WASHINGTON — Chocolate chip cookies. Baseball bats. Amazon plants. Not a game show quiz, but hypotheticals by U.S. Supreme Court justices trying to decide whether human genes should be patented.

The justices heard arguments on Monday in Association for Molecular Pathology v. Myriad Genetics, a challenge by the American Civil Liberties Union and others to Myriad’s patents on two human genes that have mutations indicating a high risk of breast or ovarian cancer. The mutated genes are known as BRCA1 and BRCA2. Myriad’s patents claim exclusive control over those genes, including related diagnostic tests to determine the risk in women.

The case has pitted biotechnology, agricultural, pharmaceutical and other industries against civil rights, women’s health organizations, the American Medical Association and others. The former contend that the patents are crucial to industry’s willingness to invest in costly research; the latter counter that the patents stifle scientific research and the monopoly on testing limits the information needed by physicians and patients.

"Patent law is filled with uneasy compromises," Justice Stephen Breyer told Myriad’s counsel, Gregory Castanias, a partner at Jones Day. The historical compromise in this area, he explained, has been, "Of course, if you get a new satisfying process to extract the sap from the plant in the Amazon, patented. Of course, if you get the sap out and you find that you can use it, you manipulate it, you use it, you figure out a way to use it to treat cancer, wonderful, patented. But what you can’t patent is the sap itself."

Breyer was referring to the so-called product of nature doctrine in patent law. Patents can be awarded for "any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement" of those inventions. But no patent can be granted for an invention that is an application of the laws of nature or natural phenomena.

During Monday’s arguments, many of the justices appeared to struggle with Myriad’s claim that its isolation of the genomic DNA created something new, a molecule with a chemical structure entirely different from DNA existing in human cells.

"You haven’t created a type of gene that does not exist in the body naturally," said Justice Antonin Scalia to Castanias.

Castanias, rejecting a hypothetical from Justice Sonia Sotomayor about the patentability of ingredients used in baking chocolate chip cookies, offered, instead, a baseball bat explanation. The bat does not exist until it is isolated from a tree, he said, adding, "But that’s still the product of human invention to decide where to begin the bat and where to end the bat."

However, Chief Justice John Roberts challenged Castanias, saying, "Here, what’s involved is snipping. You’ve got the thing there and you snip — snip off the top and you snip off the bottom and there you’ve got it. The baseball bat is quite different. You don’t look at a tree and say, well, I’ve cut the branch here and cut it there and all of a sudden I’ve got a baseball bat. You have to invent it, if you will. You don’t have to invent the particular segment of the (DNA) strand; you just have to cut it off."

"You didn’t know where to snip until Myriad invented it," said Castanias. "The invention is in the decision where to begin the gene and where to end the gene. That was not given by nature."

Christopher Hansen of the ACLU, counsel to the challengers, said Myriad had invented "nothing." The isolation process, he said, is routine and used all over the country, but what is in the genes themselves are decisions made by nature.

"Myriad unlocked the secrets of two human genes," explained Hansen. "These are genes that correlate with an increased risk of breast or ovarian cancer. But the genes themselves — where they start and stop, what they do, what they are made of, and what happens when they go wrong — are all decisions that were made by nature, not by Myriad.

Now, Myriad deserves credit for having unlocked these secrets. Myriad does not deserve a patent for it."

Justice Elena Kagan asked him what incentives would exist for Myriad to have done what it did if there were no patent protection for its work.

Hansen said other labs and researchers were anxious to do this work. "When you lock up a product of nature, it prevents this research."

Solicitor General Donald Verrilli Jr., agreeing with Hansen, told the court that isolated genetic material— gDNA — is "simply natural DNA extracted from the body. The claim that isolated DNA is a human invention rests entirely on the fact that it is no longer connected at the molecular level to what surrounded it in the body. But allowing a patent on that basis would effectively pre-empt anyone else from using the gene itself for any medical or scientific purpose."

On the other hand, complementary DNA (cDNA), he said, is patent-eligible because it is artificial DNA created in a laboratory.

Marcia Coyle is chief Washington correspondent with The National Law Journal, a Recorder affiliate.