Thomas, 38, is accused of lying when she told a federal grand jury investigating the Burlingame-based Bay Area Laboratory Co-Operative, or BALCO, in 2003 that she never took anabolic steroids and that she did not receive any products from chemist Patrick Arnold except a then-legal hormonal stimulant.
Thomas is facing five counts of making false statements and one count of obstructing justice.
This morning, before the 12-member jury was brought into the courtroom, U.S. District Court Judge Susan Illston indicated that the obstruction of justice charge might be vague and possibly inappropriate.
"I'm concerned that the defendant (Thomas) is not on notice of what exactly she's being charged with on this count," Illston told prosecutor Jeff Nedrow.
Nedrow explained that the charge showed a "pattern of evasive and misleading conduct throughout Ms. Thomas' testimony" to the grand jury.
"It is so open-ended," said Illston of the charge. "I can't say what it is she is alleged to have done."
Prosecutor Matthew Parrella argued that the obstruction of justice charge was appropriate because Thomas' testimony to the grand jury showed she was "clearly connected" to Arnold and BALCO and she was "pushing the grand jury off in another direction," he said.
Defense attorney Ethan Balogh opined that those who testify before a grand jury do so without an attorney, and said that the responsibility lay with the prosecution to ask the right questions.
"A witness is entitled to evade," said Balogh. "What a witness is not entitled to do is lie."
After the jury returned to the courtroom, prosecutors resumed their questioning of U.S. Internal Revenue Service Agent Jeff Novitzky, the chief investigator in the steroid probe.
Novitzky contended that Thomas was "the best link" between BALCO founder Victor Conte and Arnold.
Arnold last week testified that he personally mailed a steroid known as "the clear," or THG, to Thomas at least once.
Novitzky was the chief agent in a probe that began with an investigation of BALCO and eventually included indictments of 11 people, including home run champion Barry Bonds, Conte, Arnold and Thomas.
Thomas won a silver medal in the World Track Cycling Championship in Belgium in 2001, but was banned from competition for life in 2002 after tests showed she had used norbolethone, a then-obscure steroid. She is now a law student in Oklahoma.
Thomas's case is the first one in the steroids investigation to go to trial.
Eight other people, including Conte, Arnold and track star Marion Jones pleaded guilty to charges of steroid distribution, money laundering or lying and were given short prison sentences. Bonds and track coach Trevor Graham are awaiting trial on charges of lying in the investigation.
Arnold pleaded guilty in 2006 to one count of conspiring with Conte and others to distribute norbolethone. He also admitted during the plea to creating THG, which was previously undetectable on drug tests. He was sentenced to three months in prison.
Novitzky was followed on the stand this morning by Dr. John Catlin, former director of the UCLA Olympic Analytical Laboratory, which assisted in testing for doping in athletes.
Catlin said he was initially contacted by Novitzky as part of the steroid investigation in 2001 or 2002. Catlin's lab was where norbolethone and THG were first identified as anabolic steroids being used by athletes, he said.
"The FDA didn't know about it. Nobody knew about it," Catlin said.
The trial, which began last week, is expected to be handed over to the jury for deliberation by Wednesday or Thursday, Illston said today.
