Zinc Fingers Could Point to Future Cures, But Gene Patents Could Get In The Way

Jake Meyer by Jake Meyer

A December 29th, 2009 article in The New York Times describes a new technique that allows for the editing of human genes.  The technique uses natural agents called "zinc fingers," two loops of protein that can recognize specific sequences of DNA have multiple potential uses.  Zinc fingers could be used in the future to engineer new crop plants, treat human diseases, and to make alterations to sperm or egg cells –- alterations that would be inheritable. 

Zinc fingers can be used to turn on or off a gene at a specific DNA site.  An agent that turns the gene on or off can be linked to the zinc finger, which recognized and attaches to the specific DNA site.  But zinc fingers have another use which makes them a promising technology for gene therapy –- they can cut out and insert DNA from the gene sequence.

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Monsanto Hitting a Genetically Engineered Rough Patch

Patrick-Bickleyby Patrick Bickley

Although it may be hard to feel bad for a $44 billion company dominating its industry with over $11 billion in sales last year, poor Monsanto has had a rough couple of months.  Monsanto has dominated the seed market through its sales and licensing of its genetically modified seeds.  In the 1970’s, Monsanto patented a new herbicide called Roundup that quickly killed weeds and any other plants prior to planting seeds.  In the 1990’s, Monsanto isolated a gene, called CPS4, from Roundup resistant bacteria found in the company’s waste ponds and placed the gene into its patented soybeans and corn.  These Roundup Ready seeds allowed farmers to continue using Roundup even after planting.

First, in September, Judge Jeffery S. White in the Northern District of California ruled that the U.S. Department of Agriculture failed to assess the environmental impact of genetically engineered sugar beets before approving the crop for farmers to use, according to The New York Times.  The next issue to be decided in the case is what remedy should be imposed.  One possible option is ban on planting the crops until the Department of Agriculture completes the environmental impact statement.  The ban is possible, even though the plants have already been widely adopted by farmers (one survey indicated that 95% of all sugar beets planted this year were genetically engineered), a ban on planting the crops until an environmental impact statement is complete is possible.  In 2007, a different judge in the Northern District of California ruled that genetically modified alfalfa could no longer be planted until the environmental impact statement was completed.  Today, the statement has still not been completed, and the modified alfalfa is, “with rare exceptions,” not being grown.

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Supreme Court Ponders A Method of Keeping Students Awake in Anti-Trust Class and a Method of Whispering to Horses

Jake Meyer by Jake Meyer

On November 9, 2009, the U.S. Supreme Court heard oral arguments in the case Bilski v. Kappos.  This important patent case asks the question: what is the proper test for determining what is patentable subject matter for a process?  Patents are not supposed to be granted on mental processes, but Bilski’s claims are directed to a method of hedging risk in commodities trading, which the Federal Circuit has states is a “process wherein all of the process steps may be performed entirely in the human mind.”

In In re Bilski, the Federal Circuit announced that the proper test to determine whether a process was patentable subject matter under 35 U.S.C. § 101, was the machine-or-transformation test, stating that: a “process is surely patent-eligible under 101 if: (1) it is tied to a particular machine or apparatus, or (2) it transforms a particular article into a different state or thing.”  The Federal Circuit has since applied the machine-or-transformation test in a biotechnology case, Prometheus v. Mayo, which I previously blogged about.

Under the test, the Federal Circuit held that Bilski’s claims were not patentable because the claims were not tied to a machine and did not transform an article into a different state or thing.  Claims such as Bilski’s, are considered “business method” claims, and so the Court was also asked the question “[w]hether the Federal Circuit’s ‘machine-or-transformation’ test for patent eligibility, which effectively forecloses meaningful patent protection to many business methods, contradicts the clear Congressional intent that patents protect ‘method[s] of doing or conducting business.'” 35 U.S.C. § 273.  The Justices made many interesting quotes during the oral argument which shed light on the interesting and fundamental patent law question: what is patentable subject matter?

At oral argument, Bilski’s attorney, J. Michael Jakes, argued for a less rigid rule than the machine-or transformation test.

MR. JAKES: . . . I think the question can be avoided, because we don’t need a rigid test of this type based on machine-or-transformation. The question we are looking at and should be looking at is: Are we trying to patent an abstract idea?

