•Computational treatment of biological self-organisation.•Biological self-organisation requires emergence of boundaries, namely Markov blankets.•Hierarchical self-organisation entails emergence of ...Markov blankets at multiple scale.
Biological self-organisation can be regarded as a process of spontaneous pattern formation; namely, the emergence of structures that distinguish themselves from their environment. This process can occur at nested spatial scales: from the microscopic (e.g., the emergence of cells) to the macroscopic (e.g. the emergence of organisms). In this paper, we pursue the idea that Markov blankets – that separate the internal states of a structure from external states – can self-assemble at successively higher levels of organisation. Using simulations, based on the principle of variational free energy minimisation, we show that hierarchical self-organisation emerges when the microscopic elements of an ensemble have prior (e.g., genetic) beliefs that they participate in a macroscopic Markov blanket: i.e., they can only influence – or be influenced by – a subset of other elements. Furthermore, the emergent structures look very much like those found in nature (e.g., cells or organelles), when influences are mediated by short range signalling. These simulations are offered as a proof of concept that hierarchical self-organisation of Markov blankets (into Markov blankets) can explain the self-evidencing, autopoietic behaviour of biological systems.
During the early Cambrian period metazoan life forms diverged at an accelerated rate to occupy multiple ecological niches on earth. A variety of explanations have been proposed to address this major ...evolutionary phenomenon termed the “Cambrian explosion.” While most hypotheses address environmental, developmental, and ecological factors that facilitated evolutionary innovations, the biological basis for accelerated emergence of species diversity in the Cambrian period remains largely conjectural. Herein, we posit that morphogenesis by self‐organization enables the uncoupling of genomic mutational landscape from phenotypic diversification. Evidence is provided for a two‐tiered interpretation of genomic changes in metazoan animals wherein mutations not only impact upon function of individual cells, but also alter the self‐organization outcome during developmental morphogenesis. We provide evidence that the morphological impacts of mutations on self‐organization could remain repressed if associated with an unmet negative energetic cost. We posit that accelerated morphological diversification in transition to the Cambrian period has occurred by emergence of dormant (i.e., reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period.
During the early Cambrian period metazoan life forms diverged at an accelerated rate to occupy multiple ecological niches on earth. Evidence is provided that accelerated morphological diversification in transition to the Cambrian period could have occurred by emergence of dormant morphological novelties whose molecular underpinnings were seeded in the Precambrian period.
Motivated by the global pandemic of COVID-19, this study investigates the spatial factors influencing physical distancing, and how these affect the transmission of the SARS-CoV-2 virus, by ...integrating pedestrian dynamics with a modified susceptible–exposed–infectious model. Contacts between infected and susceptible pedestrians are examined by determining physical-distancing pedestrian dynamics in three types of spaces, and used to estimate the proportion of newly infected pedestrians in these spaces. Desired behaviour for physical distancing can be observed from simulation results, and aggregated simulation findings reveal that certain layouts enable physical distancing to reduce the transmission of SARS-CoV-2. We also provide policymakers with several design guidelines on how to proactively design more effective and resilient space layouts in the context of pandemics to keep low transmission risks while maintaining a high pedestrian volume. This approach has enormous application potential for other infectious-disease transmission and space assessments.
•A modified social force model was proposed for physical-distancing pedestrian dynamics.•A modified SEI model is introduced to estimate the proportion of newly infected pedestrians.•Some collective phenomena occur in the simulation for physical-distancing conditions.•Proper space organisation is suggested to curb infection spread.
Modular biofabrication strategies using microtissues or organoids as biological building blocks have great potential for engineering replacement tissues and organs at scale. Here we describe the ...development of a biofabrication strategy to engineer osteochondral tissues by spatially localising phenotypically distinct cartilage microtissues within an instructive 3D printed polymer framework. We first demonstrate that immature cartilage microtissues can spontaneously fuse to form homogeneous macrotissues, and that combining less cellular microtissues results in superior fusion and the generation of a more hyaline-like cartilage containing higher levels of sulphated glycosaminoglycans and type II collagen. Furthermore, temporally exposing developing microtissues to transforming growth factor-β accelerates their volumetric growth and subsequent capacity to fuse into larger hyaline cartilage grafts. Next, 3D printed polymeric frameworks are used to further guide microtissue fusion and the subsequent self-organisation process, resulting in the development of a macroscale tissue with zonal collagen organisation analogous to the structure seen in native articular cartilage. To engineer osteochondral grafts, hypertrophic cartilage microtissues are engineered as bone precursor tissues and spatially localised below phenotypically stable cartilage microtissues. Implantation of these engineered grafts into critically-sized caprine osteochondral defects results in effective defect stabilisation and histologically supports the restoration of a more normal articular surface after 6 months in vivo. These findings support the use of such modular biofabrication strategies for biological joint resurfacing.
Self‐organised formation of spatial patterns is known from a variety of different ecosystems, yet little is known about how these patterns affect the diversity of communities. Here, we use a food ...chain model in which autotroph diversity is described by a continuous distribution of a trait that affects both growth and defence against heterotrophs. On isolated patches, diversity is always lost over time due to stabilising selection, and the local communities settle on one of two alternative stable community states that are characterised by a dominance of either defended or undefended species. In a metacommunity context, dispersal can destabilise these states and complex spatio‐temporal patterns in the species’ abundances emerge. The resulting biomass‐trait feedback increases local diversity by an order of magnitude compared to scenarios without self‐organised pattern formation, thereby maintaining the ability of communities to adapt to potential future changes in biotic or abiotic environmental conditions.
