The Supreme Court on Monday seemed skeptical that a human gene can be patented but also worried about what a decision to bar such patents would mean for private scientific inquiry and research.

Even the normally confident justices expressed some trepidation as they considered the complexities of patent law and the mysteries of biochemistry. They talked about the introns and exons that are parts of genes, but spent more time on simpler illustrations: baseball bats, a hypothetical plant in the Amazon with miraculous powers, the recipe for chocolate-chip cookies.

The justices’ caution is warranted: The decision could shape the future of medical and genetic research and have profound effects on pharmaceuticals and genetically modified crops.

The court is considering a challenge to a decision to award a patent to Myriad Genetics for isolating human genes that indicate a hereditary disposition to breast and ovarian cancer. Doctors and patients must use the diagnostic test that Myriad has developed, and others are restricted from research in that area.

The patents are being challenged by organizations of physicians and researchers, geneticists, patients and others who say that the snippets of DNA are “products of nature” and may not be patented, even though the U.S. Patent and Trademark Office has issued such patents for decades.

The challengers were represented by Christopher A. Hansen of the American Civil Liberties Union. He told the court that Myriad did not deserve a patent because it did not invent anything.

“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,” Hansen said.

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

The justices did not so much disagree with Hansen as they did worry about the consequences of not rewarding companies that invest so much money in genetic discoveries.

“What does Myriad get out of this deal?” asked Justice Elena Kagan. “Why shouldn’t we worry that Myriad or companies like it will just say, ‘Well, you know, we’re not going to do this work anymore’?”

Hansen said that taxpayer-funded research is one answer, and that natural scientific curiosity and recognition will continue to encourage such discovery. Justice Anthony M. Kennedy said that isn’t enough.

“I just don’t think we can decide the case on the ground, ‘Oh, don’t worry about investment, it’ll come,’ ” Kennedy said.

Myriad’s attorney, Gregory A. Castanias, had more trouble convincing the court that the genetic material the company isolated was different enough from the genetic material inside the human body to warrant patent protection.

“There was invention in the decision of where to begin the gene and where to end the gene” in the strand of DNA, Castanias said. He compared it with a baseball bat.

“A baseball bat doesn’t exist until it’s isolated from a tree,” Castanias said. “But that’s still the product of human invention, to decide where to begin the bat and where to end the bat.”

The analogy did not fly with Chief Justice John G. Roberts Jr.

“You don’t look at a tree and say, ‘Well, I’ve cut the branch here and cut it here and all of a sudden I’ve got a baseball bat,’ ” he said. “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.”

Solicitor General Donald B. Verrilli Jr., representing the government, agreed mostly with the challengers and said the gene itself could not be patented. But he said ma­nipu­la­tion of the gene to produce certain results would be patentable.

Although the question of whether a gene may be patented seemed basic, Justice Samuel A. Alito Jr. wondered whether it was the one the court had to decide right now.

“Why should we jump in . . . and decide the broadest possible question?” Alito asked.

The case is Association for Molecular Pathology v. Myriad Genetics Inc .

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