The free energy principle induces intracellular compartmentalization.

Living systems at all scales are compartmentalized into interacting subsystems. This paper reviews a mechanism that drives compartmentalization in generic systems at any scale. It first discusses three symmetries of generic physical interactions in a quantum-theoretic description. It then shows that if one of these, a permutation symmetry on the inter-system boundary, is spontaneously broken, the symmetry breaking is amplified by the Free Energy Principle (FEP). It thus shows how compartmentalization generically results from permutation symmetry breaking under the FEP. It finally notes that the FEP asymptotically restores the broken symmetry, showing that the FEP can be regarded as a theory of fluctuations away from a permutation-symmetric boundary, and hence from an entangled joint state of the interacting systems.

Principled Limitations on Self-Representation for Generic Physical Systems.

The ideas of self-observation and self-representation, and the concomitant idea of self-control, pervade both the cognitive and life sciences, arising in domains as diverse as immunology and robotics. Here, we ask in a very general way whether, and to what extent, these ideas make sense. Using a generic model of physical interactions, we prove a theorem and several corollaries that severely restrict applicable notions of self-observation, self-representation, and self-control. We show, in particular, that adding observational, representational, or control capabilities to a meta-level component of a system cannot, even in principle, lead to a complete meta-level representation of the system as a whole. We conclude that self-representation can at best be heuristic, and that self models cannot, in general, be empirically tested by the systems that implement them.

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.

A Variational Synthesis of Evolutionary and Developmental Dynamics.

This paper introduces a variational formulation of natural selection, paying special attention to the nature of 'things' and the way that different 'kinds' of 'things' are individuated from-and influence-each other. We use the Bayesian mechanics of particular partitions to understand how slow phylogenetic processes constrain-and are constrained by-fast, phenotypic processes. The main result is a formulation of adaptive fitness as a path integral of phenotypic fitness. Paths of least action, at the phenotypic and phylogenetic scales, can then be read as inference and learning processes, respectively. In this view, a phenotype actively infers the state of its econiche under a generative model, whose parameters are learned via natural (Bayesian model) selection. The ensuing variational synthesis features some unexpected aspects. Perhaps the most notable is that it is not possible to describe or model a population of conspecifics per se. Rather, it is necessary to consider populations of distinct natural kinds that influence each other. This paper is limited to a description of the mathematical apparatus and accompanying ideas. Subsequent work will use these methods for simulations and numerical analyses-and identify points of contact with related mathematical formulations of evolution.

Regulative development as a model for origin of life and artificial life studies.

Using the formal framework of the Free Energy Principle, we show how generic thermodynamic requirements on bidirectional information exchange between a system and its environment can generate complexity. This leads to the emergence of hierarchical computational architectures in systems that operate sufficiently far from thermal equilibrium. In this setting, the environment of any system increases its ability to predict system behavior by "engineering" the system towards increased morphological complexity and hence larger-scale, more macroscopic behaviors. When seen in this light, regulative development becomes an environmentally-driven process in which "parts" are assembled to produce a system with predictable behavior. We suggest on this basis that life is thermodynamically favorable and that, when designing artificial living systems, human engineers are acting like a generic "environment".

Neurons as hierarchies of quantum reference frames.

Conceptual and mathematical models of neurons have lagged behind empirical understanding for decades. Here we extend previous work in modeling biological systems with fully scale-independent quantum information-theoretic tools to develop a uniform, scalable representation of synapses, dendritic and axonal processes, neurons, and local networks of neurons. In this representation, hierarchies of quantum reference frames act as hierarchical active-inference systems. The resulting model enables specific predictions of correlations between synaptic activity, dendritic remodeling, and trophic reward. We summarize how the model may be generalized to nonneural cells and tissues in developmental and regenerative contexts.

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.

Quantum Neural Networks and Topological Quantum Field Theories.

Our work intends to show that: (1) Quantum Neural Networks (QNNs) can be mapped onto spin-networks, with the consequence that the level of analysis of their operation can be carried out on the side of Topological Quantum Field Theory (TQFT); (2) A number of Machine Learning (ML) key-concepts can be rephrased by using the terminology of TQFT. Our framework provides as well a working hypothesis for understanding the generalization behavior of DNNs, relating it to the topological features of the graph structures involved.

Metacognition as a Consequence of Competing Evolutionary Time Scales.

Evolution is full of coevolving systems characterized by complex spatio-temporal interactions that lead to intertwined processes of adaptation. Yet, how adaptation across multiple levels of temporal scales and biological complexity is achieved remains unclear. Here, we formalize how evolutionary multi-scale processing underlying adaptation constitutes a form of metacognition flowing from definitions of metaprocessing in machine learning. We show (1) how the evolution of metacognitive systems can be expected when fitness landscapes vary on multiple time scales, and (2) how multiple time scales emerge during coevolutionary processes of sufficiently complex interactions. After defining a metaprocessor as a regulator with local memory, we prove that metacognition is more energetically efficient than purely object-level cognition when selection operates at multiple timescales in evolution. Furthermore, we show that existing modeling approaches to coadaptation and coevolution-here active inference networks, predator-prey interactions, coupled genetic algorithms, and generative adversarial networks-lead to multiple emergent timescales underlying forms of metacognition. Lastly, we show how coarse-grained structures emerge naturally in any resource-limited system, providing sufficient evidence for metacognitive systems to be a prevalent and vital component of (co-)evolution. Therefore, multi-scale processing is a necessary requirement for many evolutionary scenarios, leading to de facto metacognitive evolutionary outcomes.

A free energy principle for generic quantum systems.

