Investment in Energy Independence Act of 2006 - Amends the Internal Revenue Code to: (1) allow a tax credit for investment in coal-to-liquid fuels projects; (2) allow a taxpayer election to expense the cost of coal-to-liquid fuels process property and coal-fired facilities for the production of ethanol placed in service before 2016; (3) extend the election to expense oil and alternative fuel refineries until 2016; (4) include liquid fuel derived from oil shale extracted in the United States as an alternative fuel for excise tax purposes; (5) extend the excise tax credit for alternative fuels through FY2020; and (6) allow a 50% tax credit for enhanced oil recovery projects using qualified carbon dioxide.
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