Explanations for failures in designed and evolved systems

Engineers have long studied the origins of design features that make machines prone to failure, but biologists have only recently begun investigating why organisms have traits that make them susceptible to disease. This article compares explanations for vulnerability to failure in machines with explanations for traits that make bodies vulnerable to disease. Some global explanations are relevant for both: design deficiencies, corrupted plans, assembly variations, incorrect operating environment, and trade-offs. These similarities suggest that a common framework for failure analysis could be valuable. However, a closer look at each of the 10 global categories reveals fundamental differences: machines are built to match an ideal blueprint, while species have no perfect genome or form. Design trade-offs in machines involve balancing multiple factors such as performance, robustness, and costs, while biological trade-offs maximize only gene transmission, often at the expense of health and lifespan. Detailed consideration of these and other differences reveals how the metaphor of body as a designed machine fosters tacit creationism that misrepresents the nature of organically complex systems.

Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus

Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80°C and pH 2–4. It catabolizes specific carbon sources, such as D-glucose, to pyruvate via the modified Entner-Doudoroff (ED) pathway. This pathway has two parallel branches, the semi-phosphorylative and the non-phosphorylative. However, the strategy of S.solfataricus to endure in such an extreme environment in terms of robustness and adaptation is not yet completely understood. Here, we present the first dynamic mathematical model of the ED pathway parameterized with quantitative experimental data. These data consist of enzyme activities of the branched pathway at 70°C and 80°C and of metabolomics data at the same temperatures for the wild type and for a metabolic engineered knockout of the semi-phosphorylative branch. We use the validated model to address two questions: 1. Is this system more robust to perturbations at its optimal growth temperature? 2. Is the ED robust to deletion and perturbations? We employed a systems biology approach to answer these questions and to gain further knowledge on the emergent properties of this biological system. Specifically, we applied deterministic and stochastic approaches to study the sensitivity and robustness of the system, respectively. The mathematical model we present here, shows that: 1. Steady state metabolite concentrations of the ED pathway are consistently more robust to stochastic internal perturbations at 80°C than at 70°C; 2. These metabolite concentrations are highly robust when faced with the knockout of either branch. Connected with this observation, these two branches show different properties at the level of metabolite production and flux control. These new results reveal how enzyme kinetics and metabolomics synergizes with mathematical modelling to unveil new systemic properties of the ED pathway in S.solfataricus in terms of its adaptation and robustness.