This paper suggests that there is need for an amplified paradigm in nutrition, going beyond biochemistry, to accommodate new research on the effects of whole foods and complex dietary systems. It offers a brief history of nutrition science, an overview of successful applications of the reigning nutritional paradigm and a rationale for a paradigm expansion. It is suggested that complexity theory can offer the theoretical framework for such an expansion. As an example, the author offers examples for applying complexity theory to understanding food and the human body as complex adaptive systems, rather than mechanical constructs. Complexity theory brings strength to concepts such as whole foods, food synergy, and nutrient synergy. Examples are given for practical applications of the paradigm.