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Mussa Ali 2442 NW Market Street, #301 Ballard, WA 98107 (206) 427-6637 mussaali1968@gmail.

com (Pro Se) Plaintiff UNITED STATES DISTRICT COURT FOR THE WESTERN DISTRICT OF WASHINGTON ----------------------------------------------------x Mussa M. Ali, : : Plaintiff, : : vs. : : Carnegie Institution of Washington, : : Defendant. : -----------------------------------------------------x

CIVIL ACTION COMPLAINT UNDER 35 U.S.C. 256

COMPLAINT This is a Complaint 1 which has been put together in the last few days, and is being filed, by the plaintiff, Mussa Ali (plaintiff) pro se and without the assistance of counsel. NATURE OF THIS 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 Washington State claims for conversion, unfair competition, unjust enrichment and fraud related to the plaintiffs contribution to the complete conception and

The first-half of this complaint is essentially the verbatim clipping of Dr. Cimbalas letter. This Action has been cobbled together to preserve the viability of some of 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 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 litigated at/by BPAI via case no. 105,754. In an effort to lessen cluttering the court with documents and things, all of plaintiffs publically downloadable documents filed at BPAI are incorporated herein by reference; alternatively, if ordered to do so, plaintiff would furnish such documents and things. Attached as exhibits here are some of the filings with the Board or the parties in Interference case no. 105,754 which are publicly inaccessible. [Although plaintiff had used a recently filed correction of inventorshp suit as a template, plaintiff hadnt received aid (from a lay person or an attorney) in the construction of this Complaint -- neither in form nor substance.] Slides refers to plaintiffs submitted slides [and other documents] at BPAI and filed as CSIRO EXHIBIT 2082, CSIRO v. Carnegie, Interference No. 105,754

reduction to practice of the art of genetic inhibition by double-stranded ribonucleic acid (dsRNA) and claims arising from defendants action of omission of the plaintiff from being credited as a co-inventor of the said art. 2. This action is being filed at this time in an effort notwithstanding plaintiffs vigilance and the defendants documented unclean hands and inducements and their on again off again notices of inquiries (further detailed below in the body of this Complaint) to preserve the viability of plaintiffs claims. 3. For all the relevant time 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. Plaintiffs mechanistic conception and his relation of such to one of co-inventors had been witnessed. See Slide 22 4. In an acknowledgement of plaintiffs potential if not certainty to conceive or capacity to solve difficult new question, plaintiff was rated as outstanding, intelligent scientist by the defendant. (quotation from defendants evaluation) See Slide 52 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. 1338. 7. Venue is proper in this case, because the named 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-in-suit. See Slide 28

1331 and

8. Furthermore, upon knowledge and presumption, defendant has engaged in business transaction with entities in the State of Washington. THE PARTIES 9. Plaintiff is a resident of the State of Washington and a citizen of Ethiopia, who emigrated to the United States of America on November 11, 1985. 10. The defendant is presumed to have its main head quarters in Washington D. C. at 1530 P Street NW, Washington, D.C., 20005. DEFINITIONS AND TIMELINES AND PERMUTATIONS 11. The Board of Patent Appeals and Interferences may be referred to as BPAI or the Board. 12. The patents-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 has garnered since the initial patent was issued or as a generalized statement of reference. 13. The Mello group, Mello et al or Mellos lab refer to members of Dr. Craig Mellos (Dr. Mellos) laboratory, namely Mr. Samuel Sam Driver (Mr. Driver), the plaintiff and Dr. Mello who were exclusively involved in the eventual complete construction of the said art from 1995-1997. 14. The Fire group, Fire et al or Fires lab refers to Dr. Andrew Fires group, who were involved in the construction of the art-in-suit post-conception. See Slide 13 15. Dr. Nicholas Miliaras (Dr. Miliaras) refers to a member of Dr. Craig Mellos laboratory who worked at the time Plaintiff worked in Dr. Mellos laboratory in the same open laboratory space. See Slide 54

16. Mr. Paul Kokulis (Mr. Kokulis) refers to the defendants lead counsel and with whom plaintiff or his bevy of attorneys over the years has had direct communications with regarding his omission from the patents-in-suit. 17. The term single-stranded (ss) may mean double-stranded (ds) or vice versa depending on context in which they are used, i.e., pre or post recognition; and the intent of the plaintiff. 18. The word art may sometimes be substituted for patent[s]. 19. For the purpose of this action, and at all relevant times and context, plaintiff is presumed to be a co-inventor and not a sole-inventor. 20. Period I encompasses the time window between the time the plaintiff knew or should have known about his omission or from the time of the initial patent[s]-in-suit application was drafted to June 15, 2006. 21. Period II encompasses the time window between June 15, 2006 to the date of the filing of this Complaint, i.e., June 15, 2012 22. Period III encompasses the time after the filing of this suit. 23. Under Permutation I plaintiff is presumed to be the co-owner of the patents-in-suit. 24. Under Permutation II plaintiff is presumed to have forfeited his co-ownership rights to the defendant. 25. The term named co-inventors refers to the named inventors listed on the patents-in-suit 26. Patents-in-suit are Patent Nos. 6,506,559, 7,538,095, 7,560,438, 7,622,633. eg. See Slide 10 27. The word collaboration refers to largely experimental collaboration; mental collaboration between the Mello and Fire groups is implied through out the relevant 1995-1997 period. 28. When convenient the defendant may be referred to as they; defendants as their or theirs

29. Notice of Inquiry refers to the defendants 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 30. Since the early 1980s, 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. 31. In 1995, researchers at Cornell University reported that the introduction of the (control) sense RNA unexpectedly provokes sequence-specific genetic interference in C. elegans. This surprise finding prompted members of Mellos laboratory to embark on an effort to delineate the molecular mechanism underlying RNA induced genetic interference (RNAi) in C. elegans. See Slide 4 32. 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 33. These strikingly unconventional observations led Mellos 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, Mellos 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 molecule, by a putative endogenous C. elegans polymerase. See Slide 9 34. Initially, Mellos 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). Mellos group dubbed this paradigm as the RT/cDNA/dsDNA Model. See Slide 6 35. Subsequently, several experiments were carried out to prove or disprove the existence of this de novo synthesized, cDNA-sized dsDNA interfering agent. Mellos 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 36. To directly test the hypothesis that the dsDNA intermediate was the interfering agent, Mellos group tested the efficacy of dsDNA; Plaintiff was involved in the design and synthesis and carrying out of this experiment. See Slide 29 37. Despite repeated attempts, Mellos 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 38. As an alternative model, Mellos 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 39. 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, see below); 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 Plaintiff 40. What led Mellos group to the ultimate mechanistic recognition that RNAi in C. elegans is mediated by dsRNA (the interfering agent)? Upon accidentally 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 41. 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 42. With this recognition in hand, and not unlike what was done pursuant to the RT/cDNA/dsDNA Model, Mellos group along with Fires repeated the RNAi experiments to revalidate what Mello et al. had reported and published. See Slides 14 and 15 43. Indeed, all along, the one moment of recognition that was fluttering just below the radar of the Mello groups model(s) and experimental observations was the recognition that the interfering agent is dsRNA, and not dsDNA. See Slide 9

The Craig Mello Groups Reduction-to-Practice of RNAi Before the Andrew Fires Group 44. In an effort to reduce RNAi to practice with defined molecular parameters, Mellos group conducted signature molecular experiments that homed in on the mystery of RNAi. The following are highlights of original experiments performed by Mellos group: 45. 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? Mellos 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 14 and 37 46. The requirement for sequence homology between RNAs to provoke sequence specific and distinct interference was initially carried out by Mellos 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 47. 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 48. 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. Mellos group ruled out this possibility as RNAi was unable to provoke a detectable de novo methylation in C. elegans. See Slide 34

