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B."],"published-print":{"date-parts":[[2016,8,31]]},"abstract":"<jats:p>\n            Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the\n            <jats:italic>foraging<\/jats:italic>\n            gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure to light affects\n            <jats:italic>foraging<\/jats:italic>\n            expression in brood workers and foragers. Results from our field study show that the regulation of the\n            <jats:italic>foraging<\/jats:italic>\n            gene in harvester ants occurs at two time scales: levels of\n            <jats:italic>foraging<\/jats:italic>\n            mRNA are associated with ontogenetic changes over weeks in worker age, location and task, and there are significant daily oscillations in\n            <jats:italic>foraging<\/jats:italic>\n            expression in foragers. The temporal dissection of\n            <jats:italic>foraging<\/jats:italic>\n            expression reveals that gene expression changes in foragers occur across a scale of hours and the level of expression is predicted by activity rhythms: foragers have high levels of\n            <jats:italic>foraging<\/jats:italic>\n            mRNA during daylight hours when they are most active outside the nests. In the experimental study, we find complex interactions in\n            <jats:italic>foraging<\/jats:italic>\n            expression between task behaviour and light exposure. Oscillations occur in foragers following experimental exposure to 13 L : 11 D (LD) conditions, but not in brood workers under similar conditions. No significant differences were seen in\n            <jats:italic>foraging<\/jats:italic>\n            expression over time in either task in 24 h dark (DD) conditions. Interestingly, the expression of\n            <jats:italic>foraging<\/jats:italic>\n            in both undisturbed field and experimentally treated foragers is also significantly correlated with the expression of the circadian clock gene,\n            <jats:italic>cycle<\/jats:italic>\n            . Our results provide evidence that the regulation of this gene is context-dependent and associated with both ontogenetic and daily behavioural plasticity in field colonies of harvester ants. Our results underscore the importance of assaying temporal patterns in behavioural gene expression and suggest that gene regulation is an integral mechanism associated with behavioural plasticity in harvester ants.\n          <\/jats:p>","DOI":"10.1098\/rspb.2016.0841","type":"journal-article","created":{"date-parts":[[2016,8,31]],"date-time":"2016-08-31T18:59:44Z","timestamp":1472669984000},"page":"20160841","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":33,"title":["Context-dependent expression of the\n            <i>foraging<\/i>\n            gene in field colonies of ants: the interacting roles of age, environment and task"],"prefix":"10.1098","volume":"283","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4512-1549","authenticated-orcid":false,"given":"Krista K.","family":"Ingram","sequence":"first","affiliation":[{"name":"Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, 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All rights reserved.","name":"copyright","label":"Copyright"}]},{"indexed":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T00:00:40Z","timestamp":1768348840044,"version":"3.49.0"},"reference-count":68,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,3,26]],"date-time":"2019-03-26T00:00:00Z","timestamp":1553558400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,3,26]],"date-time":"2019-03-26T00:00:00Z","timestamp":1553558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Ants are abundant in desiccating environments despite their high surface area to volume ratios and exposure to harsh conditions outside the nest. Red harvester ant (<jats:italic>Pogonomyrmex barbatus<\/jats:italic>) colonies must spend water to obtain water: colonies lose water as workers forage outside the nest, and gain water metabolically through seeds collected in foraging trips. Here we present field experiments showing that hydrated<jats:italic>P. barbatus<\/jats:italic>foragers made more foraging trips than unhydrated nestmates. The positive effect of hydration on foraging activity is stronger as the risk of desiccation increases. Desiccation tests showed that foragers of colonies that reduce foraging in dry conditions are more sensitive to water loss, losing water and motor coordination more rapidly in desiccating conditions, than foragers of colonies that do not reduce foraging in dry conditions. Desiccation tolerance is also associated with colony reproductive success. Surprisingly, foragers that are more sensitive to water loss are from colonies more likely to produce offspring colonies. This could be because the foragers of these colonies conserve water with a more cautious response to desiccation risk. An ant\u2019s hydration status may influence its response to the olfactory interactions that regulate its decision to leave the nest to forage. 