WASHINGTON - Molecules and chocolate-chip cookies, baseball bats, and Amazonian tree sap were all part of a spirited Supreme Court discussion Monday as the nine justices wrestled with the question of whether one should be able to get a patent for a human gene.

If you slice up pieces of microscopic molecules, have you created new ones or just separated existing body parts, not unlike kidneys or livers, which are products of nature and not usually granted patents? And, more important in this matter, can you profit by preventing others from researching those molecules or providing lower-cost testing services?

The justices seemed to be looking for a compromise in Association for Molecular Pathology v. Myriad Genetics Inc. AMP was part of the original group of plaintiffs that represented researchers, including two from the University of Pennsylvania, patient groups, and six women, including one from Williamsport, Pa., with breast or ovarian cancer or a family history of either. The plaintiffs say Myriad's patent-provided monopoly on the BRCA1 and BRCA2 genes has stifled research because of Myriad's threats of lawsuits, and limited access to affordable testing for those cancers.

"The Patent Office seems very patent-happy," Justice Elena Kagan said to Myriad's attorney, Greg Castanias. "You have a plant. You uproot it and carry it away and isolate it. Can you now patent it?"

Plaintiffs attorney Chris Hansen later answered Kagan's question: "We do not think you should be able to get a patent on that plant you pulled from the ground."

A decision is likely before the court's term ends in June. Pharmaceutical companies and other industries with similar kinds of patents are hoping that Myriad wins. Besides arguing for deference to the wisdom of Patent Office officials, Myriad argues that its human intervention takes molecules beyond what nature provides, and it has suggested a baseball bat as an analogy, as baseball bats are inventive cutting of natural wood.

"For millions of years, trees have existed," Justice Samuel A. Alito Jr. said, pondering aloud. "But if a limb falls off, ends up in the water, is manipulated by waves, and washes up on shore, and what you have is a baseball bat?"

However, Justices Stephen G. Breyer and Sonia Sotomayor seemed uncomfortable that Myriad would retain control of the still-healthy trees in such an analogy. Breyer said he was fine with a man-made formulation that included sap from Amazonian trees, but not the sap itself.

"I create a chocolate cookie recipe and maybe I can get a patent on the recipe," Sotomayor said. "I can't imagine getting a patent on the basic elements - salt, flour, sugar."

Contact David Sell at 215-854-4506, dsell@ phillynews.com, or follow on Twitter @ phillypharma. Read his blog at www.philly.com/phillypharma.