Income Taxes (Details 2) (USD $)	3 Months Ended								12 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Tax Carryforwards
Unrecognized Tax Benefits, Reduction Resulting from Lapse of Applicable Statute of Limitations and Settlements with Taxing Authorities, Estimated in Next Fiscal Year	$ 500,000								$ 500,000
Federal statutory income tax rate (percent)									35.00%	35.00%	35.00%
Reconciliation of Income Tax Expense:
Income (loss) before provision for (benefit from) income taxes	(340,253,000)	(129,413,000)	(63,511,000)	(442,940,000)	(80,772,000)	(5,112,000)	(14,405,000)	87,908,000	(976,117,000)	(12,381,000)	60,445,000
Expected tax provision (benefit)									(341,641,000)	(4,333,000)	21,156,000
State taxes, net of federal benefit									(19,268,000)	7,075,000	10,624,000
Foreign rate differential									72,961,000	62,425,000	43,629,000
Tax credits									(16,775,000)	(1,980,000)	(51,086,000)
Unbenefited operating losses									(43,570,000)	(30,364,000)	(6,286,000)
Non-deductible expenses									9,614,000	3,198,000	1,953,000
Rate change									50,076,000	3,275,000	0
Other									36,000	(542,000)	(724,000)
Provision for (benefit from) income taxes	(155,704,000)	(751,000)	(1,799,000)	(130,313,000)	(2,696,000)	21,355,000	20,063,000	32,000	(288,567,000)	38,754,000	19,266,000
Federal net operating loss carryforward	694,800,000								694,800,000
Reconciliation of unrecognized tax benefits
Unrecognized tax benefits beginning of year				4,106,000				4,360,000	4,106,000	4,360,000
Gross change for current year positions									1,325,000	598,000
Increase for prior period positions									0	0
Decrease for prior period positions									(290,000)	0
Decrease due to settlements and payments									0	0
Decrease due to statute limitations									(185,000)	(852,000)
Deconsolidation of Alios									(2,932,000)	0
Unrecognized tax benefits end of year	2,024,000				4,106,000				2,024,000	4,106,000	4,360,000
Deferred tax assets:
Net operating loss	850,946,000				777,687,000				850,946,000	777,687,000
Tax credit carryforwards	180,380,000				147,074,000				180,380,000	147,074,000
Property and equipment	0				10,701,000				0	10,701,000
Intangible assets	26,105,000				63,353,000				26,105,000	63,353,000
Deferred revenues	25,158,000				44,867,000				25,158,000	44,867,000
Stock-based compensation	63,521,000				83,979,000				63,521,000	83,979,000
Inventories	26,278,000				56,564,000				26,278,000	56,564,000
Accrued expenses	52,470,000				27,945,000				52,470,000	27,945,000
Currency translation adjustment	217,000				0				217,000	0
Construction financing lease obligation	152,688,000				0				152,688,000	0
Gross deferred tax assets	1,377,763,000				1,212,170,000				1,377,763,000	1,212,170,000
Valuation allowance	(1,243,664,000)				(1,211,561,000)				(1,243,664,000)	(1,211,561,000)
Total deferred tax assets	134,099,000				609,000				134,099,000	609,000
Property and equipment	(134,099,000)				0				(134,099,000)	0
Deferred tax liabilities:
Unrealized gain	0				(376,000)				0	(376,000)
Contingent milestone and royalty payment obligation	0				(50,904,000)				0	(50,904,000)
Acquired intangibles	0				(229,696,000)				0	(229,696,000)
Net deferred tax liabilities	0				(280,367,000)				0	(280,367,000)
Decreased in valuation allowance									(32,100,000)
Federal
Reconciliation of Income Tax Expense:
Operating Loss	2,700,000,000								2,700,000,000
Tax Credit	120,100,000								120,100,000
State
Reconciliation of Income Tax Expense:
Operating Loss	966,800,000								966,800,000
Tax Credit	66,900,000								66,900,000
Federal net operating loss carryforward	$ 204,500,000								$ 204,500,000