Judge Richard Holwell instructed the jury that after one of their members had to be replaced for medical reasons, the entire group needed to go back to the beginning of deliberations -- already in their second week -- for the sake of the new juror.
"You must disregard your earlier deliberations," the judge said.
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"The law requires that the jurors (commence) their deliberations anew."
Rajaratnam himself was absent from the courtroom after undergoing what his attorneys said was emergency surgery on his foot last Sunday.
The Sri Lankan-born founder of the Galleon Group hedge fund has pleaded not guilty to charges of earning tens of millions of dollars on the basis of illegal insider tips.
Rajaratnam, 53, faces up to 25 years in prison if convicted on all charges in a case seen as the biggest assault on alleged insider trading in years.
More than two dozen others have been caught up in the Galleon probe, which -- unusually for a financial fraud case -- featured extensive use of telephone wi