Exhibit 10.13    December 17,
2008  Sarah
P. Cecil c/o Metabolix, Inc. 21 Erie Street Cambridge, MA 02139  Re:  Change of Control Severance Agreement  Dear
Sarah:  Metabolix, Inc. (the Company)
believes that it is in the best interests of the Company to provide you with
certain severance benefits in the event of a termination of your employment in
connection with a Change of Control, in order to provide you with financial
security and sufficient encouragement to remain with the Company
notwithstanding the possibility of a Change of Control (as defined below).  Therefore, you and the
Company agree as follows:  1.Change of Control Severance
Benefits.  1.1.In the event that your employment is terminated by the Company without
Cause or by you for Good Reason within 12 months immediately following
or 6 months immediately prior to a
Change of Control (each as defined herein), then, in addition to any accrued
salary and benefits otherwise payable to you by law or pursuant to the Companys
benefit plans as in effect at the date of termination and contingent upon your
executing a complete release of claims against the Company (the Release)
within 30 days after the date of your termination of employment:  (a) the
Company shall continue your base salary at the rate in effect at the date of
termination for a period of twelve (12) months from the date of termination,
and such salary continuation shall commence on the 37th day after the date on which your
employment terminates and shall be paid in accordance with the Companys normal
payroll practice, provided that the first payment will include all amounts
which would have been paid in the 37 days following your termination of
employment;  (b) the
Company shall pay COBRA premiums to maintain medical and dental benefits, if
any, in effect at the time of termination beginning on the date of your
termination of employment until the earlier of (i) twelve (12) months
following the date of termination, or (ii) the date you become insured
under a medical insurance plan providing similar benefits to that of the
Company plan, or (iii) the date you revoke the Release; and  Metabolix  |  21 Erie Street  | 
Cambridge  |  MA 
|  02139  |  USA tel: 617 583 1700  |  fax: 617 583 1767  | 
www.metabolix.com


(c) the Company
shall cause the full vesting of all your unvested equity, including but not
limited to any options or restricted stock granted to you under the 2006 Stock
Plan or any authorized successor stock plan, provided that the conditions to
vesting other than the passage of time have been satisfied.  1.2.Notwithstanding anything set forth in this Agreement, a termination of
employment shall be deemed not to have occurred until such time as you incur a separation
from service with the Company in accordance with Section 409A(a)(2)(A)(i) of
the Code and the applicable provisions of Treasury Regulation Section 1.409A-1(h).  1.3.Anything in this
Agreement to the contrary notwithstanding, if at the time of your separation
from service within the meaning of Section 409A of the Code, the Company
determines you are a specified employee within the meaning of Section 409A(a)(2)(B)(i) of
the Code, then to the extent any payment or benefit that you become entitled to
under this Agreement on account of your separation from service would be
considered deferred compensation subject to the 20 percent additional tax
imposed pursuant to Section 409A(a) of the Code as a result of the
application of Section 409A(a)(2)(B)(i) of the Code, such payment
shall not be payable and such benefit shall not be provided until the date that
is the earlier of (A) six months and one day after your separation from
service, or (B) your death.  The
first payment shall include a catch-up payment covering amounts that would
otherwise have been paid during the six-month period but for the application of
this provision, and the balance of the installments (if any) shall be payable
in accordance with their original schedule.  2.Definitions.  Change
of Control.  As used herein, a Change of Control shall
occur or be deemed to have occurred only upon any one or more of the following
events:  (i)            any person (as such term is used in Sections 13(d) and
14(d)(2) of the Securities Exchange Act of 1934, as amended (the Exchange
Act)) becomes a beneficial owner (as such term is defined in Rule 13d-3
promulgated under the Exchange Act) (other than the Company, any trustee or
other fiduciary holding securities under an employee benefit plan of the
Company, or any corporation owned, directly or indirectly, by the stockholders
of the Company, in substantially the same proportions as their ownership of
stock of the Company), directly or indirectly, of securities of the Company,
representing fifty percent (50%) or more of the combined voting power of the
Companys then outstanding securities; or  (ii)           persons who, as of the effective date of this Agreement,
constituted the Companys Board of Directors (the Incumbent Board) cease for
any reason including, without limitation, as a result of a tender offer, proxy
contest, merger, consolidation or similar transaction, to constitute at least a
majority of the Board of Directors, provided that any person becoming a
director of the Company subsequent to the Effective Date whose election was  2


approved by at least a
majority of the directors then comprising the Incumbent Board shall, for
purposes of this Section 6(f), be considered a member of the Incumbent
Board; or  (iii)          the consummation of a merger or consolidation of the Company
with any other corporation or other entity, other than (1) a merger or
consolidation which would result in the voting securities of the Company
outstanding immediately prior thereto continuing to represent (either by
remaining outstanding or by being converted into voting securities of the
surviving entity) more than fifty percent (50%) of the combined voting power of
the voting securities of the Company or such surviving entity outstanding
immediately after such merger or consolidation or (2) a merger or
consolidation effected to implement a recapitalization of the Company (or
similar transaction) in which no person (as hereinabove defined) acquires
more than fifty percent (50%) of the combined voting power of the Companys
then outstanding securities; or  (iv)          the stockholders of the Company approve a plan of complete
liquidation of the Company or an agreement for the sale or disposition by the
Company of all or substantially all of the Companys assets.  Termination for Cause.  Cause
for termination shall be limited to the following:  (i)    Your conviction of a felony; or  (ii)   Your commission of fraud, or misconduct that results in material
and demonstrable damage to the business or reputation of the Company; or  (iii)  Your continued, repeated, intentional and willful refusal to
perform the duties associated with your position with Company, which is not
cured within thirty (30) days following written notice to you; provided,
however, that your refusal to take any action that you reasonably believes violates
any applicable law or regulation or fiduciary duty, shall not constitute
grounds for the application of this subsection.  Good Reason. For purposes of this Agreement, Good
Reason shall mean that you have complied with the Good Reason Process (hereinafter
defined) following the occurrence of any of the following events:  (i) a material diminution in your
responsibilities, authority or duties;  (ii) a material diminution in your base salary
except for across-the-board salary reductions based on the Companys financial
performance similarly affecting all or substantially all senior management
employees of the Company; or  (iii) the requirement that you relocate to a
location more than 50 miles outside of Cambridge, Massachusetts.  3


