Norm-Establishing and Norm-Following in Autonomous Agency

Living agency is subject to a normative dimension (good-bad, adaptive-maladaptive) that is absent from other types of interaction. We review current and historical attempts to naturalize normativity from an organism-centered perspective, identifying two central problems and their solution: (1) How to define the topology of the viability space so as to include a sense of gradation that permits reversible failure, and (2) how to relate both the processes that establish norms and those that result in norm-following behavior. We present a minimal metabolic system that is coupled to a gradient-climbing chemotactic mechanism. Studying the relationship between metabolic dynamics and environmental resource conditions, we identify an emergent viable region and a precarious region where the system tends to die unless environmental conditions change. We introduce the concept of normative field as the change of environmental conditions required to bring the system back to its viable region. Norm-following, or normative action, is defined as the course of behavior whose effect is positively correlated with the normative field. We close with a discussion of the limitations and extensions of our model and some final reflections on the nature of norms and teleology in agency

Adaptation from interactions between metabolism and behaviour: self-sensitive behaviour in protocells

This thesis considers the relationship between adaptive behaviour and metabolism, using theoretical arguments supported by computational models to demonstrate mechanisms of adaptation that are uniquely available to systems based upon the metabolic organisation of self-production. It is argued how, by being sensitive to their metabolic viability, an organism can respond to the quality of its environment with respect to its metabolic well-being. This makes possible simple but powerful ‘self-sensitive’ adaptive behaviours such as “If I am healthy now, keep doing the same as I have been doing – otherwise do something else.” This strategy provides several adaptive benefits, including the ability to respond appropriately to phenomena never previously experienced by the organism nor by any of its ancestors; the ability to integrate different environmental influences to produce an appropriate response; and sensitivity to the organism’s present context and history of experience. Computational models are used to demonstrate these capabilities, as well as the possibility that self-sensitive adaptive behaviour can facilitate the adaptive evolution of populations of self-sensitive organisms through (i) processes similar to the Baldwin effect, (ii) increasing the likelihood of speciation events, and (iii) automatic behavioural adaptation to changes in the organism itself (such as genetic changes). In addition to these theoretical contributions, a computational model of self-sensitive behaviour is presented that recreates chemotaxis patterns observed in bacteria such as Azospirillum brasilense and Campylobacter jejuni. The models also suggest new explanations for previously unexplained asymmetric distributions of bacteria performing aerotaxis. More broadly, the work advocates further research into the relationship between behaviour and the metabolic organisation of self-production, an organisational property shared by all life. It also acts as an example of how abstract models that target theoretical concepts rather than natural phenomena can play a valuable role in the scientific endeavour

Modeling habits as self-sustaining patterns of sensorimotor behavior

In the recent history of psychology and cognitive neuroscience, the notion of habit has been reduced to a stimulus-triggered response probability correlation. In this paper we use a computational model to present an alternative theoretical view (with some philosophical implications), where habits are seen as self-maintaining patterns of behavior that share properties in common with self-maintaining biological processes, and that inhabit a complex ecological context, including the presence and influence of other habits. Far from mechanical automatisms, this organismic and self-organizing concept of habit can overcome the dominating atomistic and statistical conceptions, and the high temporal resolution effects of situatedness, embodiment and sensorimotor loops emerge as playing a more central, subtle and complex role in the organization of behavior. The model is based on a novel "iterant deformable sensorimotor medium (IDSM)," designed such that trajectories taken through sensorimotor-space increase the likelihood that in the future, similar trajectories will be taken. We couple the IDSM to sensors and motors of a simulated robot, and show that under certain conditions, the IDSM conditions, the IDSM forms self-maintaining patterns of activity that operate across the IDSM, the robot's body, and the environment. We present various environments and the resulting habits that form in them. The model acts as an abstraction of habits at a much needed sensorimotor "meso-scale" between microscopic neuron-based models and macroscopic descriptions of behavior. Finally, we discuss how this model and extensions of it can help us understand aspects of behavioral self-organization, historicity and autonomy that remain out of the scope of contemporary representationalist frameworks.Matthew Egbert's contributions to this research were funded by the European Commission as part of the ALIZ-E project (FP7-ICT-248116). Xabier Barandiaran's work was funded by the eSMCs: Extending Sensorimotor Contingencies to Cognition project, FP7-ICT-2009-6 no: IST-270212. Research project "Autonomia y Niveles de Organizacion" financed by the Spanish Government (ref. FFI2011-25665) and IAS-Research group funding IT590-13 from the Basque Government. The authors would also like to thank Eran Agmon as well as Lola Caliamero and the other members of the Embodied Emotion, Cognition and (Inter-)Action Lab for discussions of the research presented above. The opinions expressed are solely the authors

