Ali v. Carnegie Institution of Washington

Mussa Ali 1631 NE Broadway, # 407 Portland, OR 97232 Phone: (503) 890-9179 Email:mussaali [email protected] For the Plaintiff

UNITED STATES DISTRICT COURT

DISTRICT OF OREGON - PORTLAND DIVISION

----------------------------------------------------X Mussa Ali,

Plaintiff,

vs.

Carnegie Institution ofWashington,

Defendants. -----------------------------------------------------X

cas~42 -CV -1764 ... 51 CIVIL ACTION COMPLAINT FOR CORRECTION OF INVENTORSHIP

UNDER 35 U.S.C. § 256

JURY TRIAL DEMANDED 1

COMPLAINT

The Plaintiff, Mussa Ali ("the Plaintiff' or "Plaintiff') brings this civil cause of

action against Carnegie Institution of Washington ("the Defendant" or "Defendant") under

the Patent Laws of the United States, 35 U.S. C. § 256. This Complaine'3 is being filed, at

1 Demand stipulated at this time-only as a way of, -in order to keep Plaintiffs options open. 2 If established or procedural rule precludes the inclusion of footnotes in a Complaint, all the footnotes herein are incorporated by reference (as part of~ 120) into this Complaint's body and without losing the footnotes' referential values. Exhibits and things cited herein refer to Exhibits and Things attached to the now-voluntarily dismissed action in the United States District Court for the Western District of Washington, Case No.2: 12-CV-01046-MJP, i.e. Docket-labeled Documents 1, 6 and 13. 3 The first-half of this Complaint is essentially the verbatim clipping of Dr. Cimbala'sfactually un-responded to-letter. This Action has been cobbled together to preserve the viability of some of the Plaintiffs claims going forward. The court( s) have repeatedly rejected complainants who claimed unfamiliarity with U.S. Patent Laws or American Jurisprudence-as inexcusable excuse-to overcome the presumption of Laches attached COMPLAINT 1 Mussa Ali under 35 U.S.C. § 256 1631 NE Broadway,# 407

Portland, OR 97232 Phone: (503) 890-9179

this time, by the Plaintiff, in an effort to preserve the viability of some of the Plaintiffs

claims going forward.

NATURE OF THE ACTION

1. This is largely a correction-of-inventorship action arising out of the Patent Laws of

the United States, 35 U.S.C. § 256 and Oregon State claims for conversion, unfair

competition, unjust enrichment and fraud related to the Plaintiffs contribution to

the complete conception and reduction-to-practice of the art of genetic inhibition by

double-stranded ribonucleic acid ("dsRNA") and claims arising from Defendant's

act(s) of omission of the Plaintiff from being credited as a co-inventor of the said

art. See Exhibit 13

2. This action is being filed at this time m an effort-notwithstanding Plaintiffs

diligence and the Defendant's documented unclean hands and inducements and

their on again, 'off again notices of inquiries (further detailed below in the body of

this FA C)-to preserve the viability of Plaintiffs claims. See also ~~ 99-111, ~~

118-120

3. For all the relevant times and for the purpose of clarity, Plaintiff was working with

the named co-inventors when he contributed to the mechanistic conception of the

said art, i.e., RNAi. Plaintiff's mechanistic conception of RNAi-and or Plaintiffs

to a facially-delayed inventorship suit. Plaintiff may move to have this case be held in abeyance (after service), since Plaintiffs claim that he had contributed to the conception of RNAi is being engaged in an Interference Proceeding at/by BPAI via Interference No. 105,754. In an effort to lessen cluttering the Court with documents and things, all of Plaintiffs publicly downloadable documents filed at BPAI (Interference No. 105,754) and or documents and things furnished or being furnished to the Defendant-i.e., under the rubric Exhibit 3-are incorporated herein by reference. Additionally, Document 1, Document 6, and Document 13 are hereby incorporated by reference. COMPLAINT 2 under 35 U.S.C. § 256

MussaAli 1631 NE Broadway, # 407


contribution to such-and Plaintiffs relation of such to one of the co-inventors had

been witnessed. See Slide 22 and Exhibit 17

4. In an acknowledgement of Plaintiffs potential-ifnot certainty- to conceive and or

capacity to solve "difficult new questions", Plaintiff was rated as "outstanding,

intelligent" "scientist" by the Defendant. (quotations from Defendant's evaluation)

See Slide 52 and Exhibit 21.

JURISDICTION AND VENUE

5. This action arises under the Patent Laws of the United States, Title 35 of the United

States Code, including 35 U.S.C. § 256.

6. This Court has subject matter jurisdiction over this matter pursuant to 28 U.S.C.

§§1331 and 1338.

7. Venue is proper in this case, because the named co-inventors in the patents-in-suit

are scattered, among other places, all over the continental United States and the

relevant documentary notebooks and such have been "discarded" by the

Defendant-from the site of Plaintiffs conception and reduction to practice of the

invention(s)-in-suit. See Slide 28 and Exhibit 1, Dl: PAP 31

8. Furthermore, upon knowledge and information, Defendant has engaged in business

transaction with entities in the State of Oregon.

THE PARTIES

9. Plaintiff is a citizen of Ethiopia, and a natural person who emigrated to the United

States of America on November 11, 1985.

COMPLAINT 3 under 35 U.S.C. § 256

MussaAli 1631 NE Broadway,# 407


10. The Defendant is presumed to have its main headquarters in Washington D. C. at

1530 P Street NW, Washington, D.C., 20005. The Defendant has recently been

renamed as the Carnegie Institution for Science.

DEFINITIONS AND TIMELINES AND PERMUTATIONS

11. The Board of Patent Appeals and Interferences may be referred to as "BP AI" or

"the Board" for short.

12. "USA" or the abridged version "US" or "United States" refers to the United States

of America.

13. "Document 1" or "Dl" refers to Plaintiffs June 15, 2012 filing in the United

District Court at Seattle, i.e., case number 2: 12-CV-01046-MJP (now voluntarily

dismissed pursuant to F.R.C.P 41(a)(l)), and docket-labeled as "Document 1".

