Written at an undergraduate mathematical level, this book provides the essential theoretical tools and foundations required to develop basic models to explain collective phase transitions for a wide variety of ecosystems.

Genomic instability is a hallmark of cancer. Cancer cells that exhibit abnormal chromosomes are characteristic of most advanced tumours, despite the potential threat represented by accumulated genetic damage. Carcinogenesis involves a loss of key components of the genetic and signalling molecular networks; hence some authors have suggested that this is part of a trend of cancer cells to behave as simple, minimal replicators. In this study, we explore this conjecture and suggest that, in the case of cancer, genomic instability has (...) an upper limit that is associated with a minimal cancer cell network. Such a network would include (for a given microenvironment) the basic molecular components that allow cells to replicate and respond to selective pressures. However, it would also exhibit internal fragilities that could be exploited by appropriate therapies targeting the DNA repair machinery. The implications of this hypothesis are discussed. (shrink)

Leigh Van Valen was an American evolutionary biologist who made major contributions to evolutionary theory. He is particularly remembered for his groundbreaking paper “A New Evolutionary Law” (1973) where he provided evidence from fossil record data that the probability of extinction within any group remains essentially constant through time. In order to explain such an unexpected result, Van Valen formulated a very influential idea that he dubbed the “Red Queen hypothesis.” It states that the constant decay must be a consequence (...) of evolutionary interactions among connected species within ecological networks. In Van Valen’s picture, species do not merely evolve: they also coevolve with other species. As a consequence, when thinking about adaptation to an external environment, the other species must be considered as part (maybe a major part) of such an external world. Van Valen’s law provided the first complex systems theory of coevolutionary dynamics and inspired a whole range of theoretical and experimental developments from very diverse fields, percolating far beyond its original formulation. Red Queen arms races are nowadays considered a widespread feature of complex adaptive systems. (shrink)

Human cancers comprise an heterogeneous array of diseases with different progression patterns and responses to therapy. However, they all develop within a host context that constrains their natural history. Since it occurs across the diversity of organisms, one can conjecture that there is order in the cancer multiverse. Is there a way to capture the broad range of tumor types within a space of the possible? Here we define the oncospace, a coordinate system that integrates the ecological, evolutionary and developmental (...) components of cancer complexity. The spatial position of a tumor results from its departure from the healthy tissue along these three axes, and progression trajectories inform about the components driving malignancy across cancer subtypes. We postulate that the oncospace topology encodes new information regarding tumorigenic pathways, subtype prognosis, and therapeutic opportunities: treatment design could benefit from considering how to nudge tumors toward empty evolutionary dead ends in the oncospace. (shrink)

The search for a systems‐level picture of metabolism as a web of molecular interactions provides a paradigmatic example of how the methods used to characterize a system can bias the interpretation of its functional meaning. Metabolic maps have been analyzed using novel techniques from network theory, revealing some non‐trivial, functionally relevant properties. These include a small‐world structure and hierarchical modularity. However, as discussed here, some of these properties might actually result from an inappropriate way of defining network interactions. Starting from (...) the so‐called bipartite organization of metabolism, where the two meaningful subsets (reactions and metabolites) are considered, most current works use only one of the subsets by means of so‐called graph projections. Unfortunately, projected graphs often ignore relevant biological and chemical constraints, thus leading to statistical artifacts. Some of these drawbacks and alternative approaches need to be properly addressed. (shrink)

Fluid neural networks can be used as a theoretical framework for a wide range of complex systems as social insects. In this article we show that collective logical gates can be built in such a way that complex computation can be possible by means of the interplay between local interactions and the collective creation of a global field. This is exemplified by a NOR gate. Some general implications for ant societies are outlined. ©.