At oral argument, the Justices pushed Bilski’s attorney, J. Michael Jakes, by giving seemingly ludicrous examples of things that would be patentable under a more liberal test that did not require a machine-or-transformation.

JUSTICE BREYER: So you are going to answer this question yes. You know, I have a great, wonderful, really original method of teaching antitrust law, and it kept 80 percent of the students awake. They learned things –
JUSTICE BREYER: It was fabulous. And I could probably have reduced it to a set of steps and other teachers could have followed it. That you are going to say is patentable, too?
MR. JAKES: Potentially.

Scalia searched for some historical context.

JUSTICE SCALIA: You know, you mention that there are all these — these new areas that didn’t exist in the past because of modern business and what-not, but there are also areas that existed in the past that don’t exist today. Let’s take training horses. Don’t you think that — that some people, horse whisperers or others, had some, you know, some insights into the best way to train horses? And that should have been patentable on your theory.
MR. JAKES: They might have, yes.
JUSTICE SCALIA: Well, why didn’t anybody patent those things?

Breyer brought up concerns of the costs of patents on information.

JUSTICE BREYER: That’s exactly what I -maybe I can get you to inadvertently help my — my hypothesis you don’t like. That’s why I say it’s inadvertent.
You said there are two things. There are actually four things in the patent law which everyone accepts. There are two that are plus and two that are minus. And the two that are plus is by giving people a monopoly, you get them to produce more. As you said, you get them to disclose.
The two minuses are they charge a higher price, so people use the product less; and moreover, the act of getting permissions and having to get permission can really slow things down and destroy advance. So there is a balance.
In the nineteenth century, they made it one way with respect to machines. Now you’re telling us: Make it today in respect to information. And if you ask
me as a person how to make that balance in respect to information, if I am honest, I have to tell you: I don’t know. And I don’t know whether across the board or in this area or that area patent protection will do no harm or more harm than good.
So that’s the true situation in which I find myself in respect to your argument. And it’s in respect to that, I would say: All right, so what do I do?

Sotomayor was also concerned with the cost patents exact on the free flow of information.

JUSTICE SOTOMAYOR: But a patent limits the free flow of information. It requires licensing fees and other steps, legal steps. So you can’t argue that your definition is improving the free flow of information.

Sotomayor gave some attention to amici’s concern that a broad ruling in Bilski may hurt the biomedical world.

JUSTICE SOTOMAYOR: How about if we say something as simple as patent law doesn’t cover business matters instead of what the Federal circuit has begun to say, which is technology is tied to a machine or a transformation of the substance, but I have no idea what the limits of that ruling will impose in the computer world, in the biomedical world, all of the amici who are talking about how it will destroy industries? If we are unsure about that, wouldn’t the safer practice be simply to say it doesn’t involve business methods?

Justices Breyer and Sotomayor are right to be concerned about the effect of patents on the free flow of information.  This is particularly troublesome when patents are on information itself.  For example, with patents on gene sequences, the “invention” is the information.  It’s the A’s, C’s, T’s, and G’s that make up the sequence that are of value, and the disclosure of this information is meaningless because the patent prevents it from being built upon.

At oral argument in Bilski, the lawyer representing the patent office, Malcolm L. Stewart, argued for keeping the machine or transformation test, but to leave it open to an exception for unforeseen technologies.

MR. STEWART: Well, I think the Court could say — could do essentially what was done in Benson and Flook, namely acknowledge that there had never been a case up to this point in which a process had been held patent eligible that didn’t involve a machine or a transformation. It could leave open the possibility that some new and as yet unforeseen technology could necessitate the creation of an exception.

The government is right to be concerned about limiting unforeseen technologies, and the machine-or-transformation test could be an effective test for determining patentable subject matter of processes.  However, the Federal Circuit’s decision in Prometheus showed that the Federal Circuit considers the machine-or-transformation test to be a low hurdle, by holding that the physical step not central to the claim was transformative.  If the Supreme Court decides to keep the machine-or-transformation test, the Court shall have to give guidance to the Federal Circuit on what is to be considered transformative and what is to be considered a machine or else clever claim drafting can add a computer (machine) or other non-essential step (which could potentially be argued to be transformative) to any process claim and make it patentable, which would come with the high cost of limiting the free flow of information.

