SEC Form 4

FORM 4		UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940	OMB APPROVAL OMB Number: 3235-0287 Estimated average burden hours per response: 0.5
	Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

1. Name and Address of Reporting Person* Baker Brothers Life Sciences Capital (GP), LLC (Last) (First) (Middle) 667 MADISON AVENUE, 21ST FLOOR (Street) NEW YORK NY US 10065 (City) (State) (Zip)	2. Issuer Name and Ticker or Trading Symbol AP PHARMA INC /DE/ [ APPA ]	5. Relationship of Reporting Person(s) to Issuer (Check all applicable) Director X 10% Owner Officer (give title below) Other (specify below)
	3. Date of Earliest Transaction (Month/Day/Year) 06/30/2011
	4. If Amendment, Date of Original Filed (Month/Day/Year)	6. Individual or Joint/Group Filing (Check Applicable Line) Form filed by One Reporting Person X Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	3. Transaction Code (Instr. 8)		4. Securities Acquired (A) or Disposed Of (D) (Instr. 3, 4 and 5)			5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4)	6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)
			Code	V	Amount	(A) or (D)	Price
Common Stock(1)(2)	06/30/2011		J		1,786(10)	A	$0	5,266,568	I	Through Partnership(3)

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Transaction Date (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	4. Transaction Code (Instr. 8)		5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5)		6. Date Exercisable and Expiration Date (Month/Day/Year)		7. Title and Amount of Securities Underlying Derivative Security (Instr. 3 and 4)		8. Price of Derivative Security (Instr. 5)	9. Number of derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4)	10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)
				Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares
Senior Secured Convertible Notes due 2021(1)(2)	$0.04	06/30/2011		J		300(10)		(4)	(5)	Common Stock	7,500(7)	$0	294,600	I	Through Partnership(3)
Rights to Purchase Senior Secured Convertible Notes due 2021(1)(2)	$1,000(9)	06/30/2011		J		600(10)		(4)	(6)	Senior Secured Convertible Notes due 2021(8)(7)	600(8)(7)	$0	589,200	I	Through Partnership(3)

1. Name and Address of Reporting Person* Baker Brothers Life Sciences Capital (GP), LLC (Last) (First) (Middle) 667 MADISON AVENUE, 21ST FLOOR (Street) NEW YORK NY US 10065 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* BAKER JULIAN (Last) (First) (Middle) 667 MADISON AVENUE, 17TH FLOOR (Street) NEW YORK NY US 10021 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

1. Name and Address of Reporting Person* BAKER FELIX (Last) (First) (Middle) 667 MADISON AVENUE, 21ST FLOOR (Street) NEW YORK NY US 10065 (City) (State) (Zip) Relationship of Reporting Person(s) to Issuer Director X 10% Owner Officer (give title below) Other (specify below)

Explanation of Responses:

1. In addition to Baker Brothers Life Sciences Capital (GP), LLC, this Form 4 is being filed jointly by Julian C. Baker and Felix J. Baker, each of whom has the same business address as Baker Brothers Life Sciences Capital (GP), LLC and may be deemed to have a pecuniary interest in securities owned by it. Because of certain relationships with other security holders of the Issuer, the Reporting Persons are filing solely for informational purposes as if they were a member of a group of such shareholders. (Continued in footnote 2).

2. However, the Reporting Persons disclaim that they and any other person or persons, in fact constitute a "group" for purposes of Section 13(d)(3) of the Securities Exchange Act of 1934, as amended, or Rule 13d-5 thereunder or that they are the beneficial owners of securities owned by any such other persons, and each of them disclaims beneficial ownership of securities reported herein except to the extent of their pecuniary interest, if any, therein.

3. Represents securities owned directly by Baker Brothers Life Sciences, L.P., the sole general partner of which is Baker Brothers Life Sciences Capital, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP),LLC. Julian C. Baker and Felix J. Baker are controlling members of Baker Brothers Life Sciences Capital (GP), LLC.

4. The closing date of the purchase of the Senior Secured Convertible Notes due 2021.

5. The date that is 10 years following the closing date of the purchase of the Senior Secured Convertible Notes due 2021.

6. The date that is 2 years following the closing date of the purchase of the Senior Secured Convertible Notes due 2021.

7. Baker Brothers Life Sciences, L.P. does not have the right to convert any portion of any Senior Secured Convertible Notes due 2021, to the extent that after giving effect to such conversion, Baker Brothers Life Sciences, L.P. (together with its affiliates) would beneficially own in excess of 9.99% (subject to change as described in the note) of the number of shares of common stock outstanding immediately after giving effect to such conversion.

8. The Senior Secured Convertible Notes due 2021 underlying the Rights are convertible, at a conversion price of $0.04 per share, into an aggregate of 15,000 shares of Common Stock of the Issuer.

9. The exercise price to purchase Senior Secured Convertible Notes due 2021 represented by the Rights is $1,000 for each $1,000 principal amount of Senior Secured Convertible Notes due 2021 purchased upon exercise.

10. On June 30, 2011, Baker Bros. investments II, L.P. transferred these securities to Baker Brothers Life Sciences, LP. The general partner of Baker Bros. investments II, L.P. is Baker Bros Capital, L.P and its general partner is Baker Bros Capital, GP, LLC. The general partner of Baker Brothers Life Sciences, L.P. is Baker Brothers Life Sciences Capital, L.P. and its general partner is Baker Brothers Life Sciences capital (GP), LLC. Julian and Felix Baker are the managing members of both Baker Bros Capital (GP), LLC and Baker Brothers Life Sciences Capital (GP), LLC, and their respective pecuniary interests (if any) remain unchanged as a result of this transfer.

	/s/ Julian C. Baker, as Managing Member of Baker Brothers Life Sciences Capital (GP), LLC	07/05/2011
	/s/ Julian C. Baker	07/05/2011
	/s/ Felix J. Baker	07/05/2011
	** Signature of Reporting Person	Date
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