According to the intentions of the special issue “Advances in Philosophical and Theoretical Plant Biology” of the journal “Theoretical and Experimental Plant Physiology” plant biology is overviewed within the contrasting realms of natural science and metaphysics. Contrasting views in these realms are exemplified with modularity – emergence, reductionist – systemic, things – processes. Domains of diversity, serendipity, beauty and time are envisaged. It is concluded that separate work within these contrasting realms and domains has to be maintained for accumulating and specifying basic knowledge. However, this is not sufficient for advancing philosophical and theoretical plant biology towards an improved understanding of (plant-) life. It is shown that and how integration is possible. Integration must be approached and practiced for a better understanding of life.