**EXHIBIT 31.1**

 

**CERTIFICATION**

 
| I, Richard P. Eno certify  that: |
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| 1.                               |   | I have reviewed this  quarterly report on Form 10-Q of Metabolix, Inc.; |
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| 2.                               |   | Based on my knowledge, this  report does not contain any untrue statement of a material fact or omit to  state a material fact necessary to make the statements made, in light of the  circumstances under which such statements were made, not misleading with  respect to the period covered by this report; |
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| 3.                               |   | Based on my knowledge, the  financial statements, and other financial information included in this  report, fairly present in all material respects the financial condition,  results of operations and cash flows of the registrant as of, and for, the  periods presented in this report; |
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| 4.                               |   | The registrant’s other  certifying officer(s) and I are responsible for establishing and  maintaining disclosure controls and procedures (as defined in Exchange Act  Rules 13a-15(e) and 15d-15(e)) and internal control over financial  reporting (as defined in Exchange Act Rules 13a-15(f) and  15d-15(f)) for the registrant and have: |
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|                             |   | (a) |   | Designed such disclosure  controls and procedures, or caused such disclosure controls and procedures to  be designed under our supervision, to ensure that material information  relating to the registrant, including its consolidated subsidiaries, is made  known to us by others within those entities, particularly during the period  in which this report is being prepared; |
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|                             |   | (b) |   | Designed such internal  control over financial reporting, or caused such internal control over  financial reporting to be designed under our supervision, to provide  reasonable assurance regarding the reliability of financial reporting and the  preparation of financial statements for external purposes in accordance with  generally accepted accounting principles; |
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|                             |   | (c) |   | Evaluated the effectiveness  of the registrant’s disclosure controls and procedures and presented in this  report our conclusions about the effectiveness of the disclosure controls and  procedures, as of the end of the period covered by this report based on such  evaluation; and |
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|                             |   | (d) |   | Disclosed in this report  any change in the registrant’s internal control over financial reporting that  occurred during the registrant’s most recent fiscal quarter (the registrant’s  fourth fiscal quarter in the case of an annual report) that has materially  affected, or is reasonably likely to materially affect, the registrant’s  internal control over financial reporting; and |
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| 5.                               |   | The registrant’s other  certifying officer(s) and I have disclosed, based on our most recent  evaluation of internal control over financial reporting, to the registrant’s  auditors and the audit committee of the registrant’s board of directors (or  persons performing the equivalent functions): |
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|                             |   | (a) |   | All significant deficiencies  and material weaknesses in the design or operation of internal control over  financial reporting which are reasonably likely to adversely affect the  registrant’s ability to record, process, summarize and report financial  information; and |
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|                             |   | (b) |   | Any fraud, whether or not  material, that involves management or other employees who have a significant  role in the registrant’s internal control over financial reporting. |

 

 
| Date: November 6, 2008 |    /s/    RICHARD P. ENO |
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|                        |                                              |
|                        | Name:                                             | Richard P. Eno |
|                        | Title:                                            | *President and Chief Executive  Officer* |
|                        |                                              | *(Principal Executive Officer)* |

 

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