"Slides" refers to the (attached) Slides under the rubric Exhibit 3 or Plaintiffs filed

Slides at BPAI and filed as CSIRO EXHIBIT 2082, CSIRO v. Carnegie,

Interference No. 105,754.

14. "PAP" stands for r_laintiff Assigned r_age-number of Plaintiffs filings of June 15,

2012, i.e., case number 2:12-CV-01046-MJP; for the purpose of convenience,

Plaintiffs filings, i.e., Documents 6 and 13, bear the sequentially numbered "PAP"

tag.

15. The 1996 Rutgers University Worm Meeting ("the 1996 Worm Meeting") is a

conference of Caenorhabditis elegans ("C. elegans") researchers held in 1996 at the

Rutgers University, See Exhibit 14; the 1997 International Worm Meeting ("the

1997 Worm Meeting") refers to the May 28-June 1, 1997 International Worm

Meeting of C. elegans researchers held in Madison, Wisconsin.


Mussa Ali 1631 NE Broadway,# 407


16. Although the term RNA interference ("RNAi") was coined in June of 1997, i.e.,

after the 1997 Worm Meeting; for the purpose of ease, the term RNAi is being

used liberally here. See Slide 43

17. The term "Skeletal" is used to highlight the framework or skeleton within which

the Mello group's initial model postulated the possibility of a "double-stranded

molecule" as being the key interfering intermediate-trigger molecule mediating

RNAi in C. elegans.

18. The term "back and forth conversation" may mean a one-way flow of information,

contingent upon prospective discovery of the nature of the RNAi related

conversations that had been held between Dr. Craig Mello4 and Dr. Andrew Fire\

predating June 1, 1997.

19. The patent[s]-in-suit may sometimes be referred to as the art-in-suit or the

invention-in-suit to refer to the expandable claims the invention-in-suit has garnered

since the initial patent was issued or as a generalized statement of reference as to

the invention-in-suit's seminality.

20. The Mello['s] group or Mello et al refers to members of Dr. Craig Mello's ("Dr.

Mello's") laboratory, namely Mr. Samuel "Sam" Driver ("Mr. Driver"), the

Plaintiff and Dr. Mello who were exclusively involved in the complete construction

of the said art from 1995-1997.

4 Plaintiff has, in the past, collectively referred to them as "the co-discoverers of [Plaintiffs] conception." See Exhibit 4, footnote 48; routinely, self-styled RNAi historians (e.g. 'Zamare ofUMASS) have dubbed them as "the" co-discoverers ofRNAi. ['Za-ma-re is an Amharic word meaning one who sings praises of/to people in the limelight.] COMPLAINT 5 under 35 U.S.C. § 256



21. The Fire['s] group or Fire et al refers to Dr. Andrew Fire's laboratory members,

who were involved in the construction of the art-in-suit post-conception, i.e. post-

partum. See Slide 13

22. Dr. Nicholas Miliaras ("Dr. Miliaras") refers to a member of Dr. Craig Mello's

laboratory who worked at the time Plaintiff worked in Dr. Mello's laboratory in the

same open laboratory space. See Slide 54

23. Mr. Paul Kokulis ("Mr. Kokulis") refers to the Defendant's lead counsel and with

whom Plaintiff or Plaintiff's procession of patent-counsels over the years has had

direct communications with, regarding Plaintiffs omission from being credited as a

co-inventor on the patents-in-suit.

24. The term single-stranded ("ss") may mean double-stranded ("ds") or vice versa

depending on the context in which they are used, i.e., pre or post recognition; and

the intent ofthe Plaintiff. See illustrational e.g. Exhibitl, Dl: PAP30: Box 33, right

column.

25. The words "art" or "invention" may sometimes be substituted for "patent[s]" or

"patent[s ]-in-suit".

26. For the purpose of this action, at all relevant times and context, Plaintiff is

presumed to be a co-inventor and not a sole-inventor.

27. Period5 I encompasses the time window between the time the Plaintiff knew or

should have known about Plaintiffs omission from the being credited as a co-

inventor on the patent[ s ]-in-suit, or from the time of the initial patent[ s ]-in-suit

5 proposed permutations and timelines to give this Court the maximum flexibility in rendering prospective and or retroactive relief as [it] may deem just and proper. COMPLAINT 6 under 35 U.S.C. § 256

Mussa Ali 1631 NE Broadway, # 407


application was drafted and or the date of initiation of the first round of Defendant's

notice of inquiry into the Plaintiffs inventive contribution to the Patents-in-suit to

June 15, 2006.

28. Period II encompasses the time window between, June 15, 2006 or the end of

Period I to the date of the filing of the original Complaint, in the United District

court at Seattle, i.e., case number 2: 12-CV-01046-MJP. See fn 2

29. Period III encompasses the time after the filing of the original Complaint, namely

June 15, 2012. (!d)

30. Under Permutation5 I Plaintiff is presumed to be the co-owner of the patents-in-suit.

31. Under Permutation II Plaintiff is presumed to have forfeited Plaintiffs co-

ownership rights to the patents-in-suit to the Defendant or the State of Oregon.

32. The term "named co-inventors" refers to the named co-inventors listed on the

patents-in-suit.

33. Patents-in-suit6 are US Patent Numbers 6,506,559 Bl, 7,538,095 B2, 7,560,438 B2,

and 7,622,633 B2. See e.g. Slide 10 and Exhibit 13

34. The word "collaboration" refers largely to experimental collaboration; a one-way

mental collaboration between the Mello and Fire groups is implied or presumed

throughout the relevant 1995-1997 period.