49. The Skeletal Model put forth by Mellos 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; Mellos 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, and the validation, for the inherent amplifiable involvement of a polymerase driven and stable doublestranded intermediate. See Slides 12 and 14 50. 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 [direct] target of RNAi; Mellos group was the first to report that RNAi in C. elegans involves the targeted degradation of the endogenous mRNA. Mellos group assayed for expression of RNAi targeted gene in single cell embryos and confirmed the [target] of the RNAi machinery is the endogenous mRNA itself. See Slide 41 51. In an effort to delineate the smallest number of homologous bases required for RNAi in C. elegans, Mellos group carried out detailed size dependent RNAi experiment; as an example Mellos lab used 24, 50, 100 nucleotide long RNAi to demarcate this point of usability. See Slide 36 and 51 52. RNAi is heritable: although the bizarre nature RNA mediated inheritable interference was repeatedly observed, this phenomenon, in and of itself, didnt 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

53. 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, didnt lead to a deducible mechanistic insight. See Slides 23 and 24 A Factual Analysis of the Three Eureka[s] 54. The conception of RNAi is an exquisitely singular conception: the recognition that the interfering molecule is dsRNA. Eureka A: the Systemic Route 55. According to Dr. Mello, at the May 1997 International 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 moleculenot that there may have been a dsRNA contaminant in Mello groups in vitro RNA preparations per seupon 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 Slide 23 56. Despite its mechanistic implausibility, the biggest complication with Eureka A is the biounavailability of Mr. Driver at the May 1997 International Worm Meeting: Although he may have registered for the meeting, Mr. Driver never actually attended the 1997 International Worm Meeting. See Slide 26 57. Indeed, Dr. Mello had asked plaintiff to present the 1997 RNAi work because Mr. Driver (who had left Dr. Mellos laboratory to begin work as a technician of some sort at Hybridon Inc.) was unable to attend the Meeting. See Slide 15

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58. Having initially agreed to do so, plaintiff declined to present the abstract 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 Slide 42 59. Besides Eureka As problematic historical accuracy (i.e. the absence of Mr. Driver at the 1997 International 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 question if the interfering agent was a dsRNA molecule. 60. Additionally, at the 1996 Worm Meeting, Dr. Fire and members of his laboratory were keenly familiar with the salient features of Mello groups Skeletal Model and their seminal molecular RNAi findings; thus it is even harder to place the genesis of Dr. Fires apparent initiation and inspiration at the 1997 International Worm Meeting as if he were not familiar with RNAi (before its elucidation) in 1996. See Slide 45 61. In any case, 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. Fires inspiration didnt flow from the systemic nature of RNAi and probably didnt involve Mr. Driver. Eureka B: the RDRP/dsRNA Model 62. A few weeks before the 1997 International 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 63. 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. Fires apparent re-conception at the June 1997 International Worm Meeting. See Slide 47

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64. It is clear that the route by which one could see a dsRNA in the context of Mellos 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. 65. Do you remembermay be you do not remember this do you rememberwhen 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 Mello lab member, in early 1998 when his memory was fresher and when he was less abashed to come forward to tell the truth, and his uncued response was Yes, it was RNA dependent RNA polymerase. See Slide 22 66. 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. 67. At a meeting held in Washington D.C., on April 28, 2005, Defendants 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--vis the Skeletal Model doesnt-get-you-there argument. See CSIRO v. Carnegie, Interference No. 105,754, CSIRO Exhibit 2082, pages number 9-10 Eureka C: the dsRNA Contaminant Model 68. Lately, when asked what led Dr. Fire to his moment of recognition or his experimental involvement with RNAi, somehow upon being re-introduced to RNAi, he was inspired by Dr. Mello [and Mr. Driver] at the 1997 International Worm Meeting to wonder whether the interfering trigger molecule in Mello groups sense/antisense in vitro RNA preparation was a

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dsRNA contaminant. Subsequent to this epiphany of his, Dr. Fire holds, Fires lab entered into a collaborative work with Mellos group to test his hypothesis. See Slide 45 69. Notwithstanding the experimental approaches of Fire et al.swhether RNAi is conceived via the Skeletal Model, or re-conceived via the dsRNA contaminant-trigger model, the collaborative post-recognition experiments that Fires [and Mellos 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 Mellos groups initial conception that the interfering agent is a dsRNA molecule. See Slide 25 The Repeat [or Touch-up] Re-reduction of RNAi by The Fire Group 70. The only type of collaboration between the Fires groups and the Mellos group was a mental one: the extensive back and forth conversation between Dr. Mello and Dr. Fire. 71. Dr. Fire has denied or tried to conceal this mental collaboration between his group and Mellos group predating his alleged conception. In a 2004 speech he details how he was mesmerized by the Mellos group seminal RNAi work presented at the May 28-June 1, 1997 International Worm Meeting (Madison, Wisconsin); while he reconceived RNAi at the same locale. See Slides 45 and 50 72. Revealingly, when inquired about the conception of RNAi in a radio interview in another time, his response began by saying In Craigs case; this initial In Craigs case conception was concealed from, or was not disclosed to, BPAI in the course of the Interference case no 105,754. 73. There was a complete mechanistic conception of RNAi in Mellos laboratory before the epiphany of Dr. Fire on June 1, 1997.

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74. The Andrew Fire Groups involvement in the RNAi project was roughly 10-12 weeks. i.e., from the moment of Andrew Fires alleged conception or the date (on or about July1, 1997) plaintiff left the Mello laboratory to the date the seminal RNAi data was submitted for publication (September, 15, 1997). See Slides 20 and 26 75. The only new finding that resulted from the alleged experimental collaboration between the Mello group and Andrew Fires group was the experimental recognition that only a few molecules of dsRNA [contaminant] could or would trigger RNAi in C. elegans. See Slide 48 76. Given the above, 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 Andrew Fires group thinking by September, 15, 1997, with sufficient dsRNA to trigger RNAi. Id. 77. Owing to such finding, despite no verifiable proof of experimental collaboration, the Mello group is named as co-inventors on a patent that was largely executed by the Carnegie Institution of Washington. See Slides 10 and 27 78. In further acknowledgement of the seminal nature of Mellos group involvement, one of the listed inventors from the Fire group lauded the Mellos group for having first observed (and reported in 1996) the efficacy of exon RNAi vs intronic RNAi experiments on her personal website. Revealingly, the website additionally reveals that the Fire groups later work, i.e., from July 1997 on, was redundant. See Slide 11 Is Dr. Andrew Fires structural Eureka Sufficient or Even Necessary for the Discovery of RNAi? 79. Dr. Fires alleged conception is, in and of itself, insufficient for the complete conception of RNAi.

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80. The mere recognition that there is a dsRNA contaminant in Mellos group in vitro transcribed (IVT) RNAs is only useful after the initial recognition that the interfering molecule is dsRNA. See Slide 25 81. In a tacit acknowledgement of this, Dr. Fire himself admits that he has known about this since his graduate days, at least by or before 1991; and this knowledge didnt trigger him to conceive RNAi (allegedly) until 1997. See Slide 45 82. 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 his structural knowledge) to the possibility that the dsRNA may be the actual trigger. See Slide 35 83. As explained above Dr. Fires conception is neither necessary nor sufficient for the conception of RNAi. The Seminally-Issued RNAi Patent No. 6,506,559 B1 and its claims; The Other Related Child RNAi Patents Numbers 7,538,095, 7,560,438, 7,622,633 ; Plaintiffs Discovery of Such 84. The seminally-issued RNAi patent, Patent Number 6,506,559 (559) was issued in 2003. See Slide 10 85. Plaintiff neither read nor inspected the content of the 559 patent until after its publication. 86. 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. 87. Plaintiff had 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

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88. Accordingly, plaintiff had contributed to the subject matter embodied in claim 1 of the 559 patent. 89. A similarly situated credited co-inventor, Mr. Driver had left the Mello laboratory before the alleged experimental collaborative work commenced between the Mello group and the Fire group. Mr. Driver left the Dr. Mellos laboratory before plaintiff left the same. 90. Plaintiff became aware of the other related RNAi patents, namely patents nos. 7,538,095, 7,560,438, 7,622,633 recently. Defendants Documentarily Provable Unclean hands and Plaintiffs Initial Discovery of Such 91. 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 92. To give structure to the notice of inquiry, the Plaintiff then began an exhausting process of searching for a patent counsel with background in Biotechnology patents. 93. After securing Dr. Michelle Cimbala (Dr. Cimbala) of Sterne, Kessler, Goldstein & Fox as counsel, plaintiff then contacted the defendant. 94. In response to request for more information about plaintiff 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 95. Within weeks of the receipt of the letter, defendant abruptly closed their investigation citing unrelated incident.

