A Myriad of Questions for Biofuel Patents
The U.S. Patent Laws have long embraced the patent eligibility of biotech inventions…although biotech patent law is viewed by some as “different” than other subject areas. Patent eligibility is governed by 35 U.S.C §101. Under this statute, nucleic acids, proteins, and other naturally occurring substances were considered patentable as long as they were “isolated.” This is because such materials are typically not found isolated in nature, but rather, are the products of human intervention. Thus, claims to biological sequences are drafted to isolated molecules that are defined by an activity and a sequence:
1. An isolated nucleic acid encoding a protein having Enzyme X activity, wherein said isolated nucleic acid has a nucleotide sequence of at least 90% identity to SEQ ID NO:1.
2. An isolated protein encoded by the nucleic acid of claim 1.
3. An isolated protein having Enzyme X activity, wherein said protein has an amino acid sequence of at least 90% identity to SEQ ID NO:2.
The U.S. Patent and Trademark Office (“USPTO”) has been issuing such claims for decades. Federal Courts have been upholding them (so long as they meet the other patentability requirements).
A big test for patent eligibility, at least for nucleic acids, came with the advent of highly-automated cloning, sequencing, and characterization of biological sequences. Bioinformatic technologies allowed for the storage and analysis of vast amounts of sequence data and methods for grouping sequences into functional families. Such “in silica” data were often provided in patent specifications with little or no “wet lab” confirmation that the sequences have utility as required by §101. In response, the USPTO implemented utility guidelines for examining sequence applications. To allow claims to such sequences, their utility must be specific (well-defined and of particular benefit to the public), substantial (real world), and credible.
In 1980, the Supreme Court held that a live, human-made microorganism is patent eligible subject matter. The Court stated, however, that laws of nature are not. The latest installment in the Supreme Court’s current patent eligibility saga is AMP v. Myriad. The relevant question presented in Myriad asked whether human genes are patent eligible. The Court held that a naturally-occurring DNA segment is a product of nature and not patent eligible merely because it was isolated. The Court held that cDNA is patent eligible because it is synthetic. The Court reasoned that cDNA is "an exons-only molecule, which is not naturally occurring"
Biofuel technologies, from processing feedstocks to fermenting final products, may rely on nucleic acids that were isolated from nature or obtained as cDNA. The distinction that isolated DNA is not patent eligible but cDNA is raises many questions for Biofuel patents. For instance, are isolated, non-human sequences patent eligible? The patent laws do not distinguish between human and non-human sources in deciding patent eligibility. If isolated human sequences are not patent eligible, analogous bacterial or fungal sequences may not be either.
Furthermore, what is the status of cDNA molecules derived from genes that do not have introns (e.g. all bacterial genes)? In the lab, cDNA chemical properties and sequences are indistinguishable from “isolated, naturally-occurring DNA molecules.” The “synthetic v. isolated” distinction is entirely unclear. Moreover, the Court did not take an opinion on other biological materials isolated from nature such as proteins, hormones, or other commercially-important biochemical materials. Likewise, the Court offers no guidance for synthetic versions of naturally-occurring substances.
In light of the Myriad decision, the USPTO is revising its examination guidelines. Moreover, it could take years for the courts to sort these questions out. One should not assume, however, that claims that recite “isolated” nucleic acids or proteins are automatically invalid. Engineered sequences, cells, and methods should typically fall outside the reach of Myriad. Traditional claim construction principles will apply when deciding the meaning of claims and whether they are truly directed to patent-ineligible subject matter.
My advice to biofuel patent owners is to review their patent estates. They should adjust their claim strategies for pending applications to keep them in line with our current understanding of how Myriad has shifted the patent landscape. Likewise, such patentees should adjust their economic models and strategies because there may be new competitors in their commercial space.
Likewise, companies that seek to enter new biofuel markets or develop new technologies should take a new look at patent claims directed to isolated biological materials. They may find new market opportunities that did not exist in the pre-Myriad world. The formula for assessing patent risks has clearly changed. Until the courts sort out the questions posed above, all patent risk scenarios should be run under two competing assumptions: a more restrictive view of patent eligibility and a more expansive one.
If anybody would like to further discuss this with me, please do not hesitate to leave a comment or contact me by telephone or email.
 Ass'n for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 1747 (U.S. 2013)
 http://www.uspto.gov/web/menu/utility.pdf; Flattmann and Kaplan, Patenting Expressed Sequence Tags and Single Nucleotide Polymorphisms, Nature Biotechnology 19:683-684 (2001) (Part 1); Flattmann and Kaplan, Patenting Expressed Sequence Tags and Single Nucleotide Polymorphisms, Nature Biotechnology 19:777-779 (2001) (Part 2).
 Diamond v. Chakrabarty, 447 U.S. 303, 309 (1980)
Bilski v. Kappos, 130 S. Ct. 3218 (US 2010); Mayo Collaborative Servs. v. Prometheus Labs., Inc., 132 S. Ct. 1289 (U.S. 2012)
 The Court was careful state that the opinion is not directed to method claims, new "applications of knowledge" for BRCA1 and BRCA2 genes at issue in Myriad, and DNA sequence variants.
 I note that other countries take a different view of patent eligibility. For instance, the European Union holds biological materials isolated from nature or produced by technical processes patentable.