Interface Focus最新文献

{"title":"The scaling of goals from cellular to anatomical homeostasis: an evolutionary simulation, experiment and analysis.","authors":"Léo Pio-Lopez,&nbsp;Johanna Bischof,&nbsp;Jennifer V LaPalme,&nbsp;Michael Levin","doi":"10.1098/rsfs.2022.0072","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0072","url":null,"abstract":"<p><p>Complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behaviour science, evolutionary developmental biology and the field of machine intelligence all seek to understand the scaling of biological cognition: what enables individual cells to integrate their activities to result in the emergence of a novel, higher-level intelligence with large-scale goals and competencies that belong to it and not to its parts? Here, we report the results of simulations based on the TAME framework, which proposes that evolution pivoted the collective intelligence of cells during morphogenesis of the body into traditional behavioural intelligence by scaling up homeostatic competencies of cells in metabolic space. In this article, we created a minimal <i>in silico</i> system (two-dimensional neural cellular automata) and tested the hypothesis that evolutionary dynamics are sufficient for low-level setpoints of metabolic homeostasis in individual cells to scale up to tissue-level emergent behaviour. Our system showed the evolution of the much more complex setpoints of cell collectives (tissues) that solve a problem in morphospace: the organization of a body-wide positional information axis (the classic French flag problem in developmental biology). We found that these emergent morphogenetic agents exhibit a number of predicted features, including the use of stress propagation dynamics to achieve the target morphology as well as the ability to recover from perturbation (robustness) and long-term stability (even though neither of these was directly selected for). Moreover, we observed an unexpected behaviour of sudden remodelling long after the system stabilizes. We tested this prediction in a biological system-regenerating planaria-and observed a very similar phenomenon. We propose that this system is a first step towards a quantitative understanding of how evolution scales minimal goal-directed behaviour (homeostatic loops) into higher-level problem-solving agents in morphogenetic and other spaces.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220072"},"PeriodicalIF":4.4,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9493862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symmetry-simplicity, broken symmetry-complexity.","authors":"David C Krakauer","doi":"10.1098/rsfs.2022.0075","DOIUrl":"10.1098/rsfs.2022.0075","url":null,"abstract":"<p><p>Complex phenomena are made possible when: (i) fundamental physical symmetries are broken and (ii) from the set of broken symmetries historically selected ground states are applied to performing mechanical work and storing adaptive information. Over the course of several decades Philip Anderson enumerated several key principles that can follow from broken symmetry in complex systems. These include emergence, frustrated random functions, autonomy and generalized rigidity. I describe these as the four Anderson Principles all of which are preconditions for the emergence of evolved function. I summarize these ideas and discuss briefly recent extensions that engage with the related concept of functional symmetry breaking, inclusive of information, computation and causality.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220075"},"PeriodicalIF":3.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9496618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Embodied cognitive morphogenesis as a route to intelligent systems.","authors":"Bradly Alicea, Richard Gordon, Jesse Parent","doi":"10.1098/rsfs.2022.0067","DOIUrl":"10.1098/rsfs.2022.0067","url":null,"abstract":"<p><p>The embryological view of development is that coordinated gene expression, cellular physics and migration provides the basis for phenotypic complexity. This stands in contrast with the prevailing view of embodied cognition, which claims that informational feedback between organisms and their environment is key to the emergence of intelligent behaviours. We aim to unite these two perspectives as <i>embodied cognitive morphogenesis</i>, in which morphogenetic symmetry breaking produces specialized organismal subsystems which serve as a substrate for the emergence of autonomous behaviours. As embodied cognitive morphogenesis produces fluctuating phenotypic asymmetry and the emergence of information processing subsystems, we observe three distinct properties: acquisition, generativity and transformation. Using a generic organismal agent, such properties are captured through models such as tensegrity networks, differentiation trees and embodied hypernetworks, providing a means to identify the context of various symmetry-breaking events in developmental time. Related concepts that help us define this phenotype further include concepts such as modularity, homeostasis and 4E (embodied, enactive, embedded and extended) cognition. We conclude by considering these autonomous developmental systems as a process called connectogenesis, connecting various parts of the emerged phenotype into an approach useful for the analysis of organisms and the design of bioinspired computational agents.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220067"},"PeriodicalIF":3.