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96. Plaintiff then approached the law firm of Wilson, Sonsini, Goodrich & Rosati to approach the defendant again about their premature closure of their investigation. 97. Without disclosing the agenda in advance, defendants then requested a meeting. 98. On May 6, 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 groups Skeletal model and whether Mr. Driver attended the site of the defendants alleged conception, much less participated in its construction. See CSIRO v. Carnegie, Interference No. 105,754, CSIRO Exhibit 2082, pages number 9-10 99. 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 investigation and stated that plaintiff had nothing to do with the invention. 100. Subsequently (and among other counsels) plaintiff had Catherine Youssef (Mrs.

Youssef), currently VP and Senior Counsel at Citigroup Inc., to inquire about the nature of their investigation into plaintiffs claims. 101. In a letter dated July 5, 2006, Mrs. Youssef memorialized that she had spoken to Mr.

Kokulis on June 15, 2006 and that he had informed her that he did not speak with [Dr.] Miliaras. 102. It is clear that the defendants protestations of detailed investigation into plaintiffs

claims were not true, since they didnt even bother to interview an eyewitness that they had easy access to, after they had indicated that they would. 103. If they had indeed interviewed Dr. Miliaras and didnt like what they heard, i.e., that

Dr. Miliaras remembers plaintiffs suggestion of RDRP and plaintiffs unassailable (however inadvertent) contribution to the mechanistic conception RNAi and then the defendant

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proceeded to conceal or deceive the result of their investigation from the plaintiff, this would constitute plain fraud. Patent Interference Case Number 105, 754 and Plaintiffs Involvement in It 104. Pursuant to the invocation of plaintiffs inventorship dispute with the Senior party (in

Patent Interference Case Number 105, 754) plaintiff had produced documents and things to the parties in this case. 105. 106. Additionally Plaintiff had given a nearly 10hrs long testimony under oath. At the time of the filing of this Complaint, Patent Interference Case Number 105, 754 is

still pending. On again Off Again Notice of Inquiry by Defendant 107. 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. 108. Then in 2011 in a filing with BPAI, the defendant stated that they are open to reopen

their investigation into the nature of plaintiffs claims. See Paper 111 in Patent Interference Case Number 105, 754 109. Plaintiff had been induced to believe that he has been placed on yet another notice of

inquiry by the defendant. CLAIMS PER PERMUTATION I COUNT I Correction of Inventorship Pursuant to 35 U.S.C. 256 110. The allegations in paragraphs 1-109 are incorporated herein by reference. CLAIMS PER PERMUTATION II

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COUNT II Correction of Inventorship Pursuant to 35 U.S.C. 256 111. The allegations in paragraphs 1-109 are incorporated herein by reference. CLAIMS PER PERMUTATION I AND PERIOD I COUNT III Conversion 112. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT IV Unfair Competition 113. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT V Unjust Enrichment 114. The allegations in paragraphs 1-109 are incorporated herein by reference. CLAIMS PER PERMUTATION I AND PERIOD II COUNT VI Conversion 115. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT VII Unfair Competition 116. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT VIII Unjust Enrichment 117. The allegations in paragraphs 1-109 are incorporated herein by reference.

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COUNT IX Fraud 118. The allegations in paragraphs 1-109 are incorporated herein by reference. CLAIMS PER PERMUTATION I AND PERIOD III COUNT X Conversion 119. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XI Unfair Competition 120. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XII Unjust Enrichment 121. The allegations in paragraphs 1-109 are incorporated herein by reference. CLAIMS PER PERMUTATION II AND PERIOD I COUNT XIII Conversion 122. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XIV Unfair Competition 123. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XV Unjust Enrichment 124. The allegations in paragraphs 1-109 are incorporated herein by reference.

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CLAIMS PER PERMUTATION II AND PERIOD II COUNT XVI Conversion 125. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XVII Unfair Competition 126. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XVIII Unjust Enrichment 127. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XIX Fraud CLAIMS PER PERMUTATION II AND PERIOD III COUNT XX Conversion 128. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XXI Unfair Competition 129. The allegations in paragraphs 1-109 are incorporated herein by reference. COUNT XXII Unjust Enrichment 130. The allegations in paragraphs 1-109 are incorporated herein by reference. RELIEF REQUESTED

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RE: IN THE MATTER OF UNITED STATES PATENT AND TARDEMARK OFFICE BOARD OF PATENT APPEALS AND INTERFERENCES Patent Interference No. 105,754 COMMONWEALTH SCIENTIFIC AND INDUSTRIAL RESEARCH ORGANISATION and Bayer BioSciences (Junior party) v. CARNEGIE INSTITUTION OF WASHINGTON and the University of Massachusetts (Senior party)

MOTION1 FOR LEAVE AND A CONTINGENT MOTION1 TO FILE MUSSA M. ALIS (ALIS) RESPONSE TO THE UMASS-CARNEGIES (SENIOR PARTYS) FILED PAPER 111

UMASS-CARNEGIE (EXPANDED) MATERIAL FACTS: RE:PAPER 111 (1)to prove any type of violation of section 116, CSIRO necessarily will have the burden of proving that Carnegie deceptively and intentionally omitted Mr. Ali as a co-inventor. Page 3, lines 24-25 and page 4, line 1. (2) On page 4, line 22 of CSIROs Motion 12, CSIRO argues that Mr. Ali asserts that he conceived and helped Craig C. Mellos group see and or recognize that the dsRNA molecule was the interfering molecule. The response is that Mr. Ali has established a pattern of making sensational allegations against Dr. Mello personally and against UMass and has failed, in every instance, to substantiate any of these allegations. page 4 lines 4-8

ALIS RESPONSE TO UMASS-CARNEGIES (EXPANDED) MATERIAL FACTS: RE:PAPER 111 (1) Agreed.

(3)these baseless allegations against UMass, Dr. Mello and others began shortly after Mr. Ali was denied admission into UMMS. page 4, lines 8-9

(4) Mr. Alis baseless allegations of inventorship are, in Carnegies view, the same type of behavior that Mr. Ali has exhibited for years and are no different than the allegations Mr. Ali made in his discrimination suit against UMass and Dr. Mello. page 4 lines 10-12 (5) Carnegie and UMass have repeatedly entertained Mr. Alis assertions of his