Motion to Dismiss Denied in Breast Cancer Case: The USPTO is a Defendant in a Case Challenging the Constitutionality of Patents Granted by the USPTO

Jake Meyer by Jake Meyer

November 1, 2009, Judge Sweet of the United States District Court in the Southern District of New York issued an opinion in Association for Molecular Pathology v. United States Patent and Trademark Office.  The plaintiffs in the case, which were previously blogged about here, challenge the constitutionality and validity of patents on the BRCA1 and BRCA2 breast cancer genes owned by Myriad.  The defendants — the U.S. Patent and Trademark Office (USPTO), Myriad Genetics, and the Directors of the Utah Research Foundation — moved to dismiss the case for standing and jurisdictional issues.  Judge Sweet denied all motions to dismiss, finding there was both standing and jurisdiction.

The inclusion of the USPTO as a defendant in this case is unique to this case, as the USPTO has never been a party to a lawsuit in which the constitutionality of patents issued by the USPTO were brought into question.  The USPTO moved to dismiss for lack of subject matter jurisdiction (the USPTO also moved to dismiss for lack of standing) arguing that it had a comprehensive statutory scheme in place to redress violations of the Patent Act.  However, the cases the USPTO cited involved claims that alleged statutory violations that the Patent Act provided a remedy for.  Judge Sweet found that there was no comparable statutory scheme that provided remedies for constitutional violations.  Judge Sweet found that there was subject matter jurisdiction over the USPTO citing the novel circumstances of the action, the absence of any remedy provided in the Patent Act, and the importance of the constitutional rights asserted by the plaintiffs.

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I.B.M. Seeking to Make Sequencing of Personal Genome Available for the Low Low Price of $1,000 (Plus Millions in Royalties to Patent Holders)

Jake Meyer by Jake Meyer

I.B.M. recently announced its plans to join the race to sequence the genome for $1,000.  I.B.M. joins seventeen other companies in the race to sequence the gene.  Currently the cost to sequence the human genome ranges between $5,000 and $50,000, but these companies are yet to successfully sequence the entire genome of an individual.  I.B.M. hopes to ultimately bring the price as low as $100 to sequence an individual's entire genome.  The goal is to build a machine that can sequence an individual's genome – three billion base pairs – in several hours.  This will provide the genetic information needed by an individual for personalized diagnostic and treatment uses. 

I.B.M. is using its expertise in semiconductor manufacturing, computing, and material science to design a gene sequencer with increased speed and accuracy.  I.B.M.'s sequencer revolves around a nanoscale electric device.  The device uses an electric field to pull the DNA strand through a 3 nanometer hole in a surface, at which point the electric field holds the DNA in place for a fraction of a second while the order of the nucleotide bases (adenine, guanine, cytosine, or thymine) is determined.  After the nucleotide bases are determined, the DNA strand is pulled further through the hole and the order of the next nucleotide bases are determined.

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Prometheus Labs, Inc. v. Mayo – Administering a Drug is Transformative

Jake Meyer by Jake Meyer

Recently the Federal Circuit ruled on the case Prometheus Labs, Inc. v. Mayo, a case involving 35 U.S.C. §101 subject matter.  Prometheus came before the Federal Circuit as an appeal from a decision from the United States District Court for the Southern District of California to grant summary judgment of invalidity of Prometheus’s patents (U.S. Patents 6,355,623 and 6,680,302) finding that the claims were directed to non-statutory subject matter.   The case was a little unusual in that it was decided by two Federal Circuit judges, Michel and Lourie, and District Court Judge — Judge Clark of the United States District Court for the Eastern District of Texas.  The patents claim methods for calibrating the proper dosage of thiopurine drugs, which are used for treating autoimmune diseases.  Since the patents are directed to a process and the case involves a subject matter inquiry, the Federal Circuit was able to revisit In re Bilski (a case now before the Supreme Court) and apply the test for subject matter eligibility of a process the Federal Circuit laid out in Bilski.

