Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating activities:
Net loss	$ (101,556)	$ (141,447)	$ (162,141)
Income (loss) from discontinued operations	3,301	(3,065)	(980)
Loss from continuing operations	(104,857)	(138,382)	(161,161)
Adjustments to reconcile net loss from continuing operations to net cash used in operating activities:
Depreciation and amortization	4,753	5,832	6,274
Non-cash benefit from income taxes	(2,062)	0	0
Gain on sale of available for sale securities	57	(49)	(7)
Net amortization of premiums on marketable securities	135	1,053	1,588
Amortization of debt discount and loan fees	2,560	2,554	2,206
Warrant expense related to vesting of ADM Warrant	0	97	556
Debt conversion expense	9,770	0	1,766
Provision for doubtful accounts	321	0	0
Restructuring charges	0	2,622	2,900
Stock-based compensation expense	11,450	14,614	24,345
Loss from equity method investments	22,391	21,994	23,432
Gain from change in fair value of derivative liabilities	(82)	(1)	(8,744)
Loss on retirement of fixed assets	230	0	0
Changes in operating assets and liabilities:
Accounts receivable	(2,159)	(2,598)	(11,153)
Inventories	867	2,682	(2,696)
Prepaid expenses and other current assets	423	433	(141)
Other assets	(413)	(42)	3,582
Accounts payable	(690)	1,818	1,610
Accrued liabilities	(2,552)	(3,214)	(1,815)
Deferred revenue	(1,387)	3,460	(1,075)
Other current and long-term liabilities	818	5,363	2,172
Net cash used in operating activities — continuing operations	(60,427)	(81,764)	(116,361)
Net cash used in operating activities — discontinued operations	(4,107)	(3,351)	(1,752)
Net cash used in operating activities	(64,534)	(85,115)	(118,113)
Investing activities:
Purchases of property, plant and equipment	(1,923)	(1,241)	(7,208)
Proceeds received from the sale of equipment	51	114	0
Purchases of marketable securities	(3,013)	(24,146)	(195,987)
Proceeds from maturities of marketable securities	29,466	105,589	135,464
Proceeds from sales of marketable securities	23,981	31,196	6,541
Capital contributions in unconsolidated joint ventures	(19,342)	(22,344)	(32,550)
Capitalized interest related to unconsolidated joint venture	0	0	(620)
Restricted certificates of deposit	0	287	(731)
Net cash provided by (used in) investing activities — continuing operations	29,220	89,455	(95,091)
Net cash provided by (used in) investing activities — discontinued operations	18,837	(338)	0
Net cash provided by (used in) investing activities	48,057	89,117	(95,091)
Financing activities:
Repayments under loan agreements	0	(6)	(10,433)
Proceeds from the issuance of senior subordinated convertible notes, net of discount	0	0	143,894
Proceeds from the issuance of common stock	5,778	746	8,945
Proceeds from issuance of preferred stock, net of offering costs	27,044	0	0
Payment for loan costs and fees	0	0	(465)
Proceeds from issuance of common stock in a public offering, net of underwriting discounts and commission	0	0	59,209
Cash settlement of vested restricted stock units	0	(32)	(68)
Net cash provided by financing activities	32,822	708	201,082
Effect of exchange rate changes on cash and cash equivalents	198	(433)	(166)
Net increase (decrease) of cash and cash equivalents	16,543	4,277	(12,288)
Cash and cash equivalents—beginning of period	46,966	42,689	54,977
Cash and cash equivalents—end of period	63,509	46,966	42,689
Supplemental disclosures of cash flow information:
Interest paid in cash, net of capitalized interest	11,013	11,175	7,558
Supplemental disclosure of noncash investing and financing activities:
Purchase of property, plant and equipment in accounts payable and accrued liabilities	20	232	154
Common stock issued to Archer-Daniels-Midlands Company pursuant to termination agreement	1,206	3,052	0
Non-cash issuance of common stock options for offering costs	335	0	0
Convertible debt exchanged	30,575	0	20,147
Common Stock
Supplemental disclosure of noncash investing and financing activities:
Issuance of common stock	39,900	0	22,594
Convertible Preferred Stock
Supplemental disclosure of noncash investing and financing activities:
Issuance of common stock	$ 1,056	$ 0	$ 0