Reductionism remains the dominant philosophical framework of modern science. Within reductionism, the universe is conceived as a probabilistic and deterministic system guided solely by the laws of physics and mathematics. Under the guidance of reductionist thought, the development of the modern atomic theory and quantum mechanics has drastically changed science, medicine, and philosophy. In particular, the standard model of particle physics remains the crowning achievement of over three hundred years of reductionist thought in both physics and chemistry. Yet developments within chemistry suggest a new paradigm is required to overcome the limitations of reductionism and provide chemists a more fruitful model. This article will argue that a version of relational ontology provides an avenue for elucidating and predicting chemical and atomic phenomena. In relational ontology, the ontological status of an enduring entity in any moment is viewed as a composite of its own inherited properties and the influences of other entities, especially those closely related to it within a system. This view encompasses the causal aspects of the world without denying its dynamic and creative nature while providing a richer understanding of chemistry and other scientific fields.