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"As without, so within: how the brain's temporo-spatial alignment to the environment shapes consciousness.","authors":"Georg Northoff, Philipp Klar, Magnus Bein, Adam Safron","doi":"10.1098/rsfs.2022.0076","DOIUrl":"10.1098/rsfs.2022.0076","url":null,"abstract":"<p><p>Consciousness is constituted by a structure that includes contents as foreground and the environment as background. This structural relation between the experiential foreground and background presupposes a relationship between the brain and the environment, often neglected in theories of consciousness. The temporo-spatial theory of consciousness addresses the brain-environment relation by a concept labelled 'temporo-spatial alignment'. Briefly, temporo-spatial alignment refers to the brain's neuronal activity's interaction with and adaption to interoceptive bodily and exteroceptive environmental stimuli, including their symmetry as key for consciousness. Combining theory and empirical data, this article attempts to demonstrate the yet unclear neuro-phenomenal mechanisms of temporo-spatial alignment. First, we suggest three neuronal layers of the brain's temporo-spatial alignment to the environment. These neuronal layers span across a continuum from longer to shorter timescales. (i) The background layer comprises longer and more powerful timescales mediating topographic-dynamic similarities between different subjects' brains. (ii) The intermediate layer includes a mixture of medium-scaled timescales allowing for stochastic matching between environmental inputs and neuronal activity through the brain's intrinsic neuronal timescales and temporal receptive windows. (iii) The foreground layer comprises shorter and less powerful timescales for neuronal entrainment of stimuli temporal onset through neuronal phase shifting and resetting. Second, we elaborate on how the three neuronal layers of temporo-spatial alignment correspond to their respective phenomenal layers of consciousness. (i) The inter-subjectively shared contextual background of consciousness. (ii) An intermediate layer that mediates the relationship between different contents of consciousness. (iii) A foreground layer that includes specific fast-changing contents of consciousness. Overall, temporo-spatial alignment may provide a mechanism whose different neuronal layers modulate corresponding phenomenal layers of consciousness. Temporo-spatial alignment can provide a bridging principle for linking physical-energetic (free energy), dynamic (symmetry), neuronal (three layers of distinct time-space scales) and phenomenal (form featured by background-intermediate-foreground) mechanisms of consciousness.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220076"},"PeriodicalIF":3.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neuromodulatory control of complex adaptive dynamics in the brain.","authors":"James M Shine","doi":"10.1098/rsfs.2022.0079","DOIUrl":"10.1098/rsfs.2022.0079","url":null,"abstract":"<p><p>How is the massive dimensionality and complexity of the microscopic constituents of the nervous system brought under sufficiently tight control so as to coordinate adaptive behaviour? A powerful means for striking this balance is to poise neurons close to the critical point of a phase transition, at which a small change in neuronal excitability can manifest a nonlinear augmentation in neuronal activity. How the brain could mediate this critical transition is a key open question in neuroscience. Here, I propose that the different arms of the ascending arousal system provide the brain with a diverse set of heterogeneous control parameters that can be used to modulate the excitability and receptivity of target neurons-in other words, to act as control parameters for mediating critical neuronal order. Through a series of worked examples, I demonstrate how the neuromodulatory arousal system can interact with the inherent topological complexity of neuronal subsystems in the brain to mediate complex adaptive behaviour.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220079"},"PeriodicalIF":3.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On Bayesian mechanics: a physics of and by beliefs.","authors":"Maxwell J D Ramstead, Dalton A R Sakthivadivel, Conor Heins, Magnus Koudahl, Beren Millidge, Lancelot Da Costa, Brennan Klein, Karl J Friston","doi":"10.1098/rsfs.2022.0029","DOIUrl":"10.1098/rsfs.2022.0029","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220029"},"PeriodicalIF":3.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9598982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mixed anhydrides at the intersection between peptide and RNA autocatalytic sets: evolution of biological coding.","authors":"S A Kauffman, N Lehman","doi":"10.1098/rsfs.2023.0009","DOIUrl":"10.1098/rsfs.2023.0009","url":null,"abstract":"<p><p>We present a scenario for the origin of biological coding, a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding originated from cooperation between two, originally separate, collectively autocatalytic sets (CASs), one for nucleic acids and one for peptides. Upon interaction, a series of RNA folding-directed processes led to their joint cooperativity. The aminoacyl adenylate was the first covalent association made by these two CASs and solidified their interdependence, and is a palimpsest of this era, a relic of the original semiotic relationship between RNA and proteins. Coding was driven by selection pressure to eliminate waste in CASs. Eventually a 1 : 1 relationship between single amino acids and short RNA pieces was established, i.e. the 'genetic code'. The two classes of aaRS enzymes are remnants of the complementary information in two RNA strands, as postulated by Rodin and Ohno. Every stage in the evolution of coding was driven by the downward selection on the components of a system to satisfy the Kantian whole. Coding was engendered because there were two chemically distinct classes of polymers needed for open-ended evolution; systems with only one polymer cannot exhibit this characteristic. Coding is thus synonymous with life as we know it.