Daniel Ari Friedman, PhD Computational biologist, Active Inference researcher, cognitive security researcher, educator, and artist California, USA, Earth Email: danielarifriedman@gmail.com; daniel@activeinference.institute Sites: https://danielarifriedman.com/; https://cognitivesecurity.us GitHub: https://github.com/docxology LinkedIn: https://www.linkedin.com/in/danielarifriedman/ Google Scholar: https://scholar.google.com/citations?user=DXjPFtYAAAAJ ORCID: 0000-0001-6232-9096 Keybase: docxology ENS: docxology.eth Art portfolio: https://www.flickr.com/photos/daniel_friedman/ Voice/Text: Ask via email Variant: academic Generated: 2026-05-27T22:18:54Z Current public metrics: 124 curated works; 82 catalogued software repositories (50 owned + 32 AII); 764 Google Scholar citations, h-index 15, i10-index 17 as of 2026-05-16. SUMMARY ------- Multidisciplinary researcher and open-source builder working across social insect biology, Active Inference, cognitive security, computational frameworks, education, and art. EDUCATION --------- 2019-2023 | Postdoctoral Fellow | University of California, Davis | Davis, CA, USA - Co-mentors: Prof. Brian Johnson (UC Davis) and Prof. Tim Linksvayer (Arizona State University). - NSF Postdoctoral Research Fellowship in Biology (PRFB), award DBI-2010290; NSF budget period 2020-2022 with affiliation extending to 2023. - Genomics, epigenomics, transcriptomics, and behavior in eusocial insects, mainly ants and bees. - Science research, mentoring, participation, service, and organizing events and communities online. - Sources: NSF DBI-2010290: https://grantome.com/grant/NSF/DBI-2010290; UC Davis: https://www.ucdavis.edu/ 2014-2019 | PhD | Stanford University | Stanford, CA, USA - Advisor: Professor Deborah M. Gordon, Biology. - Research, teaching, service, and coursework from Summer 2014 to Summer 2019. - Thesis topics: ant ecology, collective behavior, brain gene expression, and neurometabolism. - Stanford Graduate Fellow (Urbanek Family Fellowship), 2014-2017. - Co-organizer of the Stanford Complexity Group, 2016-2019. - Stanford Neuroscience NeuroChoice Grant for neurometabolism in ants, 2019, $25,000. - Stanford Systems Biology Seed Grant for gene expression and behavior in ants, 2018, $25,000. - Theodore Roosevelt Memorial Award, American Museum of Natural History, 2016, $2,500. - Lewis and Clark Fund grant, American Philosophical Society, 2016, $4,000. - NSF GRFP Honorable Mention, 2015 and 2016. - Sources: Stanford dissertation: http://purl.stanford.edu/pb813wm1484 2010-2014 | BSc in Genetics | University of California, Davis | Davis, CA, USA - BSc in Genetics, University of California, Davis. - Genetics Department Citation, Highest Honors, 2014; 3.74 GPA overall. - Campus Community Service Silver Award, 2014. - Stanley and Jacqueline Schilling Award for Service, 2014. - Completed the Population Biology Graduate Group one-year base PhD curriculum, 2013. - Co-founder of The Aggie Transcript, an undergraduate biology journal, 2014. - Victoria Finnerty Award for Research in Drosophila, 2013. - Elected member of Phi Beta Kappa, UC Davis Chapter, 2014. - Co-organizer of the Chess Club at UC Davis, 2012-2014. - Research Scholars Program in Insect Biology, 2011-2014. - Provost's Undergraduate Fellowship for Drosophila research, 2011, $2,500. - Sources: UC Davis: https://www.ucdavis.edu/ EXPERIENCE ---------- 2021-ongoing | Community Organization | Active Inference Institute | Co-founder, Participant, Officer, President, Treasurer - Co-founded the Active Inference Institute; current President and Treasurer. - Sources: AII officers: https://www.activeinference.institute/officers; AII: https://activeinference.org/ 2019-2024 | Community Organization | Complexity Adventures | Co-founder, Facilitator, Participant, Organizer - Organized activities and community around learning and applying complexity science. - Sources: Complexity Adventures profile: https://www.complexityadventures.com/organizers/2 2019-ongoing | Community Organization | COGSEC | Researcher - Research facilitation