Knowing one's place: a free-energy approach to pattern regulation

Stress sharing as cognitive glue for collective intelligences: A computational model of stress as a coordinator for morphogenesis

Individual cells have numerous competencies in physiological and metabolic spaces. However, multicellular collectives can reliably navigate anatomical morphospace towards much larger, reliable endpoints. Understanding the robustness and control properties of this process is critical for evolutionary developmental biology, bioengineering, and regenerative medicine. One mechanism that has been proposed for enabling individual cells to coordinate toward specific morphological outcomes is the sharing of stress (where stress is a physiological parameter that reflects the current amount of error in the context of a homeostatic loop). Here, we construct and analyze a multiscale agent-based model of morphogenesis in which we quantitatively examine the impact of stress sharing on the ability to reach target morphology. We found that stress sharing improves the morphogenetic efficiency of multicellular collectives; populations with stress sharing reached anatomical targets faster. Moreover, stress sharing influenced the future fate of distant cells in the multi-cellular collective, enhancing cells' movement and their radius of influence, consistent with the hypothesis that stress sharing works to increase cohesiveness of collectives. During development, anatomical goal states could not be inferred from observation of stress states, revealing the limitations of knowledge of goals by an extern observer outside the system itself. Taken together, our analyses support an important role for stress sharing in natural and engineered systems that seek robust large-scale behaviors to emerge from the activity of their competent components.

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.

Active Inference for Learning and Development in Embodied Neuromorphic Agents

Taking inspiration from humans can help catalyse embodied AI solutions for important real-world applications. Current human-inspired tools include neuromorphic systems and the developmental approach to learning. However, this developmental neurorobotics approach is currently lacking important frameworks for human-like computation and learning. We propose that human-like computation is inherently embodied, with its interface to the world being neuromorphic, and its learning processes operating across different timescales. These constraints necessitate a unified framework: active inference, underpinned by the free energy principle (FEP). Herein, we describe theoretical and empirical support for leveraging this framework in embodied neuromorphic agents with autonomous mental development. We additionally outline current implementation approaches (including toolboxes) and challenges, and we provide suggestions for next steps to catalyse this important field.

Self-Improvising Memory: A Perspective on Memories as Agential, Dynamically Reinterpreting Cognitive Glue

Many studies on memory emphasize the material substrate and mechanisms by which data can be stored and reliably read out. Here, I focus on complementary aspects: the need for agents to dynamically reinterpret and modify memories to suit their ever-changing selves and environment. Using examples from developmental biology, evolution, and synthetic bioengineering, in addition to neuroscience, I propose that a perspective on memory as preserving salience, not fidelity, is applicable to many phenomena on scales from cells to societies. Continuous commitment to creative, adaptive confabulation, from the molecular to the behavioral levels, is the answer to the persistence paradox as it applies to individuals and whole lineages. I also speculate that a substrate-independent, processual view of life and mind suggests that memories, as patterns in the excitable medium of cognitive systems, could be seen as active agents in the sense-making process. I explore a view of life as a diverse set of embodied perspectives-nested agents who interpret each other's and their own past messages and actions as best as they can (polycomputation). This synthesis suggests unifying symmetries across scales and disciplines, which is of relevance to research programs in Diverse Intelligence and the engineering of novel embodied minds.

Markov Blankets and Mirror Symmetries-Free Energy Minimization and Mesocortical Anatomy

A theoretical account of development in mesocortical anatomy is derived from the free energy principle, operating in a neural field with both Hebbian and anti-Hebbian neural plasticity. An elementary structural unit is proposed, in which synaptic connections at mesoscale are arranged in paired patterns with mirror symmetry. Exchanges of synaptic flux in each pattern form coupled spatial eigenmodes, and the line of mirror reflection between the paired patterns operates as a Markov blanket, so that prediction errors in exchanges between the pairs are minimized. The theoretical analysis is then compared to the outcomes from a biological model of neocortical development, in which neuron precursors are selected by apoptosis for cell body and synaptic connections maximizing synchrony and also minimizing axonal length. It is shown that this model results in patterns of connection with the anticipated mirror symmetries, at micro-, meso- and inter-arial scales, among lateral connections, and in cortical depth. This explains the spatial organization and functional significance of neuron response preferences, and is compatible with the structural form of both columnar and noncolumnar cortex. Multi-way interactions of mirrored representations can provide a preliminary anatomically realistic model of cortical information processing.

The police hunch: the Bayesian brain, active inference, and the free energy principle in action

In the realm of law enforcement, the "police hunch" has long been a mysterious but crucial aspect of decision-making. Drawing on the developing framework of Active Inference from cognitive science, this theoretical article examines the genesis, mechanics, and implications of the police hunch. It argues that hunches - often vital in high-stakes situations - should not be described as mere intuitions, but as intricate products of our mind's generative models. These models, shaped by observations of the social world and assimilated and enacted through active inference, seek to reduce surprise and make hunches an indispensable tool for officers, in exactly the same way that hypotheses are indispensable for scientists. However, the predictive validity of hunches is influenced by a range of factors, including experience and bias, thus warranting critical examination of their reliability. This article not only explores the formation of police hunches but also provides practical insights for officers and researchers on how to harness the power of active inference to fully understand policing decisions and subsequently explore new avenues for future research.

