On the Statistical Mechanics of Life: Schrödinger Revisited

The calculus of codes - From entropy, complexity, and information to life

Exploring the core components that define living systems and their operational mechanisms within emerging biological entities is a complex endeavor. In the realm of biological systems literature, the terms matter, energy, information, complexity, and entropy are frequently referenced. However, possessing these concepts alone does not guarantee a comprehensive understanding or the ability to reconstruct the intricate nature of life. This study aims to illuminate the trajectory of these organic attributes, presenting a theoretical framework that delves into the integrated role of these concepts in biology. We assert that Code Biology serves as a pivotal steppingstone for unraveling the mechanisms underlying life. Biological codes (BCs) emerge not only from the interplay of matter and energy but also from Information. Contrary to deriving information from the former elements, we propose that information holds its place as a fundamental physical aspect. Consequently, we propose a continuum perspective called Calculus of Fundamentals involving three fundamentals: Matter, Energy, and Information, to depict the dynamics of BCs. To achieve this, we emphasize the necessity of studying Entropy and Complexity as integral organic descriptors. This perspective also facilitates the introduction of a mathematical theoretical framework that aids in comprehending continuous changes, the driving dynamics of biological fundamentals. We posit that Energy, Matter, and Information constitute the essential building blocks of living systems, and their interactions are governed by Entropy and Complexity analyses, redefined as biological descriptors. This interdisciplinary perspective of Code Biology sheds light on the intricate interplay between the controversial phenomenon of life and advances the idea of constructing a theory rooted in information as an organic fundamental.

Federated inference and belief sharing

This paper concerns the distributed intelligence or federated inference that emerges under belief-sharing among agents who share a common world-and world model. Imagine, for example, several animals keeping a lookout for predators. Their collective surveillance rests upon being able to communicate their beliefs-about what they see-among themselves. But, how is this possible? Here, we show how all the necessary components arise from minimising free energy. We use numerical studies to simulate the generation, acquisition and emergence of language in synthetic agents. Specifically, we consider inference, learning and selection as minimising the variational free energy of posterior (i.e., Bayesian) beliefs about the states, parameters and structure of generative models, respectively. The common theme-that attends these optimisation processes-is the selection of actions that minimise expected free energy, leading to active inference, learning and model selection (a.k.a., structure learning). We first illustrate the role of communication in resolving uncertainty about the latent states of a partially observed world, on which agents have complementary perspectives. We then consider the acquisition of the requisite language-entailed by a likelihood mapping from an agent's beliefs to their overt expression (e.g., speech)-showing that language can be transmitted across generations by active learning. Finally, we show that language is an emergent property of free energy minimisation, when agents operate within the same econiche. We conclude with a discussion of various perspectives on these phenomena; ranging from cultural niche construction, through federated learning, to the emergence of complexity in ensembles of self-organising systems.

Path integrals, particular kinds, and strange things

This paper describes a path integral formulation of the free energy principle. The ensuing account expresses the paths or trajectories that a particle takes as it evolves over time. The main results are a method or principle of least action that can be used to emulate the behaviour of particles in open exchange with their external milieu. Particles are defined by a particular partition, in which internal states are individuated from external states by active and sensory blanket states. The variational principle at hand allows one to interpret internal dynamics-of certain kinds of particles-as inferring external states that are hidden behind blanket states. We consider different kinds of particles, and to what extent they can be imbued with an elementary form of inference or sentience. Specifically, we consider the distinction between dissipative and conservative particles, inert and active particles and, finally, ordinary and strange particles. Strange particles can be described as inferring their own actions, endowing them with apparent autonomy or agency. In short-of the kinds of particles afforded by a particular partition-strange kinds may be apt for describing sentient behaviour.

