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Last month in San Francisco, biologists Jennifer Doudna and Emmanuelle Charpentier showed up in black gowns to receive the $3 million Breakthrough Prize, a glitzy award put on by Silicon Valley billionaires including Mark Zuckerberg. They’d won for developing CRISPR-Cas9, a “powerful and general technology” for editing genomes that’s been hailed as a biotechnology breakthrough.

Not dressing up that night was Feng Zhang (see 35 Innovators Under 35, 2013), a researcher in Cambridge at the MIT-Harvard Broad Institute. But earlier this year Zhang claimed his own prize. In April, he won a broad U.S. patent on CRISPR-Cas9 that could give him and his research center control over just about every important commercial use of the technology.

How did the high-profile prize for CRISPR and the patent on it end up in different hands? That’s a question now at the center of a seething debate over who invented what, and when, that involves three heavily financed startup companies, a half-dozen universities, and thousands of pages of legal documents.

“The intellectual property in this space is pretty complex, to put it...