what is the meaning of it in the following sentence:
These feelings are, in all likelihood, the primordial constituents of mind, based on direct signaling from the body proper.
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Per the OED, the word proper comes to us through Middle English via French and ultimately from the Latin proprius, meaning one's own or particular to. The same root gives property (something of one's own) and appropriate (to take for oneself). When the adjective follow its noun, as in your example, it signals the strict, accurate use of the noun. This is a fairly old usage: the OED attests to this use in print around 1400, only a century after its first appearance.
Your excerpt is from Self Comes to Mind: Constructing the Conscious Brain by Antonio Damasio, which deals the so-called mind-body duality. That is, the feeling we all have that our abstract mental processes (consciousness, sentience, feelings, etc.) have an existence independent from the brain, a concrete organ of the physiological, of only neurochemistry.
As Damasio puts it
The properties of minds, let alone conscious minds, appear to be so radically different from those of visible living matter that thoughtful folk wonder how one process (conscious minds working) meshes with the other process (physical cells living together in aggregates called tissues).
In the section of the book from which your excerpt is taken, Damasio is talking about the origin of feelings (which he calls "constituents of the mind and elsewhere "aspects of the mind"). These, he claims, originate from neurochemical processes in parts the brain stem, a part of the body, interpreting that word strictly to mean the biochemistry of cellular tissue.