Hierarchical network structure as the source of hierarchical dynamics (power-law frequency spectra) in living and non-living systems: How state-trait continua (body plans, personalities) emerge from first principles in biophysics

Living systems are hierarchical control systems that display a small world network structure. In such structures, many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a 'power-law' cluster size distribution (a mereology). Just like their structure, the dynamics of living systems shows fractal-like qualities: the timeseries of inner message passing and overt behavior contain high frequencies or 'states' (treble) that are nested within lower frequencies or 'traits' (bass), producing a power-law frequency spectrum that is known as a 'state-trait continuum' in the behavioral sciences. Here, we argue that the power-law dynamics of living systems results from their power-law network structure: organisms 'vertically encode' the deep spatiotemporal structure of their (anticipated) environments, to the effect that many small clusters near the base of the hierarchy produce high frequency signal changes and fewer larger clusters at its top produce ultra-low frequencies. Such ultra-low frequencies exert a tonic regulatory pressure that produces morphological as well as behavioral traits (i.e., body plans and personalities). Nested-modular structure causes higher frequencies to be embedded within lower frequencies, producing a power-law state-trait continuum. At the heart of such dynamics lies the need for efficient energy dissipation through networks of coupled oscillators, which also governs the dynamics of non-living systems (e.q., earthquakes, stock market fluctuations). Since hierarchical structure produces hierarchical dynamics, the development and collapse of hierarchical structure (e.g., during maturation and disease) should leave specific traces in system dynamics (shifts in lower frequencies, i.e. morphological and behavioral traits) that may serve as early warning signs to system failure. The applications of this idea range from (bio)physics and phylogenesis to ontogenesis and clinical medicine.

Physical Grounds for Causal Perspectivalism

We ground the asymmetry of causal relations in the internal physical states of a special kind of open and irreversible physical system, a causal agent. A causal agent is an autonomous physical system, maintained in a steady state, far from thermal equilibrium, with special subsystems: sensors, actuators, and learning machines. Using feedback, the learning machine, driven purely by thermodynamic constraints, changes its internal states to learn probabilistic functional relations inherent in correlations between sensor and actuator records. We argue that these functional relations just are causal relations learned by the agent, and so such causal relations are simply relations between the internal physical states of a causal agent. We show that learning is driven by a thermodynamic principle: the error rate is minimised when the dissipated power is minimised. While the internal states of a causal agent are necessarily stochastic, the learned causal relations are shared by all machines with the same hardware embedded in the same environment. We argue that this dependence of causal relations on such 'hardware' is a novel demonstration of causal perspectivalism.

Dynamical independence: Discovering emergent macroscopic processes in complex dynamical systems

We introduce a notion of emergence for macroscopic variables associated with highly multivariate microscopic dynamical processes. Dynamical independence instantiates the intuition of an emergent macroscopic process as one possessing the characteristics of a dynamical system "in its own right," with its own dynamical laws distinct from those of the underlying microscopic dynamics. We quantify (departure from) dynamical independence by a transformation-invariant Shannon information-based measure of dynamical dependence. We emphasize the data-driven discovery of dynamically independent macroscopic variables, and introduce the idea of a multiscale "emergence portrait" for complex systems. We show how dynamical dependence may be computed explicitly for linear systems in both time and frequency domains, facilitating discovery of emergent phenomena across spatiotemporal scales, and outline application of the linear operationalization to inference of emergence portraits for neural systems from neurophysiological time-series data. We discuss dynamical independence for discrete- and continuous-time deterministic dynamics, with potential application to Hamiltonian mechanics and classical complex systems such as flocking and cellular automata.

The Role of Thermodynamic and Informational Entropy in Improving Real Estate Valuation Methods

Price, Cost and Income (PCI) are distinct economic indicators intrinsically linked to the values they denote. These observables take center stage in the multi-criteria decision-making process that enables economic agents to convey subjective utilities of market-exchanged commodities objectively. The valuation of these commodities heavily relies on PCI-based empirical observables and their supported methodologies. This valuation measure's accuracy is critical, as it influences subsequent decisions within the market chain. However, measurement errors often arise due to inherent uncertainties in the value state, impacting economic agents' wealth, particularly when trading significant commodities such as real estate properties. This paper addresses this issue by incorporating entropy measurements into real estate valuation. This mathematical technique adjusts and integrates triadic PCI estimates, improving the final stage of appraisal systems where definitive value decisions are crucial. Employing entropy within the appraisal system can also aid market agents in devising informed production/trading strategies for optimal returns. The results from our practical demonstration indicate promising implications. The entropy's integration with PCI estimates significantly improved the value measurement's precision and reduced economic decision-making errors.

