The clause about habeous corpus was in the original constitution, not the bill of rights. It's true that in the bill of rights, specifically 6th amendment, the constitution granted the right to a fair trial to people being accused of a crime. If you read the 6th amendment it specifically says "In all CRIMINAL prosecutions..." What is controversial about the NDAA is it allows the military to detain you indefenately without even charging you with a crime. When the government detains you indefinately without charging you witha crime the ONLY legal remedy you have is a to file a writ of habeous corpus. A writ of habeous corpus is just a petition to a judge which is decided in a so called "writ hearing." A writ hearing is not even close to having a right to a trial by jury, it's just a hearing decided by a judge, without a jury. You don't have the right to call witnesses, you don't have the right to cross examine witnesses, you don't have a right to an impartial jury. The majority of writs of habeous corpus are denied. And the right for anyone to even have a writ hearing can be suspended in times of rebellion OR invasion. Lincoln, George W Bush and Obama have each personally suspended the right of habeous corpus for anyone captured by the military and the courts have upheld that. What Rand Paul's amendment does is it specifically requires all the rights of a full jury trial for any US citizen captured or detained in the US by the military, not just a writ. This is an expansion of the rights in the constitution.
The constitution is a great document but as Ron Paul said it's not perfect, it originally allowed for slavery and had no bill of rights. It has an amendment process which gave us the Bill of Rights which made it a truely remarkable document. But because the 6th amendment starts out with the clause "In all criminal prosecutions..." it's very easy for a lawyer for the government to argue to the supreme court that the right to a fair trial in the 6th amended should not apply to someone captured and detained by the military who is not formally being charged with a crime. This is exactly the argument that the Bush administration used before the supreme court and the court sided with the government. Rand Paul's amendment closes this loophole by requiring that if the military wants to capture a US civilian citizen on US soil they had better be prepared to give this person a fair trial in civilian court with all the normal rights a defendant has, rather than just hold this person indefinately and denying them due process of law.
Right now because Obama like Bush before him, has personally signed laws suspending the right of a fair trial and even the right of habeous corpus for prisoners captured by the military in the US, they can detain anyone and hold them as long they want as the "war on terror" isn't over. Rand's amendment would guarantee a fair trial for people who right now who have no legal remedy at all, not a trial or even a writ hearing, and are being held indefinately against their will.
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