Publications

The integration of active cell machinery with synthetic building blocks is the bridge toward developing synthetic cells with biological functions and beyond. Self-replication is one of the most important tasks of living systems, and various complex machineries exist to execute it. In Escherichia coli, a contractile division ring is positioned to mid-cell by concentration oscillations of self-organizing proteins (MinCDE), where it severs membrane and cell wall. So far, the reconstitution of any cell division machinery has exclusively been tied to liposomes. Here, the reconstitution of a rudimentary bacterial divisome in fully synthetic bicomponent dendrimersomes is shown. By tuning the membrane composition, the interaction of biological machinery with synthetic membranes can be tailored to reproduce its dynamic behavior. This constitutes an important breakthrough in the assembly of synthetic cells with biological elements, as tuning of membrane-divisome interactions is the key to engineering emergent biological behavior from the bottom-up.

JTD Keywords: bacterial cell division, bottom-up synthetic biology, dendrimersomes, dynamic min patterns, ftsz assembly, Bacterial cell division, Bottom-up synthetic biology, Dendrimersomes, Dynamic min patterns, Dynamics, Ftsz assembly, Ftsz filaments, Mind, Organization, Pole oscillation, Polymersome membranes, Proteins, Rapid pole, Synthetic cells, Vesicles

In cognitive science, Theory of Mind (ToM) is the mental faculty of assessing intentions and beliefs of others and requires, in part, to distinguish incoming sensorimotor (SM) signals and, accordingly, attribute these to either the self-model, the model of the other, or one pertaining to the external world, including inanimate objects. To gain an understanding of this mechanism, we perform a computational analysis of SM interactions in a dual-arm robotic setup. Our main contribution is that, under the common fate principle, a correlation analysis of the velocities of visual pivots is shown to be sufficient to characterize the self (including proximo-distal arm-joint dependencies) and to assess motor to sensory influences, and the other by computing clusters in the correlation dependency graph. A correlational analysis, however, is not sufficient to assess the non-symmetric/directed dependencies required to infer autonomy, the ability of entities to move by themselves. We subsequently validate 3 measures that can potentially quantify a metric for autonomy: Granger causality (GC), transfer entropy (TE), as well as a novel “Acceleration Transfer” (AT) measure, which is an instantaneous measure that computes the estimated instantaneous transfer of acceleration between visual features, from which one can compute a directed SM graph. Subsequently, autonomy is characterized by the sink nodes in this directed graph. This study results show that although TE can capture the directional dependencies, a rectified subtraction operation denoted, in this study, as AT is both sufficient and computationally cheaper.

JTD Keywords: agency, attention, autonomy, cognitive development, computational cognition, developmental psychology, sensorimotor learning, Agency, Attention, Autonomy, Cognitive development, Computational cognition, Developmental psychology, Model, Sensorimotor learning, Theory of mind

© 2021 Elsevier B.V. The current decline in antimalarial drug efficacy due to the evolution of resistant Plasmodium strains calls for new strategies capable of improving the bioavailability of antimalarials, especially of those whose lipophilic character imparts them a low solubility in biological fluids. Here we have designed, synthesized and characterized amphiphilic zwitterionic block copolymers forming nanoparticles capable of penetrating the intestinal epithelium that can be used for oral administration. Poly(butyl methacrylate-co-morpholinoethyl sulfobetaine methacrylate) (PBMA-MESBMA)-based nanoparticles exhibited a specific targeting to Plasmodium falciparum-infected vs. parasite-free red blood cells (74.8%/0.8% respectively), which was maintained upon encapsulation of the lipophilic antimalarial drug curcumin (82.6%/0.3%). The in vitro efficacy of curcumin upon encapsulation was maintained relative to the free compound, with an IC50 around 5 μM. In vivo assays indicated a significantly increased curcumin concentration in the blood of mice one hour after being orally fed PBMA-MESBMA-curcumin in comparison to the administration of free drug (18.7 vs. 2.1 ng/ml, respectively). At longer times, however, plasma curcumin concentration equaled between free and encapsulated drug, which was reflected in similar in vivo antimalarial activities in Plasmodium yoelii yoelii-infected mice. Microscopic analysis in blood samples of fluorescently labeled PBMA-MESBMA revealed the presence of the polymer inside P. yoelii yoelii-parasitized erythrocytes one hour after oral administration to infected animals.