(2) What UMass-Carnegie dub as sensational allegations is primarily Alis actionable suit alleging that less qualified applicants were admitted by the UMass medical school and that Dr. Mello had excluded him from authorship for a publication that Ali had made bench-work and intellectual contributions to. More importantly, limited discovery had subsequently revealed (not contested by UMass-Carnegie) that Ali was as and or more qualified than, a good portion of the admitted applicants to the medical school when he initially applied for admission. Furthermore, as it has subsequently turned out, Ali had indeed been included (after all) as an author in a Cell publication. Revealingly, when Dr. Mello was inquired about his change of heart his under oath testimony was that subsequent to his reconsideration of Alis contribution that he had concluded Ali was worthy of an authorship in Cell. Exhibit 2082, slide 44. (3) Ali filed his single-suit nearly three years after Ali received his non-admission letter from UMass Medical school. What UMassCarnegie is doing here is conflating the issue of conception with their portrayal of Ali as complainant-happy litigant. (4) If Alis allegations of inventorship are indeed baseless as UMass-Carnegie avers here, why then discard the very notebooks and other evidence that may shed light and help flesh out the baselessness of Alis allegations? See attachment, and Exhibit 2082, slide 28. (5) Ali has repeatedly (both pro se and with assistant of counsels) approached Carnegie-

plaintiff assigned page # 23

UMASS-CARNEGIE (EXPANDED) MATERIAL FACTS: RE:PAPER 111 being a co-inventor and neither institution has received any factual, verifiable proof that would substantiate Mr. Alis claims of inventorship, in spite of these repeated requests. page 4, lines 14-16

(6) For years, Carnegie and UMass have made good faith requests that Mr. Ali or his counsel provide proof of inventorship, yet Carnegie and UMass have yet to receive any verifiable, corroborated evidence of conception. page 5, lines 1-3

(7) Ms. Cimbala responded by preparing a factually incorrect letter that contained opinion and unsupported assertions that were vacant any evidence to corroborate these assertions. page 5, lines 12-14

(8) In his spam email, Mr. Ali alleged that he had proof of inventorship. In response, to Mr. Alis spam email, Mr. Aaron Lazare, then Chancellor of UMMS, responded to all recipients of Mr. Alis mass email with an email in which he addressed inventorship of the Carnegie Patents. page 5, lines 16-19

(9) In the letter, Carnegie indicted that they considered the matter closed. page 5, lines 21-22.

(10) Representatives from Carnegie attended and representatives from UMass traveled down to Washington to meet with Mr. Alis attorneys in person. page 6, lines 2-4.

ALIS RESPONSE TO UMASS-CARNEGIES (EXPANDED) MATERIAL FACTS: RE:PAPER 111 UMass in an effort to resolve his dispute of inventorship with them. At every turn they have evaded Alis gestures of trying to resolve the matter amicably. As to the production of evidence that is already in possession of Carnegie-UMass it is quite suspect that the very institutions that have the original documentations that support or refute Alis claims aver that they have not seen or received the same from Ali. Due diligence alone would have dictated that they would or should have (investigated and) concluded that Ali is a co-inventor, in stead of putting the burden and onus of proffering the evidentiary documents that they are in possession of on Ali. (6) Ali has indeed provided verifiable and corroborated evidence of his mechanistic conception of RNAi. These documents (among other things) included an audio diary of the path to the recognition (via Mellos group model and RDRP) that dsRNA is the interfering molecule; notebook extract that diagrams the conception; Dr. Mellos publicly stated assertions that he had seen dsRNA via Mellos group published model before the alleged and proffered conception date of June 1, 1997 by Dr. Fire. Exhibit 2082, slides 22 and 47. (7) Dr. Cimbalas letter detailing Alis inventive contributions, at the minimum, relied on two publicly disclosed abstracts in which Mellos group laid out the foundational thinking of their models and the data they were generating in real-time. And, of course the manuscript (which summarizes the work that was done up to the point of Mr. Drivers departure) had been corroborated by Dr. Mello himself during his deposition. Exhibit 2082, slides 14-16. (8) What UMass-Carnegie calls a spam email is a nearly verbatim clipping of Dr. Cimbalas letter. As to the then Chancellor addressing the question of inventorship, even a cursory glance at his ad hominem response shows that is not the case. What is interesting about his email is that how vacuous it sounds as it relates to the issue that was germane to Alis spam letter: i.e. whether any of the allegations contained in Dr. Cimbalas letter are factual or not. Exhibit 2082, pages 2-8 (9) According to Alis representative, Mr. Kokulis informed Dr. Cimbala that they were making progress and but now that Ali had disclosed the content of her letter (via spam e-mail) publicly that they considered the matter closed. (10) It is interesting to observe who actually attended this meeting, a meeting ostensibly organized to re-examine Alis single, unsigned, unverified notebook page. Among others Mr. John Lively, director of administration and finance at Carnegie and Chester Bisbee, acting executive director at UMass. If the meeting was about Alis contribution to the RNAi patents, what is the director of finance doing at this meeting? Exhibit 2082, page 9.

plaintiff assigned page # 24


2

UMASS-CARNEGIE (EXPANDED) MATERIAL FACTS: RE:PAPER 111 (11) Finally, fifteen months after Carnegies initial request to Mr. Ali for evidence to support his assertions, Wilson Sonsini presented a single, unsigned, unverified page allegedly from Mr. Alis laboratory notebook. page 6, lines 5-7.

(12) In May of 2005, Carnegie responded to Wilson Sonsini with an email indicating that they had completed another detailed review of inventorship with respect to Mr. Alis alleged contribution, especially with respect to the mysterious notebook page that had suddenly appeared. page 6, lines 9-11.

(13) the veracity of any new document that Carnegie or UMass has not yet seen would certainly be suspect. In other words, if Mr. Ali were to produce any new documents, and these documents actually and truly existed in 2004 when Mr. Ali initially contacted Carnegie, why has Mr. Ali not produced these documents until now? page 7, lines 17-21

ALIS RESPONSE TO UMASS-CARNEGIES (EXPANDED) MATERIAL FACTS: RE:PAPER 111 (11) Alis notebook extract showing the conception of RNAi within the context of Mellos lab model was initially presented to UMass-Carnegie not at the meeting but several months before the meeting of April 2005. In fact, the meeting was held after Mr. Kokulis had informed Mr. Norviel of Wilson Sonsini that they had concluded that Ali is not an inventor, yet again. So, to portray the meeting as the site and time in which UMassCarnegie saw the evidence of conception finally is simply not true (12) Notwithstanding the dog-and-pony nature of the April 2005 meeting, there were two leads that UMass-Carnegie indicated that they would investigate: whether an eye witness remembers Alis suggestion of RDRP to Dr. Mello directly. (At the time UMass-Carnegie was unaware of Alis conception related audio diary excerpts) and whether Mr. Driver attended the site of the UMass-Carnegie conception, much less participated in its construction. To date, Alis yet to receive the outcome of their detailed review of their investigation into these conceptionrelated matters. Exhibit 2082, page 10. (13) It is indeed the height of hypocrisy for a party that has publicly and boldly stated that they have discarded the original notebooks that laid the foundational work not just for the seminal RNAi patents but help them acquire their singular Noble Prize to question the veracity of the notebooks Ali may be in possession of. Of course, what UMass-Carnegie fails to mention is the fact that some of the pages of the notebooks extracts Ali had submitted to the Board bear the hand writings of Dr. Mello himself. Additionally, in order to carry out the molecular experiments the starting primers/oligonucleotides would have to have been ordered from a third party, so one can definitely assess the veracity of Alis notebooks in multitude of ways. Exhibit 2082, slides 22, 28-42 As to the question of producing the documents now as oppose to in the past the response is that Ali has been rebuffed and attacked ad hominem(ly) by the UMass-Carnegie. Additionally, and of course, the UMassCarnegies high-powered lawyers surely know this, i.e., one doesnt show his cards prematurely (even at this stage of the game) especially to a party that has shown time and again to be unworthy of trust. (14) Agreed.

(14) Carnegie and UMass remain, as they always have, open to reviewing any truthful, verifiable evidence of conception of the claims of the Carnegie Patents that Mr. Ali may have in his possession. Accordingly, if the Board were to grant CSIROs motion for additional discovery, Carnegie requests that the Board tailor CSIROs request for the production of documents and things to only include, dated, signed, corroborated evidence of conception. page 8,lines 3-8.

plaintiff assigned page # 25

UMASS-CARNEGIE (EXPANDED) MATERIAL FACTS: RE:PAPER 111 (15) As an initial insight, the failure to present substantiated evidence after repeated requests certainly brings into question Mr. Alis credibility. page 8,lines 12-13

(16) The court, however, was able to discern that Mr. Ali had no basis for any of his sensational allegations and granted summary judgment against him. Thus, even if Mr. Ali is allowed to testify in the present proceedings, the credibility of his testimony would be in serious question based on his past pattern of behavior. page 8. lines 19-22

(17) Of course, CSIRO failed to provide the Summary Judgment Memorandum and Order in this case in which the judge granted defendants motion for summary judgment in toto on all counts. page 9, lines 7-9.

