This is a 'phenomenon' whereby melodies and riffs from one song are repeated in another. Due to the heavily thematic story-telling nature of DT songs, this is quite a common occurence.
"Pull Me Under" and "Take The Time" share a melody, which is not quite a riff, but they are identical if juxtaposed on a corresponding major/minor scale. "Wait For Sleep" and "Learning to Live" also share a main riff. Thematically, none of the songs interconnect.
Mike Portnoy has said that the music is written out before the lyrics are written and set to melody. It is possible that they were intended to be counterparts and that the relation was either scrapped or made more subtle.
The PMU-TTT connection is not as direct as the WFS-LTL connection. The melody from PMU's "This World is spinning around me, this world is spinning without me" in a minor scale sung by LaBrie is reproduced at 4:18 of the TTT instrumental section in a major scale played by Petrucci. So, the question remains, "are the 16-note melodies reproduced completely by coincidence on the same album by the same band?"
Also, all throughout Awake, there is a lot of intentional riff sharing. Without referring to the obvious "Erotomania", which is MADE UP OF riffs from other songs, the "Space Dye Vest" piano melody was added to "The Mirror," "LSOAD," and "Scarred".
Another obvious one is MP's Alcoholics Anonymous suite: The Glass Prison, This Dying Soul and The Root of All Evil share some musical themes and melodies.
and again at 5:09 ("...make my amends. I'll never hurt you a-..." is identical to the one heard in "Lie" at 1:21 ("I won't, I swear I won't.", at 1:31 ("I'll try, I swear I'll try."
not confusing this with overture 1928? or overture?