On Bayesian mechanics: a physics of and by beliefs

The aim of this paper is to introduce a field of study that has emerged over the last decade, called Bayesian mechanics. Bayesian mechanics is a probabilistic mechanics, comprising tools that enable us to model systems endowed with a particular partition (i.e. into particles), where the internal states (or the trajectories of internal states) of a particular system encode the parameters of beliefs about external states (or their trajectories). These tools allow us to write down mechanical theories for systems that look as if they are estimating posterior probability distributions over the causes of their sensory states. This provides a formal language for modelling the constraints, forces, potentials and other quantities determining the dynamics of such systems, especially as they entail dynamics on a space of beliefs (i.e. on a statistical manifold). Here, we will review the state of the art in the literature on the free energy principle, distinguishing between three ways in which Bayesian mechanics has been applied to particular systems (i.e. path-tracking, mode-tracking and mode-matching). We go on to examine a duality between the free energy principle and the constrained maximum entropy principle, both of which lie at the heart of Bayesian mechanics, and discuss its implications.

Is information the other face of causation in biological systems?

Is information the other face of causation? This issue cannot be clarified without discussing how these both are related to physical laws, logic, computation, networks, bio-signaling, and the mind-body problem. The relation between information and causation is also intrinsically linked to many other concepts in complex systems theory such as emergence, self-organization, synergy, criticality, and hierarchy, which in turn involve various notions such as observer-dependence, dimensionality reduction, and especially downward causation. A canonical example proposed for downward causation is the collective behavior of the whole system at a macroscale that may affect the behavior of each its member at a microscale. In neuroscience, downward causation is suggested as a strong candidate to account for mental causation (free will). However, this would be possible only on the condition that information might have causal power. After introducing the Causal Equivalence Principle expanding the relativity principle for coarse-grained and fine-grained linear causal chains, and a set-theoretical definition of multiscale nested hierarchy composed of modular ⊂-chains, it is shown that downward causation can be spurious. It emerges only in the eyes of an observer, though, due to information that could not be obtained by "looking" exclusively at the behavior of a system at a microscale. On the other hand, since biological systems are hierarchically organized, this information gain is indicative of how information can be a function of scale in these systems and a prerequisite for scale-dependent emergence of cognition and consciousness in neural networks.

Low-dissipation optimization of the prefrontal cortex in the -12° head-down tilt position: A functional near-infrared spectroscopy study

Introduction

Our present study set out to investigate the instant state of the prefrontal cortex (PFC) in healthy subjects before and after placement in the -12°head-down tilt (HDT) position in order to explore the mechanism behind the low-dissipation optimization state of the PFC.

Methods

40 young, right-handed healthy subjects (male: female = 20: 20) were enrolled in this study. Three resting state positions, 0°initial position, -12°HDT position, and 0°rest position were sequentially tested, each for 10 minutes. A continuous-wave functional near-infrared spectroscopy (fNIRS) instrument was used to assess the resting state hemodynamic data of the PFC. After preprocessing the hemodynamics data, we evaluated changes in resting-state functional connectivity (rsFC) level and beta values of PFC. The subjective visual analogue scale (VAS) was applied before and after the experiment. The presence of sleep changes or adverse reactions were also recorded.

Results

Pairwise comparisons of the concentrations of oxyhemoglobin (HbO), deoxyhemoglobin (HbR), and hemoglobin (HbT) revealed significant differences in the aforementioned positions. Specifically, the average rsFC of PFC showed a gradual increase throughout the whole process. In addition, based on graph theory, the topological properties of brain network, such as small-world network and nodal degree centrality were analyzed. The results show that global efficiency and small-world sigma (σ) value were differences between 0°initial and 0°rest.

Discussion

In this study, placement in the -12°HDT had a significant effect on PFC function, mainly manifested as self-inhibition, decreased concentration of HbO in the PFC, and improved rsFC, which may provide ideas to the understanding and explanation of neurological diseases.

The energy glitch: Speculative histories and quantum counterfactuals

Energy (in all its conceptualizations and connotations) is a glitch, a bug, an error. Energy is presented here as a roadblock in efforts to articulate and formulate a coherent physical model of the universe, as well as an impediment to achieving just and equitable social relations. Energy broke physics and broke society. This article traces conundrums and uncertainties that prevail in physics today, from the irreconcilability of quantum dynamics and gravitational spacetime to the unsatisfactory postulation of dark energy, and the profusion of probabilistic reasoning. I offer a brief history of thermodynamics and its entanglement with industrial capitalism via the steam engine. I explore alternate histories of energy (hydrodynamic and metabolic) and speculate on the potential social implications of these counterfactual trajectories. Finally, building on the novel Constructor Theory paradigm, I entertain the possibility of replacing energy with informed noticing as the undergirding architecture of physics, replacing dynamics with discernment as the underbelly of the discipline. The operation within is not to argue that the current course of energy-based physics is "incorrect," but rather that it is problematic both for reasons of cosmological compatibility and the social disharmony it has wrought.

