TTIP and TPP: what's the deal with these "secret courts"?

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As a progressive/leftist/whatever, I get a lot of scare stories from Facebook, email and real life about the terrible ISDS courts that will destroy democracy and all things good. While I'm not taken in by a lot of the nonsense surrounding these treaties and the hyperbole that gets thrown around, some of the details that have trickled down to me sound ominous. Can someone give me the briefest run-down on why these things are needed in FTA's and if they can be replaced with something more palatable in the future?

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These secretive quasi judicial panels that give corporations more rights than citizens are an outrage and should be junked from free trade deals.  If corporations have problems with laws or regulations of a country they should take their case to the courts of those countries.

Here is one article one these trade tribunals from a Canadian perspective:
http://www.huffingtonpost.ca/2015/01/14/canada-sued-investor-state-dispute-ccpa_n_6471460.html

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Hopefully SCOTUS strikes down these unconstiutional courts.