Here is a portion of an interview KidsReads did with Philip Pullman. Pullman is the author of a Random House children's book Scholastic is selling called, The Golden Compass.
Bolding is, as usual, my emphasis. Go ahead and read it; I already have -- I am leaving now because it made me sick to my stomach. More posts later.
Why are all witches are female? Why are dæmons usually the opposite gender of their human counterparts? Is the fact that Lyra is a girl-child relevant to the themes HIS DARK MATERIALS?
Daemons are usually the opposite sex because we each have a bit of the opposite in our make-up, and it was one way of making that visible. Witches are female because they are --- that's the way it is. Some of their powers can be acquired by men, though, as Will inadvertently discovers, but only at the cost of suffering as witches themselves have to. As for Lyra, as soon as I thought of her I knew she had to meet Will. The two of them go through it all together, and it's vital that they come to realise their love together. The theme of the whole thing, after all, is the ending of innocence and the beginning of wisdom; and that is summed up in the third chapter of the Book of Genesis, which is the origin of this and PARADISE LOST and many other stories, in the story of Adam and Eve. Lyra is Eve; Mary Malone is the serpent, who teaches her how to fall in love, and Will is Adam.