Lyrics for the song 'Disappear' were written by James LaBrie about the subject of death it was originally titled 'Move On'.

Producers John Petrucci and Mike Portnoy were actually in a Manhattan studio conducting final mixes of the album on the day in question and made the change when all of the news reports started to refer to the site as 'Ground Zero.' It was originally titled 'Conflict at Ground Zero' based on the lyrics in the chorus but was changed at the last minute due to the 9/11 terrorist attack on New York City.

'The Great Debate' is intended to be a non-partisan song dealing with the topic of stem-cell research.

This track is in its shorter radio edit form on the cassette edition.

He then learned how to play this reversed version, and he tries to mimic the reversed version live with effects.

In the song 'Misunderstood', John Petrucci wrote and played the guitar solo, and then reversed it.

The next time would also be on Octavarium. It was also the first time he had written lyrics for more than one song on an album. It is the second longest song for which LaBrie has contributed lyrics to date, the longest being 'Sacrificed Sons' from Octavarium.

'Blind Faith' features lyrics written by James LaBrie about questioning religious belief.

Furthermore, it begins with the pink noise that ended 'Finally Free' on Metropolis Pt. 'The Glass Prison' is composed of three parts, mirroring the first three of the twelve steps of the AA program by Bill W.

The first track of the album, 'The Glass Prison', is the beginning of the Twelve-step Suite, dealing with Mike Portnoy's story of rehabilitation from alcoholism, continued in tracks on subsequent albums ('This Dying Soul' on Train of Thought, 'The Root of All Evil' on Octavarium, 'Repentance' on Systematic Chaos and 'The Shattered Fortress' on Black Clouds & Silver Linings).

Classical, folk, jazz and metal styles are present within the track. The musical styles of each section of the title track are direct reflections of the band's large variety of influences. Furthermore, the title of the album may also allude to the fact that each song on the album could be seen as a different form of inner turbulence, with the six tracks making another reference to the six degrees, along with the apparent reference to the six degrees of separation. Particularly represented are bipolar and post-traumatic stress disorder, schizophrenia, post-partum depression, autism and dissociative personality disorder.

The sixth song-a 42-minute piece occupying the second disc, separated into eight tracks-explores the stories of six individuals suffering from various mental illnesses.

The recording is a type of concept album wherein the five songs which comprise the first disc explore different themes of lifetime struggle, such as alcoholism, loss of faith, self-isolation, sanctity of life and death.

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