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We begin with an overview of Husserlian phenomenology, focusing on aspects of inner time-consciousness, namely, retention, primal impression, and protention. We then review active inference as a formal approach to modeling agent behavior based on variational (approximate Bayesian) inference. Expanding upon Husserl\u2019s model of time consciousness, we consider collective goal-directed behavior, emphasizing shared protentions among agents and their connection to the shared generative models of active inference. This integrated framework aims to formalize shared goals in terms of shared protentions, and thereby shed light on the emergence of group intentionality. Building on this foundation, we incorporate mathematical tools from category theory, in particular, sheaf and topos theory, to furnish a mathematical image of individual and group interactions within a stochastic environment. Specifically, we employ morphisms between polynomial representations of individual agent models, allowing predictions not only of their own behaviors but also those of other agents and environmental responses. Sheaf and topos theory facilitates the construction of coherent agent worldviews and provides a way of representing consensus or shared understanding. We explore the emergence of shared protentions, bridging the phenomenology of temporal structure, multi-agent active inference systems, and category theory. Shared protentions are highlighted as pivotal for coordination and achieving common objectives. We conclude by acknowledging the intricacies stemming from stochastic systems and uncertainties in realizing shared goals.<\/jats:p>","DOI":"10.3390\/e26040303","type":"journal-article","created":{"date-parts":[[2024,3,31]],"date-time":"2024-03-31T13:39:37Z","timestamp":1711892377000},"page":"303","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Shared Protentions in Multi-Agent Active Inference"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0916-4645","authenticated-orcid":false,"given":"Mahault","family":"Albarracin","sequence":"first","affiliation":[{"name":"VERSES Research Lab and Spatial Web Foundation, Los Angeles, CA 90016, USA"},{"name":"D\u00e9partement d\u2019Informatique, l\u2019Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al, Montreal, QC H3C 3P8, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4682-9573","authenticated-orcid":false,"given":"Riddhi J.","family":"Pitliya","sequence":"additional","affiliation":[{"name":"VERSES Research Lab and Spatial Web Foundation, Los Angeles, CA 90016, USA"},{"name":"Department of Experimental Psychology, University of Oxford, Oxford OX2 6GG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8317-8722","authenticated-orcid":false,"given":"Toby","family":"St. Clere Smithe","sequence":"additional","affiliation":[{"name":"VERSES Research Lab and Spatial Web Foundation, Los Angeles, CA 90016, USA"},{"name":"Topos Institute, Berkeley, CA 94704, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6232-9096","authenticated-orcid":false,"given":"Daniel Ari","family":"Friedman","sequence":"additional","affiliation":[{"name":"Active Inference Institute, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7984-8909","authenticated-orcid":false,"given":"Karl","family":"Friston","sequence":"additional","affiliation":[{"name":"VERSES Research Lab and Spatial Web Foundation, Los Angeles, CA 90016, USA"},{"name":"Wellcome Trust Centre for Neuroimaging, Institute of Neurology, University College London, London WC1N 3BG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxwell J. 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Paleolithic Rockstars were both enigmatic and sporadic: A comment on: \u2018Snakes and Ladders\u2019 in paleoanthropology: From cognitive surprise to skillfulness a million years ago","name":"articletitle","label":"Article Title"},{"value":"Physics of Life Reviews","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.plrev.2024.04.010","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"simple-article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}]},{"indexed":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T19:10:53Z","timestamp":1763665853425,"version":"3.45.0"},"posted":{"date-parts":[[2023,5,3]]},"group-title":"MetaArXiv","reference-count":0,"publisher":"Center for Open Science","license":[{"start":{"date-parts":[[2023,5,3]],"date-time":"2023-05-03T00:00:00Z","timestamp":1683072000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"content-domain":{"domain":[],"crossmark-restriction":false},"abstract":"<p>While open access publishing effectively broadens access to scientific research products, the problem of \\emph{making sense} of the volumes of new information is becoming increasingly acute. Traditional curation methods like peer-reviewed journals and recommendation services are failing to keep pace, resulting in unprecedented information overload and knowledge fragmentation. We contend that making sense of science