The theory of punctuated equilibria, introduced in paleobiology, postulates enduring morphological stability in species interrupted by rapid phenotypic change at speciation events. It played a pivotal role in evolutionary biology, reshaping perspectives and triggering a conceptual shift by redefining species as discrete and enduring entities, and paving the way for a hierarchical model of the organic world. This hierarchical approach initially faced limited attention but experienced a resurgence in the new millennium. The revived interest in hierarchical models, integrating genomics, computational methodologies, and complex systems sciences, has provided a more comprehensive theoretical foundation for understanding biological evolution. This resurgence has fueled empirical studies across various disciplines, from genomics to paleobiology, offering a potential unifying theory within the biological sciences.This paper posits the efficacy of the hierarchy theory of biology as a comprehensive, unifying framework for understanding the organic world. Despite its generality, the theory remains agnostic to specific mechanisms, allowing flexibility to accommodate diverse biological models. Through its application to speciation analysis, the hierarchy theory unveils causal processes, identifies entities and interactions, and bridges the economic and genealogical hierarchies. Acknowledging its potential for refinement based on empirical data, the hierarchy theory of biology stands as a paradigm, shaping interdisciplinary exploration and inspiring investigations across disciplines.
