TUTORIAL IT

Amicus Brief Filed By Alnylam Pharmaceuticals Argues That Funk Bros Is About Obviousness Not Patent Eligibility

Alnylam Pharmaceuticals is a biopharmaceutical company based in Cambridge, Massachusetts focused on developing synthetic "small interfering RNAs" (SiRNAs) as therapeutic agents. It has filed an amicus curiae brief in the Myriad gene patent case (AMP v. US PTO) that makes a number of insightful points, particularly in attempting to "debunk myths of Funk Brothers Seed Co. v. Kalo Inoculant Co."

Funk Brothers is generally assumed to be a case about patent eligibility. However, Alnylam points out that Funk Brothers was decided by the Supreme Court in 1948, prior to the enactment of the 1952 patent statute and thus prior to 35 USC 101, which is the statutory basis for the patent eligibility doctrine. Prior to 1952, the Court used the term “invention” to refer to "inventiveness," a concept that subsequent to 1952 and the enactment of 35 USC 103 we refer to as "nonobviousness." The Court in Funk Brothers found the claimed subject matter was not the “product of invention,” but Alnylam argues that post-1952 this statement should be interpreted a finding of obviousness, not patent ineligibility.

I have always found it extremely difficult, if not impossible, to find a principled distinction between the inventions claimed in Funk Brothers and Diamond V. Chakrabarty that would justify finding only Dr. Chakrabartys invention patent eligible. In Funk Brothers, the alleged invention was a novel and useful combination, in a single inoculant, of naturally occurring microorganisms in a combination that did not exist naturally. Chakrabarty’s invention was a novel and useful combination, in a single microorganism, of naturally occurring plasmids in a combination that did not exist naturally. It is important to bear in mind that Chakrabartys invention did not involve any genetic engineering at the molecular level.

In Funk Brothers, it has been pointed out that while the combination of bacteria in a single inoculant was novel, the bacteria function in the same manner and have the same characteristics as they would have in nature. But the same can be said regarding the plasmids Dr. Chakrabarty introduced into a single microorganism. These were naturally occurring plasmids, and in the claimed microorganism they encoded the exact same proteins, and performed the exact same function as they did in their natural state.

In a nutshell, Funk Brothers was a novel combination of naturally occurring bacteria capable of achieving novel and useful function, with the bacteria functioning in the same manner as they do in nature. Chakrabarty was a novel combination of naturally occurring plasmid DNA capable of achieving novel and useful function, with the plasmid DNA functioning in the same manner as they do in nature. I dont see how one invention can be patent eligible and the other not. However, if Funk Brothers was really decided based on obviousness rather than patent eligibility, as argued by Alnylam, the two decisions are easily reconciled.

Available link for download

Ambition but Not the Gravity Kind Derek Cianfrances The Place Beyond the Pines

The Place Beyond the Pines (2012) / US / Out on DVD now / Directed By Derek Cianfrance / Written by Derek Cianfrance, Ben Coccio and Darius Marder / Starring Ryan Gosling, Bradley Cooper, Eva Mendes, Ray Liotta, Dane DeHaan, Emory Cohen, Rose Byrne

A long while ago, when I was a young, precocious and naive girl filled with a fanciful imagination, I used to think up movies in my head. Theyd end up getting far too complex and ambitious, and then Id flag that possible masterpiece, and move on to the next creation. They werent complex in the way that say, Inception is complex. They were complex in the way that they were essentially three or four movies in one, connected by the tiniest of threads.

When I sat down to watch Derek Cianfrances sophomore effort The Place Beyond the Pines, I was prepared for this movie where Ryan Gosling and Bradley Cooper would face off for, you know, the entire movie. Alas, The Place Beyond the Pines instantly reminded me of the movies I used to work tirelessly on in my brain - and this is not at all a bad thing. It is the kind of film that is thorough in its complexity, sometimes to a fault. This is not the sort of film where Ryan Gosling plays the tattooed rebel and Bradley Cooper plays the cop trying to bring him down. It is about much, much more than that.




This is essentially three films in one, with the first act focusing on Ryan Goslings motorbike riding Luke Glanton trying to provide for the son he had with Romina (Eva Mendes), which he does by robbing banks. The second act focuses on Bradley Coopers hero cop Avery Cross, as he tries to get back into the force after his big act of heroism. The last act focuses on Lukes son, Jason (Dane DeHaan) and Averys son, AJ (Emory Cohen), who cross paths fifteen years later, and the film looks at how their fathers past affects them. This is all potentially loose sort of narrative material, which couldve been crammed into two parts, or scrapped the last part altogether. However, the beauty in The Place Beyond the Pines is that it splays the story out over three parts, so each of the very different parts can be fully realised. It is just as well that it was dealt to in this way, because Cianfrance has a lot of ideas on the go. Maybe a little too many, but it is better to have too many than not enough.

