Performance tradeoffs are ubiquitous in biology (and an essential feature of HOT). Well-studied examples include biomechanics (strength vs. speed), animal behavior (fight vs. flight), and, until recently, enzymes (stability vs. activity). The patterns of stability and activity among naturally-occurring, homologous enzymes have traditionally been attributed to flexibility tradeoffs. However, flexibility is sufficiently complex that it cannot mediate generic tradeoffs outside the active site. Furthermore, enzymes with unnatural combinations of high stability and high activity can be created in the laboratory. These enzymes are exceptionally rare among all possible amino acid sequences, suggesting that evolutionary, not physicochemical, mechanisms are responsible for the stability-activity patterns among natural homologs. Check out these slides for more information.

The relative importance of exogenous and endogenous effects in extinction has been widely debated.  We present a unifying picture based on a biotic community of evolving lattice organisms, where mutation and selection of the fittest leads to the evolution of specialized internal structure reflecting common environmental disturbances.  This is an example of Highly Optimized Tolerance (HOT), a theoretical framework supporting observations of repeatable patterns in the fossil record, in which large extinction events are triggered by rare environmental disturbances, most strongly effecting the most highly evolved, specialized organisms, followed by periods of rapid growth and diversification. Click here for more details.