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The board overseeing California’s stem cell research funding agency should redefine the role of its chairman and “let the management manage,” state Controller John Chiang said Wednesday in a letter to board members.

“The (board’s) most important role — to provide independent oversight of the California Institute for Regenerative Medicine (CIRM) management — is severely compromised when that management includes the (board) chair,” Chiang wrote.

Today, San Francisco-based CIRM operates with board Chairman Bob Klein and President Alan Trounson as co-executives. That model has led to conflicts between Klein — who engineered the 2004 passage of Proposition 71, which set up CIRM and its funding with up to $3 billion in state-sold bonds — and staff. That most notably occurred in a falling out between Klein and then-president Zach Hall in 2007.

The issue has come to a head as Klein prepares to step down from the position. He was supposed to leave the post in December, but questions arose about his hand-picked successor and the process used to select a new chairman.

In the interim, the board decided, Klein...