1.) Is this probe a violation of the Separation of Powers? Why or why not?
No. From everything I have heard, the search was conducted using proper warrants AND after an attempt to get the information using a subpeona was (for all intents and purposes) ignored.
2.) Is this search in any way a threat to the system of checks and balances?
In my opinion, no. I have yet to see or hear of anything that was improperly done with regards to this search. In actuality, it appears the FBI and Justice Department took great pains to insure that proper procedures were followed...far beyond what might take place if they were to search...say...the average american's home.
3.) Are you in favor of searches of this nature or against?
Kind of a loaded question, so let me answer it as carefully as possible. I am in favor of giving our authorities the power to conduct reasonable searches using proper procedures. I am NOT in favor of this becoming an "open door" for searches of our representatives becoming commonplace. Then again, perhaps now that a search has taken place and Senators and Congressmen now understand they are subject to the same rules of search as the rest of us, we might see a little less corruption? (Kinda sad to think that this is something to worry about though

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4.) Has Article One, Section Six of the Constitution been violated?
Seeing as how this search did not include any "arrest", then I would say no. Even if the congressman had been arrested though, it seems the alleged conduct being investigated would probably rise to the level of "felony" if charges were brought forward. So again, I would have to say no.