Active inference as a theory of sentient behavior

This review paper offers an overview of the history and future of active inference-a unifying perspective on action and perception. Active inference is based upon the idea that sentient behavior depends upon our brains' implicit use of internal models to predict, infer, and direct action. Our focus is upon the conceptual roots and development of this theory of (basic) sentience and does not follow a rigid chronological narrative. We trace the evolution from Helmholtzian ideas on unconscious inference, through to a contemporary understanding of action and perception. In doing so, we touch upon related perspectives, the neural underpinnings of active inference, and the opportunities for future development. Key steps in this development include the formulation of predictive coding models and related theories of neuronal message passing, the use of sequential models for planning and policy optimization, and the importance of hierarchical (temporally) deep internal (i.e., generative or world) models. Active inference has been used to account for aspects of anatomy and neurophysiology, to offer theories of psychopathology in terms of aberrant precision control, and to unify extant psychological theories. We anticipate further development in all these areas and note the exciting early work applying active inference beyond neuroscience. This suggests a future not just in biology, but in robotics, machine learning, and artificial intelligence.

Generating meaning: active inference and the scope and limits of passive AI

Prominent accounts of sentient behavior depict brains as generative models of organismic interaction with the world, evincing intriguing similarities with current advances in generative artificial intelligence (AI). However, because they contend with the control of purposive, life-sustaining sensorimotor interactions, the generative models of living organisms are inextricably anchored to the body and world. Unlike the passive models learned by generative AI systems, they must capture and control the sensory consequences of action. This allows embodied agents to intervene upon their worlds in ways that constantly put their best models to the test, thus providing a solid bedrock that is - we argue - essential to the development of genuine understanding. We review the resulting implications and consider future directions for generative AI.

Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance

Information for organismal patterning can come from a variety of sources. We investigate the possibility that instructive influences for normal embryonic development are provided not only at the level of cells within the embryo, but also via interactions between embryos. To explore this, we challenge groups of embryos with disruptors of normal development while varying group size. Here, we show that Xenopus laevis embryos are much more sensitive to a diverse set of chemical and molecular-biological perturbations when allowed to develop alone or in small groups, than in large groups. Keeping per-embryo exposure constant, we find that increasing the number of exposed embryos in a cohort increases the rate of survival while incidence of defects decreases. This inter-embryo assistance effect is mediated by short-range diffusible signals and involves the P2 ATP receptor. Our data and computational model emphasize that morphogenesis is a collective phenomenon not only at the level of cells, but also of whole bodies, and that cohort size is a crucial variable in studies of ecotoxicology, teratogenesis, and developmental plasticity.

Nested Selves: Self-Organization and Shared Markov Blankets in Prenatal Development in Humans

The immune system is a central component of organismic function in humans. This paper addresses self-organization of biological systems in relation to-and nested within-other biological systems in pregnancy. Pregnancy constitutes a fundamental state for human embodiment and a key step in the evolution and conservation of our species. While not all humans can be pregnant, our initial state of emerging and growing within another person's body is universal. Hence, the pregnant state does not concern some individuals but all individuals. Indeed, the hierarchical relationship in pregnancy reflects an even earlier autopoietic process in the embryo by which the number of individuals in a single blastoderm is dynamically determined by cell- interactions. The relationship and the interactions between the two self-organizing systems during pregnancy may play a pivotal role in understanding the nature of biological self-organization per se in humans. Specifically, we consider the role of the immune system in biological self-organization in addition to neural/brain systems that furnish us with a sense of self. We examine the complex case of pregnancy, whereby two immune systems need to negotiate the exchange of resources and information in order to maintain viable self-regulation of nested systems. We conclude with a proposal for the mechanisms-that scaffold the complex relationship between two self-organising systems in pregnancy-through the lens of the Active Inference, with a focus on shared Markov blankets.

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.

Bioelectric networks: the cognitive glue enabling evolutionary scaling from physiology to mind

Each of us made the remarkable journey from mere matter to mind: starting life as a quiescent oocyte ("just chemistry and physics"), and slowly, gradually, becoming an adult human with complex metacognitive processes, hopes, and dreams. In addition, even though we feel ourselves to be a unified, single Self, distinct from the emergent dynamics of termite mounds and other swarms, the reality is that all intelligence is collective intelligence: each of us consists of a huge number of cells working together to generate a coherent cognitive being with goals, preferences, and memories that belong to the whole and not to its parts. Basal cognition is the quest to understand how Mind scales-how large numbers of competent subunits can work together to become intelligences that expand the scale of their possible goals. Crucially, the remarkable trick of turning homeostatic, cell-level physiological competencies into large-scale behavioral intelligences is not limited to the electrical dynamics of the brain. Evolution was using bioelectric signaling long before neurons and muscles appeared, to solve the problem of creating and repairing complex bodies. In this Perspective, I review the deep symmetry between the intelligence of developmental morphogenesis and that of classical behavior. I describe the highly conserved mechanisms that enable the collective intelligence of cells to implement regulative embryogenesis, regeneration, and cancer suppression. I sketch the story of an evolutionary pivot that repurposed the algorithms and cellular machinery that enable navigation of morphospace into the behavioral navigation of the 3D world which we so readily recognize as intelligence. Understanding the bioelectric dynamics that underlie construction of complex bodies and brains provides an essential path to understanding the natural evolution, and bioengineered design, of diverse intelligences within and beyond the phylogenetic history of Earth.

Closing the loop on morphogenesis: a mathematical model of morphogenesis by closed-loop reaction-diffusion

Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from disturbances, such as splitting into twins. While this reliability implies some type of goal-seeking error minimization over a morphogenic field, there are many gaps with respect to detailed, constructive models of such a process. A common way to achieve reliability is negative feedback, which requires characterizing the existing body shape to create an error signal-but measuring properties of a shape may not be simple. We show how cells communicating in a wave-like pattern could analyze properties of the current body shape. We then describe a closed-loop negative-feedback system for creating reaction-diffusion (RD) patterns with high reliability. Specifically, we use a wave to count the number of peaks in a RD pattern, letting us use a negative-feedback controller to create a pattern with N repetitions, where N can be altered over a wide range. Furthermore, the individual repetitions of the RD pattern can be easily stretched or shrunk under genetic control to create, e.g., some morphological features larger than others. This work contributes to the exciting effort of understanding design principles of morphological computation, which can be used to understand evolved developmental mechanisms, manipulate them in regenerative-medicine settings, or engineer novel synthetic morphology constructs with desired robust behavior.