6 Upon knowledge and information and or belief, since or about 1997-----<iue to the high economic value of the patents-in-suit-the Defendant [and by extension the named coinventors therein] have been, for lack of a better idiom, rolling in dough. See Exhibits 20, 22 and 26. COMPLAINT under 35 U.S.C. § 256

7 Mussa Ali 1631 NE Broadway,# 407


35. When convenient, Carnegie Institution of Washington ("the Defendant" or

"Defendant") may be referred to as "they"; Defendant's as "their" or "theirs". "fn"

stands for footnote.

36. "Notice of Inquiry" refers to the Defendant's notice to the Plaintiff to investigate

into Plaintiffs claims of inventive contributions to the patents-in-suit.

BACKGROUND

The Bizarre Phenomenon of Sense RNA-mediated Genetic Interference

37. Since the early 1980's, experimental introduction of exogenous antisense RNA into

cells has been used to inhibit gene expression. A conventional complementarity

model is often used to explain antisense RNA induced gene silencing, wherein the

interfering antisense RNA is hypothesized to simply hybridize to, and inhibit the

expression of, the complementary (sense) endogenous mRNA. In such experiments

the sense RNA is often used as a control.

38. In 1995, researchers at Cornell University reported that the direct introduction of

the (control) sense RNA unexpectedly provokes sequence-specific genetic

interference in C. elegans. This surprise finding prompted members of Mello's

laboratory .i.e., the Mello's group, to embark on an effort to delineate the molecular

mechanism underlying RNA induced genetic interference ("RNAi") in C. elegans.

See Slide 4

39. The other aspects of RNA provoked interference in C. elegans were also worthy of

note: the interference effect was potent and heritable, and that both, exogenous

sense and antisense, in vitro RNA transcripts provoke interference with high degree

of fidelity and potency. See Slide 12

COMPLAINT under 35 U.S.C. § 256

8 MussaAli 1631 NE Broadway,# 407


40. These strikingly unconventional observations led the Mello's group to formulate a

Skeletal model, which attempts to explain the salient features of RNA mediated,

sequence-specific genetic inhibition in C. elegans. In an effort to account for both

the pronounced perdurance of the inhibitory effect and the fact that

complementarity appears not to play an upstream role in this pathway, Mello's

group put forth a model wherein the exogenously introduced sense or antisense

RNA would be converted into a "double-stranded molecule" i.e., the interfering-

trigger molecule, by a putative endogenous C. elegans polymerase. See Slide 9

41. Initially, Mello's group tested the possibility of the existence of a double-stranded

DNA (dsDNA) [instead of dsRNA] interfering intermediate, which would have

been formed by the polymerizing activity of the putative Reverse Transcriptase

("RT"). Mello's group dubbed this paradigm as the "RT/cDNA/dsDNA" Model.

See Slide 6

42. Subsequently, several experiments were carried out to prove or disprove the

existence of this de novo synthesized, eDNA-sized dsDNA interfering agent.

Mello's group was initially in favor of this model because of the durability and

heritability of silencing. The logic being, if the interference effect is heritable, the

interfering intermediate "has" to be a dsDNA molecule. (quoting Dr. Mello) See

Slides 14,16,30 and 31

43. To directly test the hypothesis that the dsDNA intermediate was the interfering-

trigger agent, Mello's group tested the efficacy of dsDNA; Plaintiff was involved in

the initiation, design [and synthesis] and carrying out of this experiment. See Slide

29


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44. Despite repeated attempts, Mello's group was unable to conclusively detect the

putative dsDNA intermediate, which would have been formed had there been RNA-

induced RT-like polymerizing activity within the cell. See Slide 31

45. As an alternative model, Mello's group briefly entertained the possibility of

interference within the nucleus, that is, RNA induced transcriptional silencing at the

level of the gene. Not unlike the "RT/cDNA/dsDNA" model, this transcriptional

gene silencing ("TGS") model would (if proven) still explain the salient features of

RNA mediated interference detailed above. For example, one could speculate that

the interfering sense or antisense RNA would interfere with the transcriptional

activity of the endogenous gene at the level of the silenced gene locus either

directly or indirectly by provoking epigenetic changes. See Slide 7

46. Such exogenous RNA transcripts induced transcriptional silencing and epigenetic

changes have previously been described in plants. Although, much of the work

garnered in this regard was negative (methylation, promoter targeting experiments);

inadvertently, the data generated pursuing the possibility of transcriptional silencing

cemented the possibility and likelihood that RNA induced silencing in C. elegans

was a post transcriptional gene silencing ("PTGS") event, and distinct from other

related RNA induced silencing phenomenon observed in other systems. See Slides

32, 33, 34 and 37

THE LATTER-DAY MECHANISTICALLY-VINDICATED CONCEPTION OF RNAi BY THE PLAINTIFF

47. What led Mello's group to the ultimate mechanistic recognition that RNAi in C.

elegans is mediated by dsRNA (the interfering agent)? Upon accidentally


10 Mussa Ali 1631 NE Broadway, # 407


encountering an enzyme called RNA Replicase or RNA dependent RNA

polymerase, (in an MCAT book) Plaintiff recognized that this enzyme (instead of

RT) might be involved in RNAi pathways in C. elegans. See Slide 22

48. Subsequently, and within the context of the Skeletal Model, Plaintiff informed Dr.

Mello that dsRNA might be the active interfering agent triggering RNAi in C.

elegans. See Slide 22 and Exhibit 17

49. With this recognition7 in hand, and not unlike what was done pursuant to the

"RT/cDNA/dsDNA" Model, the Mello's group [along] with Fire's 'repeated' the

RNAi experiments to revalidate what Mello et a/. had reported and published. See

Slides 14 and 15

50. Indeed, all along, the one moment of recognition that was fluttering just below the

radar of the Mello group's model(s) and experimental observations was the

recognition that the interfering agent is dsRNA (via RDRP), and not dsDNA (via

RT). See Slide 9

THE MELLO GROUP'S REDUCTION-TO-PRACTICE OF RNAi BEFORE THE FIRE'S GROUP

51. In an effort to reduce RNAi to practice with defined molecular parameters, Mello's

group conducted signature molecular experiments that homed in on the mystery of

7 Plaintiff had repeatedly suggested to Dr. Mello (at the time discounted as unlikely by Dr. Mello) that both strands of RNAs be introduced into the cell, at the same time. This experiment, that Plaintiff suggested, involved RNA strands that were ofthe appropriate size for inducing RNA in C. elegans. Also, the proposed injected two strands ofRNAs were such that their sequence were complementary and corresponded to the sequence of at least a portion of the double-stranded sequence of the target gene, with the expectation of achieving the inhibition of the expression of the desired target gene within the cell. COMPLAINT 11 Mussa Ali under 35 U.S.C. § 256 1631 NE Broadway,# 407


