From the recommended reading material I found the following points useful.
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You use the coordinate numbers to define distance units to be used and the size of spaces. So you can come up with your own distance system based on the coordinates
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For design purposes, origins can be a location or landmark
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Using directional cues the axis are fixed except for the one axis that is to be rotated. So you can only rotate one axis at a time.
I spoke to my brother the industrial chemist about chirality and handedness. He said its used all the time in chemistry, where you think of molecules as a key in a lock. So nature uses it all the time.