"Your suspicions aren't enough to warrant a jury conviction," Judge Ellis told the father.
Because there is no such thing as an unbiased scientist, Judge Ellis said, "you put your thumb on the scale of justice when you pick an expert."
Nonetheless, Judge Ellis explicitly rejected the argument that the prosecution was unfairly flawed because this practice goes on regularly in Washington.
After two decades of work as a full-time federal district judge, Judge Ellis took Senior Status in April 2007.
"We're not going to proceed as if this was some sort of show business here," Judge Ellis angrily replied.
The Clinton Administration urged Judge Ellis to defer to the board's expertise on this issue.
On June 11, prosecutors asked Judge Ellis to reduce Franklin's sentence to eight years for his cooperation.
In his three-year tenure on the bench, Judge Ellis frequently ruled in favor of segregationists.
Mr. Brosnahan suggested that part of his reason for negotiating a plea agreement was Judge Ellis.
On Monday, a clerk in the chamber of Judge Ellis would not discuss the matter, saying that no one in the judge's office spoke to reporters.