Competency in Navigating Arbitrary Spaces as an Invariant for Analyzing Cognition in Diverse Embodiments

One of the most salient features of life is its capacity to handle novelty and namely to thrive and adapt to new circumstances and changes in both the environment and internal components. An understanding of this capacity is central to several fields: the evolution of form and function, the design of effective strategies for biomedicine, and the creation of novel life forms via chimeric and bioengineering technologies. Here, we review instructive examples of living organisms solving diverse problems and propose competent navigation in arbitrary spaces as an invariant for thinking about the scaling of cognition during evolution. We argue that our innate capacity to recognize agency and intelligence in unfamiliar guises lags far behind our ability to detect it in familiar behavioral contexts. The multi-scale competency of life is essential to adaptive function, potentiating evolution and providing strategies for top-down control (not micromanagement) to address complex disease and injury. We propose an observer-focused viewpoint that is agnostic about scale and implementation, illustrating how evolution pivoted similar strategies to explore and exploit metabolic, transcriptional, morphological, and finally 3D motion spaces. By generalizing the concept of behavior, we gain novel perspectives on evolution, strategies for system-level biomedical interventions, and the construction of bioengineered intelligences. This framework is a first step toward relating to intelligence in highly unfamiliar embodiments, which will be essential for progress in artificial intelligence and regenerative medicine and for thriving in a world increasingly populated by synthetic, bio-robotic, and hybrid beings.

Bayesian mechanics for stationary processes

This paper develops a Bayesian mechanics for adaptive systems. Firstly, we model the interface between a system and its environment with a Markov blanket. This affords conditions under which states internal to the blanket encode information about external states. Second, we introduce dynamics and represent adaptive systems as Markov blankets at steady state. This allows us to identify a wide class of systems whose internal states appear to infer external states, consistent with variational inference in Bayesian statistics and theoretical neuroscience. Finally, we partition the blanket into sensory and active states. It follows that active states can be seen as performing active inference and well-known forms of stochastic control (such as PID control), which are prominent formulations of adaptive behaviour in theoretical biology and engineering.

Permutation Entropy as a Universal Disorder Criterion: How Disorders at Different Scale Levels Are Manifestations of the Same Underlying Principle

What do bacteria, cells, organs, people, and social communities have in common? At first sight, perhaps not much. They involve totally different agents and scale levels of observation. On second thought, however, perhaps they share everything. A growing body of literature suggests that living systems at different scale levels of observation follow the same architectural principles and process information in similar ways. Moreover, such systems appear to respond in similar ways to rising levels of stress, especially when stress levels approach near-lethal levels. To explain such communalities, we argue that all organisms (including humans) can be modeled as hierarchical Bayesian controls systems that are governed by the same biophysical principles. Such systems show generic changes when taxed beyond their ability to correct for environmental disturbances. Without exception, stressed organisms show rising levels of 'disorder' (randomness, unpredictability) in internal message passing and overt behavior. We argue that such changes can be explained by a collapse of allostatic (high-level integrative) control, which normally synchronizes activity of the various components of a living system to produce order. The selective overload and cascading failure of highly connected (hub) nodes flattens hierarchical control, producing maladaptive behavior. Thus, we present a theory according to which organic concepts such as stress, a loss of control, disorder, disease, and death can be operationalized in biophysical terms that apply to all scale levels of organization. Given the presumed universality of this mechanism, 'losing control' appears to involve the same process anywhere, whether involving bacteria succumbing to an antibiotic agent, people suffering from physical or mental disorders, or social systems slipping into warfare. On a practical note, measures of disorder may serve as early warning signs of system failure even when catastrophic failure is still some distance away.