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.

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.

Cellular signaling pathways as plastic, proto-cognitive systems: Implications for biomedicine

Many aspects of health and disease are modeled using the abstraction of a "pathway"-a set of protein or other subcellular activities with specified functional linkages between them. This metaphor is a paradigmatic case of a deterministic, mechanistic framework that focuses biomedical intervention strategies on altering the members of this network or the up-/down-regulation links between them-rewiring the molecular hardware. However, protein pathways and transcriptional networks exhibit interesting and unexpected capabilities such as trainability (memory) and information processing in a context-sensitive manner. Specifically, they may be amenable to manipulation via their history of stimuli (equivalent to experiences in behavioral science). If true, this would enable a new class of biomedical interventions that target aspects of the dynamic physiological "software" implemented by pathways and gene-regulatory networks. Here, we briefly review clinical and laboratory data that show how high-level cognitive inputs and mechanistic pathway modulation interact to determine outcomes in vivo. Further, we propose an expanded view of pathways from the perspective of basal cognition and argue that a broader understanding of pathways and how they process contextual information across scales will catalyze progress in many areas of physiology and neurobiology. We argue that this fuller understanding of the functionality and tractability of pathways must go beyond a focus on the mechanistic details of protein and drug structure to encompass their physiological history as well as their embedding within higher levels of organization in the organism, with numerous implications for data science addressing health and disease. Exploiting tools and concepts from behavioral and cognitive sciences to explore a proto-cognitive metaphor for the pathways underlying health and disease is more than a philosophical stance on biochemical processes; at stake is a new roadmap for overcoming the limitations of today's pharmacological strategies and for inferring future therapeutic interventions for a wide range of disease states.

The mesoanatomy of the cortex, minimization of free energy, and generative cognition

Capacity for generativity and unlimited association is the defining characteristic of sentience, and this capacity somehow arises from neuronal self-organization in the cortex. We have previously argued that, consistent with the free energy principle, cortical development is driven by synaptic and cellular selection maximizing synchrony, with effects manifesting in a wide range of features of mesoscopic cortical anatomy. Here, we further argue that in the postnatal stage, as more structured inputs reach the cortex, the same principles of self-organization continue to operate at multitudes of local cortical sites. The unitary ultra-small world structures that emerged antenatally can represent sequences of spatiotemporal images. Local shifts of presynapses from excitatory to inhibitory cells result in the local coupling of spatial eigenmodes and the development of Markov blankets, minimizing prediction errors in each unit's interactions with surrounding neurons. In response to the superposition of inputs exchanged between cortical areas, more complicated, potentially cognitive structures are competitively selected by the merging of units and the elimination of redundant connections that result from the minimization of variational free energy and the elimination of redundant degrees of freedom. The trajectory along which free energy is minimized is shaped by interaction with sensorimotor, limbic, and brainstem mechanisms, providing a basis for creative and unlimited associative learning.

Darwin's agential materials: evolutionary implications of multiscale competency in developmental biology

A critical aspect of evolution is the layer of developmental physiology that operates between the genotype and the anatomical phenotype. While much work has addressed the evolution of developmental mechanisms and the evolvability of specific genetic architectures with emergent complexity, one aspect has not been sufficiently explored: the implications of morphogenetic problem-solving competencies for the evolutionary process itself. The cells that evolution works with are not passive components: rather, they have numerous capabilities for behavior because they derive from ancestral unicellular organisms with rich repertoires. In multicellular organisms, these capabilities must be tamed, and can be exploited, by the evolutionary process. Specifically, biological structures have a multiscale competency architecture where cells, tissues, and organs exhibit regulative plasticity-the ability to adjust to perturbations such as external injury or internal modifications and still accomplish specific adaptive tasks across metabolic, transcriptional, physiological, and anatomical problem spaces. Here, I review examples illustrating how physiological circuits guiding cellular collective behavior impart computational properties to the agential material that serves as substrate for the evolutionary process. I then explore the ways in which the collective intelligence of cells during morphogenesis affect evolution, providing a new perspective on the evolutionary search process. This key feature of the physiological software of life helps explain the remarkable speed and robustness of biological evolution, and sheds new light on the relationship between genomes and functional anatomical phenotypes.

Really radical?

I enjoyed reading this compelling account of Conviction Narrative Theory (CNT). As a theoretical neurobiologist, I recognised - and applauded - the tenets of CNT. My commentary asks whether its claims could be installed into a Bayesian mechanics of decision-making, in a way that would enable theoreticians to model, reproduce and predict decision-making.