Using enactive robotics to think outside of the problem-solving box: How sensorimotor contingencies constrain the forms of emergent autononomous habits

We suggest that the influence of biology in 'biologically inspired robotics' can be embraced at a deeper level than is typical, if we adopt an enactive approach that moves the focus of interest from how problems are solved to how problems emerge in the first place. In addition to being inspired by mechanisms found in natural systems or by evolutionary design principles directed at solving problems posited by the environment, we can take inspiration from the precarious, self-maintaining organization of living systems to investigate forms of cognition that are also precarious and self-maintaining and that thus also, like life, have their own problems that must be be addressed if they are to persist. In this vein, we use a simulation to explore precarious, self-reinforcing sensorimotor habits as a building block for a robot's behavior. Our simulations of simple robots controlled by an Iterative Deformable Sensorimotor Medium demonstrate the spontaneous emergence of different habits, their re-enactment and the organization of an ecology of habits within each agent. The form of the emergent habits is constrained by the sensory modality of the robot such that habits formed under one modality (vision) are more similar to each other than they are to habits formed under another (audition). We discuss these results in the wider context of: (a) enactive approaches to life and mind, (b) sensorimotor contingency theory, (c) adaptationist vs. structuralist explanations in biology, and (d) the limits of functionalist problem-solving approaches to (artificial) intelligence.This work was supported in part via funding from the Digital Life Institute, University of Auckland. XB acknowledges funding from the Spanish Ministry of Science and Innovation for the research project Outonomy PID2019-104576GB-I00 and IAS-Research group funding IT1668-22 from Basque Government

Behavioral metabolution: the adaptive and evolutionary potential of metabolism-based chemotaxis

We use a minimal model of metabolism-based chemotaxis to show how a coupling between metabolism and behavior can affect evolutionary dynamics in a process we refer to as behavioral metabolution. This mutual influence can function as an in-the-moment, intrinsic evaluation of the adaptive value of a novel situation, such as an encounter with a compound that activates new metabolic pathways. Our model demonstrates how changes to metabolic pathways can lead to improvement of behavioral strategies, and conversely, how behavior can contribute to the exploration and fixation of new metabolic pathways. These examples indicate the potentially important role that the interplay between behavior and metabolism could have played in shaping adaptive evolution in early life and protolife. We argue that the processes illustrated by these models can be interpreted as an unorthodox instantiation of the principles of evolution by random variation and selective retention. We then discuss how the interaction between metabolism and behavior can facilitate evolution through (i) increasing exposure to environmental variation, (ii) making more likely the fixation of some beneficial metabolic pathways, (iii) providing a mechanism for in-the-moment adaptation to changes in the environment and to changes in the organization of the organism itself, and (iv) generating conditions that are conducive to speciatio

A Minimal Model of Metabolism Based Chemotaxis

Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption. Recent studies have shown, however, that many metabolism-dependent chemotactic patterns occur in bacteria. We hereby present the simplest artificial protocell model capable of performing metabolism-based chemotaxis. The model serves as a proof of concept to show how even the simplest metabolism can sustain chemotactic patterns of varying sophistication. It also reproduces a set of phenomena that have recently attracted attention on bacterial chemotaxis and provides insights about alternative mechanisms that could instantiate them. We conclude that relaxing the metabolism-independent assumption provides important theoretical advances, forces us to rethink some established pre-conceptions and may help us better understand unexplored and poorly understood aspects of bacterial chemotaxis