Equality and Freedom as Uncertainty in Groups

In this paper, I investigate a connection between a common characterisation of freedom and how uncertainty is managed in a Bayesian hierarchical model. To do this, I consider a distributed factorization of a group's optimization of free energy, in which each agent is attempting to align with the group and with its own model. I show how this can lead to equilibria for groups, defined by the capacity of the model being used, essentially how many different datasets it can handle. In particular, I show that there is a "sweet spot" in the capacity of a normal model in each agent's decentralized optimization, and that this "sweet spot" corresponds to minimal free energy for the group. At the sweet spot, an agent can predict what the group will do and the group is not surprised by the agent. However, there is an asymmetry. A higher capacity model for an agent makes it harder for the individual to learn, as there are more parameters. Simultaneously, a higher capacity model for the group, implemented as a higher capacity model for each member agent, makes it easier for a group to integrate a new member. To optimize for a group of agents then requires one to make a trade-off in capacity, as each individual agent seeks to decrease capacity, but there is pressure from the group to increase capacity of all members. This pressure exists because as individual agent's capacities are reduced, so too are their abilities to model other agents, and thereby to establish pro-social behavioural patterns. I then consider a basic two-level (dual process) Bayesian model of social reasoning and a set of three parameters of capacity that are required to implement such a model. Considering these three capacities as dependent elements in a free energy minimization for a group leads to a "sweet surface" in a three-dimensional space defining the triplet of parameters that each agent must use should they hope to minimize free energy as a group. Finally, I relate these three parameters to three notions of freedom and equality in human social organization, and postulate a correspondence between freedom and model capacity. That is, models with higher capacity, have more freedom as they can interact with more datasets.

A Drive towards Thermodynamic Efficiency for Dissipative Structures in Chemical Reaction Networks

Dissipative accounts of structure formation show that the self-organisation of complex structures is thermodynamically favoured, whenever these structures dissipate free energy that could not be accessed otherwise. These structures therefore open transition channels for the state of the universe to move from a frustrated, metastable state to another metastable state of higher entropy. However, these accounts apply as well to relatively simple, dissipative systems, such as convection cells, hurricanes, candle flames, lightning strikes, or mechanical cracks, as they do to complex biological systems. Conversely, interesting computational properties-that characterize complex biological systems, such as efficient, predictive representations of environmental dynamics-can be linked to the thermodynamic efficiency of underlying physical processes. However, the potential mechanisms that underwrite the selection of dissipative structures with thermodynamically efficient subprocesses is not completely understood. We address these mechanisms by explaining how bifurcation-based, work-harvesting processes-required to sustain complex dissipative structures-might be driven towards thermodynamic efficiency. We first demonstrate a simple mechanism that leads to self-selection of efficient dissipative structures in a stochastic chemical reaction network, when the dissipated driving chemical potential difference is decreased. We then discuss how such a drive can emerge naturally in a hierarchy of self-similar dissipative structures, each feeding on the dissipative structures of a previous level, when moving away from the initial, driving disequilibrium.

Metacode: One code to rule them all

The code of codes or metacode is a microcosm where biological layers, as well as their codes, interact together allowing the continuity of information flow in organisms by increasing biological entities' complexity. Through this novel organic code, biological systems scale towards niches with higher informatic freedom building structures that increase the entropy in the universe. Code biology has developed a novel informational framework where biological entities strive themselves through the information flow carried out through organic codes consisting of two molecular or functional landscapes intertwined through arbitrary linkages via an adaptor whose nature is autonomous from molecular determinism. Here we will integrate genomic and epigenomic codes according to the evidence released in ENCODE (phase 3), psychENCODE and GTEx project, outlining the principles of the metacode, to address the continuous nature of biological systems and their inter-layered information flow. This novel complex metacode maps from very constrained sets of elements (i.e., regulation sites modulating gene expression) to new ones with greater freedom of decoding (i.e., a continuous cell phenotypic space). This leads to a new domain in code biology where biological systems are informatic attractors that navigate an energy metaspace through a complexity-noise balance, stalling in emergent niches where organic codes take meaning.

A Brief on Biological Thermodynamics for Human Physiology

Thermodynamics, the science of energy interactions, governs the direction of processes found in nature. While the subject finds wide applications in science and technology, its connection to biological sciences and in particular to bio-engineering is becoming increasingly important. In this work, after a brief introduction to the fundamental concepts in thermodynamics, we focus on its application in human physiology. A review of application of thermodynamics to the interaction between human body and environment is presented. Research works on biological systems such as the nervous system and the cardiovascular systems are summarized. The thermodynamics of metabolism is reviewed, and finally, the role of the subject in understanding and combating diseases is highlighted.