There’s Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-Scale Machines

The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic view. Such a view dissolves the contingent dichotomies driven by human cognitive biases (e.g., a tendency to oversimplify) and prior technological limitations in favor of a more continuous view, necessitated by the study of evolution, developmental biology, and intelligent machines. Form and function are tightly entwined in nature, and in some cases, in robotics as well. Thus, efforts to re-shape living systems for biomedical or bioengineering purposes require prediction and control of their function at multiple scales. This is challenging for many reasons, one of which is that living systems perform multiple functions in the same place at the same time. We refer to this as “polycomputing”—the ability of the same substrate to simultaneously compute different things, and make those computational results available to different observers. This ability is an important way in which living things are a kind of computer, but not the familiar, linear, deterministic kind; rather, living things are computers in the broad sense of their computational materials, as reported in the rapidly growing physical computing literature. We argue that an observer-centered framework for the computations performed by evolved and designed systems will improve the understanding of mesoscale events, as it has already done at quantum and relativistic scales. To develop our understanding of how life performs polycomputing, and how it can be convinced to alter one or more of those functions, we can first create technologies that polycompute and learn how to alter their functions. Here, we review examples of biological and technological polycomputing, and develop the idea that the overloading of different functions on the same hardware is an important design principle that helps to understand and build both evolved and designed systems. Learning to hack existing polycomputing substrates, as well as to evolve and design new ones, will have massive impacts on regenerative medicine, robotics, and computer engineering.

Active inference, morphogenesis, and computational psychiatry

Active inference is a leading theory in neuroscience that provides a simple and neuro-biologically plausible account of how action and perception are coupled in producing (Bayes) optimal behavior; and has been recently used to explain a variety of psychopathological conditions. In parallel, morphogenesis has been described as the behavior of a (non-neural) cellular collective intelligence solving problems in anatomical morphospace. In this article, we establish a link between the domains of cell biology and neuroscience, by analyzing disorders of morphogenesis as disorders of (active) inference. The aim of this article is three-fold. We want to: (i) reveal a connection between disorders of morphogenesis and disorders of active inference as apparent in psychopathological conditions; (ii) show how disorders of morphogenesis can be simulated using active inference; (iii) suggest that active inference can shed light on developmental defects or aberrant morphogenetic processes, seen as disorders of information processing, and perhaps suggesting novel intervention and repair strategies. We present four simulations illustrating application of these ideas to cellular behavior during morphogenesis. Three of the simulations show that the same forms of aberrant active inference (e.g., deficits of sensory attenuation and low sensory precision) that have been used to explain psychopathological conditions (e.g., schizophrenia and autism) also produce familiar disorders of development and morphogenesis when implemented at the level of the collective behavior of a group of cells. The fourth simulation involves two cells with too high precision, in which we show that the reduction of concentration signaling and sensitivity to the signals of other cells treats the development defect. Finally, we present the results of an experimental test of one of the model's predictions in early Xenopus laevis embryos: thioridazine (a dopamine antagonist that may reduce sensory precision in biological systems) induced developmental (anatomical) defects as predicted. The use of conceptual and empirical tools from neuroscience to understand the morphogenetic behavior of pre-neural agents offers the possibility of new approaches in regenerative medicine and evolutionary developmental biology.

Counting with Cilia: The Role of Morphological Computation in Basal Cognition Research

"Morphological computation" is an increasingly important concept in robotics, artificial intelligence, and philosophy of the mind. It is used to understand how the body contributes to cognition and control of behavior. Its understanding in terms of "offloading" computation from the brain to the body has been criticized as misleading, and it has been suggested that the use of the concept conflates three classes of distinct processes. In fact, these criticisms implicitly hang on accepting a semantic definition of what constitutes computation. Here, I argue that an alternative, mechanistic view on computation offers a significantly different understanding of what morphological computation is. These theoretical considerations are then used to analyze the existing research program in developmental biology, which understands morphogenesis, the process of development of shape in biological systems, as a computational process. This important line of research shows that cognition and intelligence can be found across all scales of life, as the proponents of the basal cognition research program propose. Hence, clarifying the connection between morphological computation and morphogenesis allows for strengthening the role of the former concept in this emerging research field.

Cognition as Morphological/Morphogenetic Embodied Computation In Vivo

Cognition, historically considered uniquely human capacity, has been recently found to be the ability of all living organisms, from single cells and up. This study approaches cognition from an info-computational stance, in which structures in nature are seen as information, and processes (information dynamics) are seen as computation, from the perspective of a cognizing agent. Cognition is understood as a network of concurrent morphological/morphogenetic computations unfolding as a result of self-assembly, self-organization, and autopoiesis of physical, chemical, and biological agents. The present-day human-centric view of cognition still prevailing in major encyclopedias has a variety of open problems. This article considers recent research about morphological computation, morphogenesis, agency, basal cognition, extended evolutionary synthesis, free energy principle, cognition as Bayesian learning, active inference, and related topics, offering new theoretical and practical perspectives on problems inherent to the old computationalist cognitive models which were based on abstract symbol processing, and unaware of actual physical constraints and affordances of the embodiment of cognizing agents. A better understanding of cognition is centrally important for future artificial intelligence, robotics, medicine, and related fields.

Endless forms most beautiful 2.0: teleonomy and the bioengineering of chimaeric and synthetic organisms

The rich variety of biological forms and behaviours results from one evolutionary history on Earth, via frozen accidents and selection in specific environments. This ubiquitous baggage in natural, familiar model species obscures the plasticity and swarm intelligence of cellular collectives. Significant gaps exist in our understanding of the origin of anatomical novelty, of the relationship between genome and form, and of strategies for control of large-scale structure and function in regenerative medicine and bioengineering. Analysis of living forms that have never existed before is necessary to reveal deep design principles of life as it can be. We briefly review existing examples of chimaeras, cyborgs, hybrots and other beings along the spectrum containing evolved and designed systems. To drive experimental progress in multicellular synthetic morphology, we propose teleonomic (goal-seeking, problem-solving) behaviour in diverse problem spaces as a powerful invariant across possible beings regardless of composition or origin. Cybernetic perspectives on chimaeric morphogenesis erase artificial distinctions established by past limitations of technology and imagination. We suggest that a multi-scale competency architecture facilitates evolution of robust problem-solving, living machines. Creation and analysis of novel living forms will be an essential testbed for the emerging field of diverse intelligence, with numerous implications across regenerative medicine, robotics and ethics.