(18) the courts memorandum and order in the civil case involving Mr. Alis credibility is telling. page 9, lines 1012.

(19) When presenting evidence to the court, however, Mr. Ali submitted a copy of a medical school application on which a checkbox had been marked indicating that his certificate of residence had been received. page 9, lines 19-22 (20) So, on one hand, Mr. Ali failed to dispute that he did not have the proper residency or citizenship status, yet on the other hand Mr. Ali produced a questionable medical school application indicating that his certificate of residence had been received. The single notebook page that Carnegie and UMass received from Wilson Sonsini 15 months after they asked Mr. Ali for proof of conception is no different than the medical school application Mr. Ali

ALIS RESPONSE TO UMASS-CARNEGIES (EXPANDED) MATERIAL FACTS: RE:PAPER 111 (15) This simply is not true. As recently as the first week of January 2011, Ali called Mr. Kokulis and informed him that it may be wise for the validity of the patents that they should look into the documentation and evidence that he has before Ali joins the other side or publicly discloses them. Mr. Kokulis demurred --a fact UMass-Carnegie conveniently left out in their submission to the Board. (16) The bevy of lawyers for UMass-Carnegie should know that the summary judgment axe could be swung or brought down for multitude of reasons: inadequate representation, incomplete discovery etc. Just because one loses a case at the summary judgment stage (before trial) doesnt mean one lacks credibility. In fact, there is nothing in the body of the courts memorandum or order where the credibility of Ali was questioned or undermined. (17) What UMass-Carnegie fails to mention is the courts implausible conclusion that Ali was allowed discovery of the very discarded Mello lab notebooks. (See exhibit 1114, last two pages of Memorandum) In fact it could be argued that the court may have erred in its discovery-related rulings in that it may have denied Alis discovery related motions on the intent that [it] had already allowed Ali the very same discovery requests. (18) This is interesting: what UMass-Carnegie cites from the Courts memorandum to question Alis credibility is a document that was bate-stamped and produced by UMass-Carnegie themselves. Additionally, the question was not whether Ali was in possession of a green card at the time of his initial application for admission (Ali was an asylum-applicants at the time) but whether UMass-Carnegie had approved his Massachusetts residency status and then proceeded to admit less qualified applicants in his place. The fact remains, and not contested by UMass-Carnegie, that applicants with as low as a combined subjective and objective score of 11 out of 100 were admitted whereas Ali, with combined score of 81, at the time of his initial application, was rejected (19) Again this is an UMass-Carnegie document produced by them in response to request to any and all documents related to Alis initial application to the UMass medical school. What is almost perjurious here is the UMass-Carnegie implied assertion that Ali may have produced a doctored document. (20) The question germane to the Alis case was not whether Ali had a permanent residency status at the time, but whether UMass medical school had approved his Massachusetts residency status and then proceeded to accepted grossly less qualified applicants. As to the question of conveying Alis conception to anyone else: the response is: just listen to the conception audio diary. Additionally, [as it appears Dr. Miliaras is practically on the pay roll of UMassCarnegie], even a cursory investigation would

plaintiff assigned page # 26

plaintiff assigned page # 27

UMASS-CARNEGIE (EXPANDED) MATERIAL FACTS: RE:PAPER 111 UMass or the Board does not demonstrate or even suggest that he conceived of the notion that introduction of doublestranded RNA (dsRNA) triggers sequence specific gene silencing. page. 11, lines 11-16

(25) This model that Mr. Ali allegedly proposed utilizes RDRP and is based on the introduction of single-stranded RNA (ssRNA) into a cell, not dsRNA. In this model that Mr. Ali allegedly proposed, introduction of ssRNA would have been the key triggering event and RDRP would have acted upon the ssRNA to produce complementary copies of the introduced ssRNA. Thus, even if the assertions in Ms. Cimbalas letter are true, which Carnegie disputes, this model of ssRNA being the triggering agent to initiate sequence specific gene silencing misses the point of the invention entirely. page 12, lines 2-8.

(26) The invention is that the introduction of dsRNA into a cell will trigger sequence specific gene silencing. The notebook page and the unsupported allegations in the Cimbala letter thus fail to show evidence of conception of the invention at issue. P. 12, lines 811.

(27) No issued claim in any of the Carnegie Patents recites the use of the RDRP enzyme. Footnote 4, page 12

(28) Footnote 1 in the Cimbala letter states that Mr. Ali was a graduate student and a research assistant at the University of Massachusetts and Dr. Mellos laboratory from 1994 to 1997. Mr. Ali, however, was never enrolled in graduate school at UMass and was never a graduate student at UMass. In addition, Mr. Ali worked in Dr. Mellos lab from September 1995 to June 1997. MF41. Thus footnote 1, which appears in the very first sentence of the Cimbala letter, is simply wrong. If the Cimbala letter is factually incorrect at its outset, how credible could the rest of the letter be? page 13, lines 12-18

ALIS RESPONSE TO UMASS-CARNEGIES (EXPANDED) MATERIAL FACTS: RE:PAPER 111 conception) had revealed publicly that double stranded molecule is indeed the interfering molecule. Initially, the Mello group was leaning toward the possibility that it is mediated by (via RT) dsDNA and not dsRNA. It is within this milieu that Alis suggestion of RDRP directly to Dr. Mello paved the way for the ultimate upstream recognition that dsRNA is the interfering molecule. Exhibit 2082, pages 3-5 and slides 1, 6-8, 16, 16. (25) It may be noteworthy here to look at the timeline of the UMass-Carnegie ever shifting positions. Specifically: a) in or about 1998, Ali averred that if UMass-Carnegie were to produce his notebooks it would specifically show he conceived dsRNAi first; b) subsequently, in 2002, UMass-Carnegie responded that they have discarded the notebooks; c) in [or by] 2005 Ali produced an extract from his notebook documenting his mechanistic conception and other documentation showing that his contribution was multifold; d) Through his representatives Dr. Mello denied or unremembered that Ali had suggested RDRP to him directly; while authoring a Nature RNAi article where Dr. Mello claims to have seen dsRNA via Mellos group model; e) Ali then forwarded the RDRP audio diary to UMass-Carnegie; f) and now UMass-Carnegie, reverting to form, attempt to plug Alis suggestion into some other groups model. (26) It is clear from the corroborated two abstracts and the Dr. Mello corroborated manuscript Mellos group working model was that double stranded molecule was the key molecule that was mediating interference. Within this context, Alis suggestion of RDRP would directly trigger one skilled in the art to see dsRNA as a mediator of interference. And nothing else. Of course, it defies logic as to why UMass-Carnegie would bother to investigate the two leads if they had concluded Alis notebook page and RDRP do not get one to the conception of RNAi. Exhibit 2082, page 10, slides 14-16 and 22. (27) Neither is Fuzzy logic cited. The Fuzzy logic mediated UMass-Carnegies proffered conception is the twin of RDRP mediated recognition of Mellos group. Exhibit 2082, slides 21 and 24. (28) Ali was indeed a graduate student. (Post-baccalaureate students taking Medical school courses are registered, and matriculated as gradate students at UMass.) So Alis status was a graduate student and a member of Mellos lab within the to time window enumerated in Dr. Cimbalas letter. Speaking of graduate students, UMassCarnegie, of course, failed to mention that Mr. Driver left the graduate program at UMass abruptly and involuntarily to become a technician of some sort at Hybridon inc. More importantly, his ex-graduate student or technician status or the fact that he couldnt have participated in the alleged

plaintiff assigned page # 28

UMASS-CARNEGIE (EXPANDED) MATERIAL FACTS: RE:PAPER 111 It is likely that Ms. Cimbala relied upon Mr. Alis representations that he made to her regarding his status as a graduate student at UMass and his dates of employment in the Mello lab. Such reliance, however, begs the question of what other of Mr. Alis assertions did Ms. Cimbala rely upon, without any investigation on her part? page 13,lines 19-22 (29) It is clear that Mr. Ali is using hindsight in an attempt to reconstruct the invention and claim that he had the concept that introduction of doublestranded RNA was the triggering event for induction of sequence-specific gene silencing. page 1, lines 19-21

ALIS RESPONSE TO UMASS-CARNEGIES (EXPANDED) MATERIAL FACTS: RE:PAPER 111 collaborative experiments did not preclude him from being credited as an inventor. Exhibit 2082, slides 15, 27 and 54.