Answering Schrödinger's "What Is Life?"

In his “What Is Life?” Schrödinger poses three questions: (1) What is the source of order in organisms? (2) How do organisms remain ordered in the face of the Second Law of Thermodynamics? (3) Are new laws of physics required? He answers his first question with his famous “aperiodic solid”. He leaves his second and third questions unanswered. I try to show that his first answer is also the answer to his second question. Aperiodic solids such as protein enzymes are “boundary conditions” that constrain the release of energy into a few degrees of freedom in non-equilibrium processes such that thermodynamic work is done. This work propagates and builds structures and controls processes. These constitute his causally efficacious “code script” controlling development. The constrained release of energy also delays the production of entropy that can be exported from cells as it forms. Therefore, cells remain ordered. This answers his second question. However, “What is life?” must also ask about the diachronic evolution of life. Here, the surprising answer to this extended version of Schrödinger’s third question is that there are no new entailing laws of physics. No laws at all entail the evolution of ours or any biosphere.

Transitions in Brain Evolution: Space, Time and Entropy

How did brains evolve to become so complex, and what is their future? Brains pose an explanatory challenge because entropy, which inexorably increases over time, is commonly associated with disorder and simplicity. Recently we showed how evolution is an entropic process, building structures – organisms – which themselves facilitate entropy growth. Here we suggest that key transitional points in evolution extended organisms’ reach into space and time, opening channels into new regions of a complex multidimensional state space that also allow entropy to increase. Brain evolution enabled representation of space and time, which vastly enhances this process. Some of these channels lead to tiny, dead-ends in the state space: the persistence of complex life is thus not thermodynamically guaranteed.

Evolution of brain complexity is (counterintuitively) an entropy-enhancing process leading organisms to new regions of a space of states, which in turn allow access through channels to additional new spaces, and thus entropy to continue growing.

Step transitions in evolution have occurred as organisms acquired new abilities to reach out in space and time, vastly increasing the visitable space of states, and thereby access to new channels.

The ability of brains to represent space and time, culminating in human language and hence human technological civilisation, was an important set of transitions that magnified this process.

Continued evolution of biological complexity is not assured, because some newly accessible regions of the state space may be small and have no exits, resulting in extinction.

Bright-Dark and Multi Solitons Solutions of (3 + 1)-Dimensional Cubic-Quintic Complex Ginzburg-Landau Dynamical Equation with Applications and Stability

In this paper, bright-dark, multi solitons, and other solutions of a (3 + 1)-dimensional cubic-quintic complex Ginzburg–Landau (CQCGL) dynamical equation are constructed via employing three proposed mathematical techniques. The propagation of ultrashort optical solitons in optical fiber is modeled by this equation. The complex Ginzburg–Landau equation with broken phase symmetry has strict positive space–time entropy for an open set of parameter values. The exact wave results in the forms of dark-bright solitons, breather-type solitons, multi solitons interaction, kink and anti-kink waves, solitary waves, periodic and trigonometric function solutions are achieved. These exact solutions have key applications in engineering and applied physics. The wave solutions that are constructed from existing techniques and novel structures of solitons can be obtained by giving the special values to parameters involved in these methods. The stability of this model is examined by employing the modulation instability analysis which confirms that the model is stable. The movements of some results are depicted graphically, which are constructive to researchers for understanding the complex phenomena of this model.

On Markov blankets and hierarchical self-organisation

Biological self-organisation can be regarded as a process of spontaneous pattern formation; namely, the emergence of structures that distinguish themselves from their environment. This process can occur at nested spatial scales: from the microscopic (e.g., the emergence of cells) to the macroscopic (e.g. the emergence of organisms). In this paper, we pursue the idea that Markov blankets - that separate the internal states of a structure from external states - can self-assemble at successively higher levels of organisation. Using simulations, based on the principle of variational free energy minimisation, we show that hierarchical self-organisation emerges when the microscopic elements of an ensemble have prior (e.g., genetic) beliefs that they participate in a macroscopic Markov blanket: i.e., they can only influence - or be influenced by - a subset of other elements. Furthermore, the emergent structures look very much like those found in nature (e.g., cells or organelles), when influences are mediated by short range signalling. These simulations are offered as a proof of concept that hierarchical self-organisation of Markov blankets (into Markov blankets) can explain the self-evidencing, autopoietic behaviour of biological systems.