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20230009"},"PeriodicalIF":4.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9508054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symmetry and complexity in object-centric deep active inference models.","authors":"Stefano Ferraro, Toon Van de Maele, Tim Verbelen, Bart Dhoedt","doi":"10.1098/rsfs.2022.0077","DOIUrl":"10.1098/rsfs.2022.0077","url":null,"abstract":"<p><p>Humans perceive and interact with hundreds of objects every day. In doing so, they need to employ mental models of these objects and often exploit symmetries in the object's shape and appearance in order to learn generalizable and transferable skills. Active inference is a first principles approach to understanding and modelling sentient agents. It states that agents entertain a generative model of their environment, and learn and act by minimizing an upper bound on their surprisal, i.e. their free energy. The free energy decomposes into an accuracy and complexity term, meaning that agents favour the least complex model that can accurately explain their sensory observations. In this paper, we investigate how inherent symmetries of particular objects also emerge as symmetries in the latent state space of the generative model learnt under deep active inference. In particular, we focus on object-centric representations, which are trained from pixels to predict novel object views as the agent moves its viewpoint. First, we investigate the relation between model complexity and symmetry exploitation in the state space. Second, we do a principal component analysis to demonstrate how the model encodes the principal axis of symmetry of the object in the latent space. Finally, we also demonstrate how more symmetrical representations can be exploited for better generalization in the context of manipulation.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220077"},"PeriodicalIF":3.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making and breaking symmetries in mind and life","authors":"A. Safron, D. A. R. Sakthivadivel, Z. Sheikhbahaee, Magnus Bein, A. Razi, Michael Levin","doi":"10.1098/rsfs.2023.0015","DOIUrl":"https://doi.org/10.1098/rsfs.2023.0015","url":null,"abstract":"Symmetry is a motif featuring in almost all areas of science. Symmetries appear throughout the natural world, making them particularly important in our quest to understand the structure of the world around us. Symmetries and invariances are often first principles pointing to some lawful description of an observation, with explanations being understood as both ‘satisfying’ and potentially useful in their regularity. The sense of aesthetic beauty accompanying such explanations is reminiscent of our understanding of intelligence in terms of the ability to efficiently predict (or compress) data; indeed, identifying and building on symmetry can offer a particularly elegant description of a physical situation. The study of symmetries is so fundamental to mathematics and physics that one might ask where else it proves useful. This theme issue poses the question: what does the study of symmetry, and symmetry breaking, have to offer for the study of life and the mind?","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43396725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chiral conformity emerges from the least-time free energy consumption.","authors":"Arto Annila","doi":"10.1098/rsfs.2022.0074","DOIUrl":"10.1098/rsfs.2022.0074","url":null,"abstract":"<p><p>The prevalence of chirally pure biological polymers is often assumed to stem from some slight preference for one chiral form at the origin of life. Likewise, the predominance of matter over antimatter is presumed to follow from some subtle bias for matter at the dawn of the universe. However, rather than being imposed from the start, handedness standards in societies emerged to make things work. Since work is the universal measure of transferred energy, it is reasoned that standards at all scales and scopes emerge to consume free energy. Free energy minimization, equal to entropy maximization, turns out to be the second law of thermodynamics when derived from statistical physics of open systems. This many-body theory is based on the atomistic axiom that everything comprises the same fundamental elements known as quanta of action; hence, everything follows the same law. According to the thermodynamic principle, the flows of energy <i>naturally select</i> standard structures over less-fit functional forms to consume free energy in the least time. Thermodynamics making no distinction between animate and inanimate renders the question of life's handedness meaningless and deems the search for an intrinsic difference between matter and antimatter pointless.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220074"},"PeriodicalIF":4.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9496617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}