We consider meta‐food webs in which autotroph diversity is described by a distribution of a functional trait that affects both growth and defence against grazing. When dispersal between habitat patches is low, stabilising selection leads to low functional diversity (trait variance) in the local communities. However, when dispersal is above a critical threshold, complex spatio‐temporal patterns in the distribution of the species' abundances across patches emerge. The resulting biomass‐trait feedback increases local diversity by an order of magnitude, which helps to maintain the ability of communities to adapt to potential future changes in environmental conditions.
Mouse embryonic stem cells (mESCs) are clonal populations derived from preimplantation mouse embryos that can be propagated in vitro and, when placed into blastocysts, contribute to all tissues of ...the embryo and integrate into the normal morphogenetic processes, i.e. they are pluripotent. However, although they can be steered to differentiate in vitro into all cell types of the organism, they cannot organise themselves into structures that resemble embryos. When aggregated into embryoid bodies they develop disorganised masses of different cell types with little spatial coherence. An exception to this rule is the emergence of retinas and anterior cortex-like structures under minimal culture conditions. These structures emerge from the cultures without any axial organisation. Here, we report that small aggregates of mESCs, of about 300 cells, self-organise into polarised structures that exhibit collective behaviours reminiscent of those that cells exhibit in early mouse embryos, including symmetry breaking, axial organisation, germ layer specification and cell behaviour, as well as axis elongation. The responses are signal specific and uncouple processes that in the embryo are tightly associated, such as specification of the anteroposterior axis and anterior neural development, or endoderm specification and axial elongation. We discuss the meaning and implications of these observations and the potential uses of these structures which, because of their behaviour, we suggest to call 'gastruloids'.
Paradoxes of cancer: Survival at the brink Erenpreisa, Jekaterina; Salmina, Kristine; Anatskaya, Olga ...
Seminars in cancer biology,
June 2022, 2022-06-00, 20220601, Volume:
81
Journal Article
Peer reviewed
Open access
The fundamental understanding of how Cancer initiates, persists and then progresses is evolving. High-resolution technologies, including single-cell mutation and gene expression measurements, are now ...attainable, providing an ever-increasing insight into the molecular details. However, this higher resolution has shown that somatic mutation theory itself cannot explain the extraordinary resistance of cancer to extinction. There is a need for a more Systems-based framework of understanding cancer complexity, which in particular explains the regulation of gene expression during cell-fate decisions. Cancer displays a series of paradoxes. Here we attempt to approach them from the view-point of adaptive exploration of gene regulatory networks at the edge of order and chaos, where cell-fate is changed by oscillations between alternative regulators of cellular senescence and reprogramming operating through self-organisation. On this background, the role of polyploidy in accessing the phylogenetically pre-programmed “oncofetal attractor” state, related to unicellularity, and the de-selection of unsuitable variants at the brink of cell survival is highlighted. The concepts of the embryological and atavistic theory of cancer, cancer cell “life-cycle”, and cancer aneuploidy paradox are dissected under this lense. Finally, we challenge researchers to consider that cancer “defects” are mostly the adaptation tools of survival programs that have arisen during evolution and are intrinsic of cancer. Recognition of these features should help in the development of more successful anti-cancer treatments.
Objective
The purpose of this study was to identify self‐organised dynamics in sessions with dialogical patterns (i.e. reflective interactions of self‐states associated with psychological change) ...within long‐term psychotherapy. One of the hallmarks of self‐organisation is the presence of an Inverse Power Law (IPL) in the frequency distribution of relevant events, which reflect better adaptation to internal and environmental changes, produced by psychotherapy.
Methods
A case study of successful psychotherapy (44 weekly sessions) with a patient diagnosed with borderline personality disorder (BPD) and the therapist was conducted. The expressions of the subjectivity (i.e. voices) in the patient and therapist were identified through the Model of Analysis of Discursive Positioning in Psychotherapy (MAPP). State Space Grids (SSG) identified sessions that presented dialogical patterns acting as attractors (8 sessions) and those with non‐dialogical patterns acting as attractors (12 sessions). Finally, Orbital Decomposition (ORBDE) produced statistics of self‐organisation in both groups of sessions and the degree of fit to an IPL.
Results
Both groups of sessions presented an acceptable fit to the IPL distributions (R2 = .853 and .938), and statistics placed them in different self‐organised regions.
Conclusions
Although dialogical patterns are an emergent property of therapy, their structure is similar to sessions of other types, in that dynamic processes occur in them that can be empowered in patients to consolidate psychological change. The nonlinear and emergent character of these self‐organised processes and their clinical implications for activating the patients' psychological resources are discussed.
Micropatterning encompasses a set of methods aimed at precisely controlling the spatial distribution of molecules onto the surface of materials. Biologists have borrowed the idea and adapted these ...methods, originally developed for electronics, to impose physical constraints on biological systems with the aim of addressing fundamental questions across biological scales from molecules to multicellular systems. Here, I approach this topic from a developmental biologist's perspective focusing specifically on how and why micropatterning has gained in popularity within the developmental biology community in recent years. Overall, this Primer provides a concise overview of how micropatterns are used to study developmental processes and emphasises how micropatterns are a useful addition to the developmental biologist's toolbox.
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