In the final scene where Jane is walking past a stand of orange trees, he stops at one of the trees and plucks an orange which he begins to peel. This is a very visual allegory concerning the "tree of life." It implies that possibly Jane is considering Lisbon's earlier statement in the cellar about choosing life over his own self-destructive quest for Red John. Although the tree of life is prevalent in many cultures and religions, this particular tree is most likely the tree of life mentioned in both the Old Testament and New Testament of the Bible. Considering that Lisbon's cross is plainly in view when she confronts Jane in the cellar and that the background music playing when Jane takes the orange was composed by J.S. Bach (he wrote church music as an expression of his own religious feelings), the allegorical context is Judeo-Christian in nature.
In the cellar scene, Lisbon subdues Sheriff Hardy and begins to handcuff him with his face down and his hands behind his back. Later, Sheriff Hardy is seen on the floor of the cellar, face up and handcuffs in front of him.
In one of the final scenes when Sheriff Hardy and Jane arrive at the farm, Hardy pumps his shotgun once making it ready to fire. He then pumps it a second time in the cellar with Jane. This was unnecessary since he didn't discharge the weapon after the first pump.
The piano piece played by Alicia Witt (Rosalind Harker) is "Well-Tempered Clavier, Book 1, Prelude in C major" by Johann Sebastian Bach.
Gaia, the name of the company in this episode, is an alternate spelling for the Greek goddess of the earth, who bore Uranus.
When Lisbon, Van Pelt and Cho arrive at Jenny Didrikson's house and get out of the car, you can see that only Lisbon's badge is clipped on her belt. However, in the next scene when they decide to go into the house she's wearing her gun and holster on her right hip.
During one of the location shots at the beginning of the episode, an advertisement for Studio 60 on the Sunset Strip, which was ended nearly two years before the episode was set, can be clearly seen. The producers most likely used old stock clips for the shot.
Carnelian, the name of the company in this episode, is a a pale to deep red or reddish-brown semi-precious gemstone used in jewelry.
When Jane goes looking for the car with the bomb in it, the cars are dry. When it pans to the parking lot with the van and the bomb, all the cars have large water droplets on them.
Patrick's blue and white car is a Citroën DS, actually a French car produced by the manufacturer Citroën between 1955 and 1975.
When we see the victim fall, she ends face up over a table. When the team shows up, she is lying face down on the floor.
At the end of the episode when Jackie Shaper shows up at CBI HQ for her date with Wayne, she is wearing a very sexy black and grey dress. Two days later on 2/19/2009 a Burn Notice episode, "Truth and Reconciliation" aired. In that episode, when Fi is at the home of Jean-Pierre Duman to spy on him, she is wearing the exact same dress.
"Trouble" by Bitter:Sweet (Opening scenes)
Grace Van Pelt's father is a football coach.
When Lisbon and Patrick questioned Brad, they did so without his parental permission and without their presence, anything he said would be inadmissible at court.
Red Rum spelled backwards is Murder.
Goof: When Grace Van Pelt looks up Undine's mother, her name on screen is listed as "Marisa Kopecki", although everyone refers to her name as "Mariska".
When interviewing Tommy/Thomas at the end both claim that at the end of "Moby Dick" that Moby Dick dies, but this is not the case. In the end Moby Dick destroys the Peaquod, drags Ahab into the water, and then escapes.
When Jane tells Lisbon he's going to read her mind, he tells her to think of shape other than a square -- while he is telling her this, he is holding his hands in front of him with his fingers outlining an invisible triangle. He then tells her to think of a shape that circumscribes the first shape; as he tells her this, his index fingers draw an invisible circle in the air. She then admits that her shapes were a triangle in a circle and it appears that Jane has read her mind.
The motel used as crime scene in this episode is the same set as the motel used in popular comedy series My Name Is Earl.