Patent Docs

Moderna Sues Pfizer and BioNTech over mRNA Vaccine Technology

August 31, 2022

By Kevin E. Noonan –

On Friday, August 26th, Moderna Tx, Inc. and Moderna US, Inc. filed a complaint for patent infringement in Federal district court for the District of Massachusetts against Pfizer, Inc., BioNTech SE, BioNTech Manufacturing GmbH, and BioNTech US, Inc. (A parallel suit was filed in Germany asserting Moderna's corresponding German patents.) There are several interesting aspects to this complaint, and perhaps of even greater interest has been the reaction to the filing in light of Moderna's earlier "pledge" to refrain from asserting any of its patents "during the pandemic."

The complaint asserts three patents, identified herein in the context of the claims set forth in the complaint itself:

U.S. Patent No. 10,898,574

Claim 2. A pharmaceutical composition comprising:
    a plurality of lipid nanoparticles comprising a cationic lipid, a sterol, and a PEG-lipid,
    wherein the lipid nanoparticles comprise an mRNA encoding a polypeptide,
    wherein the mRNA comprises one or more uridines, one or more cytidines, one or more adenosines, and one or more guanosines and wherein substantially all uridines are modified uridines.

Claim 9. The pharmaceutical composition of claim 2, wherein the modified uridine is 1-methyl-pseudouridine.

U.S. Patent No. 10,702,600

Claim 1. A composition, comprising:
    a messenger ribonucleic acid (mRNA) comprising an open reading frame encoding a betacoronavirus (BetaCoV) S protein or S protein subunit formulated in a lipid nanoparticle.

U.S. Patent No. 10,933,127

Claim 1. A method comprising administering to a subject
    a messenger ribonucleic acid (mRNA) comprising an open reading frame encoding a betacoronavirus (BetaCoV) S protein or S protein subunit formulated in a lipid nanoparticle
    in an effective amount to induce in the subject an immune response to the BetaCoV S protein or S protein subunit
    wherein the lipid nanoparticle comprises 20-60 mol% ionizable cationic lipid, 5-25 mol% neutral lipid, 25-55 mol% cholesterol, and 0.5-15 mol% PEG-modified lipid.

Of these three asserted patents, the '574 patent has the broadest claims, not being limited to a particular virus or antigenic protein thereof, while the '600 and '127 patents expressly recite mRNAs encoding a b-coronavirus Spike protein; these claims would encompass vaccines to SARS-CoV-1 (the original SARS pandemic vaccine) as well as MERS and SARS-CoV-2 (COVID19). These claims in particular form a basis for Moderna's allegations of infringement by the Pfizer/BioNTech Comirnaty® vaccine, as recited in several paragraphs in the complaint. In particular, Moderna alleges that the Comirnaty® vaccine was a direct copy of their vaccine (a path taken over three other competing candidate vaccines), citing public statements by Pfizer CEO Albert Bourla on June 9, 2020, at Goldman Sachs Virtual 41st Annual Global Healthcare Conference (¶20 of the complaint).

Perhaps in recognition of the post-pandemic patent zeitgeist, the complaint has two remarkable features. The first is a long expostulatory section explaining the long antecedents of the technology Moderna was able to apply towards making its Spike mRNA SARS-CoV-2 vaccine (and the skepticism those efforts elicited pre-pandemic). This portion of the complaint includes a history of Moderna's development of the underlying mRNA technology as well as its efforts to develop its vaccine (unnoted is that Moderna abjured participation in "Operation Warp Speed" with its attendant Federal government financial support) during the pandemic (and makes the point that their technology is not limited to vaccines against COVID infections). The complaint also makes the case that the company's IP was both the technical foundation for its successful and rapid development of the COVID vaccine and provided protection against the significant financial and investment risk occasioned by Moderna's development of its vaccine.

The second remarkable feature of the complaint, and Moderna's strategy in bringing suit, is in the Prayer for Relief (and certain sections explaining the limitations of the remedy Moderna asks the Court to grant). In addition to a judgment that Pfizer and BioNTech infringe by sales of its Comirnaty® vaccine (and that such infringement was willful), Moderna seeks money damages that expressly exclude damages it would be entitled to from "sales to the U.S. government that are subject to 28 U.S.C. § 1498 or to the 92 low- and middle-income countries in the Gavi COVAX Advance Market Commitment (AMC)." And in the litany of other remedies routinely requested in patent infringement cases (a finding that this is an exceptional case, with an award of attorneys' fees, costs, and expenses under 35 U.S.C. § 285, and treble damages for willful infringement under 35 U.S.C. § 284), expressly excluded is an injunction from "such other relief the Court may deem just and proper." Deigning to forego compensation for sales to the government under 28 U.S.C. § 1498 is likely done in an effort to avoid any attempt by Pfizer or BioNTech to have the case adjudicated under the statute in the Court of Federal Claims; disclaiming any interest in sales outside the U.S. to countries falling within the scope of the COMAX AMC avoids (or at least tries to) allegations that Moderna is putting its profits and patent rights over the health and lives of the citizens of those countries.

The complaint also addresses Moderna's promises regarding assertion of its IP, specifically quoting its October 8, 2020 press release stating that "while the pandemic continues, Moderna will not enforce our COVID-19 related patents against those making vaccines intended to combat the pandemic" (italics in original) (¶22). The complaint also provides Moderna's rationale and justification for filing this complaint at this time:

By early 2022, however, the collective fight against COVID-19 had entered a new endemic phase and vaccine supply was no longer a barrier to access in many parts of the world, including the United States. In view of these developments, Moderna announced on March 7, 2022, that it expected companies such as Pfizer and BioNTech to respect Moderna's intellectual property and would consider a commercially-reasonable license should they request one. This announcement was widely publicized, including through coverage in The Wall Street Journal. Critically, however, and to further its belief that intellectual property should never be a barrier to access, as part of this announcement, Moderna committed to never enforce its patents for any COVID-19 vaccine used in the 92 low- and middle-income countries in the Gavi COVAX Advance Market Commitment ("AMC"). This includes any product manufactured outside the AMC countries, such as the World Health Organization's project in South Africa, with respect to COVID-19 vaccines destined for and used in the AMC-92 countries. Although they have continued to use Moderna's intellectual property, Pfizer and BioNTech have not reached out to Moderna to discuss a license. (¶23)

