially if it is dominated by a single ideology.
Under the agreement, signed last month on the sidelines of an African Union summit in Ethiopia, five independent judges will investigate the 1994 bombing.
He is also working hard on plans to remove the mystique and patronage surrounding the appointment of judges through the introduction of an independent judicial appointments commission.
Composed of seven independent judges, the court has broad powers, though these have never been used before in a presidential election.
But that would only have meaning if the judges were known to be independent.
This one seeks to put the delineation of political constituencies in the hands of an independent panel of retired judges instead of self-interested politicians.
Article III judges are independent of the executive branch of government.
Mr Clarke told the BBC that British judges were very independent and they would have to be convinced there was a genuine "danger" to the public or to informants from evidence being heard in public to justify holding closed sessions.
Once the nomination period has ended, an independent panel of judges will choose 500 finalists.
The ConnectU founders accused their lawyers of malpractice but an independent panel of judges found otherwise.
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"MAS has betrayed the electorate and especially our hope that this would be an election of truly independent judges, " he says.
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Appointments of independent fiduciaries by courts have often amounted to invitations to steal and the judges overseeing these arrangements have been blind to skimming happening right under their noses.
Kaplan says Donziger himself might have criminal or professional liability for his alleged involvement in pressuring judges and preparing a report by a supposedly independent expert for the court.
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An independent judicial appointments commission, favoured by many reformers and some senior judges, would be a step in the right direction.
An independent judiciary is welcome, says Samina Ahmed of the International Crisis Group, yet it is striking how hard the judges fought to reject any elected oversight.
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