Today’s oral arguments in Association for Molecular Pathology v. Myriad Genetics were wide-ranging–and often-times confusing. Almost all of the Justices seemed struggled with basic principles of laboratory genetics, and several seemed hung up on various points of basic patent law. Nonetheless, Myriad’s composition claims–that is, gene patent–claims seem in jeopardy. Whether that jeopardy will translate into five or more votes, however, remains to be seen.

To briefly recap the facts: In 1994, researchers at the University of Utah discovered that several mutations in the genes BRCA1 and 2 corresponded to a significantly elevated risk of breast and ovarian cancer. They patented various aspects this discovery, such as methods for using the sequence of these mutations to test for breast cancer, a kit to perform that test, and–now at issue before the Supreme Court–the “genes” themselves. In reality, the claims directed toward the genes were of a variety of types: the genes isolated from chromosome 17, the so called “isolated DNA” claims; the same genes as in the isolated DNA but missing their non-coding portions, or the cDNA (cloned DNA) claims; and primers, or short DNA sequences, 15 nucleotides in length, used to clone BRCA1 and 2. The researchers then exclusively licensed their patents to Myriad Genetics.

Out of concern, a consortium of BRCA researchers, labeled the Association of Molecular Pathology, in conjunction with the ACLU, filed suit against the PTO and Myriad Genetics to invalidate the patents. The district court had concluded that almost all of Myriad’s patents’ claims were invalid, but, on appeal, the Federal Circuit mostly reversed, affirming only the district court’s invalidation of one type of method claim. The parties petitioned the Supreme Court for certiorari in 2011, which, in 2012, the Supreme Court granted, vacated, and remanded in light of Mayo v. Prometheus. On remand, the Federal Circuit issued an almost identical decision, which the parties again appealed, and the Supreme Court again took up.

The lead petition presented three questions: (1) Are human genes patentable? (2) Did the court of appeals err in upholding a method claim that is irreconcilable with Mayo?; and (3) a question related to the extent of declaratory judgment jurisdiction after MedImmune. Interestingly, the Court limited its acceptance of the case to the first and, consequently, broadest question–not its typical practice.

Based on the Court’s acceptance of this loaded question–and based on Justice Breyer’s recent foray into patent law–good money going into the argument was on the Court striking down Myriad’s gene claims. Christopher A. Hansen, of the ACLU, argued in favor of AMP; the government, who requested an appearance in this case, was represented by Solicitor General Donald J. Verrilli; and Gregory A. Castanias, of Jones Day, argued for Myriad.

Mr. Hansen began, and lead his argument with the proposition that Myriad didn’t actually invent anything; it unlocked the secrets of two genes but that those were not, themselves, patentable inventions. This led to some strange confusion among the Justices about the difference between product and product-by-process patents, which in turn led Mr. Hansen to respond that if the product were identical to that found in nature, a product-by-process patent would be unobtainable as well. This then led to some brief confusion among the judges as to whether invalidated claims were divisible from the remainder of the patent. (The answer is Yes, as explicitly stated in 35 U.S.C. § 288.) Seeming to lead this conversation away from a morass of confusion, Justice Kagan then asked Mr. Hansen to respond to the incentive issue–whether anyone in Myriad’s position would have invested in such research were it not for the possibility of patent protection. Mr. Hansen attempted to suggest that scientific curiosity would normally play a role, but it appeared that the Justices rejected this position. Mr. Hansen then tried to flip the issue on its head, suggesting that DNA patents in fact hindered the commercialization of other, similar recombinant DNA, but it was unclear whether the Justices agreed with that either.

Out of this mire, Justice Sotomayor jumped in, and cut straight to the heart of the matter, asking why cDNA, as a synthetic molecule, should not be patentable. In doing so, the Justice nailed the cDNA synthesis process perfectly, even up to saying the words “introns” and “exons,” perhaps a Supreme Court first. Mr. Hansen’s response suggested that this was essentially no different from what happened in nature, because the exon removal process–also known as splicing–occurred in the cell’s transcription of DNA to mRNA. (Side point: This is technically incorrect; splicing occurs either immediately following transcription or during post-transcription processing, not during transcription itself.)  Justice Breyer then fumbled around with what seemed like a meaningless distinction between RNA’s inclusion of uracil rather than DNA’s thymine.