Resourceful Event-Predictive Inference: The Nature of Cognitive Effort

Pursuing a precise, focused train of thought requires cognitive effort. Even more effort is necessary when more alternatives need to be considered or when the imagined situation becomes more complex. Cognitive resources available to us limit the cognitive effort we can spend. In line with previous work, an information-theoretic, Bayesian brain approach to cognitive effort is pursued: to solve tasks in our environment, our brain needs to invest information, that is, negative entropy, to impose structure, or focus, away from a uniform structure or other task-incompatible, latent structures. To get a more complete formalization of cognitive effort, a resourceful event-predictive inference model (REPI) is introduced, which offers computational and algorithmic explanations about the latent structure of our generative models, the active inference dynamics that unfold within, and the cognitive effort required to steer the dynamics-to, for example, purposefully process sensory signals, decide on responses, and invoke their execution. REPI suggests that we invest cognitive resources to infer preparatory priors, activate responses, and anticipate action consequences. Due to our limited resources, though, the inference dynamics are prone to task-irrelevant distractions. For example, the task-irrelevant side of the imperative stimulus causes the Simon effect and, due to similar reasons, we fail to optimally switch between tasks. An actual model implementation simulates such task interactions and offers first estimates of the involved cognitive effort. The approach may be further studied and promises to offer deeper explanations about why we get quickly exhausted from multitasking, how we are influenced by irrelevant stimulus modalities, why we exhibit magnitude interference, and, during social interactions, why we often fail to take the perspective of others into account.

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.

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.

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.

Design for an Individual: Connectionist Approaches to the Evolutionary Transitions in Individuality

The truly surprising thing about evolution is not how it makes individuals better adapted to their environment, but how it makes individuals. All individuals are made of parts that used to be individuals themselves, e.g., multicellular organisms from unicellular organisms. In such evolutionary transitions in individuality, the organised structure of relationships between component parts causes them to work together, creating a new organismic entity and a new evolutionary unit on which selection can act. However, the principles of these transitions remain poorly understood. In particular, the process of transition must be explained by “bottom-up” selection, i.e., on the existing lower-level evolutionary units, without presupposing the higher-level evolutionary unit we are trying to explain. In this hypothesis and theory manuscript we address the conditions for evolutionary transitions in individuality by exploiting adaptive principles already known in learning systems. Connectionist learning models, well-studied in neural networks, demonstrate how networks of organised functional relationships between components, sufficient to exhibit information integration and collective action, can be produced via fully-distributed and unsupervised learning principles, i.e., without centralised control or an external teacher. Evolutionary connectionism translates these distributed learning principles into the domain of natural selection, and suggests how relationships among evolutionary units could become adaptively organised by selection from below without presupposing genetic relatedness or selection on collectives. In this manuscript, we address how connectionist models with a particular interaction structure might explain transitions in individuality. We explore the relationship between the interaction structures necessary for (a) evolutionary individuality (where the evolution of the whole is a non-decomposable function of the evolution of the parts), (b) organismic individuality (where the development and behaviour of the whole is a non-decomposable function of the behaviour of component parts) and (c) non-linearly separable functions, familiar in connectionist models (where the output of the network is a non-decomposable function of the inputs). Specifically, we hypothesise that the conditions necessary to evolve a new level of individuality are described by the conditions necessary to learn non-decomposable functions of this type (or deep model induction) familiar in connectionist models of cognition and learning.

Technological Approach to Mind Everywhere: An Experimentally-Grounded Framework for Understanding Diverse Bodies and Minds

Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved and designed material and software. These advances are disrupting familiar concepts in the philosophy of mind, and require new ways of thinking about and comparing truly diverse intelligences, whose composition and origin are not like any of the available natural model species. In this Perspective, I introduce TAME-Technological Approach to Mind Everywhere-a framework for understanding and manipulating cognition in unconventional substrates. TAME formalizes a non-binary (continuous), empirically-based approach to strongly embodied agency. TAME provides a natural way to think about animal sentience as an instance of collective intelligence of cell groups, arising from dynamics that manifest in similar ways in numerous other substrates. When applied to regenerating/developmental systems, TAME suggests a perspective on morphogenesis as an example of basal cognition. The deep symmetry between problem-solving in anatomical, physiological, transcriptional, and 3D (traditional behavioral) spaces drives specific hypotheses by which cognitive capacities can increase during evolution. An important medium exploited by evolution for joining active subunits into greater agents is developmental bioelectricity, implemented by pre-neural use of ion channels and gap junctions to scale up cell-level feedback loops into anatomical homeostasis. This architecture of multi-scale competency of biological systems has important implications for plasticity of bodies and minds, greatly potentiating evolvability. Considering classical and recent data from the perspectives of computational science, evolutionary biology, and basal cognition, reveals a rich research program with many implications for cognitive science, evolutionary biology, regenerative medicine, and artificial intelligence.

Multi-scale Chimerism: An experimental window on the algorithms of anatomical control

Despite the immense progress in genetics and cell biology, major knowledge gaps remain with respect to prediction and control of the global morphologies that will result from the cooperation of cells with known genomes. The understanding of cooperativity, competition, and synergy across diverse biological scales has been obscured by a focus on standard model systems that exhibit invariant species-specific anatomies. Morphogenesis of chimeric biological material is an especially instructive window on the control of biological growth and form because it emphasizes the need for prediction without reliance on familiar, standard outcomes. Here, we review an important and fascinating body of data from experiments utilizing DNA transfer, cell transplantation, organ grafting, and parabiosis. We suggest that these are all instances (at different levels of organization) of one general phenomenon: chimerism. Multi-scale chimeras are a powerful conceptual and experimental tool with which to probe the mapping between properties of components and large-scale anatomy: the laws of morphogenesis. The existing data and future advances in this field will impact not only the understanding of cooperation and the evolution of body forms, but also the design of strategies for system-level outcomes in regenerative medicine and swarm robotics.