RNAi. The following are highlights of original experiments performed by Mello's

group:

52. Are RNAs, targeting exonic sequences, sufficient to induce RNAi in C. elegans? If

RNAi is mediated by TGS, then one could arguably target intronic sequences and

still induce silencing? Could one target (upstream) promoter sequences and induce

RNAi? Mello's group was the first to report, while exonic sequences were

compatible with RNAi; RNAi targeted against intronic or promoter sequences were

ineffective. These molecular data strongly suggested that RNAi is PTGS. See Slides

11, 14 and 37; and See also Exhibit 19

53. The requirement for sequence homology between RNAs to provoke sequence

specific and distinct interference was initially carried out by Mello's group. Two

related genes that were "80%" homologous to each other gave a distinct and non-

overlapping loss of function phenotype. Additionally, almost all the genes tested

phenocopied the known loss of function phenotype for the gene targeted. See Slides

38 and 39 and Exhibit 10, fn 13

54. Mutation was undetectable within RNAi targeted gene locus. One possibility of

RNAi that needed to be explored was the possibility that RNAi could induce de

novo mutation at the gene locus by some unknown homology dependent

RNA/DNA or 'DNA'/DNA interaction. See Slide 33 and Exhibit 10, PAP 124

55. Previous reports in the literature indicated that in some cases RNA mediated

silencing provokes de novo methylation at the level of the gene, including promoter

regions. Mello's group ruled out this possibility as RNAi was unable to provoke a

detectable de novo methylation in C. elegans. See Slide 34




56. The Skeletal Model put forth by Mello's group dictates that both the sense and

antisense RNA should exhibit equal level of inhibitions, i.e., both sense and

antisense RNA have equal dose response properties. Indeed, this was the case;

Mello's group reported their findings that for all the concentrations of RNA tested,

both sense and antisense preparation of RNA provoked equal level of inhibitory

effects. Coincidentally, this finding served as the basis for the stable double-

stranded intermediate-trigger hypothesis. See Slides 12 and 14; See also Exhibit 10

57. Although it was clearly established that RNAi results in the disappearance of the

endogenous protein and several of the data generated strongly suggest that is a

PTGS event, it was still unknown if the endogenous mRNA coexisted, and was

compatible, with interference or the mRNA was the target of RNAi; Mello's group

was the first to report that RNAi in C. elegans involves the absence of the

endogenous mRNA. Mello's group assayed for expression of RNAi targeted gene

in single cell embryos and ruled out-while not precluding the twin possibilities of

a pre/co transcriptional silencing mechanism-a post-translational mechanism

wherein RNAi is compatible with the co-existence the [target] endogenous

messenger RNA ("mRNA"). See Slide 41

58. In an effort to delineate the smallest number of homologous bases required for

RNAi in C. elegans, Mello's group carried out detailed size dependent RNAi

experiment; as an example Mello's lab used 24, 50, 100 nucleotide long RNAi to

demarcate this point of usability. See Slide 36 and 51 and Exhibit 10, PAP 124

59. RNAi is 'heritable': although the bizarre nature RNA mediated inheritable

interference was repeatedly observed, this phenomenon, m and of itself, didn't


13 MussaAli 1631 NE Broadway, # 407


directly lead, or significantly contribute, to the ultimate upstream recognition that

RNAi is mediated by dsRNA. Ironically, the heritability of RNAi served as a ruse

for the formation of the initial [biased] hypothesis, that the interfering agent is a

dsDNA, instead of dsRNA. See Slide 42

60. Somewhat intriguing at the time, RNAi was found to be able to cross cellular

boundaries, i.e., that it is "systemic"; this finding, in and of itself, didn't lead to a

deducible mechanistic insight. See Slides 23 and 24

A FACTUAL ANALYSIS OF THE THREE EUREKA[SJ

61. The conception of RNAi is an exquisitely monadic conception: the recognition that

the interfering molecule is dsRNA.

Eureka A: the Systemic Route

62. According to Dr. Mello, at the 1997 Worm Meeting, in discussion with Dr. Mello

and Sam Driver, Dr. Fire was "prompted" to ask the question if the interfering agent

was, in fact, a dsRNA molecule-not that there may have been a dsRNA

contaminant in Mello group's in vitro RNA preparations per se-upon being told

that RNAi is systemic by Mr. Driver. Dr. Fire echoes this 'conception' scenario at a

World Talk Radio interview he gave on July 23, 2003 and in an interview with a

Wall Street Journal reporter in 2002; while Dr. Mello recounts in detail the same

story of conception in an interview posted on an Ambion website. See Slides 23 and

24 and Exhibit 18

63. Despite its mechanistic implausibility, the biggest complication with Eureka A is

the bio-unavailability of Mr. Driver at the 1997 Worm Meeting: Although he may




have registered for the meeting, Mr. Driver never actually attended the 1997 Worm

Meeting. See Slide 26

64. Indeed, Dr. Mello had asked Plaintiff to present the Mello group's RNAi findings at

the1997 Worm Meeting because Mr. Driver (who had abruptly left Dr. Mello's

laboratory to begin work as a technician of some sort at Hybridon Inc.) was unable

to attend the Meeting. See Slide 15

65. Having initially agreed to do so, Plaintiff declined to present the RNAi data because

Plaintiff was unable to reproduce what Dr. Mello and Mr. Driver claimed in the

submitted abstract, namely that they could propagate RNAi "indefinitely." See e.g.