Thiopurine drugs are used to treat inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis.  Thiopurine drugs include 6-mercaptopurine (6-MP), and azathiopurine, which upon administration to the patient converts to 6-MP.  The body breaks down 6-MP into different metabolites, such as 6-methyl-mercaptopurine (6-MMP) and 6-thioguanine (6-TG).  Prometheus’s patents involve the measurement of these metabolites.  For example, claim 1 of patent 6,355,623 is representative of the claims in the Prometheus:

1. A method of optimizing therapeutic efficacy for treatment of an immune-mediated gastrointestinal disorder, comprising:
(a) administering a drug providing 6-thioguanine to a subject having said immune-mediated gastrointestinal disorder; and
(b) determining the level of 6-thioguanine in said subject having said immune-mediated gastrointestinal disorder,
wherein the level of 6-thioguanine less than about 230 pmol per 8.times.10.sup.8 red blood cells indicates a need to increase the amount of said drug subsequently administered to said subject and
wherein the level of 6-thioguanine greater than about 400 pmol per 8.times.10.sup.8 red blood cells indicates a need to decrease the amount of said drug subsequently administered to said subject.

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Patent Infringement Case May Be Damaging to Microsoft and My Preferred Word Processor

Jake Meyer by Jake Meyer

Microsoft is currently involved in a patent infringement case involving its word processor program Microsoft Word.  The outcome of this case could determine the fate of Microsoft's most well-known software.  In fact, this very blog post was composed on Microsoft Word.

Microsoft's Word program allegedly infringes Canadian software developer i4i's U.S. Patent No. 5,787,449.  The asserted claim (claim 14) of this patent is directed to "markup languages" for computers.  A markup language inserts "tags" that indicate how a text should be displayed between the tags.  XML, HTML, and SGML are all examples of markup languages.  Microsoft’s brief to the Federal Circuit gives an example of markup language. "For example, <Para> is a computer markup code that indicates the start of a paragraph and </Para> indicates the end of a paragraph."  Claim 14 claims this markup language as a method for producing a "map of metacodes":

A method for producing a first map of metacodes and their addresses of use in association with mapped content and stored in distinct map storage means, the method comprising: providing the mapped content to mapped content storage means; providing a menu of metacodes; compiling a map of the metacodes in the distinct storage means, by locating, detecting and addressing the metacodes; and providing the document as the content of the document and the metacode map of the document.

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Will Patent Court Police the Boundaries of the Statute?: Federal Circuit to Look at Written Description Requirement

Jake Meyer by Jake Meyer

A panel of Federal Circuit judges previously heard the case of Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co., 2007 WL 2712087 (Fed. Cir. 2009) and held that Ariad failed to provide adequate written description for its claims to methods of the regulation of the expression of certain genes.  The Federal Circuit has granted a request to hear the case Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co., en banc and in doing so will interpret a section of the Patent Act.  The questions before the Federal Circuit en banc are now:

1. Whether 35 U.S.C. § 112, paragraph 1, contains a written description requirement separate from enablement?
2. If a separate written description requirement is set forth in the statute, what is the scope and purpose of the requirement?

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Dyslexia Gene eneG aixelsyD

Jake Meyer by Jake Meyer

The other day I while doing some patent law related research, I stumbled across a patent in the U.S. Patent and Trademark's patent database on a gene linked to dyslexia—U.S. Patent No. 7,355,022.  Dyslexia has been defined as a learning disability.  It can manifest itself in many different ways, but usually appears as some type of difficulty with reading and/or writing. 

After I found the patent on a dyslexia gene, I started to think about the types of inventions a company licensing this patent might be.  After a gene is "discovered," lab tests for the gene can be developed.  These genetic tests could be used to determine if someone has this dyslexia gene and therefore a predisposition to dyslexia.  Tests could also be used to preselect embryos to help ensure a child might be born without dyslexia.  Or perhaps in the future genetic therapies or a cure to dyslexia could be found. 

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“Generic” Versions of Expensive Biologic Drugs Would Benefit Consumers

Patrick-BickleyGUEST BLOGGER Pat Bickley

Competition from generic drugs has substantially reduced the prices of many prescription drugs.  However, under current law, the FDA can only apply the expedited testing of a generic designation to certain classes of drugs, generally those that are chemically synthesized, small-molecule products.  Larger and more complex drugs, such as biologics, are not allowed to receive generic designations. Biologics are protein-based and produced in living cells.  They also tend to be much more expensive.  Annual costs can be as high as $48,000 for the breast cancer drug Herceptin and $20,000 for the rheumatoid arthritis drug Remicade.  Manufacturers of biologics, such as Amgen and Genentech, justify these costs as necessary to recoup their substantial investments in developing and gaining approval for the drug.

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