Linking Brain Structure, Activity, and Cognitive Function through Computation

Understanding the human brain is a “Grand Challenge” for 21st century research. Computational approaches enable large and complex datasets to be addressed efficiently, supported by artificial neural networks, modeling and simulation. Dynamic generative multiscale models, which enable the investigation of causation across scales and are guided by principles and theories of brain function, are instrumental for linking brain structure and function. An example of a resource enabling such an integrated approach to neuroscientific discovery is the BigBrain, which spatially anchors tissue models and data across different scales and ensures that multiscale models are supported by the data, making the bridge to both basic neuroscience and medicine. Research at the intersection of neuroscience, computing and robotics has the potential to advance neuro-inspired technologies by taking advantage of a growing body of insights into perception, plasticity and learning. To render data, tools and methods, theories, basic principles and concepts interoperable, the Human Brain Project (HBP) has launched EBRAINS, a digital neuroscience research infrastructure, which brings together a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits.

"Project for a Spatiotemporal Neuroscience" - Brain and Psyche Share Their Topography and Dynamic

What kind of neuroscience does psychoanalysis require? At his time, Freud in his "Project for a Scientific Psychology" searched for a model of the brain that could relate to incorporate the psyche's topography and dynamic. Current neuropsychoanalysis builds on specific functions as investigated in Affective and Cognitive (and Social) Neuroscience including embodied approaches. The brain's various functions are often converged with prediction as operationalized in predictive coding (PC) and free energy principle (FEP) which, recently, have been conceived as core for a "New Project for Scientific Psychology." We propose to search for a yet more comprehensive and holistic neuroscience that focuses primarily on its topography and dynamic analogous to Freud's model of the psyche. This leads us to what we describe as "Spatiotemporal Neuroscience" that focuses on the spatial topography and temporal dynamic of the brain's neural activity including how they shape affective, cognitive, and social functions including PC and FEP (first part). That is illustrated by the temporally and spatially nested neural hierarchy of the self in the brain's neural activity (second and third part). This sets the ground for developing our proposed "Project for a Spatiotemporal Neuroscience," which complements and extends both Freud's and Solms' projects (fourth part) and also carries major practical implications as it lays the ground for a novel form of neuroscientifically informed psychotherapy, namely, "Spatiotemporal Psychotherapy." In conclusion, "Spatiotemporal Neuroscience" provides an intimate link of brain and psyche by showing topography and dynamic as their shared features, that is, "common currency."

Bayesian theories of consciousness: a review in search for a minimal unifying model

The goal of the paper is to review existing work on consciousness within the frameworks of Predictive Processing, Active Inference, and Free Energy Principle. The emphasis is put on the role played by the precision and complexity of the internal generative model. In the light of those proposals, these two properties appear to be the minimal necessary components for the emergence of conscious experience-a Minimal Unifying Model of consciousness.

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.

A review of regulated self-organizing approaches for tissue regeneration

Tissue and organ regeneration is the dynamic process by which a population of cells rearranges into a specific form with specific functions. Traditional tissue regeneration utilizes tissue grafting, cell implantation, and structured scaffolds to achieve clinical efficacy. However, tissue grafting methods face a shortage of donor tissue, while cell implantation may involve leakage of the implanted cells without a supportive 3D matrix. Cell migration, proliferation, and differentiation in structured scaffolds may disorganize and frustrate the artificially pre-designed structures, and sometimes involve immunogenic reactions. To overcome this limitation, the self-organizing properties and innate regenerative capability of tissue/organism formation in the absence of guidance by structured scaffolds has been investigated. This review emphasizes the growing subfield of the regulated self-organizing approach for neotissue formation and describes advances in the subfield using diverse, cutting-edge, inter-disciplinarity technologies. We cohesively summarize the directed self-organization of cells in the micro-engineered cell-ECM system and 3D/4D cell printing. Mathematical modeling of cellular self-organization is also discussed for providing rational guidance to intractable problems in tissue regeneration. It is envisioned that future self-organization approaches integrating biomathematics, micro-nano engineering, and gene circuits developed from synthetic biology will continue to work in concert with self-organizing morphogenesis to enhance rational control during self-organizing in tissue and organ regeneration.

Active Inferants: An Active Inference Framework for Ant Colony Behavior

In this paper, we introduce an active inference model of ant colony foraging behavior, and implement the model in a series of in silico experiments. Active inference is a multiscale approach to behavioral modeling that is being applied across settings in theoretical biology and ethology. The ant colony is a classic case system in the function of distributed systems in terms of stigmergic decision-making and information sharing. Here we specify and simulate a Markov decision process (MDP) model for ant colony foraging. We investigate a well-known paradigm from laboratory ant colony behavioral experiments, the alternating T-maze paradigm, to illustrate the ability of the model to recover basic colony phenomena such as trail formation after food location discovery. We conclude by outlining how the active inference ant colony foraging behavioral model can be extended and situated within a nested multiscale framework and systems approaches to biology more generally.

