Tool's "Forty Six and Two" is based on the teachings of Carl Jung and the ideas expanded by Drunvalo Melchizadek in which they talk about human evolution resulting is our species having 46 autosomes and 2 sex chromosomes as compared to our current 44 and 2.
Melchizadek says, "There are three totally different kinds of humans on the Earth, meaning that they perceive the One reality in three different ways, interpreted differently. The first kind of human has a chromosome composition of 42+2. They comprise a unity consciousness that does not see anything outside themselves as being separate from themselves. To them, there is only one energy - one life, one beingness that moves everywhere. Anything happening anywhere is within them, as well. They are like cells in the body. They are all connected to a single consciousness that moves through all of them. These are the aboriginals in Australia. There might be a few African tribes left like this. Then, there is our level, comprising 44+2 chromosomes. We are a disharmonic level of consciousness that is used as a steppingstone from the 42+2 level to the next level, 46+2...These two additional chromosomes change everything."
The song also refers to a wish to experience change through the "shadow"; an idea which represents the parts of one's identity that one hates, fears, and represses, this is a theme in Carl Jung's work.