(29) Although (at the very outset) UMassCarnegie make the assertion that Ali was using hindsight to re-conceive RNAi, there, quite literally, is not a single supporting argument or documentation in the UMassCarnegies 20-plus paged response to support such averment. A simple glance at the history of Alis documented assertions leads one to conclude hindsight is an impossibility; to wit: Ali would have to have suggested RDRP in 1997 anticipating that Dr. Mello would claim publicly that he saw dsRNA via RDRP in 2004, while un-remembering Alis suggestion; plant the RDRP idea in Dr. Miliaras mind in 1997 and somehow (uncued) provoke Dr. Miliaras to remember his suggestion of RDRP to Dr. Mello in 1998 and of course, Ali, all the while, would have to have foreseen that UMass-Carnegie would publicly claim that they have discarded the Mellos lab RNAi notebooks in 2002. (30) The data presented lists mostly the molecular work that was carried out in Mellos lab. Naturally, since virtually all of the molecular work in Mellos lab was carried out by Ali, it is reasonable to expect Ali would have his hand in those experiments. If, on the other hand, the experiments had to do with the genetics of RNAi the table would have Dr. Mellos and Mr. Drivers work prominently displayed. This assertion of Ali is also borne out by his notebooks extract submitted to the Board. Exhibit 2082, page 8 and slides 18, 19, 22, 28-42. As to the assertion Ali had no part in any experiment: this assertion simply defies logic. (31) The published working hypothesis of Mellos group was that double-stranded molecule was the interfering molecule. The smoking gun of the Mellos group thinking: when they initially thought RNAi was being mediated by dsDNA (via RT) and not dsRNA (via RDRP), Mellos Group directly introduced dsDNA into cell (the distal arm of the gonad) to see if dsDNA was indeed the interfering molecule. Exhibit 2082, page 6, footnote 18 and see the Notes in slide 14. (32) This is noteworthy for several reasons: 1. the Mellos lab from day one had indeed done experiments with sufficient dsRNA to induce RNAi. The biggest give away to this is

(30) The Cimbala letter also contains a summary of 9 experiments on pages 5 to 7. The manner in which the letter is written implies, of course, that Mr. Ali had a central role in virtually every experiment listed on these pages. Yet, when these experiments are viewed in their proper context and time frame, it is clear that Mr. Ali had no part in any experiment involving the introduction of dsRNA into a cell to trigger sequence specific gene silencing. page 15. Lines 12-16.

(31) During this time (between the fall of 1995 and the spring of 1997), however, the working hypothesis in Dr. Mellos laboratory was that ssRNA was the trigger to initiating sequence specific gene silencing. Thus, Mr. Alis involvement in the experiments listed on pages 5-7 of the Cimbala letter that were performed between the fall of 1995 and the spring of 1997 would have only been with ssRNA and not dsRNA. page 16, lines 1-5 (32) The Mello lab did not perform any of the experiments listed on pages 5-7 of the Cimbala letter using dsRNA until after Dr. Fire proposed to the Mello lab

7 plaintiff assigned page # 29

plaintiff assigned page # 30

plaintiff assigned page # 31

RE: IN THE MATTER OF UNITED STATES PATENT AND TARDEMARK OFFICE BOARD OF PATENT APPEALS AND INTERFERENCES (BPAI or the Board) Patent Interference No. 105,754 COMMONWEALTH SCIENTIFIC AND INDUSTRIAL RESEARCH ORGANISATION and Bayer BioSciences (Junior party) v. CARNEGIE INSTITUTION OF WASHINGTON and the University of Massachusetts (Senior party)

STATEMENT OF MUSSA ALI RE: MY AUGUST 3, 2011 DEPOSITION AND MY REPLY (UNDER OATH) TO DRS. CRAIG C. MELLOS AND CHRISTIAN ROCHELEAUS DECLARATIONS (CARNEGIE EXHIBIT 1118 AND 1094 RESPECTIVELY) SUBMITTED TO THE BOARD My deposition: 1. Pursuant to the third party subpoena initiated by the Junior party, I was deposed on August 3, 2011. My deposition began around 9AM and ended in the evening around 7PM. At my deposition I was represented by attorney Mr. Matt McFarlane (attorney McFarlane). Several weeks before my deposition I had instructed attorney McFarlane to relay my wishes that I would like an audio-taped deposition, citing as the potential issue associated with my accented English; it is not clear to me that attorney McFarlane had relayed my request and or my intent that I would be audio recording my own deposition to the deposing parties. On several occasions before and after August 3, 2011 attorney McFarlane had informed me in writing that pursuant to Fed. Rule. Civ. Pro. 30 (e) that I would have the opportunity to review and make changes to my deposition transcript as to either form or substance; however he never informed me that I would/could have had the opportunity to review the rough draft of my deposition transcript and make changes as to form, i.e., correct errors due to incorrect transcription before the final transcript was available. See a representative Fed. Rule. Civ. Pro. 30 (e) email I had received from attorney McFarlane. MA 525 During my testimony attorney McFarlane job essentially entailed surveilling for incorrectly transcribed words or phrases; I met him for the first time a day before my deposition where we had conversation about the general mechanics of depositions. During my deposition, the court reporter was audio taping my testimony; as such the official audio version of my testimony is available with the court reporter. I had requested attorney McFarlane on several occasions and in writing to contact the court reporter to inquire about the botched nature of the final deposition transcript at least as it relates to the numerous incorrect transcriptional errors* that coat my deposition transcript. Attorney McFarlane had repeatedly refused to help me in this regard. See email exchanges. MA 526-MA 527

2. 3.

4.

5.

6.

plaintiff assigned page # 32

7.

In some cases, the rough draft of my deposition transcript is of a better quality than the sonamed final transcript. For example, in the initial rough draft my testimony is accurately transcribed as there was no biochemical data but in the final transcript it reads as there was biochemical data; in another instance the initial rough draft accurately conveyed what I actually uttered as would be a better suggestion yet in the final draft it reads as wouldnt be a better suggestion. I also remember informing the court reporter that he had incorrectly transcribed the terms effector molecule as effect on molecule yet the final deposition transcript still bears the same defect. See final deposition transcript page 150, line 18. [Dr. North might have overheard this particular exchange: my conversation with the court reporter about changing effect on molecule to effector molecule.] Additionally, in my conversation with the court reporter during recess, he had specifically informed me that what he was typing was just a rough draft and that I would have the opportunity to review it and make changes. I have lived in the Unites States since November 11, 1985. So far as people tell me, I enunciate my words just fine. In fact in support of this assertion of mine, and as an example, the court reporter heard me enunciate the word intermediate correctly more than 20 times and yet it is incorrectly transcribed as inter media in at least one instance; it is also clear, in few instances, the court reporter heard me utter the word perdure or perdurance and transcribed it correctly as such and in another line the same utterance is transcribed as procure.