The complaint has nonetheless raised the issue of the status of Moderna's promise in the context of patent pledges in other industries, notably for standard-essential patents (SEP) and FRAND ("fair, reasonable, and non-discriminatory") agreements. Academics (in particular, Jacob Sherkow from the University of Illinois Law School and Jorge Contreras, S.J. Quinney College of Law, University of Utah Law School) have raised the specter of successful suit by Moderna in the face of its earlier promise as creating a challenge threatening the substantial edifice of patent pledges used in these other contexts. Some distinctions immediately come to mind, however. One is that the patent pledges in the SEP/FRAND context are associated with consideration for the pledging party, that consideration consisting of, inter alia, compliance by companies licensing SEPs owned by the pledging patentee that provide stability and consistency in licensing regimes and create impediments against non-compliant companies. Moderna received no such consideration for its pledge (and the effects of any "good will" it might have hoped to gain was ephemeral; after all, all the pledges in the world did not deter the WTO from adopting a patent waiver agreement at the behest of India, South Africa, and other countries who could expect to benefit and did benefit from agreements like the one in Moderna's complaint exempting sales to the COVAX AMC countries from any damages claims sought by Moderna). Another distinction is that a fair reading of Moderna's promise-by-press-release was its essentially contingent nature; forgoing (or postponing exercise of) its patent rights was always limited to during the pandemic (although it is a fair question to ask who decides when the pandemic is over). Finally it is not unfair to say that the SEP/FRAND situation is vastly different from patenting vaccines against a pandemic virus; there is, after all, no analogous risk to global health and welfare arising from patent pledges relating to such patents.

On the other hand, if a court does hold Moderna's patent promise to be enforceable (under the doctrine of promissory estoppel, for example), it most likely will be the last time any biotechnology or pharmaceutical company makes such a promise.

There is one other consideration here that may explain Moderna's willingness to file suit at this time that abjures the lion's share of any damages it could reasonably have expected to receive. Moderna has achieved something of a Holy Grail of patenting: true platform patents that can be and will be used for the next vaccine, and the one after that, etc. Bringing a successful suit might result in a healthy damages award but these may pale compared with what could happen during the ~10 -15 years of patent life remaining. Of course, any suit brings risks and it is not unlikely that Pfizer/BioNTech will petition for inter partes review; indeed, at least one patent owned by the University of Pennsylvania, U.S. Patent No. 8,691,966 (naming BioNTech principal Katalin Kariko as an inventor), discloses and claims mRNA modifications comprising 1-methylpseudouridine (albeit outside the SARS context); this patent has an earliest priority date about 4 years prior to Moderna's patents asserted in the litigation.

All these considerations make for a compelling story that will almost certainly be the subject of future posts.
Guest Post — AI and Inventorship — Will Next Blockbuster Drug Be Denied Patent Protection?

August 28, 2022

By Brian A. Pattengale* and Anthony D. Sabatelli** —

Decades after the science-fiction visions of Stanley Kubrick’s 2001: A Space Odyssey and Isaac Asimov’s I, Robot, artificial intelligence ("AI") is finally moving to the mainstream. Many of us use digital assistants like Apple's Siri or Google's Alexa every day, and we gape, with a mixture of awe and terror, over videos of the feats of robotic animals and stories over whether AI being developed at Google is displaying signs of sentience. Along with this, we have finally reached the point in the development of AI where we must confront the legal and policy questions of whether AI can (or should) be able to be an inventor on a patent.

That very question was recently addressed by the Court of Appeals for the Federal Circuit ("CAFC") in Thaler v. Vidal.¹ The patent applicant in the Thaler case argued that he did not invent the subject matter of his patent applications; rather, he asserted they were invented solely by an AI system.² In its decision, the CAFC swiftly came to the conclusion that the answer to this question is clear from the statute. U.S. Patent Law clearly and unambiguously states that only natural persons can be named as inventors on patents. The Court stated ". . . .it might seem that resolving this issue would involve an abstract inquiry . . . however we need not ponder these aphysical matters . . . [i]nstead, our task begins — and ends — with consideration of the . . . statute." The Court reiterated that the Patent Act requires that inventors are "individuals" and therefore limited to human beings. End of story.

In this article we consider what this very clear pronouncement by the CAFC means for drug discovery: Will the next blockbuster drug potentially be denied patent protection if it is discovered solely through highly sophisticated AI methods?

According to a 2020 study, it generally takes on the order of 10 years and over a billion dollars to bring a new drug to market, from initial discovery in the lab through preclinical and clinical testing, to eventual approval of the new drug application ("NDA"), and then to marketing and sales.³ Furthermore, the success rate is very low — only approximately 10% of drug candidates make it all the way through the process to approval for marketing. The drug discovery process is still very empirical, often involving medicinal chemists and their teams synthesizing and evaluating thousands of compounds. The process also typically relies upon numerous structure activity relationship ("SAR") decisions by those involved to direct the process. Computer-aided drug discovery ("CADD") technologies have significantly improved this very empirical process, allowing for more efficient utilization of bio- and chemoinformatic information to propose, screen, and perform target-based analyses on drug candidates. AI-based technologies represent the next forefront of drug discovery, offering the potential to identify optimized drug molecules based on training data without further human input during the identification process.⁴ To be clear, scenarios such as this are not science fiction — the German biotechnology company Evotec recently partnered with UK-based Exscientia to use AI to identify a new anticancer drug candidate that is currently in Phase I clinical trials.⁵ Pharma giant Merck is also highly invested in utilizing AI platforms for drug discovery.⁶

Experts in the field generally utilize AI systems to perform machine learning or what is known as "deep learning" to make decisions and predictions based upon correlations in training data provided to the system. For example, in the field of drug discovery, one could start with a general core structure for a drug compound and add to it a large set of chemical substituents for altering the properties of the compound. With appropriate training data, AI can be used to predict and sift through several tens of thousands, if not millions, of theoretical substituent combinations to identify a limited set of compounds– or even a single specific compound — having selected target properties. In this scenario, would AI then be the rightful "inventor" of the target compound, which otherwise might never have been identified but for the use of AI?

