I don't know if this has been said before but there's this one aspect of Signalis that's chilled me for a while and that's the complete absence of nature. The only suggestions we see in the game of anything natural are pictures of Vineta, which is a desolate hell planet derived from human-
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One could argue that this plant is sheltered from that very hostile and sterile world, but you're right, it is also indeed in captivity in its enclosed box; which is sad.
Though they see it in more romantic light, without the actual reality of living under an excavator.