The rapid development of "complexity science," together with the revolutionary advances of "omics" and systems biology at the turn of the 20th and 21st centuries, has actualized the question of the structure of biological theory and practice and the place of biology in the tree of knowledge. The anti-reductionist arguments, which were initially directed against positivist and physicalist attempts to explain emergent phenomena from higher levels with components (molecules) from lower levels of matter organization (weak or epistemological reductionism), were further strengthened by the results of systems biology. Most authors agree that post-genomic systems biology is a reliable ally of anti-reductionists in fighting against reductionism, especially in rejecting epistemological and methodological reductionism. Some philosophers and scientists even go a step further and claim that it is possible to justify a strong thesis about biological reality based on the available knowledge about the living world. According to this thesis, biological processes and phenomena cannot be fully explained by the physicochemical properties of the components of living systems without assuming emergent laws (ontological holism and strong (ontological) emergence). In such a constellation of strong empirical support for the anti-reductionist stream within philosophy, which could even imply a new metaphysics, the defense of both weak and strong reductionism is called into question and requires reforming reductionist strategies.