The Glass Prison” was written about the first three steps in the Alcoholics Anonymous 12-Step Program, and after Six Degrees of Inner Turbulence came out Mike said he would like to write a song on each album that continued with that theme. “This Dying Soul” is about steps four and five (and “The Root of All Evil” from Octavarium is about steps six and seven, “Repentance” from Systematic Chaos being eight and nine, and “The Shattered Fortress” on Black Clouds & Silver Linings being ten, elevent and twelve.)
The two songs share some lyrics and a riff, and there is also some small references to “The Mirror”, which is written around the same themes.
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