Inventorship in the U.S. is based upon conception of an invention. Activities undertaken simply to reduce an invention to practice are not sufficient to confer inventorship. The Manual of Patent Examination Procedures ("MPEP"), provides unambiguous guidance for inventorship, even specifically for chemical compounds. MPEP § 2109 II states: "General knowledge regarding the anticipated biological properties of groups of complex chemical compounds is insufficient to confer inventorship status with respect to specifically claimed compounds".⁷ Therefore, in a simplified scenario, a medicinal chemist having expert knowledge of a broad genus of compounds would not necessarily be the inventor of a specific chemical compound falling under that genus, if that compound was discovered by another chemist on the team. That other chemist would most likely be the inventor. Suppose now, instead of that compound having been identified by another chemist, it is identified by AI. Following the same logic, would not AI now likely be the rightful inventor?

For the sake of discussion, let's assume that AI fully predicts a previously unknown compound as a particular drug target. That target compound is tested for efficacy, safety, etc. and becomes a candidate that is eventually approved for use and reaches blockbuster sales status. Even though humans were involved in the synthesis, testing, clinical trials, and approval process, none of those activities would constitute conception (i.e., invention) of this drug compound. The humans were "told" by AI exactly which compound to make and would only be reducers to practice, having therefore not contributed to the original conception of that particular drug compound.

Taking this scenario to its seemingly perverse conclusion, under current U.S. Patent Law as recently pronounced by the CAFC, the AI-discovered target compound would be unpatentable because AI cannot be an inventor on the patent and no human could specifically be identified as the discoverer of that compound. In the absence of patent protection, this AI-identified compound could then likely end up in the public domain. This result is at odds with the public policy standpoint of our patent system which rewards innovation by placing patented inventions before the public to encourage further innovation, while providing the patentee with an exclusivity for the term of the patent, which is generally twenty years.⁸

The above thought exercise, to our knowledge, has not yet played out. But it soon could. There may, however, be a solution to this apparent dilemma, albeit not one that is completely satisfying or sufficiently tested through litigation. Because U.S. inventorship is based upon the patent claims, and a co-inventor need only contribute to the conception of a single patent claim to be listed as an inventor on a patent, it is entirely possible that a human inventor could conceive of a single claim or claim limitation, or even an alternative claimed embodiment, in order to be rightfully included on a patent otherwise directed to an AI-generated compound. For example, the chemists on the AI project may conceive of or discover salts or solvates of the compound, functional limitations related to the compound, closely related compounds, methods of using the compound, methods of synthesizing the compound, etc., which could likely be sufficient for establishing human inventorship — at least to those claims reciting these limitations.

In Thaler, the Federal Circuit intentionally left certain questions unresolved by stating that the Court was " . . . not confronted today with the question of whether inventions made by human beings with the assistance of AI are eligible for patent protection". It seems that there are arguments that a human being would have contributed to the inventions (i.e., claims) thereby meeting the inventorship threshold of the Patent Act. Time will only tell how this scenario plays out. Perhaps the more important million-dollar question (or, rather, multi-billion dollar question with respect to drug discovery) is whether or not a patent claim directed to a drug compound identified solely through AI, and having no human inventor, would be valid in view of Thaler.

¹Thaler v. Vidal, U.S. Court of Appeals for the Federal Circuit, 2022, case number 21-2347

²Mr. Thaler was issued a patent in South Africa with his AI system DABUS listed as the inventor, a world first, and Europe and Australia both rejected the applications. An Australian judge initially ruled that AI can be an inventor, and that decision was overturned earlier this year by a higher court.

³https://www.biospace.com/article/median-cost-of-bringing-a-new-drug-to-market-985-million/

⁴Paul, D. et al. "Artificial intelligence in drug discovery and development", 2021, Drug Discov. Today, 26:1, pp. 80–93

⁵https://www.fiercebiotech.com/medtech/merck-selects-saama-add-machine-learning-tech-drug-development-process; https://www.emdgroup.com/en/research/science-space/envisioning-tomorrow/precision-medicine/generativeai.html

⁶https://www.nature.com/articles/d43747-021-00045-7

⁷Ex parte Smernoff, 215 U.S.P.Q. 545, 547 (Bd. App. 1982)

⁸In Thaler v. Vidal, Mr. Thaler did include related policy arguments, which the Federal Circuit dismissed in view of its reliance on the statutory language that Congress chose.

* Dr. Pattengale is a patent agent at Wiggin and Dana. Dr. Pattengale received his Ph.D., Physical and Materials Chemistry from Marquette University, and his B.S., Biochemistry from Carroll University.
** Dr. Sabatelli is Patent Counsel at Wiggin and Dana. Dr. Sabatelli received his J.D., cum laude, from the Salmon P. Chase College of Law. He received his Ph.D., with Honors, in Organic Chemistry from Yale University, and his B.S., summa cum laude, in Chemistry from Fairfield University.

This article was originally published on the Wiggin and Dana website on August 17, 2022.
Oral Arguments Rescheduled in CRISPR Interferences

August 28, 2022

By Kevin E. Noonan –

On August 16th, the Patent Trial and Appeal Board rescheduled back-to-back oral hearings for interferences between ToolGen Inc. (Senior Party) and Junior Party The Broad Institute, Massachusetts Institute of Technology, and The President and Fellows of Harvard College (collectively, "Broad," Interference No. 106,126) and Junior Party The Regents of the University of California, University of Vienna, and Emmanuelle Charpentier (collectively, "CVC," Interference No. 106,127). In the '126 Interference, the hearing will commence at 1:00 pm EDT on September 12th, and for the '127 interference, the hearing will start at 3:00 pm EDT that day. The hearings will be conducted by telephone. In the Notices in each interference, the Board’s Order stated that postponement was at Senior Party ToolGen’s request.

Interested members of the public may be granted access by request sent to PTABHearings@uspto.gov at least five business days prior to the hearing date.