requires open access to diverse sources of scientific sensemaking data, and that current frictions and failures of scientific sensemaking arise from deficiencies in reckoning with these kinds of data. Sensemaking data are the digital traces of sensemaking processes, in which individuals and groups organize and structure new information to improve subsequent decision-making and actions. Sensemaking data include explicit annotations (tags, votes, ratings, marginal comments) and commentaries made by researchers, as well implicit behavioral data generated through app usage (reference managers, website metrics, etc). Crucially, sensemaking data is currently scattered and siloed across a multitude of apps and formats, and also increasingly enclosed by publishers for profit. We provide an outline for Open Science Sensemaking (OSSm), an interoperable and decentralized annotation network. Such a system would enable researchers to record, own, and share their sensemaking data, thus contributing to the network while remaining resilient to platform capture. Shared annotation data will greatly benefit individual and collective sensemaking by enabling development of diverse content discovery services, from simple aggregation of reviews and ratings (e.g., ``Goodreads for scientific research'') to more advanced AI-augmented scientific intelligence systems.<\/p>","DOI":"10.31222\/osf.io\/9nb3u","type":"posted-content","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T01:01:20Z","timestamp":1683162080000},"source":"Crossref","is-referenced-by-count":0,"title":["Open Access science needs Open Science Sensemaking (OSSm): open infrastructure for sharing scientific sensemaking data"],"prefix":"10.31222","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6049-591X","authenticated-orcid":true,"given":"Ronen","family":"Tamari","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6232-9096","authenticated-orcid":true,"given":"Daniel","family":"Friedman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"15934","deposited":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T19:02:06Z","timestamp":1763665326000},"score":0.0,"resource":{"primary":{"URL":"https:\/\/osf.io\/9nb3u_v1"}},"issued":{"date-parts":[[2023,5,3]]},"references-count":0,"URL":"https:\/\/doi.org\/10.31222\/osf.io\/9nb3u","published":{"date-parts":[[2023,5,3]]},"subtype":"preprint"},{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T04:02:40Z","timestamp":1760241760574,"version":"build-2065373602"},"reference-count":57,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2018,8,13]],"date-time":"2018-08-13T00:00:00Z","timestamp":1534118400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Arts"],"abstract":"<jats:p>Healthy romantic relationships contribute to human physical health and emotional well-being. Technologies that catalyze human sexuality such as silicone sex toys and video-conferencing are increasingly common today, and disruptive sexological artifacts such as sexbots are speculated to eventually compete directly with human-human sexuality. The consequences of these evolutionary transitions in human sociosexual behavior are entirely unknown at the individual or collective scale. Here we introduce Partner Pen Play in Parallel (PPPiP), the act of simultaneous improvisational drawing on paper without clinical supervision. In this prospective article we sketch out what PPPiP is, then provide interdisciplinary evidence from art therapy, sexology, affective neuroscience, and aesthetics to support PPPiP as a useful strategy for relationship development. PPPiP combines the advantages of individuated artistic practice with the established frameworks of improvisation and dyadic relationship interventions. Relative to traditional art therapy practices, PPPiP is less clinically oriented, features fewer external constraints, and directly encourages the dynamic integration of artistic creation with relationship co-creation. PPPiP emphasizes the importance of narrative structure and controlled novelty at multiple scales in intimate partnerships, connecting art therapy practices more directly to recent neuropsychological research. Evidence from brain imaging in improvisational and aesthetic contexts supports a model in which PPPiP synergistically activates motor and cortico-limbic neural circuits associated with skilled emotive-creative processes. PPPiP thus represents a transdisciplinary answer to the question of what will we carry from our sociosexual past towards a healthier textosexual future.