Good Reason Process shall mean that (i) you
reasonably determine in good faith that a Good Reason condition has occurred;
(ii) you notify the Company in writing of the occurrence of the Good
Reason condition within 60 days of the occurrence of such condition; (iii) you
cooperate in good faith with the Companys efforts, for a period not less than
30 days following such notice (the Cure Period), to remedy the condition; (iv) notwithstanding
such efforts, the Good Reason condition continues to exist; and (v) you
terminate your employment within 60 days after the end of the Cure Period.  If the Company cures the Good Reason
condition during the Cure Period, Good Reason shall be deemed not to have
occurred.  3.             At-Will Employment. 
The Company and you acknowledge that, notwithstanding anything contained in
this Agreement, your employment with the Company shall be at-will, as defined
under applicable law.  Nothing in this letter agreement is intended to
provide you with any right to continue in the employ of the Company for any
period of specific duration or interfere with or otherwise restrict in any way
your rights or the rights of the Company, which rights are hereby expressly
reserved by each, to terminate your employment at any time and for any reason.
If your employment terminates for any reason, you shall not be entitled to any
payments, benefits, damages, awards or compensation other than as provided by
this Agreement, or as may otherwise be established under the Companys then
existing employee benefit plans or policies at the time of termination.  4.General.  4.1.Entire Agreement.  This
Agreement embodies the entire agreement and understanding between you and the
Company with respect to the subject matter hereof and supersedes all prior oral
or written agreements and understandings relating to the subject matter hereof.  4.2.Modifications, Amendments, Waivers.  The
terms and provisions of this Agreement may be modified or amended only by
written agreement executed by you and the Company. The terms and provisions of
this Agreement may be waived, or consent for the departure therefrom granted,
only by written document executed by the party entitled to the benefits of such
terms or provisions.  4.3.Assignment.  The Company shall cause its rights and obligations hereunder to be assumed by any person or entity that succeeds to all or substantially all of the Companys business or that aspect of the Companys business in which you are principally involved or to any Company affiliate.  You may not assign your rights and obligations under this Agreement without the prior written consent of the Company and any such attempted assignment by you without the prior written consent of the Company will be void.  Notwithstanding the foregoing, the terms of this Agreement and your rights hereunder shall inure to the benefit of, and be enforceable by, your personal or legal representatives, executors, administrators, successors, heirs, and legatees.  4


4.4.Governing Law.  This
Agreement and the rights and obligations of the parties hereunder will be
construed in accordance with and governed by the law of Massachusetts, without
giving effect to the conflict of law principles thereof.  4.5.Jurisdiction, Venue and Service of Process.  Any
legal action or proceeding with respect to this Agreement will be brought in
the courts of Massachusetts or of the United States of America for theDistrict of Massachusetts.  By execution and delivery of this Agreement,
each of the parties hereto accepts for itself and in respect of its property,
generally and unconditionally, the exclusive jurisdiction of the aforesaid
courts.  4.6.Jury Waiver. You and the Company agree to waive trial by jury in connection with
any action arising from or relating to this Agreement.  4.7.Severability.  The
parties intend this Agreement to be enforced as written.  However, if any portion or provision of this
Agreement is to any extent declared illegal or unenforceable by a duly
authorized court having jurisdiction, then the remainder of this Agreement, or
the application of such portion or provision in circumstances other than those
as to which it is so declared illegal or unenforceable, will not be affected
thereby, and each portion and provision of this Agreement will be valid and
enforceable to the fullest extent permitted by law.  4.8.Taxes.  All payments required to be
made by the Company to you under this Agreement shall be subject to the
withholding of such amounts for taxes and other payroll deductions as the
Company may reasonably determine it should withhold pursuant to any applicable
law or regulation.  To the extent applicable, it is intended that this
Agreement be exempt from, or comply with, the provisions of Section 409A
of the Code, and this Agreement shall be construed and applied in a manner
consistent with this intent.  In the
event that any severance payments or benefits hereunder are determined by the
Company to be in the nature of nonqualified deferred compensation payments, you
and the Company hereby agree to take such actions as may be mutually agreed to
ensure that such payments or benefits comply with the applicable provisions of Section 409A
of the Code and the official guidance issued thereunder.  Notwithstanding the foregoing, the
Company does not guarantee the tax treatment or tax consequences associated
with any payment or benefit arising under this Agreement.  5


If the foregoing accurately
sets forth our agreement, please so indicate by signing and returning to us the
enclosed copy of this Agreement.  Very truly yours,Metabolix, Inc.By:
  /s/ Richard P. EnoRichard P. EnoPresident & CEOAccepted
  and agreed:/s/
  Sarah P. CecilSarah
  P. CecilDate:
  12/18/08  6