The issues to be discussed can be found on the PTAB website and in several prior Patent Docs posts.
Conference & CLE Calendar

August 28, 2022

August 30, 2022 – "Litigating Inventorship — When and How to Change Named Inventors on an Issued Patent" (IPWatchdog and Ludwig, APC) – 12:00 pm (ET)

September 1, 2022 – "Computer-Implemented Inventions in the EPO" – Part I (Schwegman Lundberg & Woessner) -12:00 pm (CT)

September 1, 2022 – "Telling Stories to Clients with IP Intelligence" (IPWatchdog and PatSnap) – 12:00 pm (ET)

September 29, 2022 – "Computer-Implemented Inventions in the EPO" – Part II (Schwegman Lundberg & Woessner) -12:00 pm (CT)
Webinar on Litigating Inventorship

August 27, 2022

IPWatchdog and Ludwig, APC will be offering a webinar entitled "Litigating Inventorship — When and How to Change Named Inventors on an Issued Patent" on August 30, 2022 at 12:00 pm (ET). Gene Quinn of IPWatchdog, Inc. will moderate a panel consisting of Pattric Rawlins of Procopio Cory Hargreaves & Savitch and Eric Ludwig of Ludwig, APC. The panel will examine the following:

• Who may apply for a patent — a joint inventor or author?
• How would a joint inventor amend or contest inventorship of an issued patent?
• What are the most significant issues facing a would-be joint inventor or patent owner, when it comes to litigating an inventorship contest?
• What does case law have to say about a prospective inventor’s standing to sue, in face of an invention assignment agreement?

There is no registration fee for this webinar. However, those interested in registering for the webinar, should do so here.
Webinar on Computer-Implemented Inventions in the EPO

August 27, 2022

Schwegman Lundberg & Woessner will be offering a two-part webinar on "Computer-Implemented Inventions in the EPO" on September 1 and September 29, 2022 at 12:00 pm (CT). In Part I, Daniel Closa from the European Patent Office will explore a problem-solution approach to computer-implemented inventions in the EPO, will discuss pertinent parts of the EPO's Guidelines for Examination, as well as the EPO's current examination practice, and cover topics such as: inventive step and claims with technical and non-technical features; a problem-solution approach for mixed-type inventions; analysis of features contributing to the technical character; the objective technical problem; and technical effects. Attendees of Part I will have a chance to vote on what specific subject matter they would like to see covered in Part II, for example AI or computer games. Maureen Kinsler of SLW International will moderate both sessions.

While there is no cost to participate in the program, those interested in attending the webinar can register here.
Webinar on Developing Compelling Narratives

August 27, 2022

IPWatchdog and PatSnap will be offering a webinar entitled "Telling Stories to Clients with IP Intelligence" on September 1, 2022 at 12:00 pm (ET). Chad Gilman of Fish & Richardson, Sam Wiley of PatSnap, and Gene Quinn of IPWatchdog, Inc. will explore the tools and tactics for synthesizing IP, and legal and business intelligence into compelling narratives. The panel will also discuss the following:

• The IP and legal data resources available to build data-driven, visual narratives;
• How leveraging data can strengthen existing, and create new, client relationships; and
• Why research and analysis using multiple, seamless intelligence sources is critical for high-stakes legal practices.

There is no registration fee for this webinar. However, those interested in registering for the webinar, should do so here.
Penguin Genetics Suggests Complex History

August 25, 2022

By Kevin E. Noonan —

Penguins are unique among bird species, having lost the ability to fly more than 60 million years ago and adopting a "hyperspecialized marine body plan" consistent with their unique habitat in the higher latitudes of the Southern Hemisphere. Key geological events are believed to be in part responsible, with major climate oscillations that led the penguins to find ecological refuge and then recolonize previous niches.

A recent study by an international team of scientists* reported specifics of penguin natural history and genetic structure in a paper entitled "Genomic insights into the secondary aquatic transition of penguins," in the journal Nature Communications (13: 3912 (2022). A significant difference between this study and earlier studies is that this one includes fossil penguins, which make up almost 75% of all penguin species (earlier studies were limited to mitochondrial genes or a few nuclear genes) "combining genomes from all extant and recently-extinct penguin lineages (27 taxa) (Table 1), stratigraphic data from fossil penguins (47 taxa), and morphological and biogeographic data from all species (extant and extinct)."

The data from these analyses support the origin of penguins in New Zealand, originating in stem penguins with extensive local radiation followed by dispersing to Antarctica and South America in multiple invasions of these environments. Crown penguins, on the other hand, originated in South Africa — 14Mya from these migrations, followed by dispersal back to New Zealand at least three times, with two of these inferred migrations occurring before the prevailing Antarctica Circumpolar Current had been established (west to east, which would have facilitated these migrations). The origin of these species coincides with global cooling in the middle Miocene; during at least some of the time periods relevant to penguin evolution there were no polar ice sheets.

These researchers found "incongruities" between phylogenetic trees created by genetic versus conventional morphology-based phylogenies. They found evidence that rapid speciation of Crown penguins was associated with incomplete lineage sorting (ILS) (due in part to the persistence of polymorphisms across different speciation events) or introgression (transfer of genetic material between related species) resulted from 5% ILS content within ancestors of several penguin species (Spheniscus, Eudyptula, Eudyptes, and several subgroups within Eudyptes). These results are consistent with closely related penguin species can hybridize in the wild and "provides a temporal framework for this rapid radiation: the four extant Spheniscus taxa are all inferred to have split from one another within the last ~3 Ma, and likewise the nine extant Eudyptes taxa likely split from one another in that same time."

This observed pattern of relatively recent divergence of penguin species within the past 3 million years is a consistent feature among penguin lineages and is correlated with post-speciation introgression events between these populations (events not detected between species that are geographically disparate). These researchers found "a genomic signature of a period of physical isolation during the Last Glacial Period (LGP) with increased climate fluctuation and environmental uncertainty, followed by postglacial contact and introgression as Earth warmed once again"; similar evidence can be seen in other marine taxa during this period, where penguins and other species moved north away from the South Pole and then back as the earth warmed.

The authors also analogize their historical evidence of climate change during this period with the effects of man-made climate change recently, stating that taxa capable of migration survived better than taxa that were "residential" and foraged close to shore.