The Place Beyond the Pines works most because it is ambitious. Not in the way it uses technology, or aims for a super long running time or something out of the ordinary, but in the way that it aims to comment on so many different themes and wind them up all into one story. No, it isnt perfect. I dont particularly think the story involving Ray Liottas character really served the main narrative as much as Cianfrance perhaps wanted it to, and it wasnt as closely tied as the rest of it was (and I dont say this because Liotta and I have a strange relationship). But it was as realistic as possible. Our lives arent movies. Movies have the luxury of editing lives into narratives. The Place Beyond the Pines doesnt feel like it is made up from some fantastical dream world that will give us all of the answers to humanity. It just happens to feel like something that is real. Particularly the final act, which really floored me when I first saw the film. Instead of leaving the film with just Ryan Gosling and Bradley Cooper, it dares to look at the consequences that resonate through the years. Though both Romina and Avery tuck the past away, it is interesting to see what they treat as a fragment of the past comes back to the surface in the present to their two sons. Of course, the film wouldnt have been near as effective if we didnt have the parts that just focused on Luke and Avery, but I felt like the film really came to fruition in that final act. Ambitious, yes, but it was this certain kind of uniqueness that could make The Place Beyond the Pines either wonderful to some or tiring to others. Luckily, I fell in the former category, particularly due to the great performances from Emory Cohen and especially man of the moment, Dane DeHaan.


Sure, this isnt perhaps as closely tied as a narrative as Blue Valentine was, but theres such an enigmatic beauty about this film. It has a lot to say, and doesnt choose to take out ideas in order to have an easier viewing experience. Ryan Gosling, Bradley Cooper and Eva Mendes are on the top of their games here, shedding their considerably glossy movie star exterior to create real characters, in this wonderfully life-like (well I think it is, anyway) film. Double Cianfrances down-to-Earth writing with some brilliant cinematography by Sean Bobbitt, who is perhaps most famous for being the man behind the camera on all of Steve McQueens films, and heres a film is different because it dares, without being overt about it.

Ambition bleeds through every frame of this film. And at the end of the day, its ambition that keeps everything moving forward.

How I felt about this one:

Available link for download

All that glisters is not gold

At the end of the nineteenth century, a rich gold strike near the Mexican town of Tlalpujahua meant that for a few years in the early twentieth century, it was the largest producer of gold in the world. The mine was a huge industry, and the population grew to a quarter of a million. Then, in 1937, a major landslide buried the mine, and much of the town. The mine closed, and the townspeople were forced to go elsewhere in search of work. Within ten years, the population was under a thousand.

One of the men who left was Joquaín Muñoz Orta, who in the fifties ended up in Chicago, working in a factory making artificial Christmas trees. When he returned to Mexico, he set up a workshop making first trees, and then baubles to go with them. The baubles were far more popular, and the workshop grew into a factory... which is now the fifth largest producer of baubles in the world. There is also a second bauble factory in the town, as well as over a hundred small family workshops. The population of Tlapujahua is now back up to about a quarter of a million... and around 70% of the towns economy comes from bauble-making.

I just thought that was nice. Happy New Year.

Available link for download

AMP v PTO Does Not Appear to Invalidate Very Many Gene Patent Method Claims

In this post, I explain why my recent analysis of 533 patents identified by Jensen and Murray as "gene patents" (described in a previous post) suggests the Federal Circuit’s recent decision in AMP v. PTO implicates the validity of very few gene patent method claims.

Background

As I pointed out in a blog post last December, the patent eligibility of Myriads claims to methods of detecting mutations in the BRCA gene by "analyzing" or "comparing" DNA sequences hinged entirely on the courts interpretation of the word "sequence" as it appears in the claims. In the field of molecular biology, the term "sequence" is routinely used not only to refer to the description of the chemical structure of a DNA molecule, but also to the actual DNA molecule as well.


For example, a scientist might say that "I determined the sequence of the BRCA gene." In this context, she is using the word sequence in reference to the abstract description of the order of nucleotides appearing in the gene. But the same scientist might also say that "I cloned the BRCA sequence into an expression vector," in which case she is using the term "sequence" to refer to the DNA molecule itself.

In the first example, "sequence" refers to abstract information describing a chemical structure, while in the second "sequence" is used to refer to a physical object, i.e., a specific DNA molecule. Molecular biologists are usually not bothered by the dual meaning of "sequence," because in practice the meaning of the term is understood based on the context in which it is used. However, it can lead to ambiguity, as seen in AMP v. PTO.

In AMP v. PTO, Myriad argued that as used in its claims the term "sequence" refers to an actual DNA molecule, and thus that analyzing or comparing "sequences of the BRCA gene" would involve physically manipulating and processing molecules in a manner that would render the claims patent eligible under Prometheus. I think it is clear that if the court had adopted this interpretation of "sequence" it would have upheld the validity of the claims. The ACLU plaintiffs never argued that a method claim that requires the analysis of physical DNA molecules would be patent ineligible.

Instead, as explained in a previous post, the ACLUs case was based on its argument that the term "sequence" in the claims refers to information, not to a physical molecule, and hence would cover the mental activity of analyzing or comparing genetic information. The court adopted the ACLUs interpretation of "sequence,” and ruled the claims patent ineligible for claiming nothing more than a mental step. This outcome was specifically dictated by the Federal Circuit’s earlier Prometheus decision, where it stated that a claim directed only to mental analysis of information is patent ineligible.