Slide 42

66. Besides Eureka A's problematic historical accuracy (i.e. the absence of Mr. Driver

at the 1997 Worm Meeting), to many in the field, it may be hard to imagine that the

suggestion of the systemic nature of RNAi could have provoked Dr. Fire to re-

conceive RNAi or prompted him to ask the question if the interfering agent was, in

fact, a dsRNA molecule.

67. Additionally, at the 1996 Worm Meeting, Dr. Fire and members of Dr. Fire's

laboratory were keenly familiar with the salient features of Mello group's Skeletal

Model and Mello group's seminal molecular RNAi findings; thus it is even harder

to place the genesis of Dr. Fire's apparent initiation and inspiration at the 1997

Worm Meeting -as if Dr. Fire were not familiar with the Mello group's RNAi data

and models (before its elucidation) in 1996. See Slide 45

68. Although it is plausible that an illogic or even serendipity could provoke one to

discover RNAi, it is fair to state, taken together, that Dr. Fire's alleged inspiration,


15 MussaAii 1631 NE Broadway,# 407


didn't flow from the systemic nature of RNAi and, didn't involve Mr. Driver,

neither directly nor indirectly.

Eureka B: the RDRP/dsRNA Model

69. A few weeks before the 1997 Worm Meeting, Plaintiff suggested to Dr. Mello that

RDRP may play a role in RNA interference and that dsRNA via RDRP (instead of

dsDNA via RT) could be the interfering agent. See Slide 22

70. In support of this, and in a tacit admission, Dr. Mello writes that "our initial" model

"saw" a dsRNA molecule as an interfering agent, before Dr. Fire's apparent re-

conception at the 1997 Worm Meeting. See Slide 47 and Exhibits 23 and 29

71. It is clear that the route by which one could see a dsRNA ntermediate-trigger in the

context of Mello's group published Skeletal Model is via RDRP. It is also

unassailable that Plaintiff was the one who suggested RDRP/dsRNA as an

alternative to RT/dsDNA to Dr. Mello directly. See Exhibit 17

72. "Do you remember ... may be you do not remember this ... do you remember ... when

I told this to [Dr. Mello], I remember winking at you at the time ... I remember,

telling you ... when I tell this to [Dr. Mello], he would probably say it is [nothing]

and then suggest it the very next day?" Plaintiff asked Dr. Miliaras, a Dr. Mello

laboratory member, in early 1998 when Dr. Miliaras' memory was fresher and

when he was less abashed to come forward to tell the truth, and Dr. Miliaras' un-

cued response was "Yes, it was RNA dependent RNA polymerase." See Slide 22

73. Dr. Miliaras then continued on to recollect that after Plaintiffs suggestion of the

role of RDRP, Dr. Mello retorted by saying "this must be it; I am going to tell

Sam about this." This was a verbatim recounting of what Dr. Miliaras said




happened when Plaintiff told Dr. Mello about the role of RDRP within the context

of the Skeletal Model. See Exhibit 5, P AP98a

74. At a meeting held in Washington D.C., on April 28, 2005, Defendant's

representatives denied that Plaintiff had ever suggested RDRP to Dr. Mello in the

laboratory or that Dr. Mello "does not recall" such, while concomitantly presenting

a mechanistically flawed RDRP vis-a-vis the Skeletal Model 'doesn't-get-you-

there' argument. See CSIRO v. Carnegie, Interference No. 105,754, CSIRO Exhibit

2082, pages number 9-10; or See Exhibit 3, PAP35-PAP36.

Eureka C: the dsRNA Contaminant 'Model'

75. When asked what led Dr. Fire to Dr. Fire's alleged moment of recognition or Dr.

Fire's experimental involvement with RNAi, somehow upon being re-introduced to

RNAi, Dr. Fire was inspired by Dr. Mello [and Mr. Driver] at the 1997 Worm

Meeting to wonder whether the interfering trigger molecule in Mello group's

sense/antisense in vitro RNA preparation was a dsRNA contaminant. Subsequent to

this epiphany of Dr. Fire's, Dr. Fire holds, Fire's lab entered into a collaborative

work with Mello's group to test Dr. Fire's hypothesis. See Slide 45

76. Notwithstanding the doubtful veracity of Dr. Fire's alleged conception-whether

RNAi is conceived via the Skeletal Model, or re-conceived via the dsRNA

contaminant-trigger 'model'-the collaborative post-recognition experiments that

the Fire's [and Mello's groups] carried out were neither to test for the existence of

the dsRNA contaminant nor to directly test that the dsRNA contaminant is the

actual trigger, but to confirm Mello's group's initial conception that the interfering

agent is a dsRNA molecule. See Slides 25, 45 and 50.




THE REPEAT (OR TOUCH-UP8) RE-REDUCTION-TO-PRACTICE

OF RNAi BY THE FIRE GROUP

77. The only type of collaboration between the Fire group and the Mello group was a

mental one: the extensive back and forth conversation between Dr. Mello and Dr.

Fire. According to Dr. Mello, Dr. Mello spoke "to Andy so often-almost every

week or every couple of weeks-talking about this silencing phenomenon" until Dr.