Using the integrated evolutionary speed hypothesis (IESH) (which assesses the effects of temperature, water availability, population size, and spatial heterogeneity) these researchers concluded that penguins have the slowest evolutionary rate of all bird species, something these scientists attributed to their "increasing aquatic ecology." Paradoxically perhaps this perceived evolutionary slowdown could be seen in crown penguins over the first 10 million years of its history but then an uptick in evolutionary rates around 2 million years ago, correlating with the glacial-interglacial cycles during that time has something to do with it.

Turning to genes associated with penguin evolution, these scientists report correlations between phenotypic adaptations (including "their locomotory strategy, thermoregulation, sensory perception, and diet"). They identified three classes of genetic sources of these adaptations: positively selected genes (PSGs); rapidly evolving genes (REGs); and pseudogenes. These results showed 15 PSGs and six REGs were penguin-specific adaptations (Fig. 4a) below, five genes containing penguin-specific substitutions, seven pseudogenes, and two gene expansions, illustrated in this figure:

Three of these genes (TBXT and FOXP1, relating to cartilage, tendons, and limb bone and SMAD3, encoding transforming growth factor 3 are related in penguins (and other flightless birds) to "shortening, rigidity, and increased density of the forelimb bones." Also implicated in limb formation and adaptations was TNMD, a PSG, which the authors speculate may be the cause of "wholesale replacement of penguin distal wing musculature by tendons." And the authors note that KCNU1 and KCNMA1 genes related to calcium sequestration have been expanded in the genomes of penguins (as well as grebes).

Other genes are implicated in phenotypic features such as densely-packed waterproof feathers, thick skin, and a layer of subcutaneous fat which enables the animals to thermoregulate in cold environments. These genes include APPL1, TRPC1, EVPL, wherein the APPL1 and TRPC1 genes are involved in glucose levels and fatty acid breakdown through adiponectin; the authors hypothesize these genes promote white adipose fat storage which provide both insulation and an energy reserve. Another important adaptation is the capacity to withstand hypoxic conditions, and in this regard the transferrin receptor 1 gene TFRC was found to be under positive selection pressure (consistent with expression of this gene in an oxygen-dependent manner even in domesticated cattle). The FIBB and ANO6 genes, which are involved in blood coagulation, were found to be selected for in species having the capacity for the deepest dives (>500m). Hemoglobin genes HBA-αA (A140S) and HBB-βA (L87M) had the noted penguin-specific amino acid sequence variations found conserved in all penguin species as were modification in myoglobin genes. Finally, in this regard a gene that may help widen blood vessels to decrease blood pressure during deep dives, TRPC4, was found to be a PSG.

Vision, particularly low-light vision, is another phenotype hshowing penguin-specific adaptations. It was known that penguins have only three functional cone photoreceptor types, and the green cone opsin gene RH2, was found in all penguin species to have a 12bp deletion encoding a lysine residue critical for chromophore binding. These researchers also found specific genetic alterations in red cones associated with blue-shifting the pigment and facilitating a shift in optimum wavelength consistent with ambient underwater light (and having implications for foraging under such conditions). And deactivation of CYP2J19, a gene that encodes a carotenoid ketolase responsible for producing red oil droplets in avian cone, the authors surmise "likely allows for higher retinal sensitivity when foraging in dim light conditions, as seen in nocturnal owls and kiwis." Finally, other genes thought responsible for visual sensitivity at low light levels (including TMEM30A (PSG), KCNV2 (REG), CNGB1, and GNB3) show evidence of selection and/or mutations specific to penguins.

Diet is another aspect of penguin lifestyle associated with genetic changes. This implicates penguin taste sensitivities, and these authors report that penguins have retained the capacity to taste only sour and salty flavors (and the genes associated with these capacities); the genes for sweet, bitter and umami have been lost in all penguin species. Curiously, according to the authors, the penguin genome contains no active chitinase genes and only one pseudogene, which is inconsistent with a diet comprising crustaceans (because many species are known to consume large amounts of these animals. The researchers propose (based on fossil evidence) that penguins lost their chitinase genes during ~50 million year interval where they did not consume this prey.

Immune-related genes were also assessed, and 51 PSGs were detected for such genes. The authors speculate that the selective pressure may be the result of host-pathogen co-evolution. Examples of such genes include bacterial-recognizing Toll-like receptors TLR4 and TLR5 and within these genes site proximal to the lipopolysaccharide-binding site of TLR4 and the flagellin-binding site of TLR5. A gene involved in viral RNA detection, IFIT5 is also under positive selection in penguins with positively selected amino acid sites in the protein analogous to similar sites in the human ortholog of this gene. A similar pattern of selection was found in the penguin gene encoding glycoprotein-mediated hepatitis C viral entry (CD81) with a cluster of positively selected amino acid sites that correspond to similar sites in humans. Finally, the transferrin gene has undergone positive selection in penguins, which the authors speculate reflects resistance to Corynebacterium infection and diphtheritic stomatitis which are known to cause increased chick mortality.

The authors conclude that penguins acquired most of the genetic adaptations associated with their unique (for birds) aquatic habitat early in their speciation from other birds and that the strong positive selection for these traits is responsible for the low amount of evolutionary change in all penguin taxa. But their strong adaptation to the colder climate in the peri-South Pole region puts them at risk in the current warming climate trends. Accordingly these authors suggest that the canary in the global warming coal mine might actually be a penguin.

*Researchers from Demark, Norway, France, the UK, Germany, various European countries, the United States, Argentina, South Africa, New Zealand, China, and Australia reported the results of their studies in a paper entitled "Genetic Insights into the Secondary Aquatic Transition of Penguins," Nature Communications 13: 1-13
The EFF is Patently Wrong

August 24, 2022

By Michael Borella —

The Electronic Frontier Foundation (EFF) is at it again, gaslighting the public in its ongoing crusade against patents. While the EFF does perform some commendable work, mostly in the areas of individual privacy rights, its track record on patents amounts to little more than a hit job. In particular, the EFF has few qualms with providing heavily slanted opinion pieces on patent policy and making statements that are misleading or outright wrong. This is nothing new, unfortunately.

The EFF's latest screed covers Senator Tillis' recent proposed legislation to reform 35 U.S.C. § 101, but is full of falsehoods, deceptiveness, and bias. It was written by Joe Mullin, a former journalist and current policy analyst for the EFF. As far as I can tell, Mr. Mullin is not a patent attorney and has never practiced patent law. His EFF job title is "Mark Cuban Chair to Eliminate Stupid Patents" (you can't make this stuff up), which pretty much says all you need to know about his positions.