The Federal Circuit based its interpretation of “sequence” on its finding that Myriads patent specifications implicitly defined “sequence” broadly to cover pure information, as set forth in this excerpt from the case:

The patent specifications make clear that “sequence” does not exclusively specify a DNA molecule, but refers more broadly to the linear sequence of nucleotide bases of a DNA molecule. For example, Figure 10A–10H is described as showing the “genomic sequence of BRCA1.” ?473 patent col.5 l.66. Figure 10 does not show a physical DNA molecule; the figure lists a series of letters (Gs, As, Ts, and Cs) corresponding to the nucleotides guanine, adenine, thymine, and cytosine of a DNA molecule. Similarly, the patent specifications state that “[t]he nucleotide sequence for BRCA1 exon 4 is shown in SEQ ID NO: 11.” Id. col.53 ll.50–53. SEQ ID NO: 11 again lists a series of Gs, As, Ts, and Cs corresponding to the nucleotide sequence of BRCA1 exon 4.

Thus, Myriad’s claims might very well have been found patent eligible if the specification had defined the term "sequence" to refer only the DNA molecule itself. Alternatively, the claim probably would have been found patent eligible if it recited analyzing "DNA molecules" instead of analyzing sequences. If the claims could only be infringed by someone who physically analyzes the DNA molecule, it would certainly be patent eligible under the Federal Circuits interpretation of Bilski as set forth in Prometheus.

Claims that could be infringed by merely analyzing genetic data appear to be rare in Jensen and Murray dataset

In essence, Myriad’s method claims were patent ineligible because, as interpreted by the court, they could be infringed by analysis of genetic information. However, my research suggests that few if any of the gene patents identified by Jensen and Murray fall into this category. To the contrary, the vast majority of the claims in these patents would appear to be patent eligible.

Of the 533 patents I analyzed in my study, I only found 12 that included a claim reciting a method of analyzing a DNA sequence for a mutation or variation, and most if not all of those claims appear to require a physical manipulation of a patients DNA in order for there to be infringement.

In 8 of the 12 patents (6,395,482; 6,087,107; 6,458,541; 6,743,579; 5,830,649; 5,840,486; 5,955,265; and 6,410,226) the broadest claims specifically require obtaining a sample from a patients body, or analyzing for the genetic variation directly in a patients body.

For example, Claim 1 of US patent number 6,395,482 recites:

1. A method for determining susceptibility in a human subject to schizophrenia wherein the method comprises the steps of:

(a) removing a bodily sample from the subject, wherein the sample comprises a polynucleotide sequence of a PRODH gene;

(b) determining whether the PRODH gene of the bodily sample comprises a DNA sequence comprising a variation in SEQ ID NO:1 consisting of a T to C transition in the first position of codon 497, such that the presence of said variation in said PRODH gene is indicative of said subjects susceptibility to schizophrenia.

These eight claims would all appear to be patent eligible under AMP and Prometheus because they all involve physically manipulating a human sample obtained from patient.

The remaining four of the 12 patents (5,916,748; 6,630,304; 5,989,815; 6,432,644) are a little more ambiguous, and do not explicitly recite obtaining or analyzing a bodily sample. But arguably all of these claims do require physical manipulation of a sample, depending upon how a court interprets the claim, which will depend in part on how the claim terms were used in the patent specification

For example, Claim 1 of 6,432,644 recites:

1. A method for diagnosing the presence of a polymorphism in human KCNE1 (the coding region of which is bases 193-579 of SEQ ID NO:3) which causes long QT syndrome wherein said method is performed by means which identify the presence of said polymorphism, wherein said polymorphism is one which results in the presence of a KCNE1 polypeptide of SEQ ID NO:4 with an altered amino acid, said altered amino acid being selected from the group consisting of: a) a Leu at residue 74.

Note that this claim uses "means plus function" language, and would probably be interpreted to only cover means for identifying polymorphisms (a polymorphism is a genetic variation) that are described in the specification. If the only means for identifying polymorphisms described in the specification rely on physically analyzing DNA molecules, the claim would appear to be so-limited and thus patent eligible.

Similarly, Claim 1 of 6,630,304 recites:

1. A method of diagnosing a susceptibility to osteoporosis in an individual, comprising detecting a polymorphism in a human BMP2 gene of SEQ ID NO: 1, wherein the presence of a "T" at nucleotide position 11980 is indicative of a susceptibility to osteoporosis, compared with an individual having an "A" at nucleotide position 11980.

This claim refers to detecting a genetic variation in a "gene," as opposed to a "sequence" (the language used by Myriad). If a court were to interpret the claim limitation "detecting a polymorphism in the gene" as requiring actual analysis of a DNA molecule (which could depend upon how the term "gene" is using the specification), the claim would appear to be patent eligible. However, if the claim is interpreted to encompass detecting a polymorphism by analyzing genetic sequence data, it would appear to be patent ineligible.

Available link for download