The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on surprisal (a.k.a., self-information). This upper bound can be read as a Bayesian prediction error. Equivalently, its negative is a lower bound on Bayesian model evidence (a.k.a., marginal likelihood). In short, certain random dynamical systems evince a kind of self-evidencing. Here, we reformulate the FEP in the formal setting of spacetime-background free, scale-free quantum information theory. We show how generic quantum systems can be regarded as observers, which with the standard freedom of choice assumption become agents capable of assigning semantics to observational outcomes. We show how such agents minimize Bayesian prediction error in environments characterized by uncertainty, insufficient learning, and quantum contextuality. We show that in its quantum-theoretic formulation, the FEP is asymptotically equivalent to the Principle of Unitarity. Based on these results, we suggest that biological systems employ quantum coherence as a computational resource and - implicitly - as a communication resource. We summarize a number of problems for future research, particularly involving the resources required for classical communication and for detecting and responding to quantum context switches.

Minimal physicalism as a scale-free substrate for cognition and consciousness.

Theories of consciousness and cognition that assume a neural substrate automatically regard phylogenetically basal, nonneural systems as nonconscious and noncognitive. Here, we advance a scale-free characterization of consciousness and cognition that regards basal systems, including synthetic constructs, as not only informative about the structure and function of experience in more complex systems but also as offering distinct advantages for experimental manipulation. Our "minimal physicalist" approach makes no assumptions beyond those of quantum information theory, and hence is applicable from the molecular scale upwards. We show that standard concepts including integrated information, state broadcasting via small-world networks, and hierarchical Bayesian inference emerge naturally in this setting, and that common phenomena including stigmergic memory, perceptual coarse-graining, and attention switching follow directly from the thermodynamic requirements of classical computation. We show that the self-representation that lies at the heart of human autonoetic awareness can be traced as far back as, and serves the same basic functions as, the stress response in bacteria and other basal systems.

Metabolic limits on classical information processing by biological cells.

Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis.

Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 µm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

Fitness Beats Truth in the Evolution of Perception.

Does natural selection favor veridical percepts-those that accurately (if not exhaustively) depict objective reality? Perceptual and cognitive scientists standardly claim that it does. Here we formalize this claim using the tools of evolutionary game theory and Bayesian decision theory. We state and prove the "Fitness-Beats-Truth (FBT) Theorem" which shows that the claim is false: If one starts with the assumption that perception involves inference to states of the objective world, then the FBT Theorem shows that a strategy that simply seeks to maximize expected-fitness payoff, with no attempt to estimate the "true" world state, does consistently better. More precisely, the FBT Theorem provides a quantitative measure of the extent to which the fitness-only strategy dominates the truth strategy, and of how this dominance increases with the size of the perceptual space. The FBT Theorem supports the Interface Theory of Perception (e.g. Hoffman et al. in Psychon Bull Rev https://doi.org/10.3758/s13423-015-0890-8 , 2015), which proposes that our perceptual systems have evolved to provide a species-specific interface to guide adaptive behavior, and not to provide a veridical representation of objective reality.

Fact, Fiction, and Fitness.

A theory of consciousness, whatever else it may do, must address the structure of experience. Our perceptual experiences are richly structured. Simply seeing a red apple, swaying between green leaves on a stout tree, involves symmetries, geometries, orders, topologies, and algebras of events. Are these structures also present in the world, fully independent of their observation? Perceptual theorists of many persuasions-from computational to radical embodied-say yes: perception veridically presents to observers structures that exist in an observer-independent world; and it does so because natural selection shapes perceptual systems to be increasingly veridical. Here we study four structures: total orders, permutation groups, cyclic groups, and measurable spaces. We ask whether the payoff functions that drive evolution by natural selection are homomorphisms of these structures. We prove, in each case, that generically the answer is no: as the number of world states and payoff values go to infinity, the probability that a payoff function is a homomorphism goes to zero. We conclude that natural selection almost surely shapes perceptions of these structures to be non-veridical. This is consistent with the interface theory of perception, which claims that natural selection shapes perceptual systems not to provide veridical perceptions, but to serve as species-specific interfaces that guide adaptive behavior. Our results present a constraint for any theory of consciousness which assumes that structure in perceptual experience is shaped by natural selection.

Scale-free architectures support representational diversity.

Gilead et al. propose an ontology of abstract representations based on folk-psychological conceptions of cognitive architecture. There is, however, no evidence that the experience of cognition reveals the architecture of cognition. Scale-free architectural models propose that cognition has the same computational architecture from sub-cellular to whole-organism scales. This scale-free architecture supports representations with diverse functions and levels of abstraction.

Do Process-1 simulations generate the epistemic feelings that drive Process-2 decision making?

We apply previously developed Chu space and Channel Theory methods, focusing on the construction of Cone-Cocone Diagrams (CCCDs), to study the role of epistemic feelings, particularly feelings of confidence, in dual process models of problem solving. We specifically consider "Bayesian brain" models of probabilistic inference within a global neuronal workspace architecture. We develop a formal representation of Process-1 problem solving in which a solution is reached if and only if a CCCD is completed. We show that in this representation, Process-2 problem solving can be represented as multiply iterated Process-1 problem solving and has the same formal solution conditions. We then model the generation of explicit, reportable subjective probabilities from implicit, experienced confidence as a simulation-based, reverse engineering process and show that this process can also be modeled as a CCCD construction.

Scale-Free Biology: Integrating Evolutionary and Developmental Thinking.

When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and selection become, for example, bidirectional information flows between scales, while the notions of "cooperation" and "competition" become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale-free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system.