JTD Keywords: curcumin, drug delivery, malaria, pbma-mesbma, plasmodium, zwitterionic block copolymers, Curcumin, Drug delivery, Malaria, Pbma-mesbma, Plasmodium, Zwitterionic block copolymers

© 2020, Springer Nature Limited. The human gut microbiome has emerged as a major player in human health and disease. The liver, as the first organ to encounter microbial products that cross the gut epithelial barrier, is affected by the gut microbiome in many ways. Thus, the gut microbiome might play a major part in the development of liver diseases. The common end stage of liver disease is decompensated cirrhosis and the further development towards acute-on-chronic liver failure (ACLF). These conditions have high short-term mortality. There is evidence that translocation of components of the gut microbiota, facilitated by different pathogenic mechanisms such as increased gut epithelial permeability and portal hypertension, is an important driver of decompensation by induction of systemic inflammation, and thereby also ACLF. Elucidating the role of the gut microbiome in the aetiology of decompensated cirrhosis and ACLF deserves further investigation and improvement; and might be the basis for development of diagnostic and therapeutic strategies. In this Review, we focus on the possible pathogenic, diagnostic and therapeutic role of the gut microbiome in decompensation of cirrhosis and progression to ACLF.

JTD Keywords: albumin, decreases intestinal permeability, hepatic-encephalopathy, portal-vein thrombosis, rifaximin improves, secondary bile-acids, systemic inflammation, translocation, venous-pressure gradient, Spontaneous bacterial peritonitis

Can machines be endowed with morality? We argue that morality in the descriptive or epistemic sense can be extended to artificial systems. Following arguments from evolutionary game-theory, we identify two main ingredients required to operationalize this notion of morality in machines. The first, being a group theory of mind, and the second, being an assignment of valence. We make the case for the plausibility of these operations in machines without reference to any form of intentionality or consciousness. The only systems requirements needed to support the above two operations are autonomous goal-directed action and the ability to interact and learn from the environment. Following this we have outlined a theoretical framework based on conceptual spaces and valence assignments to gauge latent morality in autonomous machines and algorithms.

JTD Keywords: Autonomous systems, Ethics of algorithms, Goal-directed action, Philosophy of morality, Qualia, Theory of mind

The components of a Living Machine must be integrated into a functioning whole, which requires a detailed understanding of the architecture of living machines. This chapter starts with a conceptual and historical analysis which from Plato brings us to nineteenth-century neuroscience and early concepts of the layered structure of nervous systems. These concepts were further captured in the cognitive behaviorism of Tolman and came to full fruition in the cognitive revolution of the second half of the twentieth century. Verschure subsequently describes the most relevant proposals of cognitive architectures followed by an overview of the few proposals stemming from modern neuroscience on the architecture of the brain. Subsequently, we will look at contemporary contenders that mediate between cognitive and brain architecture. An important challenge to any model of cognitive architectures is how to benchmark it. Verschure proposes the Unified Theories of Embodied Minds (UTEM) benchmark which advances from Newell’s classic Unified Theories of Cognition benchmark.

JTD Keywords: Architecture, Mind, Brain, Organization, System, Virtualization, Abstraction layers

A major challenge in cognitive science and AI is to understand how intelligent agents might be able to predict mental states of other agents during complex social interactions. What are the computational principles of such a Theory of Mind (ToM)? In previous work, we have investigated hypotheses of how the human brain might realize a ToM of other agents in a multi-agent social scenario. In particular, we have proposed control-based cognitive architectures to predict the model of other agents in a game-theoretic task (Battle of the Exes). Our multi-layer architecture implements top-down predictions from adaptive to reactive layers of control and bottom-up error feedback from reactive to adaptive layers. We tested cooperative and competitive strategies among different multi-agent models, demonstrating that while pure RL leads to reasonable efficiency and fairness in social interactions, there are other architectures that can perform better in specific circumstances. However, we found that even the best predictive models fall short of human data in terms of stability of social convention formation. In order to explain this gap between humans and predictive AI agents, in this work we propose introducing the notion of trust in the form of mutual agreements between agents that might enhance stability in the formation of conventions such as turn-taking.

JTD Keywords: Cognitive Architectures, Game Theory, Multi-Agent Models, Reinforcement Learning, Theory of Mind