He reiterated that his client had always abided by the rules for his first planting, but chose to save money and go to the grain elevator for the risky second planting.
Several of the justices focused not on the purchase of the seed from the grain elevator, but the replanting of those seeds for subsequent crops.
"You know, there are certain things that the law prohibits. What is prohibited here is making a copy of the patented invention. And that is what he did. So it's generation 3 that concerns us," Justice Stephen Breyer said.
"The Exhaustion Doctrine permits you to use the goods that you buy," Justice Sonia Sotomayor said. "It never permits you to make another item from the item that you bought."
Assistant to the Solicitor General Melissa Arbus Sherry argued on behalf of the Department of Justice in support of Monsanto.
"If the concept is the sale of a parent plant exhausts the patent holder's rights not only with respect to that seed but with respect to all the progeny seed," then patented protections would be eviscerated, she argued.
Monsanto lawyer Seth P. Waxman said the company would never have commercialized its invention and "never would have produced what is, by now the most popular agricultural technology in America" if the patent had been so easily exhausted.
Supporters of Bowman say the case highlights a troubling and dangerous situation in which a handful of large agrichemical corporations own a large share of seeds.
"The essence of the case is this: who should control and own seeds, the very product of life," said Debbie Barker, whose group Center for Food Safety has filed a friend of the court brief on behalf of Bowman. "Corporations are saying that they own seed, but in fact seeds have been bred, exchanged and saved by farmers over the centuries."
But Scott McBride, a partner at Chicago-based law firm McAndrews, Held & Malloy, filed an amicus brief on behalf of universities eager to ensure innovative biotechnology continues to be made available for the public benefit.
"If the Supreme Court were to side with Bowman, existing biotechnology patents would be devalued, and the incentive to innovate in biotechnology going forward would be severely harmed," he argued.
The Supreme Court decision could affect many areas of biotechnology, including vaccines, DNA and treatments for cancer, he said.
As for Bowman, he says he's not afraid of losing.
"I know it's a possibility," he said. "I have one good thing going for me: I'm poor as nothing, I was lucky when they brought a suit against me that I was broke anyway. "