The different forms of duality in Robert Ulanowicz’s (2009) book A Third Window are compared to the notion of neo-duality found in Logan and Schumann (2005). The influence of Heraclitus on the formulation Ulanowicz’ duality is described. It is argued that the origin of language, which led to conceptualization and emotional intelligence, also gave rise to human spirituality, cooperation and altruism all of which contributed to human survival. The four mysteries of the existence of 1) matter/energy, 2) life, 3) human intelligence, and 4) human spirituality are identified. It is suggested that physics and chemistry deal with mystery number one; that Ulanowicz’s process ecology describes mystery number two and the relation of life to energy/matter. Mystery number three entails process ecology and consideration of the effects of language. The emergence of the fourth mystery of spirituality and/or a belief in God is shown to have emerged from two uniquely human attributes, namely the abstract form of language-based intelligence and altruism. It is suggested rather than as an agent that influences events in the universe God, an idea that arises in the minds of humankind as a metaphor of all that is good in humankind.