This all then led to the greater question of whether this case wouldn’t be more properly received under nonobviousness rather than patent eligibility. Hansen partially disagreed, saying that it was the sequence that made these genes valuable, and that that sequence was no different from that found in nature, and therefore more a matter of eligibility rather than nonobviousness. Justice Breyer again pressed a point about the chemical differences between cDNA and DNA, but Mr. Hansen reminded him that the patent defined “DNA” as including both.

General Verrilli then took the podium, and took up the cause that while isolated DNA should not be patentable, cDNA should be. Justice Sotomayor, quickly becoming an existentialist, then asked, “Are we fighting over nothing?” lamenting the lack of a significant difference between the two, at least in this case. The argument then again turned to whether obviousness was a better invalidator than eligibility. General Verrilli stated simply, that the Court’s own precedents appeared to make it so, and refused to express an opinion–exercising his amicus’s privilege–on whether the government believed the patents would nonetheless be invalid for obviousness. Justice Alito then expressed his concern that eligibility was, essentially, the broadest question, and if the Court could avoid resolving it, that would seem to be for the best.

Mr. Castanias then began his argument but was quickly cut off by Justice Sotomayor. Justice Sotomayor asked him to respond to the contention that gene sequences–the heart of Myriad’s patents–were little more than binary sequences, which the Court had long held unpatentable. Mr. Castanias disagreed, analogizing them to new chemical compounds–things–as opposed to abstract ideas. Justice Breyer then attempted to clarify whether tiny portions of isolated DNA molecules were in fact present in cells as a probabilistic matter. Mr. Castanias then tried to analogize the case to carving a baseball bat (patentable) from a tree (unpatentable), which then led to Justice Alitor’s hypothetical of whether it would matter that a piece of driftwood, sometime in geological history, happened to be exactly like a baseball bat. Mr. Castanias then tried again, comparing the gene to the extract of an exotic Amazonian plant, rather than the plant itself, which seemed to only lead to more confusion as to whether Myriad’s gene patents were more like the extract or the plant. When this all failed–through, it seems, much more the fault of the Justices than Mr. Castanias–Mr. Castanias relied on that all stalwart of prudence–reliance–claiming thirty years of it when it came to DNA patents. The Justices, still enamored with the various analogies being pasted on the walls, tried for another: isolating an organ from a human body. Was the organ patentable? Mr. Castanias answered No–because it performed the same function as the organ inside the body.

Mr. Hansen, with his reserved time, again took the podium, and Justice Sotomayor pressed him for a Yes or No answer to whether isolated DNA, as opposed to cDNA, was patentable. Mr. Hansen answered No, and his response ensued into a debate as to whether cDNA is “recombinant DNA,” a question that seemed to turn, in the Justices’ minds, as whether nature or a scientist decided the cDNA’s sequence. Mr. Hansen pressed his nature point, but–like much of the rest of the argument–it became further lost in analogies.

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Reading oral argument tea leaves is always a difficult proposition. And Breyer–who many had pegged as the Court’s anti-intellectual property stalwart–seemed, only next to Justice Alito, to provide the most salient (if scientifically inept) defense of some of Myriad’s claims. Nonetheless, I count at least five votes decidedly on board to invalidate Myriad’s claims: Chief Justice Roberts, and Justices Kennedy, Ginsburg, Sotomayor, and Kagan. All bets are off when it comes to Justice Scalia and anything scientific, and Justice Thomas has, much to many’s surprise, shown to be an apt and even-handed student of the history of patent law. And lastly, Justice Alito seemed ready to defend Myriad’s claims to their logical absurdities.

So, like so many other revolutions before, the Breyer revolution in patent law may have claimed its leader.