what is the "philosopher's stone", "elixer of life" and "soul of the world"

The Philosophers Stone is the solid portion of the Master Work. The Philosopher's Stone has the ability to turn any metal into gold, an ability which the Alchemist uses to generate gold at the Coptic monastery in Egypt before taking his leave of Santiago.

The Elixir of Life is the liquid portion of the Master Work, the goal of all alchemists. The Elixir of Life heals diseases and grants long life when ingested. The Alchemist carries some in a flask through the desert.

Soul of the World

A term which comes up repeatedly in the text, the Soul of the World is sometimes equated with God. It is a spiritual force that binds all of us together and governs all things and that speaks with us in the language of signs or omens.