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Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are examples where apparently robust behaviour emerges from highly complex and stochastic sub-cellular processes. Here we attempt to make connections between different theoretical perspectives to gain qualitative insights into the types of cell-fate decision making processes that are at the heart of stem cell and developmental biology. We discuss both dynamical systems as well as statistical mechanics perspectives on the classical Waddington or epigenetic landscape. We find that non-equilibrium approaches are required to overcome some of the shortcomings of classical equilibrium statistical thermodynamics or statistical mechanics in order to shed light on biological processes, which, almost by definition, are typically far from equilibrium.
The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddingtons landscape, consisting of hills and valleys. The smooth top and valley-strewn botto
Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To address this
Directed fibroblast migration is central to highly proliferative processes in regenerative medicine and developmental biology, such as wound healing and embryogenesis. However, the mechanisms by which single fibroblasts affect each others directional
Studying the development of malignant tumours, it is important to know and predict the proportions of different cell types in tissue samples. Knowing the expected temporal evolution of the proportion of normal tissue cells, compared to stem-like and
Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to harmonise an