Mello's ears "would be hurting". See Exhibit 7, PAP 101

78. Dr. Fire has denied or tried to conceal this mental collaboration between the Fire

group and the Mello group predating Dr. Fire's alleged conception. In a 2004

speech he details how he was mesmerized by "the basics of' the Mello's group

RNAi work presented at the May 28-June 1, 1997 Worm Meeting (Madison,

Wisconsin); while he reconceived RNAi at the same locale via "fuzzy logic"

(quoting Dr. Fire); See also Slides 45 and 50 and Exhibit 24, PAP 211

79. Revealingly, when inquired about the conception of RNAi in a radio interview8 in

another time, Dr. Fire's response began by saying "In Craig's case"; this initial "In

Craig's [lab] case" conception was concealed from, or was not disclosed to, BPAI

in the course of the Motions Phase of Interference No. 1 05,754; while the "fuzzy-

logic" mediated and the largely mythologized (alleged) conception of Dr. Fire's had

been proffered as the genuine article. See Patent Interference No. 105,754 (Paper

50) or Exhibit 7, PAP 102 and Exhibits 16, Exhibit 24, PAP 211

8 To the extent that the Fire group was involved in RNAi, it is clear that the Fire group's involvement was after the recognition that RNAi is mediated by dsRNA: any later reduction to practice simply inures to the benefits of the Plaintiffs initial mechanistic conception ofRNAi-or Plaintiffs contribution to such-in this regard. See Slides 11, 13, 19, 20, 25, 47, 49; Dr. Fire was being interviewed by Dr. David Lemberg and Mr. Sam Kephart. See Exhibit 5, PAP98b and Exhibit 16 COMPLAINT 18 under 35 U.S.C. § 256



80. There was a complete mechanistic conception ofRNAi in Mello's laboratory before

the alleged epiphany of Dr. Fire on June 1, 1997.

81. The Fire group's experimental involvement in the RNAi project was roughly 10

weeks. i.e., from the moment of Dr. Fire's alleged conception or the date (on or

about July 1, 1997) Plaintiff left the Dr. Mello's laboratory to the date the seminal

RNAi data was submitted for publication (September, 16, 1997). See Slides 20 and

26 and Exhibit 11, PAP 130

82. The only new finding that resulted from the alleged experimental collaboration

between the Mello and the Fire groups was the experimental recognition that only a

few molecules of dsRNA [contaminant] could or would trigger RNAi in C. elegans.

See Slide 48 and Exhibit 11, PAP 128

83. Given the above, i.e. ,-r 82, the nearly 2 years worth of seminal RNAi data

generated by the Mello group would have been done, as a practical matter and as a

matter of the Fire group's thinking by September 16, 1997, with sufficient dsRNA

to trigger RNAi. (!d.)

84. Owing to such finding, despite no verifiable proof of experimental collaboration,

the Mello group (minus the Plaintiff) is named as co-inventors on a patent that was

largely executed by the Carnegie Institution of Washington. See Slides 10 and 27

and Exhibit 13

85. In further acknowledgement of the seminal nature of Mello's group involvement,

one of the listed co-inventors from the Fire group lauded the Mello's group for

having "first" "observed" (and reported in 1996) the efficacy of exon RNAi vs.

intron RNAi experiments on her personal website. Interestingly, the website




additionally reveals that the Fire group's later work, i.e., from July 1997 on, was

redundant. See Slide 11 and Exhibit 19, PAP 174

IS DR. FIRE'S STRUCTURAL EUREKA SUFFICIENT OR EVEN NECESSARY FOR THE DISCOVERY OF RNAi?

86. Dr. Fire's alleged conception is, in and of itself, insufficient for the complete

conception of RNAi.

87. The mere recognition that there is a dsRNA contaminant in Mello's group in vitro

transcribed ("IVT") RNAs, is only useful after the initial recognition that the

interfering molecule is dsRNA. See Slide 25

88. In a tacit acknowledgement of this, Dr. Fire himself admits that he has known about

the co-synthesis of a dsRNA subpopulation in an IVT reaction in which the dsDNA

template has a 3' protruding ends, since Dr. Fire's "graduate" days, at least by or

before 1991; and this knowledge didn't trigger Dr. Fire to conceive RNAi

(allegedly) until June 1, 1997. See Slides 45 and 46 and Exhibit 24, PAP 211

89. Plaintiff holds that what triggered Dr. Fire to put two and two together was a

negative data that was generated by the Plaintiff that awakened Dr. Fire (owing to

Dr. Fire's structural knowledge) to the possibility that the dsRNA may be the actual

trigger. See Slides 49 and 50 and Exhibit 25; also, see Exhibit 9, Deposition

transcript pages 89-90

90. Additionally, Dr. Fire's alleged conception was neither immaculately conceived nor

inspired by a "fuzzy logic", as Dr. Fire holds. See Slides 45, 47, 49 and 50 and

Exhibit 24, PAP 211




91. Moreover, the tenures of some of the co-inventors status are so tenuous that even a

benign poking into their alleged contributions would show that they are meritless 9 •

See e.g. slide 48

THE SEMINALLY -ISSUED RNAi US PATENT NUMBER 6,506,559 Bl AND ITS CLAIMS; THE OTHER RELATED CHILD RNAi US PATENT

NUMBERS 7,538,095 B2, 7,560,438 B2, AND 7,622,633 B2; PLAINTIFF'S DISCOVERY OF SUCH

92. The seminally-issued RNAi patent, US Patent Number 6,506,559 Bl ("'559") was

issued in 2003. See Slide 10 and Exhibit 13

93. Plaintiff neither read nor inspected the content of the '559 patent until after the '559

patent's issuance and publication.

94. The mother claim, i.e., claim 1, of the '559 patent reads as follows:

A method to inhibit expression of a target gene in a cell comprising introduction of a ribonucleic acid in an amount sufficient to inhibit expression of the target gene, wherein the RNA comprises a double-stranded structure with an identical nucleotide sequence as compared to a portion of the target gene. (See Exhibit 13, PAP 163)

95. Plaintiff had contributed to the complete conception of, and designed and carried

out numerous experiments, using -sufficient- dsRNA to inhibit the expression of

target gene. See Slides 14-16, 18-20, and 29-42

96. Accordingly, Plaintiff had contributed to the subject matter embodied in claim 1 of

the '559 patent. Exhibit 13, PAP 163

97. A similarly situated credited co-inventor, Mr. Driver, had left the Mello laboratory

before the alleged experimental collaborative work commenced between the Mello

9 Plaintiff is not a patent counsel-neither imagined nor real. That being said, the naming of H. Tabara as a co-inventor is certainly curious; simply put: Mr. Tabara was not there at site of the invention's invention, when RNAi was, conceived and or reduced to practice. COMPLAINT 21 Mussa Ali under 35 U.S.C. § 256 1631 NE Broadway, # 407


group and the Fire groups. Mr. Driver left the Dr. Mello's laboratory before

Plaintiff left the same. See Slide 26 and Exhibit 13, PAP 142 and Exhibit 9,

Deposition Transcript page 37

98. Plaintiff became aware of the other related child RNAi patents, namely US patent

numbers 7,538,095 B2, 7,560,438 B2, and 7,622,633 B2 recently.

