Motivated by reductionism's current inability to encompass the quantum theory we explore an indivisible and dynamical wholeness as an underlying foundation for physics. After reviewing the role of wholeness in the quantum theory we set a philosophical background aiming at introducing an ontology, based on a dynamical wholeness. Equipped with the philosophical background we then propose a mathematical realization by representing the dynamics with a non-trivial elementary embedding from the mathematical universe to itself. By letting the embedding interact with itself through application we obtain a left-distributive universal algebra that is isomorphic to special braids. Via the connection between braids and quantum and statistical physics we show that a the mathematical structure obtained from wholeness yields known physics in a special case. In particular we point out the connections to algebras of observables, spin networks, and statistical mechanical models used in solid state physics, such as the Potts model. Furthermore we discuss the general case and there the possibility of interpreting the mathematical structure as a dynamics beyond unitary evolution, where entropy increase is involved.