Cancer Niches and Their Kikuchi Free Energy

Biological forms depend on a progressive specialization of pluripotent stem cells. The differentiation of these cells in their spatial and functional environment defines the organism itself; however, cellular mutations may disrupt the mutual balance between a cell and its niche, where cell proliferation and specialization are released from their autopoietic homeostasis. This induces the construction of cancer niches and maintains their survival. In this paper, we characterise cancer niche construction as a direct consequence of interactions between clusters of cancer and healthy cells. Explicitly, we evaluate these higher-order interactions between niches of cancer and healthy cells using Kikuchi approximations to the free energy. Kikuchi's free energy is measured in terms of changes to the sum of energies of baseline clusters of cells (or nodes) minus the energies of overcounted cluster intersections (and interactions of interactions, etc.). We posit that these changes in energy node clusters correspond to a long-term reduction in the complexity of the system conducive to cancer niche survival. We validate this formulation through numerical simulations of apoptosis, local cancer growth, and metastasis, and highlight its implications for a computational understanding of the etiopathology of cancer.

Brain Entropy During Aging Through a Free Energy Principle Approach

Neural complexity and brain entropy (BEN) have gained greater interest in recent years. The dynamics of neural signals and their relations with information processing continue to be investigated through different measures in a variety of noteworthy studies. The BEN of spontaneous neural activity decreases during states of reduced consciousness. This evidence has been showed in primary consciousness states, such as psychedelic states, under the name of "the entropic brain hypothesis." In this manuscript we propose an extension of this hypothesis to physiological and pathological aging. We review this particular facet of the complexity of the brain, mentioning studies that have investigated BEN in primary consciousness states, and extending this view to the field of neuroaging with a focus on resting-state functional Magnetic Resonance Imaging. We first introduce historic and conceptual ideas about entropy and neural complexity, treating the mindbrain as a complex nonlinear dynamic adaptive system, in light of the free energy principle. Then, we review the studies in this field, analyzing the idea that the aim of the neurocognitive system is to maintain a dynamic state of balance between order and chaos, both in terms of dynamics of neural signals and functional connectivity. In our exploration we will review studies both on acute psychedelic states and more chronic psychotic states and traits, such as those in schizophrenia, in order to show the increase of entropy in those states. Then we extend our exploration to physiological and pathological aging, where BEN is reduced. Finally, we propose an interpretation of these results, defining a general trend of BEN in primary states and cognitive aging.

The 2-D Cluster Variation Method: Topography Illustrations and Their Enthalpy Parameter Correlations

One of the biggest challenges in characterizing 2-D image topographies is finding a low-dimensional parameter set that can succinctly describe, not so much image patterns themselves, but the nature of these patterns. The 2-D cluster variation method (CVM), introduced by Kikuchi in 1951, can characterize very local image pattern distributions using configuration variables, identifying nearest-neighbor, next-nearest-neighbor, and triplet configurations. Using the 2-D CVM, we can characterize 2-D topographies using just two parameters; the activation enthalpy (ε0) and the interaction enthalpy (ε1). Two different initial topographies (“scale-free-like” and “extreme rich club-like”) were each computationally brought to a CVM free energy minimum, for the case where the activation enthalpy was zero and different values were used for the interaction enthalpy. The results are: (1) the computational configuration variable results differ significantly from the analytically-predicted values well before ε1 approaches the known divergence as ε1→0.881, (2) the range of potentially useful parameter values, favoring clustering of like-with-like units, is limited to the region where ε0<3 and ε1<0.25, and (3) the topographies in the systems that are brought to a free energy minimum show interesting visual features, such as extended “spider legs” connecting previously unconnected “islands,” and as well as evolution of “peninsulas” in what were previously solid masses.

Uncovering cognitive similarities and differences, conservation and innovation

This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.

Deeply Felt Affect: The Emergence of Valence in Deep Active Inference

The positive-negative axis of emotional valence has long been recognized as fundamental to adaptive behavior, but its origin and underlying function have largely eluded formal theorizing and computational modeling. Using deep active inference, a hierarchical inference scheme that rests on inverting a model of how sensory data are generated, we develop a principled Bayesian model of emotional valence. This formulation asserts that agents infer their valence state based on the expected precision of their action model-an internal estimate of overall model fitness ("subjective fitness"). This index of subjective fitness can be estimated within any environment and exploits the domain generality of second-order beliefs (beliefs about beliefs). We show how maintaining internal valence representations allows the ensuing affective agent to optimize confidence in action selection preemptively. Valence representations can in turn be optimized by leveraging the (Bayes-optimal) updating term for subjective fitness, which we label affective charge (AC). AC tracks changes in fitness estimates and lends a sign to otherwise unsigned divergences between predictions and outcomes. We simulate the resulting affective inference by subjecting an in silico affective agent to a T-maze paradigm requiring context learning, followed by context reversal. This formulation of affective inference offers a principled account of the link between affect, (mental) action, and implicit metacognition. It characterizes how a deep biological system can infer its affective state and reduce uncertainty about such inferences through internal action (i.e., top-down modulation of priors that underwrite confidence). Thus, we demonstrate the potential of active inference to provide a formal and computationally tractable account of affect. Our demonstration of the face validity and potential utility of this formulation represents the first step within a larger research program. Next, this model can be leveraged to test the hypothesized role of valence by fitting the model to behavioral and neuronal responses.