DEFENDANT'S DOCUMENTARILY PROVABLE UNCLEAN HANDS AND PLAINTIFF'S INITIAL DISCOVERY OF SUCH

99. Plaintiff, having learnt about and inspected the '559 patent, contacted the Defendant

to initiate notice of inquiry into Plaintiffs assertion that he had made inventive

contribution to the patent[s]-in-suit in or around 2003; Plaintiff contacted Mr.

Kokulis and Defendant indicated that they would "look into the matter".

100. To give structure to the notice of inquiry, the Plaintiff then began an

exhausting process of searching for a patent counsel with background m

Biotechnology patents.

101. After securing Dr. Michelle Cimbala ("Dr. Cimbala") of STERNE,

KESSLER, GOLDSTEIN & FOX as counsel, Plaintiff then contacted the

Defendant.

102. In response to request for "more" information about Plaintiffs claims, Dr.

Cimbala sent a detailed analysis ("the letter") of the Plaintiff claims, relying, among

other things on two published abstracts, bearing Plaintiff as a co-author, in which

the Mello group laid down the foundational thinking of their models and the data

they were generating in real-time. See CSIRO v. Carnegie, Interference No.

105,754, CSIRO Exhibit 2082, pages number 2-8; or See Exhibit 3, PAP28-PAP34.




103. Within weeks of the receipt of the letter, Defendant abruptly closed their

investigation citing unrelated incident. See Exhibit!, Dl: PAP24: Box 19, right

column; and Exhibit 30

104. Plaintiffthen approached the law firm ofWILSON, SONSINI, GOODRICH

& ROSATI ("WSGR") to approach the Defendant again about their premature

closure of their investigation.

105. Subsequently: Plaintiffs counsel forwarded, among other things, the

notebook extract which documented the mechanistic conception of RNAi (via

RDRP) to the Defendant; notwithstanding the Defendants' now aspersions of doubt

on the "veracity" of the said extract, according to Mr. Vern Norviel ("Mr. Norviel")

of WSGR, upon the receipt of the said document, the first utterance 10 of Mr.

Kokulis was that "UMASS has nothing to do" with the patents-in-suit and that he

would get back to Mr. Norviel as soon as possible; several months later Mr. Kokulis

informed Mr. Norviel that they, had completed their alleged investigation and, had

concluded that Plaintiff has nothing to do with the invention-in-suit; and then,

strangely 11 and without disclosing the agenda in advance, Defendant then requested

a meeting.

106. On April 28, 2005 a meeting was held and at this meeting the Defendant

clearly stated that they would investigate whether Dr. Miliaras still remembers

Plaintiffs suggestion of RDRP in the context of the Mello group's Skeletal model

10 It is presumed that Mr. Kokulis has never seen a direct documentary evidence of experimental collaboration between the Mello and Fire groups, hence the telling utterance; utterance ran-by and or fact-checked with Mr. Norviel, via e-mail. 11 See Exhibit 1, Dl: PAP24, Box 10, right column. COMPLAINT 23 under 35 U.S.C. § 256

MussaAii 1631 NE Broadway, # 407


and whether Mr. Driver attended the site of the Defendant's alleged conception,

much less participated in its construction. See CSIRO v. Carnegie, Interference No.

105,754, CSIRO Exhibit 2082, pages number 9-10; or See Exhibit 3, PAP36.

107. A few weeks later, in response to a request for update on the status of their

alleged investigation, the Defendant sent an e-letter to Plaintiffs counsel stating

that they had completed their "detailed" investigation and stated that Plaintiff had

nothing to do with the invention-in-suit. See Exhibit 6

108. Subsequently (and among other counsels) Plaintiff had Mrs. Catherine

Youssef ("Mrs. Youssef'), currently VP and Senior Counsel at Citigroup Inc., to

mqmre about the nature of their investigation into Plaintiffs invention-related

claims.

109. In a letter dated July 5, 2006, Mrs. Youssef memorialized that she had

spoken to Mr. Kokulis on June 15, 2006 and that Mr. Kokulis had informed her that

"[Mr. Kokulis] did not speak with [Dr.] Miliaras". Exhibit 15, PAP 169

110. It is clear that the Defendant's protestations of "detailed" investigation into

the Plaintiffs invention-related claims were not true, since they didn't even bother

to interview Dr. Miliaras, whom they had easy access to, after they had indicated

that they would. Exhibit 3, PAP 36

111. If they had indeed interviewed Dr. Miliaras and hadn't like what they heard,

1.e., that Dr. Miliaras still remembered Plaintiffs suggestion of RDRP and

Plaintiffs unassailable 12 (however inadvertent) contribution to the mechanistic

12 Notwithstanding the then Defendant's evaluation of the Plaintiff as an "outstanding, intelligent" "scientist" who "often devis[ed]* innovative approaches to difficult new COMPLAINT 24 Mussa Ali under 35 U.S.C. § 256 1631 NE Broadway,# 407


conception RNAi, and then if the Defendant had, in fact, proceeded to conceal -or

deceive- the result of their investigation from the Plaintiff, this would constitute

plain fraud. Alternatively, if the Defendant had completed their alleged "detailed"

investigation of the Plaintiffs inventive claims without interviewing the Plaintiffs

conception witness, after they had clearly indicated that they would as part of their

"detailed" investigation, this would also constitute the same.

