The first ruling in the case came on November 1, 2009. Judge Sweet (who once upon a time was deputy mayor of New York) rejected the motions to dismiss. He said that the plaintiffs did have a right to challenge the constitutionality of the USPTO's polices and practices as well as to evaluate the legitimacy of Myriad's specific patents. In a footnote, tellingly, he wrote: "Although the USPTO suggests that finding ... jurisdiction over Plaintiffs' constitutional claims would open the gates to a flood of challenges to patents based on alleged constitutional violations, it is difficult to see how a colorable claim ... could arise out of patents for more commonly patented inventions, such as computer chips or carburetors."

Having rejected the defendants' move to toss the case out on procedural grounds, Judge Sweet then moved on to the merits of the plaintiffs' claims. His next ruling, in late March 2010, invalidated the patents and sent the biomedical and venture capital worlds into a tizzy. It is a long opinion, full of facts about molecular biology that even the judge acknowledged were often difficult to follow. But Judge Sweet was clear about the results: The USPTO had been too lax in issuing patents like these and Myriad's patents were legally invalid. The judge wrote:

The claims ... directed to "isolated DNA" containing human BRCA1/2 gene sequences reflect the USPTO's practice of granting patents on DNA sequences so long as those sequences are claimed in the form of "isolated DNA." This practice is premised on the view that DNA should be treated no differently from any other chemical compound, and that its purification from the body, using well-known techniques, renders it patentable by transforming it into something distinctly different in character. Many, however, including scientists in the field of molecular biology and genomics, have considered this practice a "lawyer's trick" that circumvents the prohibitions on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result.... It is concluded that DNA's existence in an "isolated" form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes.

Gary Cohen (no relation), who is Vice President of Bioethics, Law & Policy at Foundation Medicine, takes no official position on the case. But he recognized in Judge Sweet's ruling a shifting of paradigms in this area of law and science. Cohen told me:

We've been accustomed to thinking of DNA as a molecule, a chemical entity (which, of course, it is). But in this more sophisticated era, we understand that DNA is not "just" a molecule; its an information-carrying molecule. Genes are better thought of as packets of information, not mere molecules, Judge Sweet reasoned. This reasoning is key to his decision -- because the information encoded by a gene is the same, whether its sitting amongst its natural neighbor genes, or in isolated form. That's why researchers want to isolate genes -- because they are useful in all sorts of ways, but only because the isolated form contains the same genetic instructions as the naturally-occuring form. Using this information paradigm, the judge reasoned that "isolation" does not render a naturally-occurring gene something novel, something patentable. This part of the ruling is what makes it so interesting -- its very much consistent with "information age" thinking -- bits, bytes, genetic base pairs, genes: all information carriers.

There have been dozens of amici briefs filed for one side or the other, all arguing over the policy choices inherent at the intersection of patent law, medicine and science. Should we be tinkering with the free market by allowing patents for such things? Is this how the government wants to exercise its prerogative to offer 20-year monopolies? Good questions. For now, all Uncle Sam will say is that it does not want to endorse either side in the argument. However, in a court filing in advance of Monday's argument, Justice Department officials undercut the USPTO's initial determination, perhaps fatally. The feds now argue:

The district court correctly held, however, that genomic DNA that has merely been isolated from the human body, without further alteration or manipulation, is not patent-eligible.... The chemical structure of native human genes is a product of nature, and it is no less a product of nature when that structure is "isolated" from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth.

So many people in so many different industries and for so many different reasons are waiting for a ruling in this case from the Federal Circuit -- and then perhaps from the United States Supreme Court. In a case over molecular biology, from small things, truly, big things one day come. Monday is the next big day in this case. It surely will not be the last.