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Let me be absolutely clear that I think that the Patriot Act provision relating to the "interim" appointment of US Atty's was terrible, both in its substance and with respect to the fact that it was not offered as a separate amendment.
HOwever, a few things (and only a few things) seem clear from the published legislative history of the Patriot Act reauthorization.
First, the provision relating to the appointment of US Attorneys was added to the legislation during the House/Senate conference to resolve differences in the versions of the Patriot Act reauthorization previously passed by the House and Senate. The earliest reference to the interim US Atty's provision that I can find is in the Conference Report of December 8, 2005. That report contains the new language as well as one-sentence explanation describing the provision as "a new section" that "addresses an inconsistency in the appointment process of United States Attorneys" (this description it seems to me is misleading at best).
The House approved this language on December 14; the bill then moved to the Senate for consideration, but an attempt at cloture failed. It was not until March 2 that the standoff was resolved and the Senate passed the bill, which then went to chimpy for his signature on March 8.
In short, the US Atty language was not slipped in after enactment -- it was added to the bill before the Conference REport was voted on by either House and was sitting there for three months before the Senate acted.
Sure, its a big bill, but changes to a bill in conference, including the addition of new and often extraneous matter, is hardly unusual. It was there to be seen by anyone who looked (although, as noted the one sentence explanation was misleading).
There is blame all around for this, including on members of Congress and their staff who failed to notice or comprehend what this provision was even though it was there for three months.
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