PATENT INTERFERENCE NUMBER 105, 754 AND PLAINTIFF'S INVOLVEMENT IN IT

112. Pursuant to the invocation of Plaintiffs inventorship dispute with the Senior

Party (in Patent Interference No. 105, 754) Plaintiff had produced documents and

things to the Parties in this case, i.e., Patent Interference No. 105,754. See Patent

Interference No. 105,754 (Papers 26 and 74) and or Exhibit 8.

113. Additionally, on August 3, 2011, Plaintiff had given a day long testimony

under oath; the number of redirect question posed to Plaintiff was zero. See Exhibit

9

114. Dr. Mello was present at the site of Plaintiffs deposition, apparently to

furnish with help in the Senior Party's cross-examination of Plaintiff. See Exhibit 9,

Deposition Transcript page 4

questions"; even if it were to be presumed that the Plaintiff, indeed, were incapable of 'thinking' on his own, as the Defendant aver(s) now, the mere-witnessed-suggestion of RDRP by the Plaintiff directly to Dr. Mello would have been the kindling event that led to the initial mechanistic recognition that the interfering intermediate-trigger molecule was dsRNA. See also Exhibit 1, D1: PAP27: Box 21, right column.

*According to Merriam-Webster Dictionary the word DEVISE is defined as "to form in the mind by new combinations or applications of ideas or principles" and is synonymous with the word INVENT. COMPLAINT under 35 U.S.C. § 256



115. On August 10, 2011, a meeting was held, between the Junior Party's

attorneys and Plaintiff's bro bono 13 counsels-Ronald M. Daignault and David

Leichtman 14 of the Law Firm of ROBINS, KAPLAN, MILLER & CIRESI-to

discuss the possibility of Plaintiff's active involvement in aiding the Junior Party (in

Patent Interference No. 105, 754) construct a motion in support of Plaintiffs

inventorship claims.

116. Should the Junior Party opt to exercise its prerogative -and should there be

a need for a Priority Phase proceeding- Plaintiffs inventorship claim is slated to

be brought in as an issue at the beginning of the Priority Phase of Patent

Interference No. 105, 754.

117. At the time of the filing of this suit, Patent Interference No. 105, 754 is still

pending.

THE ON AGAIN, 'OFF' AGAIN AND THE ON AGAIN, 'OFF' AGAIN,

ON AGAIN NOTICE OF INQUIRY BY THE DEFENDANT

118. In or about 2003 Defendant put Plaintiff on notice of inquiry; the Defendant

then abruptly closed it; then (without explanation) in or about 2006 they re-opened

their investigation only to close it without even interviewing the Plaintiffs

conception eyewitness.

119. Then in 2011 in a filing with BP AI, the Defendant stated that they are open

to 'reopen' their investigation into the nature of Plaintiff's claims. See Patent

13 quality costs money; also, see Interference No. 105,754, Paper 451, last~-14 after the fact and cursory investigation had revealed that Mr. David Leichtman used to work with Mr. Kokulis at Morgan Lewis' Washington D.C office, within the same practice group, which would tum the doctrine/concept of avoiding conflict-of-interest in legal representation on its head. COMPLAINT under 35 U.S.C. § 256



Interference No. 105, 754, Paper 111, page 8, lines 3-8; or See Exhibit1, D1:

PAP25: Box 14, left column.

120. Plaintiff had been induced (by the Defendant) into believing that he has

been put on yet another notice of inquiry by the Defendant. In fact, no 6 years

window has elapsed in which, Plaintiff has not been placed on notice of inquiry by

the Defendant, and or, the Plaintiff hasn't inquired about the status or outcome of

the Defendant's alleged investigation into the nature of Plaintiffs RNAi invention-

in-suit-related claims.

CLAIMS PER PERMUTATION I

COUNT I

Correction ofinventorship Pursuant to 35 U.S.C. § 256

121. The allegations in paragraphs 1-120 & fns 1-12 are incorporated herein by

reference.

CLAIMS PER PERMUTATION II

COUNT II

Correction of Inventorship Pursuant to 35 U.S.C. § 256


reference.

CLAIMS PER PERMUTATION I AND PERIOD I

COUNT III

Conversion


reference.




COUNT IV

Unfair Competition


reference.

COUNTV

Unjust Enrichment


reference.

CLAIMS PER PERMUTATION I AND PERIOD II

COUNT VI

Conversion


reference.

COUNT VII

Unfair Competition


reference.

COUNT VIII

Unjust Enrichment


reference.


COUNT IX

Fraud

28 Mussa Ali 163 I NE Broadway,# 407



reference.

CLAIMS PER PERMUTATION I AND PERIOD III

COUNT X

Conversion

13 0. The allegations in paragraphs 1-120 & fns 1-12 are incorporated herein by

reference.

COUNT XI

Unfair Competition


reference.

COUNT XII

Unjust Enrichment


reference.

CLAIMS PER PERMUTATION II AND PERIOD I

COUNT XIII

Conversion


reference.


COUNT XIV

Unfair Competition




reference.

COUNT XV

Unjust Enrichment


reference.

CLAIMS PER PERMUTATION II AND PERIOD II

COUNT XVI

Conversion


reference.

COUNT XVII

Unfair Competition


reference.

COUNT XVIII

Unjust Enrichment


reference.

COUNT XIX

Fraud


reference.




CLAIMS PER PERMUTATION II AND PERIOD III

COUNT XX

Conversion

140. The allegations in paragraphs 1-120 & fus 1-12 are incorporated herein by

reference.

COUNT XXI

Unfair Competition


reference.

COUNT XXII

Unjust Enrichment


reference.

RELIEF REQUESTED

Any and all equitable relief as this Court deems just and proper under the Patent

Laws ofthe United States and the Laws ofthe State of Oregon.

Dated: September 28, 2012 By: ·~ Portland, Oregon. Mussa Ali


1631 NE Broadway, #407 Portland, OR 97232 Phone: (503) 890-9179 E-mail: mussaali [email protected] Plaintiff (Pro Se)

