Truth
This novel is challenging its readers to scrutinize beliefs. Although there are many reasons why someone would want to command a person to believe one thing or another, there is only one reason to use the truth—for truth's sake. That means that Lyra is asked to judge between people's motives, in an attempt to understand how trust should work. She uses an "alethiometer," which is just Greek for "truth meter," and she communicates with elements of her higher self, symbolized by her "daemon," or spirit.
Death and malice
The problem of human evil gets lumped into a bigger problem in this book—human death. If no one could ever die, then what would the danger of violence be? When the witch kills John, Will is left to mourn the actual pain of lost life. Is Lyra alive or not? The book ends on a cliff-hanger, but he receives her tool for truth measuring, the "alethiometer," and the challenge of finding out whether she lived. He is challenged to encounter real death and Lyra's disappearance in one fell swoop.
Misdirection
The novel is clearly a portrait of various entities competing for the young people's minds. Why? Because by swaying a reasonable person, they gain resources for their own interests. So the image is of misdirection and manipulation. Although there are violent villains who harm Lyra and her friends, those are all people who tried to manipulate them but failed. The witch desperately wants Lyra's mind for her own purposes. The battle is for sanity and level-headedness in a maelstrom of competing information.