8.

9.

10. The table below contain samples of what I uttered* vs. what was transcribed: WHAT I UTTERED* WHEN BOTH 70 RDRP COMMUNICATED DR. ANDREW FIRE WERE THAT IS A IT IS MIGHTY STRANGE ALL RNA CONSTRUCT SEQUENCES US PRIMER WERENT LEVEL IN READ PERDURANCE EXPERIMENTAL TAKE HOME MESSAAGE GIVING RISE TO CODE THAT PART OF CELL GONAD I WASNT WHAT THE COURT REPORTER TYPED WHAT THOSE 17 VRR COMMENTED UNDER ANDREW FIRE ARE IS THAT THE IT IS -- MIGHT BE STRANGE THE RNA CONSTRUCTION CONSEQUENCES IN PRIME WERE LIFE TO RE-READ PERDURE EXPERIMENT TAKE ON MESSAGE GIVING RIGHTS TO CAUSE THE PARTIES SALE GOING OUT IT WAS

plaintiff assigned page # 33

WHAT I UTTERED* EXPERIMENTS SYNTHESIZED SIZE RNA PRINT RDRP ORDERED THE WHEN FOUND OUT HOW mRNA INTERMEDIATE LOSS-OF-FUNCTION RUN TO CARRY OUT LADDER SIZE CARRY OUT GENEROUS RNAi RNA REPLICASE SINKING TWO SYNTHESIZED RNAs CYNDI BROADENED MACHINERY GENE OF INTEREST PROPAGATED PHENOTYPE FLOURESCING WORCESTER WHAT PERDURES SCHEMATICS GRAHAM RNAi SAM SALEINT COMPLETELY GIVE RISE TO TALKING AMPLIFYING NO BIOCHEMICAL DATA WOULD

WHAT THE COURT REPORTER TYPED EXPERIMENTING SYNTHESIZER SITE RNAi IMPRINT R TOWARD THEN WHAT FIND WHO RNA INTER MEDIA ALSO FUNCTION WRITE TAKE CARE OF LATTERY SIDE CARRY GENERIS RNAis RNA REPLICATES SICKENING TO SYNTHESIZER RNAs SYDNEY BROUGHT IN MACHINE GENOPHENO INTEREST PROPERLY PHONE TYPE FORESTING WESTERN WHO PROCURES SEMANTICS VON RNA SAMMY SILENT COMPLETE USED AS FAR AS TAKING APPLYING BIOCHEMICAL DATA WOULDNT

* these are samples; an official back-up audio version of my deposition available with the court reporter; my request (in writing) to contact the court reporter in an effort to clear up the confusion surrounding what I uttered and what was transcribed has been denied by my counsel, Mr. McFarlane, repeatedly. **that is neither here nor there.

plaintiff assigned page # 34

11. For the purpose of definition and as a legend to the (attached) filled-errata sheet, under the reason for change incorrect transcription denotes change in form and clarification denoted change in substance. However, I cannot rule out the possibility that some of the changes made under clarification are due to incorrect transcription and hence, a change in form only or vice versa. This, of course, could have been easily sorted out had** I had an attorney who was a bit vigilant and performed his rudimentary duty of surveilling for incorrectly transcribed words or even been willing to contact the court reporter to clarify this confusion after the fact. As an aside: 12. My reply (under oath) to Craig Mellos statement to the Board: DR. CRAIG C. MELLOS DECLARATION (CARNEGIE EXHIBIT 1118) Paragraph 46. To the best of my recollection, I gave Mr. Ali positive employee evaluations throughout his tenure in my laboratory. ALIS REPLY (UNDER OATH) TO DR. CRAIG C. MELLOS DECLARATION (CARNEGIE EXHIBIT 1118) Notwithstanding the hoopla surrounding whether I can think independently and come up with new ideas and propose models, it is quite informative to closely examine Dr. Mellos evaluation of my work in his lab. The only demerit that he mentioned in his evaluation of my performance was my inability to organize the work of others or delegate to other members of the lab the routine task of lab maintenance. Indeed when looked as a whole, it could be argued that Dr. Mellos evaluation of my work, ostracized me for having failed to carry out my routine technician responsibilities while extolling me for devising innovate approaches to difficult new questions. Quoting Dr. Mello. MA 288-MA 289 and MA 141 By July 1997, Dr. Mellos laboratory was anything but overcrowded, as three members of his lab namely Mr. Sam driver, myself and Dr. Claudia Wittman had all abruptly left within a span of few months, which would have left it with a skeleton staff of not more than 5 people. Additionally, Dr. Mellos laboratory was an open space lab that bled into the adjoining lab without walls to separate the lab spaces. The lab also had numerous shelf spaces as each rows of bench had an adjoining shelf space that spanned the length/width of the lab. See Dr. Mellos 2002 deposition/testimony about the number of people (technicians, graduate students, post-docs etc) that worked in his lab. MA 534. It was Dr. Mello himself who declared in court filings that he had discarded the lab notebooks (according to him) prior to my filing of an action. Additionally he had attested to the fact that I had handed him my notebooks as a condition of getting a release from UMASS and his lab on the very last day of my employ there. MA 644 I filed my complaint just few months after I left Dr. Mellos lab in 1997. That alone should have provoked Dr. Mello and UMass to preserve the lab notebooks as they related to the very heart of my claims, i.e., the exclusion of authorship claims for the work I

Paragraph 32. By 1997 my laboratory was extremely overcrowded and had very limited shelf space for journals and notebooks.

Paragraph 33. I understand that Mr. Ali is claiming that UMass or I have discarded his notebooks. While I can attest that no one, to my knowledge, knowingly discarded Mr. Alis notebooks, we have been unable to locate the notebooks that Mr. Ali kept while he was member of my laboratory. Paragraph 34. Other laboratory notebooks, however, from that same time frame are also missing. I am not certain why Mr. Alis and several other notebooks from that time are missing. It is possible that some were taken

plaintiff assigned page # 35

DR. CRAIG C. MELLOS DECLARATION (CARNEGIE EXHIBIT 1118) without permission.

Paragraph 74. With respect to Experiment 4 listed on page 6 of the Cimbala letter, this appears to be incorrect. To my knowledge, no one in my laboratory performed any experiments to detect levels of DNA methylation in C. elegans.

Paragraph 75. With respect to Experiment 6 listed on page 6 of the Cimbala letter, this appears to be incorrect or at least an incorrect interpretation of the data we generated. The experiments conducted during this relevant time frame, between the fall of 1995 and 1997, could not definitely prove that the target of the RNAi machinery is the endogenous mRNA itself. Such a statement from Mr. Ali indicates to me that he did not understand the data generated or how to interpret this data.