Valuing what happens: a biogenic approach to valence and (potentially) affect

Valence is half of the pair of properties that constitute core affect, the foundation of emotion. But what is valence, and where is it found in the natural world? Currently, this question cannot be answered. The idea that emotion is the body's way of driving the organism to secure its survival, thriving and reproduction runs like a leitmotif from the pathfinding work of Antonio Damasio through four book-length neuroscientific accounts of emotion recently published by the field's leading practitioners. Yet while Damasio concluded 20 years ago that the homeostasis-affect linkage is rooted in unicellular life, no agreement exists about whether even non-human animals with brains experience emotions. Simple neural animals-those less brainy than bees, fruit flies and other charismatic invertebrates-are not even on the radar of contemporary affective research, to say nothing of aneural organisms. This near-sightedness has effectively denied the most productive method available for getting a grip on highly complex biological processes to a scientific domain whose importance for understanding biological decision-making cannot be underestimated. Valence arguably is the fulcrum around which the dance of life revolves. Without the ability to discriminate advantage from harm, life very quickly comes to an end. In this paper, we review the concept of valence, where it came from, the work it does in current leading theories of emotion, and some of the odd features revealed via experiment. We present a biologically grounded framework for investigating valence in any organism and sketch a preliminary pathway to a computational model. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.

Neural and phenotypic representation under the free-energy principle

The aim of this paper is to leverage the free-energy principle and its corollary process theory, active inference, to develop a generic, generalizable model of the representational capacities of living creatures; that is, a theory of phenotypic representation. Given their ubiquity, we are concerned with distributed forms of representation (e.g., population codes), whereby patterns of ensemble activity in living tissue come to represent the causes of sensory input or data. The active inference framework rests on the Markov blanket formalism, which allows us to partition systems of interest, such as biological systems, into internal states, external states, and the blanket (active and sensory) states that render internal and external states conditionally independent of each other. In this framework, the representational capacity of living creatures emerges as a consequence of their Markovian structure and nonequilibrium dynamics, which together entail a dual-aspect information geometry. This entails a modest representational capacity: internal states have an intrinsic information geometry that describes their trajectory over time in state space, as well as an extrinsic information geometry that allows internal states to encode (the parameters of) probabilistic beliefs about (fictive) external states. Building on this, we describe here how, in an automatic and emergent manner, information about stimuli can come to be encoded by groups of neurons bound by a Markov blanket; what is known as the neuronal packet hypothesis. As a concrete demonstration of this type of emergent representation, we present numerical simulations showing that self-organizing ensembles of active inference agents sharing the right kind of probabilistic generative model are able to encode recoverable information about a stimulus array.

Why isn't sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution

Animals that can reproduce vegetatively by fission or budding and also sexually via specialized gametes are found in all five primary animal lineages (Bilateria, Cnidaria, Ctenophora, Placozoa, Porifera). Many bilaterian lineages, including roundworms, insects, and most chordates, have lost the capability of vegetative reproduction and are obligately gametic. We suggest a developmental explanation for this evolutionary phenomenon: obligate gametic reproduction is the result of germline stem cells winning a winner-take-all competition with non-germline stem cells for control of reproduction and hence lineage survival. We develop this suggestion by extending Hamilton's rule, which factors the relatedness between parties into the cost/benefit analysis that underpins cooperative behaviors, to include similarity of cellular state. We show how coercive or deceptive cell-cell signaling can be used to make costly cooperative behaviors appear less costly to the cooperating party. We then show how competition between stem-cell lineages can render an ancestral combination of vegetative reproduction with facultative sex unstable, with one or the other process driven to extinction. The increased susceptibility to cancer observed in obligately-sexual lineages is, we suggest, a side-effect of deceptive signaling that is exacerbated by the loss of whole-body regenerative abilities. We suggest a variety of experimental approaches for testing our predictions.

How Do Living Systems Create Meaning?

Meaning has traditionally been regarded as a problem for philosophers and psychologists. Advances in cognitive science since the early 1960s, however, broadened discussions of meaning, or more technically, the semantics of perceptions, representations, and/or actions, into biology and computer science. Here, we review the notion of “meaning” as it applies to living systems, and argue that the question of how living systems create meaning unifies the biological and cognitive sciences across both organizational and temporal scales.

Life, death, and self: Fundamental questions of primitive cognition viewed through the lens of body plasticity and synthetic organisms

Central to the study of cognition is being able to specify the Subject that is making decisions and owning memories and preferences. However, all real cognitive agents are made of parts (such as brains made of cells). The integration of many active subunits into a coherent Self appearing at a larger scale of organization is one of the fundamental questions of evolutionary cognitive science. Typical biological model systems, whether basal or advanced, have a static anatomical structure which obscures important aspects of the mind-body relationship. Recent advances in bioengineering now make it possible to assemble, disassemble, and recombine biological structures at the cell, organ, and whole organism levels. Regenerative biology and controlled chimerism reveal that studies of cognition in intact, "standard", evolved animal bodies are just a narrow slice of a much bigger and as-yet largely unexplored reality: the incredible plasticity of dynamic morphogenesis of biological forms that house and support diverse types of cognition. The ability to produce living organisms in novel configurations makes clear that traditional concepts, such as body, organism, genetic lineage, death, and memory are not as well-defined as commonly thought, and need considerable revision to account for the possible spectrum of living entities. Here, I review fascinating examples of experimental biology illustrating that the boundaries demarcating somatic and cognitive Selves are fluid, providing an opportunity to sharpen inquiries about how evolution exploits physical forces for multi-scale cognition. Developmental (pre-neural) bioelectricity contributes a novel perspective on how the dynamic control of growth and form of the body evolved into sophisticated cognitive capabilities. Most importantly, the development of functional biobots - synthetic living machines with behavioral capacity - provides a roadmap for greatly expanding our understanding of the origin and capacities of cognition in all of its possible material implementations, especially those that emerge de novo, with no lengthy evolutionary history of matching behavioral programs to bodyplan. Viewing fundamental questions through the lens of new, constructed living forms will have diverse impacts, not only in basic evolutionary biology and cognitive science, but also in regenerative medicine of the brain and in artificial intelligence.