Principles of seed banks and the emergence of complexity from dormancy

Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.

Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel

Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources—particularly oxygen—and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.

Biological matter as a material

Although it is usually obvious whether matter is animate or inanimate, it is far from easy to define life. Here we adopt as a definition the three principles identified by Paul Nurse in his recent book ‘What is life?’ There is a resurgence in the physics of life, in particular the materials science of animate matter and the emergence of complexity. This is a departure from molecular biology to a more holistic approach to understanding living matter as a self-organised complex system comprising energy-consuming, purposeful molecular machines, or agents, working collectively. An ultimate goal of synthetic biology is to create animate matter from inanimate matter. First steps have been taken, but there is still a long way to go.

4 SPECIES OF BACTERIA DETERMINISTICALLY FORM A STABLE BIOFILM IN A MILLIFLUIDIC CHANNEL: ASSEMBLY PRINCIPLES

Multispecies microbial adherent communities are widespread in nature and organisms but the principles of their assembly and development remain unclear. Yet, the demand to understand and predict the responses of such living communities to environmental changes is increasing, calling for new approaches. Here, we test the possibility to establish a simplified but relevant model of multispecies biofilm in a laboratory setup enabling in situ real-time monitoring of the community development and control of the environmental parameters in order to decipher the mechanisms underlying the formation of the community. Using video-microscopy and species combinatorial approach, we assess the global and individual species spatiotemporal development in millifluidic channels under constant flow of nutrients. Based on quantitative measurements of expansion kinetics, local dynamics and spatial distribution, we demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians and Rhodocyclus sp.) form a dynamical community that deterministically reaches its equilibrium after about 30 hours of growth. We evidence the emergence of complexity in this simplified community as reported by spatial heterogeneity rise and non-monotonic developmental kinetics. We find interspecies interactions consisting in competition for resources - in particular oxygen - and both direct and indirect physical interactions but no positive feedback. Thereby, we introduce a model of multispecies adherent community where effective couplings result from individual species quest for fitness optimization in a moving and heterogenous environment. This control and the understanding of this simplified experimental model shall open new avenues to apprehend adherent bacterial communities behavior in a context of rapid global change.

Information-theoretic analysis of complex systems modeled by two dimensional pairwise Ising models

Stochastic complex systems are composed by a large number of seemingly simple variables that exhibit non-linear interactions with each other, causing the emergence of complexity and non-deterministic dynamics in the edge between order and chaos. Hence, the evolution of these systems seems to be completely out of control, with unpredictable behaviors. In this paper, using information geometry as a mathematical approach to chaos and complexity, we investigate how information theory can be used to analyze the dynamics of pairwise Ising random fields along Markov Chain Monte Carlo simulations in which phase transitions are observed. Our experiments indicate that Fisher information regarding the inverse temperature parameter can bring important insights, since it signalizes changes in the global spatial dependence structure. Information-theoretic curves are built to show that, despite the random nature of the system, it is possible to identify an asymmetric pattern of evolution when the system moves towards different entropic states.

Emergence of complexity in hierarchically organized chiral particles

The structural complexity of composite biomaterials and biomineralized particles arises from the hierarchical ordering of inorganic building blocks over multiple scales. Although empirical observations of complex nanoassemblies are abundant, the physicochemical mechanisms leading to their geometrical complexity are still puzzling, especially for nonuniformly sized components. We report the self-assembly of hierarchically organized particles (HOPs) from polydisperse gold thiolate nanoplatelets with cysteine surface ligands. Graph theory methods indicate that these HOPs, which feature twisted spikes and other morphologies, display higher complexity than their biological counterparts. Their intricate organization emerges from competing chirality-dependent assembly restrictions that render assembly pathways primarily dependent on nanoparticle symmetry rather than size. These findings and HOP phase diagrams open a pathway to a large family of colloids with complex architectures and unusual chiroptical and chemical properties.

A Uniquely Complex Mitochondrial Proteome from Euglena gracilis

Euglena gracilis is a metabolically flexible, photosynthetic, and adaptable free-living protist of considerable environmental importance and biotechnological value. By label-free liquid chromatography tandem mass spectrometry, a total of 1,786 proteins were identified from the E. gracilis purified mitochondria, representing one of the largest mitochondrial proteomes so far described. Despite this apparent complexity, protein machinery responsible for the extensive RNA editing, splicing, and processing in the sister clades diplonemids and kinetoplastids is absent. This strongly suggests that the complex mechanisms of mitochondrial gene expression in diplonemids and kinetoplastids occurred late in euglenozoan evolution, arising independently. By contrast, the alternative oxidase pathway and numerous ribosomal subunits presumed to be specific for parasitic trypanosomes are present in E. gracilis. We investigated the evolution of unexplored protein families, including import complexes, cristae formation proteins, and translation termination factors, as well as canonical and unique metabolic pathways. We additionally compare this mitoproteome with the transcriptome of Eutreptiella gymnastica, illuminating conserved features of Euglenida mitochondria as well as those exclusive to E. gracilis. This is the first mitochondrial proteome of a free-living protist from the Excavata and one of few available for protists as a whole. This study alters our views of the evolution of the mitochondrion and indicates early emergence of complexity within euglenozoan mitochondria, independent of parasitism.

Brian Ferneyhough’s ‘Transit’, The London Sinfonietta, and the Emergence of Complexity in 1977

In November 1977 the London Sinfonietta began its tenth-anniversary season with a performance in London of Transit by Brian Ferneyhough. The concert marks a significant moment in the formation of Ferneyhough’s public persona, just as the tenth-anniversary season marked a turning point for the London Sinfonietta. In this article I undertake a microhistory of this performance in order to ascertain how Ferneyhough’s reputation for complexity was forged in Britain. Rooted in performance and reception history, and based around close readings of key tropes, I show that early critical opinion ranged from sympathetic to ambivalent or curious; yet it never developed into the type of hostility commonly referenced in critiques of New Complexity. The historical detail of this pivotal performance, I argue, suggests the need for a broader cultural history attuned to the transitional state that characterizes both the history and the historiography of new music in the late 1970s.