The Neurochemistry of Baroques
As addressed several times in-game, a Baroque is a distorted view of the world - a delusion - that helps a person cope with the hardships of life. For example, the Box Thing's only reason to continue living is the idea that his daughter lives on inside his box and will one day be returned to life - something he knows deep down is false.
The Research Angel declines to inject more CCK at the beginning of the game, as "it's difficult to live in this world without some sort of Baroque." "Baroque Report Gold" clarifies that the creative staff were operating under the idea that CCK has ties to memory, and therefore could be used to repress memories. However, CCK is also responsible for feelings of anxiety and stress, much like noradrenaline which (although it does have various effects on the immune system as the game states a bit inaccurately) is a chemical mainly produced in reaction to stressors for the purpose of preparing the body to take action and confront obstacles. To put it more simply, your levels of noradrenaline are lowest while you sleep, and get higher the closer you are to waking. These chemicals are the opposite of a Baroque - people's natural inclination to create a delusional version of the world in order to cope with (but not confront) problems in their lives. CCK and noradrenaline help you to combat problems but in the long term can lead to stress and degraded mental health. Baroques on the other hand, allow you to recover peace of mind and relax, but allow problems to grow further out of control. This is what HP (physical health) and VT (will to live) are representing - and why cooked versions of food causes a polarizing effect in these stats. They're largely opposites, and a reason why injecting CCK represses your natural Baroque (the other - official - reason being that repressing memories would also repress memories of a Baroque). They're stressing the protagonist out to a point where he can no longer ignore his guilt, thus leaving him vulnerable to the Archangel's manipulation. This jittery anxiety is the reason for the "nervous twitching in my eyes won’t stop" line at the start of the game.
This anxiety vs escapism axis is also embodied in the lobotomization of God. The Archangel describes the noradrenaline they are removing as being responsible for signaling the body to heal illness, or as he initially phrases it, "distortion". Without noradrenaline, God will have no way of knowing it is going mad, and will complacently allow the Archangel to slowly feed it delusional data.
More evidence of this relationship comes in the Idea Sefirah crystals produced by purifying Abnormals. You, like the other NPCs still capable of rational thought, can experience the contents of these crystals by holding them. Since Abnormals think of nothing but their own delusions, you're taking that delusion into yourself when you pick up the crystals. This influx of delusion is why you regain a small amount of VT when picking up the Idea Sefirot of Abnormals. However, you gain nothing when picking up the crystals of NPCs, likely because they're so riddled with guilt that holding these crystals is not at all an uplifting experience. Several characters will confirm that the contents of NPC crystals are not remotely pleasant. In his PS1 Guidebook interview, Yonemitsu clarifies that it is the weight of this guilt that causes NPCs to sink into the soil.* It is also this guilt that makes NPC Idea Sefirot such effective throwing weapons against Abnormals. The placid delusions that have consumed these monstrous beings cannot withstand the sudden and devastating influx of pain and guilt contained within these crystals. The "purified" states of these people still containing so much delusion and emotional damage also provides subtle foreshadowing to the game's ending, in which you discover that this ugly and distorted world is, in actuality, the natural state of things.
*Yonemitsu further expanded on the concept of NPCs sinking into the soil during one of his Baroque livestreams. He explains the process as a retreat into oneself, likening it to hikikomori (a large population of unemployed adults in Japan who live off their parents). Buried characters in Baroque are literally burying their problems and emotionally withdrawing until they become totally unresponsive to the outside world. Contrary to popular fan theories, this has absolutely nothing to do with suicide. As Yonemitsu states, "it's comfortable in the soil."