<\/jats:p>","DOI":"10.3390\/arts7030039","type":"journal-article","created":{"date-parts":[[2018,8,13]],"date-time":"2018-08-13T11:27:13Z","timestamp":1534159633000},"page":"39","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Partner Pen Play in Parallel (PPPiP): A New PPPiParadigm for Relationship Improvement"],"prefix":"10.3390","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8699-7125","authenticated-orcid":false,"given":"Alexandra","family":"Mikhailova","sequence":"first","affiliation":[{"name":"Center for Neuroscience, University of California, Davis, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6232-9096","authenticated-orcid":false,"given":"Daniel A.","family":"Friedman","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2018,8,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"85","DOI":"10.3389\/fnhum.2014.00085","article-title":"What Does the Brain Tell Us about Abstract Art?","volume":"8","author":"Aviv","year":"2014","journal-title":"Frontiers in Human Neuroscience"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.tics.2017.01.005","article-title":"The Depressed Brain: An Evolutionary Systems Theory","volume":"21","author":"Badcock","year":"2017","journal-title":"Trends in Cognitive Sciences"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e168","DOI":"10.2196\/resprot.6271","article-title":"A Dyadic Behavioral Intervention to Optimize Same Sex Male Couples\u2019 Engagement Across the HIV Care Continuum: Development of and Protocol for an Innovative Couples-Based Approach (Partner Steps)","volume":"5","author":"Bazzi","year":"2016","journal-title":"JMIR Research Protocols"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.anbehav.2016.10.007","article-title":"A Preference to Bond? 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This hierarchical model, structured as nested Markov blankets, comprises three interconnected levels: (i) knowledge domains as information repositories, (ii) the Thoughtseed Network where thoughtseeds compete, and (iii) meta-cognition regulating awareness. It simulates focused-attention Vipassana meditation via rule-based training informed by empirical neuroscience research on attentional stability and neural dynamics. Four states\u2014breath_control, mind_wandering, meta_awareness, and redirect_breath\u2014emerge organically from thoughtseed interactions, demonstrating self-organizing dynamics. Results indicate that experts sustain control dominance to reinforce focused attention, while novices exhibit frequent, prolonged mind_wandering episodes, reflecting beginner instability. Integrating Global Workspace Theory and the Intrinsic Ignition Framework, the model elucidates how thoughtseeds shape a unitary meditative experience through meta-awareness, balancing epistemic and pragmatic affordances via active inference. Synthesizing computational modeling with phenomenological insights, it provides an embodied perspective on cognitive state emergence and transitions, offering testable predictions about meditation skill development. The framework yields insights into attention regulation, meta-cognitive awareness, and meditation state emergence, establishing a versatile foundation for future research into diverse meditation practices (e.g., Open Monitoring, Non-Dual Awareness), cognitive development across the lifespan, and clinical applications in mindfulness-based interventions for attention disorders, advancing our understanding of the nature of mind and thought.<\/jats:p>","DOI":"10.3390\/e27050459","type":"journal-article","created":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T08:08:41Z","timestamp":1745482121000},"page":"459","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics in Meditative States"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5582-0431","authenticated-orcid":false,"given":"Prakash Chandra","family":"Kavi","sequence":"first","affiliation":[{"name":"Center for Brain and Cognition, Universitat Pompeu Fabra, 08005 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gorka","family":"Zamora-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Center for Brain and Cognition, Universitat Pompeu Fabra, 08005 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6232-9096","authenticated-orcid":false,"given":"Daniel Ari","family":"Friedman","sequence":"additional","affiliation":[{"name":"Active Inference Institute, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1977-9101","authenticated-orcid":false,"given":"Gustavo","family":"Patow","sequence":"additional","affiliation":[{"name":"Center for Brain and Cognition, Universitat Pompeu Fabra, 08005 Barcelona, Spain"},{"name":"Department of Computer Science, Applied Mathematics and Statistics, University of Girona, 17003 Girona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Varela, F.J., Thompson, E., and Rosch, E. 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This allows us to naturalise the scientific process in terms of dynamics that can be read as inference or Bayesian belief updating, i.e., processes that maximize the evidence for a generative model of the sensed and measured world. Our goal is to ground a computational framework that elucidates how individual cognitive processes contribute to the emergence of the scientific system, and reciprocally, how collective values, practices and technological advancements guide individual scientific cognition. Epistemologically, it also addresses some key questions, e.g., is science a special? And in what ways is scientific pursuit an existential imperative for all beings? 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