So let's go through Mr. Mullin's article, line-by-line, categorizing each based on where it falls on a spectrum ranging from mostly true to deceptive to false. Hint: very little he writes comes close to being mostly true.

"A recently introduced patent bill would authorize patents on abstract ideas just for including computer jargon . . ."

False. Frankly, this statement is almost too vague to be meaningful. But if Mr. Mullin is referring to just adding processors, memory, and the like to claims otherwise involving a business, mathematical, or mental process, the Tillis bill would still result in such inventions being unpatentable.

". . . and would even legalize the patenting of human genes."

Deceptive. The Tillis bill would make unmodified human genes (e.g., those appearing naturally in the human body) unpatentable, but would allow patenting of genes that are "isolated, purified, enriched, or otherwise altered by human activity." In other words, if you do something new and inventive with a human gene, then the result of labor by human hands might be patentable.

"The 'Patent Eligibility Restoration Act,' sponsored by Sen. Thom Tillis (R-NC), explicitly overrides some of the most important Supreme Court decisions of the past 15 years, and would tear down some of the public's only protections from the worst patent abuses."

False. The public has many protections from those trying to unethically exploit the patent system that the Tillis bill would not touch. Like the other parts of the patent statute that define additional requirements for patentability.

"Pro-patent maximalists are trying to label the Tillis bill as a 'consensus,' but it's nothing of the sort."

Deceptive. And likely a straw man argument. "Pro-patent maximalist" is a made up term that remains undefined and meaningless. Therefore, it is irrelevant to attribute any particular viewpoint to this hypothetical group of people.

"We need EFF supporters to send a message to Congress that it isn't acceptable to allow patent trolls, or large patent-holders, to hold our technology hostage."

Deceptive. Non-practicing entities (let's call them that rather than the pejorative term "trolls") and large patent holders do not hold technology hostage. Anyone is permitted to file patent applications on inventions they wish to protect. If granted, they have approximately 20 years to exclude others from practicing the invention in return for publicly disclosing the fruits of their labors. This is a carefully-designed quid-pro-quo, not a hostage negotiation.

"Starting in the late 1990s, the U.S. Court of Appeals for the Federal Circuit essentially did away with any serious limits on what could be patented. This court, the top patent appeals court in the U.S., allowed patents on anything that produced a 'useful result,' even when that result was just a number."

False. Claims that are not directed to novel, non-obvious, and properly described inventions have been unpatentable since at least 1952 if not the earliest days of our republic. In the 1990s, the Federal Circuit clarified that the broadly-drafted § 101 included certain types of business methods, thereby making such business methods patent-eligible. But these inventions still needed to satisfy the other statutory requirements of patentability, which are indeed "serious limits" that prevent the patenting of just any useful result.

"This allowed for a period of more than a decade during which the U.S. Patent Office issued, and the courts enforced, all kinds of ridiculous patents."

Deceptive. Again, a vacuous statement. The USPTO has always issued patents that it should not and still does. The USPTO also makes it unduly hard to obtain patents on legitimate inventions. There is no such thing as a ridiculous patent, only patents that are valid and those that are invalid. And making this determination requires more work than just reading the title or abstract.

"Several Supreme Court decisions eventually limited the power of bad patents."

Deceptive. Another ill-defined characterization. Yes, the Alice Corp. v. CLS Bank case, among others, made it harder to obtain certain types of patents, including vaguely-claimed business methods as well as many that represent legitimate technical inventions.

"Most importantly, the Supreme Court's 2014 Alice Corp. v. CLS Bank decision made a clear rule—just adding 'on a computer' to an abstract idea isn't enough to make it patentable."

False. First of all, this is a poor characterization of Alice, as the rule is much more nuanced than that. But the larger issue is that the Alice decision is notoriously vague, confusing and unworkable in practice. Eight years later, the Federal Circuit judges still argue about what it means and how to interpret it — and these are not minor disputes. The distance between their positions on Alice can be measured in astronomical units.

"The Alice Corp. decision was not a panacea. It did not eliminate the serious problem of patent trolls—that is, companies that have no products or services, but simply sue and threaten others over patents. But it did put a big dent in the patent trolling business. Vaguely worded software patents can still be used to extort money from software developers and small businesses. But when those patents can be challenged in court, they now rarely survive."

Mostly True. Well, finally something that Mr. Mullin and I almost agree about. But why the negative view of software patents? The modern economy is largely driven by software, so protecting the rights of innovators from copyists and efficient infringers should be important to a policy analyst. Besides, is software inherently horrible? Why not pick on inventions using plastic instead?

"That's been a huge benefit for individuals and small businesses. Our 'Saved by Alice' project details the stories of several small businesses that managed to overcome unjustified patent troll demands because of the Alice Corp. precedent."

False. A recent paper by Mark Lemley and Samantha Zyontz concludes that "[once in court] the entities most likely to lose their patents at this stage are not patent trolls but individual inventors and inventor-started companies." Oops. Further, the Saved by Alice project currently lists just nine stories — this is anecdotal evidence at best and is not statistically significant.

"It's now been eight years since the Alice Corp. decision, and judges have thrown out hundreds of bad patents that couldn't stand up to this test. It's likely that many more bad patents have been abandoned because their owners know they can't keep using them to threaten people. The patents knocked down by Alice Corp. include [list]"

Deceptive. Once more, whether a patent should be considered "bad" is subjective. Further, Mr. Mullin complains about aggressive litigation tactics, which is a separate issue from whether a patent should or should not have been granted.

"Ten years ago, there weren't effective legal mechanisms to throw out the worst types of patents. If someone targeted by a patent troll felt the patent was wrongly granted, they'd likely have to pay millions of dollars in patent litigation costs just to take their chances in front of a jury."

False. Even ten years ago, few patent cases made it to jury trial. Many cases were effectively decided by a judge's Markman ruling or on summary judgment. And cases with poorly-drafted complaints could be dismissed on the pleadings. Further, we are less than one month away from the ten-year anniversary of when the USPTO's inter partes review (IPR) proceedings began, a process that can be used to pause litigation while the USPTO reevaluates the validity of a patent.

"The Tillis bill will make it easier to use exactly the types of weak, overbroad patents that often threaten startups and small businesses."

False. The bill's text is vague enough that it could end up being a codification of some of the worst aspects of Alice (the ones that Mr. Mullin probably likes), such as the USPTO refusing to grant patents on innovative technologies and courts invalidating patents based on nonsensical reasoning.

"Since the Alice Corp. decision, it's much harder to demand money using questionable patents. That's why patent trolls, among others, don't like the decision, and would like to see a bill like this pass to override it. But the Senate should not grant this wish."

Deceptive. It is harder to stop infringement of any patent thanks to Alice, because that case and the Federal Circuit's expansion of the exclusions to eligibility made it easier to invalidate patents, period. Overruling Alice would be a step in the right direction but the Tillis bill falls short.

"The Tillis bill encodes a version of the old rule that virtually any kind of 'business method' is worthy of a patent. It explicitly allows for patents on 'non-technological economic, financial, business, social, cultural, or artistic process,' as long as those are embodied in a 'machine or manufacture.' In other words, you can take basic human 'methods' of doing business, or even socializing, and just add a generic purpose computer (or another machine). The Tillis bill does specify that the machine must do more than 'merely storing or executing,' but that's an unclear if not meaningless narrowing. That will merely allow patent lawyers to avoid using those exact verbs—'storing' and 'executing'—when they're writing patents.

Deceptive. If it were only that easy. This provision of the bill is unclear and if passed as is, the courts (especially the Supreme Court) are likely to call upon stare decisis to keep things as they are under Alice. In fact, I have yet to hear from a patent attorney who can describe what is or is not patentable based on the proposed language.

"Software patents are drafted by patent lawyers, who have come up with a lot more ways to describe manipulating data than just 'storing' and 'executing.' To take just one of the stupid patents above, the first claim in the Ultramercial ad-watching patent described an Internet-based process of 'receiving' media products, 'selecting' a sponsor message, 'providing' the media to the public for sale, 'restricting' general access, 'facilitating' display of the ad, 'recording the transaction,' and also 'receiving payment.'"

Deceptive. The term "stupid patent" is just as vacuous and overused as the term "bad patent". If you don't like it, just say so. There is much more to the Ultramercial claims, which should have been deemed patent-eligible as they materially change a technological process. Also, all of the verbs that Mr. Mullin lists are not magic words that suddenly make unpatentable claims eligible for patenting. If there is anything that we have learned over the eight years since Alice, it is that there is no rote procedure for drafting successful software claims when the evaluation of said claims is largely subjective.

"The Tillis bill even implicitly authorizes patents on a 'mental process,' saying the only kind that wouldn't be eligible is one that takes place 'solely in the human mind.' That would seem to imply that even adding trivial steps like writing things down or communicating information could make a 'mental process' patentable."

Deceptive. The problem with the current mental process exclusion to patentability is that literally everything that a computer does boils down to a handful of calculations performed by a microprocessor. Theoretically, a human could perform these operations in their mind, though too slowly to be practically useful. Nonetheless, mental process doctrine has been used to refuse applicants patents on otherwise innovative and complex software inventions. Machine learning, a particularly critical competitive technology for the U.S., is often targeted in this fashion.

"If Congress passes the Patent Eligibility Restoration Act, it will destroy one of our best safeguards against abusive patents. The Tillis bill will give an explicit green light to the most aggressive patent trolls, the funders of their litigation, and the attorneys who work for them. They'll get more outrageous business method patents, and use them to demand payments from working software developers."

Deceptive. As noted above, it is quite unclear whether the Tillis bill would have this impact, and aggressive litigation is an orthogonal issue with respect to patent eligibility. Limiting the scope of what is patentable would make it harder for bad faith actors to disrupt software companies, but it would also prevent small companies from stopping the giants from stealing inventions. The sword is double-edged, so let's be honest about how it cuts both ways.

Mr. Mullin goes on to criticize the bill's partial codification of Association for Molecular Pathology v. Myriad Genetics, in that it prevents unmodified natural DNA from being patented but allows the patenting of certain modifications. I'll leave rebuttal of his claims in this area to my learned colleagues with advanced life sciences degrees (something that neither I nor Mr. Mullin have).

While everyone is entitled to their opinions and adversarial debate can be a healthy predecessor of progress, Mr. Mullin's unsupported claims, playing loose with the facts, and outright falsehoods are dangerous. A layperson reading Mr. Mullin's article might assume that it is easy to get a broad patent granted on something that you did not invent. This is not the case.

In the patent community, we have a duty to accurately represent the current state of the law, as well as the potential unintended consequences of proposed litigation. In this way, policymakers can reach informed conclusions based on rational debate rather than sky-is-falling histrionics. Taking advice from someone who touts being the "Chair to Eliminate Stupid Patents" is ill-advised if the goal is to avoid glaring bias.
Click-to-Call Technologies LP v. Ingenio, Inc. (Fed. Cir. 2022)

August 23, 2022

By Kevin E. Noonan —

For most of the past decade, the Supreme Court has been marking out the metes and bounds of the Patent Trial and Appeal Board's execution of the post-grant review provisions of the Leahy-Smith America Invents Act, particularly with regard to inter partes reviews (see "Oil States Energy Services, LLC. v. Greene's Energy Group, LLC (2018)"; "Return Mail, Inc. v. U.S. Postal Service (2019)"; "SAS Institute Inc. v. Iancu (2018)"; "Cuozzo Speed Technologies, LLC v. Lee (2016)"; and "Teva Pharmaceuticals USA, Inc. v. Sandoz Inc. (2015)"). In its most recent decision, Thryv, Inc. v. Click-to-Call Technologies, LP (2020), the Court ruled that 35 U.S.C. § 315(b), which precludes a petitioner from filing an inter partes review petition more than one year after being served with a complaint alleging infringement, are barred from judicial review under 35 U.S.C. § 314(d). The Court's decision reversed an en banc Federal Circuit opinion that the time bar was reviewable.

Last week, the Federal Circuit heard an appeal from a related patent infringement lawsuit between the parties that had been stayed during the IPR and lengthy appeals they spawned. In the opinion, Click-to-Call Technologies LP v. Ingenio, Inc., the Federal Circuit held that infringement defendant Ingenio was barred by the statutory estoppel codified at 35 U.S.C. § 315(e)(2) from challenging validity of a claim for which the PTAB refused to institute the IPR, under what the Court characterized as "a rather unusual set of facts."

As set forth in the opinion, in response to Click's assertion of patent infringement of its U.S. Patent No. 5,818,836, Ingenio sought to institute an IPR based on two grounds: one for anticipation and/or obviousness over the Dezonno reference, and the other for obviousness over the Freeman reference. The Board instituted the IPR only on the first Dezonno ground; as a consequence only one claim (claim 27) was not within the scope of declared IPR, and the Board ultimately issued a Final Written Decision that all the challenged claims were invalid.

However, the Supreme Court's decision in SAS Institute v. Iancu intervened, in which the Court held the PTAB was compelled to render a Final Written Decision (FWD) on all claims challenged by a petitioner in its IPR petition. Ingenio did not respond to this decision by seeking remand at the Board to include claim 27 in the IPR (it being relevant to note that the Court's SAS decision did not mandate that the Board arrive at any different conclusion regarding validity of claim 27 and that if the Board had joined claim 27 it could have and likely would have held Ingenio had not shown this claim to be invalid in view of the Freeman reference).

After the District Court lifted the stay at the final conclusion of the IPR and its appeals, Ingenio moved for summary judgment that claim 27 was invalid based on the Dezonno reference. The District Court rejected Click's argument that Ingenio was estopped under § 315(e)(2) from challenging validity of claim 27, and granted summary judgment of invalidity against Click; this was the principal issue on appeal. (A secondary issue was whether the District Court had abused its discretion by refusing to allow Click to amend its complaint to include two additional '836 claims not involved in the IPR; these claims had been asserted in Click's complaint but removed from consideration pursuant to the district court's order that Click reduce the number of claims to be tried, prior to the IPR being instituted.)

The Federal Circuit reversed-in-part (as to the estoppel issue), affirmed-in-part (as to the abuse of discretion issue) and remanded, in an opinion by Judge Stoll joined by Judges Schall and Cunningham. The District Court erred, according to the Federal Circuit, by addressing Click's estoppel argument solely under the common law principle of issue preclusion, and failing to address Click's argument that the estoppel arose under the statute. In addition, the panel found error in the District Court's reliance on Click's failure to satisfy the requirement for common law estoppel that the "issue must have been fully and vigorously litigated in the prior action," citing United States v. Shanbaum, 10 F.3d 305, 311 (5th Cir. 1994). This requirement can be found nowhere in § 315(e)(2) and moreover it would have been unreasonable to apply this requirement in view of the provision that the estoppel arises on grounds that "reasonably could have [been] raised" by the express language of the statute. Reaching what the opinion calls the merits of Click's estoppel argument, the opinion asserts that invalidity of claim 27 over the Dezonno reference is one that Ingenio "reasonably could have raised" in the IPR (but did not). The Court also rejected Ingenio's argument that the estoppel should not apply because the Board had not rendered a FWD against that claim, based on a statutory construction argument regarding § 315(e)(2). The opinion's basis for finding the estoppel applied was in the context of what it termed "the unusual procedural posture" of this case; the opinion notes:

Ingenio included claim 27 in its [IPR] petition, and the IPR did result in a final written decision[ as to that claim]. The fact that the Board, due to a legal error corrected by SAS, failed to include claim 27 in its final written decision does not absolve Ingenio of the estoppel triggered by its choice to challenge claim 27 at the Board.

The Federal Circuit also indicated the panel was influenced by the equities here, because "Ingenio was not helpless to remedy the Board's institution error" and could have moved to have claim 27 included in the IPR after the SAS decision was handed down. "Ingenio's choice to leave unremedied the Board's mistake does not shield it from estoppel as to a claim it included in its IPR petition" according to the Court. The case was remanded for the District Court to deny Ingenio's motion and hold that clam 27 was not invalid as being anticipated by the Dezonno reference.

Turning to the District Court's denial of Click's motion to amend its complaint to include claims not involved in the IPR, the Federal Circuit based its determination that this was not an abuse of discretion in part because it implicated the district court's management of its docket, for which the opinion states its review uses "a highly deferential lens," citing 5th Circuit (S&W Enters., L.L.C. v. SouthTrust Bank of Ala., NA, 315 F.3d 533, 535 (5th Cir. 2003)), as well as Federal Circuit (Alpek Polyester, S.A. de C.V. v. Polymetrix AG, No. 2021-1706, 2021 WL 5974163, at *8 (Fed. Cir. Dec. 16, 2021)) precedent. Another basis for the Court's opinion was the length of time the case was pending prior to Click's motion. As noted in the opinion, Click filed its lawsuit against Ingenio on May 29, 2012 and the District Court granted Ingenio's motion to stay on December 5, 2013. The stay was in place for more than six years as noted in the opinion and during that time there were several status reports filed with the District Court in which Click never asked for leave to add additional claims. And the Board's Final Written Decision issued in 2014, informing Click of the Board's reasoning in finding the challenged claims unpatentable over the Dezonno reference. Yet Click "did not request leave to amend its asserted claims until six years later" in response to Ingenio's summary judgment motion (the panel stating that Click's request was "cursory" and lacking in justification for the request). These facts, according to the Court, supported their conclusion that the District Court did not abuse its discretion in denying Click's motion to amend. Specifically, the Court rejected Click's reliance on S&W Enters., L.L.C. v. SouthTrust Bank of Ala., NA, inter alia, because Click's terse and cursory motion did not itself cite S&W Enterprises in support of its motion ("We will not fault the district court for failing to apply a case that Click-to-Call did not even present to the district court") and the panel refused to consider the S&W Enterprises factors for the first time on appeal.

The Court remanded the case to the District Court for further considerations, which under the circumstances should be limited to infringement.

Click-to-Call Technologies LP v. Ingenio, Inc. (Fed. Cir. 2022)
Panel: Circuit Judges Stoll, Schall, and Cunningham
Opinion by Circuit Judge Stoll

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