This essay re-examines the enduring conceptual landscape of self-organization with the objective of clarifying the fundamental role of emergence and holism in contemporary biology. A deeper appreciation of these concepts can help biologists establish a solid theoretical foundation, avoiding biases that may occur when such perspectives are incomplete. The essay begins by exploring the historical roots of self-organization in biology and then discusses relevant theories of self-organization in the biological sciences. A comprehensive understanding of these historical foundations and the significance of self-organization is used to explore and conceptually connect self-organization to emergence and holism. Throughout the essay, these theoretical frameworks are illustrated with significant examples from biology and other scientific fields. In conclusion, the essay emphasizes the need for deeper conceptual reflection to clarify many controversial issues at the intersection of self-organization, emergence, and holism in biology and, more broadly, within science.
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