ALT Fig. 1: Phylogenetic distribution of cooperative breeding and diversity of life history traits among lamprologine cichlids.

ALT A diagram showing how canalization creates a coherence gap in Waddington’s epigenetic landscape. On the bottom is a horizontal line labeled phenotypic space and on the left side is a vertical line labeled developmental time. On the right are two color scale bars. The first shows fitness, with high values shown in blue, then transitioning to green, yellow, and with low fitness shown in light beige. The second shows stability to perturbations, with low stability in white, then transitioning to light red, and high stability in dark red. The diagram shows that while canalization increases both basin and attractor coherence in absolute terms, it increases basin coherence more, creating a stability gradient within each valley. Attractors, representing mature cell types or phenotypes, are positioned closer to basin boundaries relative to transient states in their developmental trajectories. The ridges between valleys become relatively flatter near attractors compared to mid-trajectory.

ALT An illustration of the topics covered in this tutorial. Labeled Sec. II in the upper left corner is classical proteome allocation theory, which introduces the phenomenology of growth laws. Below, Sec. III explores the dependence of the translation elongation rate and ribosomal activity on growth. Section IV further extends the framework by incorporating transcriptional dynamics and traffic theory, while Sec. V to the right includes protein degradation. In the center, Sec. VI examines the mechanistic regulation of ribogenesis in both prokaryotes and eukaryotes. In the lower left corner, Section VII illustrates how to model cellular behavior in fluctuating environments. The final three sections on the far right address broader topics beyond the classical theory: density homeostasis and volume-mass coupling (Sec. VIII); the interplay between growth laws and cell-cycle progression (Sec. IX); and the insights gained from a community and ecological perspective (Sec. X).