Washington ( CNN ) -- Dueling scientists , a former trainer , friends and family are among the witnesses whose testimony a jury will consider as they decide if famed baseball pitcher Roger Clemens lied to Congress during an investigation of steroid use among major league players . The case against Clemens involves one count of obstruction of Congress , three counts of making false statements and two counts of perjury . He is not charged with illicit use of performance-enhancing drugs , but his denial of such use is part of the case against him . Federal prosecutor Courtney Saleski , in closing arguments Tuesday , told the jury Clemens `` wanted to protect his brand , he wanted to protect his livelihood , '' in denying the use of steroids during a 2008 investigation by the U.S. House of Representatives into the problem . `` He did that at the expense of our Congress . He threw sand in their eyes . He stole the truth from them , '' Saleski said . She said a guilty verdict would give that truth back to lawmakers . The Clemens defense team disputed whether the government has made its case , telling the jury all the evidence came through a former personal trainer , Brian McNamee , who had incentive to lie . `` You saw Brian McNamee , the only witness in the history of the world who says he gave or saw an injection of that man , '' said defense attorney Michael Attanasio . `` One person in the entire world . '' During closing arguments , the defense cited the lack of corroborating witnesses , which they said would be a basis for reasonable doubt against any conviction . `` McNamee defines reasonable doubt , '' Attanasio said , because of perceived inconsistencies , retractions and corrections he made while testifying . After verbally providing instructions to the jury late Tuesday , U.S. District judge Reggie Walton sent the jury back to begin deliberations , while acknowledging they may only have time to select a foreperson before letting them go for the day . The trial has run longer than envisioned , and one juror was moved to alternate status Tuesday because of a fellowship in Germany for which he must depart next week . An alternate was then sent back to join the others . It took about eight weeks for the prosecution and defense to question 46 witnesses , and the most direct conflict came among expert witnesses as to how to interpret a collection of discarded medical items that allegedly link Clemens to steroid use . Soiled medical wrappings , cotton balls , drug vials and hypodermic needles that McNamee kept were interpreted differently by both sides . Witnesses for the government said genetic material linked with Clemens suggested it was impossible for McNamee to fabricate the evidence . But defense witnesses on the same topic said storage in a beer can for years allowed commingling and contamination of materials , making reliable conclusions impossible , and the evidence nearly worthless . `` If you have garbage at the start , you 'll have garbage at the end , '' said defense expert witness Dr. Bruce Goldberger , who said his lab would refuse to test such materials without a solid basis for their storage and handling before analysis . Prosecution witness Dr. Cynthia Morris-Kukoski , an FBI toxicologist , said it is not up to the toxicology lab to make judgments about the materials submitted for testing , with their job only to determine the substances and any genetic identifiers involved . Former teammate and friend Mike Boddicker testified as to whether Clemens had ever accepted injections , providing an eyewitness account that he had . `` I think it was either 1989 or 1990 , '' Boddicker said , referring to their time together with the Boston Red Sox , describing that he `` came into the training room , and saw Roger bent over the table with his pants down , getting a shot . '' The vial , Boddicker said , was clearly marked `` B-12 '' a substance said to provide a pick-me-up after a game or workout . This is the second trial for Clemens . A year ago , a mistrial was declared before the case reached the jury . The government 's lawyers played video evidence the judge had already banned . Prosecutors said it was an editing mistake , but the Clemens defense team suggested prosecutors were unprepared and had gotten off to a bad start . `` This was a mistake , a regretful mistake , '' government attorney David Goodhand said in September in arguing for a new trial . But Walton blasted prosecutors for letting inadmissible evidence be shown . `` I would hate to believe they just blatantly disregarded rulings that I made , but it 's hard for me to reach any other conclusion , '' Walton said , before rejecting a defense request that he dismiss the indictment entirely . After consideration , Walton then ordered the new trial . Several pretrial hearings this time included protests from defense attorneys that the prosecution was trying to take advantage of having heard the initial opening statement last summer by the defense . In the latest trial , defense attorneys expressed concern that prosecutors were trying to `` do over '' certain efforts the defense may have refuted . Deliberations Wednesday were set to begin at 1:30 p.m .
Second trial involves 46 witnesses over eight weeks . Jury will weigh opposing `` expert witnesses '' on DNA evidence . Clemens declines to testify in his defense .