Interface Focus

Organisms are non-equilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy (FE) principle describes an organism's homeostasis as the regulation of biochemical work constrained by the physical FE cost. By contrast, recent research in neuroscience and theoretical biology explains a higher organism's homeostasis and allostasis as Bayesian inference facilitated by the informational FE...

How is the massive dimensionality and complexity of the microscopic constituents of the nervous system brought under sufficiently tight control so as to coordinate adaptive behaviour? A powerful means for striking this balance is to poise neurons close to the critical point of a phase transition, at which a small change in neuronal excitability can manifest a nonlinear augmentation in neuronal activity. How the brain could mediate this critical transition is a key open question in neuroscience. Here, I propose that the different arms of the ascending arousal system provide the brain with a diverse set of heterogeneous control parameters that can be used to modulate the excitability and receptivity of target neurons-in other words, to act as control parameters for mediating critical neuronal order...

The embryological view of development is that coordinated gene expression, cellular physics and migration provides the basis for phenotypic complexity. This stands in contrast with the prevailing view of embodied cognition, which claims that informational feedback between organisms and their environment is key to the emergence of intelligent behaviours. We aim to unite these two perspectives as embodied cognitive morphogenesis , in which morphogenetic symmetry breaking produces specialized organismal subsystems which serve as a substrate for the emergence of autonomous behaviours...

Since Newton, classical and quantum physics depend upon the 'Newtonian paradigm'. The relevant variables of the system are identified. For example, we identify the position and momentum of classical particles. Laws of motion in differential form connecting the variables are formulated. An example is Newton's three laws of motion. The boundary conditions creating the phase space of all possible values of the variables are defined. Then, given any initial condition, the differential equations of motion are integrated to yield an entailed trajectory in the prestated phase space...

The prevalence of chirally pure biological polymers is often assumed to stem from some slight preference for one chiral form at the origin of life. Likewise, the predominance of matter over antimatter is presumed to follow from some subtle bias for matter at the dawn of the universe. However, rather than being imposed from the start, handedness standards in societies emerged to make things work. Since work is the universal measure of transferred energy, it is reasoned that standards at all scales and scopes emerge to consume free energy...

Humans perceive and interact with hundreds of objects every day. In doing so, they need to employ mental models of these objects and often exploit symmetries in the object's shape and appearance in order to learn generalizable and transferable skills. Active inference is a first principles approach to understanding and modelling sentient agents. It states that agents entertain a generative model of their environment, and learn and act by minimizing an upper bound on their surprisal, i.e. their free energy. The free energy decomposes into an accuracy and complexity term, meaning that agents favour the least complex model that can accurately explain their sensory observations...

Consciousness is constituted by a structure that includes contents as foreground and the environment as background. This structural relation between the experiential foreground and background presupposes a relationship between the brain and the environment, often neglected in theories of consciousness. The temporo-spatial theory of consciousness addresses the brain-environment relation by a concept labelled 'temporo-spatial alignment'. Briefly, temporo-spatial alignment refers to the brain's neuronal activity's interaction with and adaption to interoceptive bodily and exteroceptive environmental stimuli, including their symmetry as key for consciousness...

The most immediately salient asymmetry in our experience of the world is the asymmetry of causation. In the last few decades, two developments have shed new light on the asymmetry of causation: clarity in the foundations of statistical mechanics, and the development of the interventionist conception of causation. In this paper, we ask what is the status of the causal arrow, assuming a thermodynamic gradient and the interventionist account of causation? We find that there is an objective asymmetry rooted in the thermodynamic gradient that underwrites the causal asymmetry: along a thermodynamic gradient, interventionist causal pathways-scaffolded intervention-supporting probabilistic relationships between variables-will propagate influence into the future, but not into the past...

The paper studies principles behind structured, especially symmetric, representations through enforced inter-agent conformity. For this, we consider agents in a simple environment who extract individual representations of this environment through an information maximization principle. The representations obtained by different agents differ in general to some extent from each other. This gives rise to ambiguities in how the environment is represented by the different agents. Using a variant of the information bottleneck principle, we extract a 'common conceptualization' of the world for this group of agents...

Complex phenomena are made possible when: (i) fundamental physical symmetries are broken and (ii) from the set of broken symmetries historically selected ground states are applied to performing mechanical work and storing adaptive information. Over the course of several decades Philip Anderson enumerated several key principles that can follow from broken symmetry in complex systems. These include emergence, frustrated random functions, autonomy and generalized rigidity. I describe these as the four Anderson Principles all of which are preconditions for the emergence of evolved function...

Life is a constant battle against equilibrium. From the cellular level to the macroscopic scale, living organisms as dissipative systems require the violation of their detailed balance, i.e. metabolic enzymatic reactions, in order to survive. We present a framework based on temporal asymmetry as a measure of non-equilibrium. By means of statistical physics, it was discovered that temporal asymmetries establish an arrow of time useful for assessing the reversibility in human brain time series. Previous studies in human and non-human primates have shown that decreased consciousness states such as sleep and anaesthesia result in brain dynamics closer to the equilibrium...

Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach...

Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution...

In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput reconstruction of GEMs relies on accurate gap filling of metabolic pathways using automated algorithms. Here, we systematically explore how the composition of the media (specification of the available nutrients and metabolites) during gap filling influences the resulting GEMs concerning predicted auxotrophies for fully sequenced model organisms and environmental isolates...

[This corrects the article DOI: 10.1098/rsfs.2022.0019.][This corrects the article DOI: 10.1098/rsfs.2022.0019.].

Properties of microbial communities emerge from the interactions between microorganisms and between microorganisms and their environment. At the scale of the organisms, microbial interactions are multi-step processes that are initiated by cell-cell or cell-resource encounters. Quantification and rational design of microbial interactions thus require quantification of encounter rates. Encounter rates can often be quantified through encounter kernels-mathematical formulae that capture the dependence of encounter rates on cell phenotypes, such as cell size, shape, density or motility, and environmental conditions, such as turbulence intensity or viscosity...

This paper identifies time calibration points for accurately rooting and dating the phylogeny of Arawakan, the largest Indigenous linguistic family of the Americas. We present and model a methodology for extracting calibration points from the archaeological record, based on principles of geographical overlap between archaeological sites and Arawakan peoples, and on continuity in material culture between archaeological finds and modern Arawakan practices. Based on a consensus model of the expansion of the Arawakan family from Central Amazonia, we focus on archaeological finds in Arawakan expansion zones, where Arawakan material culture abruptly appears in a given region, and where only a single major Arawakan subgroup/clade is present...

[This corrects the article DOI: 10.1098/rsfs.2021.0072.][This corrects the article DOI: 10.1098/rsfs.2021.0072.].

Although language-family specific traits which do not find direct counterparts outside a given language family are usually ignored in quantitative phylogenetic studies, scholars have made ample use of them in qualitative investigations, revealing their potential for identifying language relationships. An example of such a family specific trait are body-part expressions in Pano languages, which are often lexicalized forms, composed of bound roots (also called body-part prefixes in the literature) and non-productive derivative morphemes (called here body-part formatives)...

The Upper Rio Negro regional social system is made up of more than 30 languages belonging to six linguistic families. This results from socio-historical processes stretching back at least two millennia, which have built a system with different levels of autonomy and hierarchy associated with a mythical and ritual complex, and with social and linguistic exchanges. The analysis of these processes require an interdisciplinary outlook to understand the ways in which people from different linguistic families interacted and created it...