Which patients with ES-SCLC are most likely to benefit from more aggressive radiotherapy: A secondary analysis of the Phase III CREST trial

Introduction: In ES-SCLC patients with residual intrathoracic disease after first-line chemotherapy, the addition of thoracic radiotherapy reduces the risk of intrathoracic recurrence, and improves 2-year survival. To identify patient subgroups for future trials investigating higher dose (extra)thoracic radiotherapy, we investigated the prognostic importance of number and sites of metastases in patients included in the CREST trial. Materials/methods: Additional data on sites and numbers of metastases were collected from individual records of 260 patients from the top 9 recruiting centers in the randomized CREST trial (53% of 495 study patients), which compared thoracic radiotherapy (TRT) to no TRT in ES-SCLC patients after any response to chemotherapy. All patients received prophylactic cranial irradiation. Results: The clinical characteristics and outcomes of the 260 patients analyzed here did not differ significantly from that of the other 235 patients included in the CREST trial, except that fewer patients had a WHO = 0 performance status (24% vs 45%), and a higher proportion had WHO = 2 (15% vs 5%; p <0.0001). No distant metastases were recorded in 5%, 39% had metastases confined to one organ, 34% to two, and 22% to three or more organ sites. Metastases were present in the liver (47%), bone (40%), lung (28%), extrathoracic (non-supraclavicular) lymph nodes (19%), supraclavicular nodes (18%), adrenals (17%) and other sites (12%). The OS (p = 0.02) and PFS (p = 0.04) were significantly better in patients with 2 or fewer metastases, with OS significantly worse if liver (p = 0.03) and/or bone metastases (p= 0.04) were present. Discussion: This analysis of patients recruited from the top 9 accruing centers in the CREST trial suggests that future studies evaluating more intensive thoracic and extra-thoracic radiotherapy in ES-SCLC should focus on patients with fewer than 3 distant metastases. (C) 2017 The Author(s). Published by Elsevier Ireland Ltd

Storm-induced upwelling of high pCO2 waters onto the continental shelf of the western Arctic Ocean and implications for carbonate mineral saturation states

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 39 (2012): L07606, doi:10.1029/2012GL051574.The carbon system of the western Arctic Ocean is undergoing a rapid transition as sea ice extent and thickness decline. These processes are dynamically forcing the region, with unknown consequences for CO2 fluxes and carbonate mineral saturation states, particularly in the coastal regions where sensitive ecosystems are already under threat from multiple stressors. In October 2011, persistent wind-driven upwelling occurred in open water along the continental shelf of the Beaufort Sea in the western Arctic Ocean. During this time, cold (32.4) halocline water—supersaturated with respect to atmospheric CO2 (pCO2 > 550 μatm) and undersaturated in aragonite (Ωaragonite < 1.0) was transported onto the Beaufort shelf. A single 10-day event led to the outgassing of 0.18–0.54 Tg-C and caused aragonite undersaturations throughout the water column over the shelf. If we assume a conservative estimate of four such upwelling events each year, then the annual flux to the atmosphere would be 0.72–2.16 Tg-C, which is approximately the total annual sink of CO2 in the Beaufort Sea from primary production. Although a natural process, these upwelling events have likely been exacerbated in recent years by declining sea ice cover and changing atmospheric conditions in the region, and could have significant impacts on regional carbon budgets. As sea ice retreat continues and storms increase in frequency and intensity, further outgassing events and the expansion of waters that are undersaturated in carbonate minerals over the shelf are probable.Funding for this work was provided by the National Science Foundation (ARC1041102 – JTM, OPP0856244-RSP, and ARC1040694- LWJ), the National Oceanic and Atmospheric Administration (CIFAR11021- RHB) and the West Coast & Polar Regions Undersea Research Center (POFP00983 – CLM and JM).2012-10-1

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions