Within the scope of this investigation, educational instruments grounded on materialist ontology were employed to undertake a semantic analysis of the concepts of cell and the mechanisms of living organisms as they appear in biology and natural science textbooks. Drawing upon the ontological categories applied to distinct biological system levels, our findings demonstrate that the dominant approach for introducing the concept of cell and living organisms is via a holistic approach. However, prevalent inaccuracies relate to the presentation of tissue or organ properties, which neglect to reference the types of cells and their interactions responsible for emergent properties at this level. Our findings suggest that the use of a holistic approach to teach the functioning of living beings, may partially account for the difficulties when transitioning between levels of reality to construct explanations by students in this field of study. Our work provides tools to transition towards a biology education with a systemic approach to the content of cells and living organisms.