Mainstream ecological thought is explored in three sections: (i) Epistemological traits. Given the typical scientific development and the necessity of preserving our intellectual heritage, the conservatism outlined in (i) is cyclical, so its stages are graphically summarized. (ii) Methodological benchmarks antithetically derived from (i), in order to get faster advancement consistent with the growing environmental challenges which spur ecological development. (iii) The renaissance of an old paradigm. This section exposes the misunderstanding of the physical concept of equilibrium by the mainstream ecological thought; this explains its current state. Consequently, section (iii) also summarizes the evolution of a recent set of proposals (organic biophysics of ecosystems) that rescues the foundational paradigm of ecosystem ecology based on physics, neglected by the mainstream thought before producing its most valuable results. We highlight that the main problems emerge from the weakness of integration between ecology, physics and epistemology, and spurious links between ecology and neoclassical economics.