CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Operating activities:
Net loss	$ (65,478)	$ (84,801)	$ (61,251)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation	7,074	6,594	4,840
Amortization of patents	1,224	1,938	1,961
Amortization of licenses	2,457	3,252	2,376
Amortization of premium on investments, net	4,193	5,410	5,075
Amortization of debt issuance costs	619	507	507
Amortization of 2 5/8 percent convertible subordinated notes discount	6,169	8,553	7,795
Amortization of 2 3/4 percent convertible subordinated notes discount	2,268
Amortization of long-term financing liability for leased facility	6,503	2,872
Share-based compensation expense	8,571	9,845	12,159
Equity in net loss of Regulus Therapeutics Inc.	1,406	3,554	6,879
Gain on investment in Regulus Therapeutics Inc.	(18,356)		(4,651)
Loss on early retirement of debt	4,770
Gain from the sale of property, plant and equipment			(72)
(Gain) loss on investments, net	(1,465)	(4,182)	713
Non-cash losses related to patents, licensing and property, plant and equipment	825	1,924	1,512
Tax benefit from other unrealized gains on securities	(9,111)
Changes in operating assets and liabilities:
Contracts receivable	6,399	(5,679)	10,479
Inventories	(1,982)	(1,655)	284
Other current and long-term assets	279	914	(943)
Accounts payable	1,292	875	1,325
Accrued compensation	(1,305)	2,352	394
Income taxes payable			(7,178)
Deferred rent	255	382
Accrued liabilities	(3,254)	6,273	1,013
Deferred contract revenue	48,523	(70,857)	(46,810)
Net cash provided by (used in) operating activities	1,876	(111,929)	(63,593)
Investing activities:
Purchases of short-term investments	(217,877)	(371,108)	(530,137)
Proceeds from the sale of short-term investments	242,659	488,918	577,533
Purchases of property, plant and equipment	(1,479)	(10,203)	(13,237)
Proceeds from the sale of property, plant and equipment			185
Proceeds from land sold to BioMed			10,147
Reduction of cash due to deconsolidation of Regulus Therapeutics Inc. upon adoption of a new accounting standard			(16,228)
Acquisition of licenses and other assets, net	(3,691)	(3,667)	(4,319)
Investment in Regulus Therapeutics Inc.	(3,000)
Purchases of strategic investments	(790)	(359)	(250)
Proceeds from the sale of strategic investments	2,177	4,445
Net cash provided by investing activities	17,999	108,026	23,694
Financing activities:
Proceeds from issuance of equity	9,470	3,567	4,356
Proceeds from issuance of 2 3/4 percent convertible senior notes, net of issuance costs	194,697
Principal and premium payment on redemption of the 2 5/8 percent convertible subordinated notes	(163,718)
Proceeds from equipment financing arrangement	9,100	1,625	4,694
Principal payments on debt and capital lease obligations	(10,419)	(5,864)	(4,354)
Net cash provided by (used in) financing activities	39,130	(672)	4,696
Net increase (decrease) in cash and cash equivalents	59,005	(4,575)	(35,203)
Cash and cash equivalents at beginning of year	65,477	70,052	105,255
Cash and cash equivalents at end of year	124,482	65,477	70,052
Supplemental disclosures of cash flow information:
Interest paid	5,770	4,804	4,889
Income taxes paid, net of refund received	2	2	7,270
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	647	902	922
Capital lease obligations			770
Capitalized costs and financing liability associated with leased facility		$ 59,730