The foray of punctuated equilibria into paleobiology was a pivotal point in the history of the discipline and became one of the cornerstones of contemporary evolutionary theory with far-reaching ramifications that echoed across natural and social sciences. Its most prominent and long-lasting impact was the reinvigorating the study of patterns and mechanisms of evolution in biological (and, later, socio-cultural) systems by highlighting long-term morphological stasis of species and offering a new perspective on evolutionary trends. More subtly, punctuated equilibria triggered a tectonic shift in the conceptual core of the entire field of biology. Recognizing species as discrete and stable entities invited a plethora of hypotheses about diversification dynamics involving distinct processes at the species and population levels. Implicit in the original contribution on punctuated equilibria, this insight paved the way for the development of a full-fledged hierarchical model of the organic world, the significance of which is yet to be acknowledged. Fueled by the nascent field of biological complexity, new ideas in philosophy pertaining to species ontology and the replicator-interactor dichotomy, and the revision of the explanation for large-scale patterns in the fossil record, the hierarchical model was formalized in mid 1980s in a series of works (written individually and in collaboration) by Niles Eldredge, an invertebrate paleontologist and the principal architect of the punctuated equilibria hypothesis, and Stanley Salthe, a biologist and a philosopher of science. Possibly, owing to its primarily theoretical and philosophical outlook, the model did not initially receive much traction. The beginning of the new millennium has seen a renaissance of the hierarchical approaches to evolution with the emergence of a new synthesis, integrating advances in genomics, computational approaches, complex systems sciences (network theory in particular), and recent philosophical developments in the ontology of levels of biological organization. The present contribution will describe the principal features of the current hierarchical model, clarify its relation to punctuated equilibria, and attempt to demonstrate the promise it holds for creating an overarching general theory of biological sciences.