Paragraph 76. Although a post-transcriptional gene silencing (PTGS) mechanism in which the endogenous mRNA was targeted for degradation was a possibility, we could not rule out gene silencing through a transcriptional process in which the production of the endogenous mRNA is itself inhibited. The interpretation of the experiments discussed in numbered paragraph 6 of the Cimbala letter is incorrect. Paragraph 82. Dr. Fire first contacted me about some curious results with RNAmediated interference on 7 July 1997, after Mr. Ali had left my laboratory. Thus Mr. Ali was not present at any time in my laboratory when we repeated our previous experiments

ALIS REPLY (UNDER OATH) TO DR. CRAIG C. MELLOS DECLARATION (CARNEGIE EXHIBIT 1118) performed in Dr. Mellos lab. As to his now assertion that Dr. Mellos lab notebooks are missing and that they might have been taken without permission: to the extent this assertion implicates me: the response is: I have never been back to the UMass Medical school campus --much less to Dr. Mellos lab-- after I left it on or around July 1, 1997. In fact, I left to Atlanta, GA immediately following my resignation from Dr. Mellos lab; additionally all I have are copies. This is quite interesting in many respects: 1) Dr. Mello himself was the one who initiated the methylation assay experiments and 2) when I went over to his office to tell him that there was no-methylation I could detect, his first utterance --even before I actually showed him the data--was, Mussa, are we going to be famous?!. 3) Additionally the methylation data contained in my notebook pages bear Dr. Mellos hand writing. In his 2004 Heineken prize speech, tallying up whodid-what in his lab, Dr. Andrew Fire states plainly that Mary Montgomery [] showed that the effect of double-stranded RNA injection in early embryo was to destabilize target mRNAs. MA560. Given the fact that Dr. Fire was citing the repeat data done with in situ hybridization designed to assay for the presence of the endogenous mRNA, the conclusion is one and the same. To answer the very same question, I carried out RT-PCR on single-cell embryos, and showed that the mRNA is no longer detectable in embryos that displayed the silencing molecular and or loss-offunction phenotype. Indeed, this data was published in the 1997 worm abstract bearing my name and Dr. Mellos name and in the manuscript that bears Mr. Driver, myself and Dr. Mellos name. MA287, MA309 Dr. Mello is correct here in speculating that the absence of the mRNA doesnt necessarily preclude the twin possibilities of a pre/co-transcriptional or post transcriptional silencing mechanism. However, what it ruled out for us at the time was the possibility of a post-translational mechanism wherein RNAi is compatible with the co-existence of the [targeted] endogenous mRNA.

The repeat experiments that Dr. Fire (allegedly in collaboration with Dr. Mello) carried out were done with dsRNAs much the same way the RNAi experiments I carried out were done with sufficient dsRNAs to induce potent and sequence specific RNA mediated silencing in C. elegans.

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DR. CRAIG C. MELLOS DECLARATION (CARNEGIE EXHIBIT 1118) using dsRNA. Appendix D.

ALIS REPLY (UNDER OATH) TO DR. CRAIG C. MELLOS DECLARATION (CARNEGIE EXHIBIT 1118) It is also curious to point out here that in the July 7, 1997 email Dr. Fire uses the term RNA-mediated interference or RNAi before the Cell paper which bears the seminally coined term (RNAi) was submitted for publication on July 15, 1997. MA 586 It is also strange that Dr. Fire [and Dr. Mello] fail to mention the Cell paper in the Nature published dsRNA mediated interference publication. See footnotes of the Nature paper.

13. My reply (under oath) to Christian Rocheeleaus statement to the Board: CHRISTIAN ROCHELEAUS DECLARATION (CARNEGIE EXHIBIT 1094) Paragraph 3. I am the co-primary author of the publication Wnt Signaling and an APC Related Gene Specify Endoderm in Early C. elegans Embryos that was published in the journal Cell, in Volume 90, pages 707-716 in 1997. ALIS REPLY (UNDER OATH) TO CHRISTIAN ROCHELEAUS DECLARATION (CARNEGIE EXHIBIT 1094) Rocheleau didnt write the Cell paper cited here. His primary authorship was tantamount to the following: I would write my name as Chris North; Dr. Mello then scratches off what I had written as my name and then would write the publishable version of my name which is Mussa Ali; Now, I could claim that I had written my name, but in reality what I had written as my name and what was actually published as my real name had no relations other than the fact that they are both used to name after homo sapiens on two different continents. Rocheleau seems to be unaware of the fact the templates that were used to synthesize the RNAs bear the signature dsDNAs with 3 protruding ends which invariably give rise to a subpopulation of a perfectly annealed dsRNAs. MA 178-MA 179.This is a byproduct of the TdT activity of the Taq DNA polymerase enzyme we used for PCR amplifying the gene-of-interest in generating the templates, which were subsequently used to in vitro transcribe the RNAs. MA 571-MA 584. Again Rocheleau seems to be unaware of the simple fact that when we generated complementary strands in our IVT reactions that they would invariably anneal. This is because the transcription buffer could double as an annealing buffer and as such an extra step or resuspension in annealing buffer is largely unnecessary. This assertion of Rocheleau is fantastic for the simple reason that he tried to synthesize the RNAs and failed, much the same way he tried to carry out the molecular experiments (e.g. the cloning of the mom-implicated genes) and failed miserably. So if he never succeeded in synthesizing the RNAs to begin with, how could he detail and declare to the Board what his intent and

Paragraph 4. sentence 4. while I agree that there is a possibility of the presence of doublestranded RNA in my experiments, I believe that it is inaccurate to conclude that doublestranded RNA was necessarily present and that double-stranded RNA alone was causing the observed effects.

Paragraph 5. sentence 3. However, both Dr. Vances and Dr. Weigels opinions are overly simplistic in concluding that (1) reverseoriented strands were always necessarily made; (2) that such strands necessarily hybridized to each other to form a doublestranded RNA Paragraph 6. sentence 2 and 3. At no point did I mix either of these samples, nor did I attempt to produce both strands simultaneously in the same solution. There was no intent or design in my experiments to produce a doublestranded RNA.

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CHRISTIAN ROCHELEAUS DECLARATION (CARNEGIE EXHIBIT 1094)

ALIS REPLY (UNDER OATH) TO CHRISTIAN ROCHELEAUS DECLARATION (CARNEGIE EXHIBIT 1094) purpose was. MA 101, MA 593 and MA 531 listing the pages in my notebooks that bear the very same RNAs used for the Cell paper, In fact, Dr. Mellos instructed him to give me a list of the RNAs that needed to be synthesized and per that instruction Rocheleau wrote on a piece of paper titled RNA requests the RNAs that needed to be synthesized. Subsequent to which I synthesized all of the RNAs that were used in his experiments. See MA 529 Dr. Fire need not to speculate here since he had, not just knowledge of the existence of the dsRNA subpopulation in our IVT preps but had actually observed the dsRNA-trigger and commented on it as far back as 1991. MA 659. The assertion that random pieces of RNAs could have given us reproducible and sequence-specific silencing is just plainly impossible. If random pieces of RNAs were responsible for the silencing, the sequence specificity of the silencing phenomenon we had observed would have been non-specific and irreproducible. This is quite frankly unintelligent: if the pre-annealed dsRNAs we were injecting were to dissociate upon introduction into the cell, then the much acclaimed Nature published Fire et al pre-annealed dsRNAi paper would have suffered the same travails since it would have, also, dissociated upon introduction into the cell. As to the assertion made by Rocheleau that in his experiments that he didnt perform[] additional procedures to ensure annealing, this simply falls apart because he never successfully synthesized the RNAs to begin with, much less began to worry about carrying out additional procedures to ensure anything. This again shows the Mello/Fire flawed mechanistic argument promulgated by Rocheleau: the very genesis of all the RNAi experiments we carried out from the outset was because we treated both sense and antisense mediated RNA interference as one and the same. This was largely a byproduct of the experimental data we generated as to dose, perdurance or heritability etc. In fact it is because the canonical antisense mechanism could not explain[] the fact that the sense RNA induced silencing and more importantly that both sense and antisense RNAs provoked silencing in exactly the same manner that we had hypothesized that they would enter the RNAi

Paragraph 7. sentence 2. In both the Nobel Lecture and Fire et al., Dr. Fire proposes only a possibility that double-stranded RNA molecules were present, based on the possibility that a bacteriophage polymerase may produce random pieces of RNA.

Paragraph 9. sentence 1 and sentence 3. Further there is no possibility that complementary pieces of RNA would have hybridized. While the rules of Watson-Crick base pairing apply to complementary strands of RNA, that they inherently anneal, particularly in a diverse environment such as a cell is not an absolute law of science as both Dr. Vance and Dr. Weigel seem to imply. In my experiments, I performed no additional procedures to ensure annealing.

Paragraph 10. sentence 2. In my experiments where I injected single-stranded antisense RNA, the results can possibly explained by known single-stranded RNA antisense mechanism.

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MA528

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