and participation on initiatives related to cognitive security. - Sources: COGSEC: https://www.cogsec.org/ 2014-2019 | Community Organization | Stanford Complexity Group | Organizer, Participant - Organized the Stanford Complexity Group while it was active. - Sources: Stanford: https://www.stanford.edu/; verification: https://danielarifriedman.com/resume/verify.html 2019-2023 | Research | Johnson Lab / Linksvayer Lab | Mentor, Researcher - Postdoctoral position during NSF fellowship with Brian Johnson at UC Davis and Tim Linksvayer at Arizona State University. - Sources: Johnson Lab: https://johnsonlab.ucdavis.edu/; UC Davis: https://www.ucdavis.edu/ 2014-2019 | Research | Gordon Lab | Mentor, Researcher - Graduate research, field work, wet lab, bioinformatics, and mentoring of high schoolers, undergraduates, graduate students, and non-academics. - Sources: Gordon Lab: https://web.stanford.edu/~dmgordon/ 2010-2014 | Research | Kopp Lab | Researcher - Undergraduate research assistant with Prof. Artyom Kopp in Ecology and Evolution at UC Davis, studying non-coding DNA elements in the evolution of the Drosophila foreleg sex comb. - Sources: UC Davis Biology: https://biology.ucdavis.edu/ 2015-2016 | Teaching | Stanford University | Teacher, Organizer, Graduate Teaching Assistant - Graduate Teaching Assistant for undergraduate and graduate courses: General Biology: Cell and Molecular Biology (2015) and Ethics of Evolutionary Biology (2016). - Sources: Stanford Biology: https://biology.stanford.edu/ 2014 | Teaching | UC Davis | Teacher, Organizer, Course Co-developer - Student teacher and developmental biology course co-developer with Prof. Susan Keen at UC Davis. - Sources: UC Davis Biology: https://biology.ucdavis.edu/ AWARDS AND FELLOWSHIPS ---------------------- 2020 | NSF Postdoctoral Research Fellowship in Biology - Award DBI-2010290; NSF budget period 2020-2022. - Sources: NSF DBI-2010290: https://grantome.com/grant/NSF/DBI-2010290 2014 | Stanford Graduate Fellow, Urbanek Family Fellowship - Stanford University, 2014-2017. - Sources: Stanford Graduate Fellowship: https://vpge.stanford.edu/fellowships-funding/sgf 2019 | Stanford Neuroscience NeuroChoice Grant - Neurometabolism in ants, $25,000. - Sources: Stanford Neurosciences Institute: https://neuroscience.stanford.edu/ 2018 | Stanford Systems Biology Seed Grant - Gene expression and behavior in ants, $25,000. - Sources: Stanford Systems Biology: https://sysbio.stanford.edu/ 2016 | Theodore Roosevelt Memorial Award - American Museum of Natural History, $2,500. - Sources: AMNH Theodore Roosevelt Grants: https://www.amnh.org/research/richard-gilder-graduate- school/academics-and-research/fellowships-and-grants/theodore-roosevelt-memorial-grants 2016 | Lewis and Clark Fund grant - American Philosophical Society, $4,000. - Sources: APS Lewis and Clark Fund: https://www.amphilsoc.org/grants/lewis-and-clark-fund- exploration-and-field-research 2015 | NSF GRFP Honorable Mention - Honorable Mention in 2015 and 2016. - Sources: NSF GRFP: https://www.nsfgrfp.org/ 2014 | UC Davis Genetics Department Citation - Highest Honors. - Sources: UC Davis Genetics: https://genetics.ucdavis.edu/ 2013 | Victoria Finnerty Award for Research in Drosophila - UC Davis. - Sources: UC Davis Genetics: https://genetics.ucdavis.edu/ 2014 | Phi Beta Kappa - Elected member, UC Davis Chapter. - Sources: Phi Beta Kappa: https://www.pbk.org/ 2011 | Provost's Undergraduate Fellowship - Drosophila research, $2,500. - Sources: UC Davis Undergraduate Research Center: https://urc.ucdavis.edu/puf WORKS AND PUBLICATIONS (124) ---------------------------- [001] 2026 | Paper | A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication | Zenodo | 10.5281/zenodo.19139090 [002] 2026 | Series | Active Inference Journal — 500+ videos on Active Inference with transcripts | YouTube | https://video.activeinference.institute/ [003] 2026 | Paper | Before Pragmatism Had a Name: Blake's "America A Prophecy" Anticipates American Anticipatory Epistemology | Zenodo | 10.5281/zenodo.18807970 [004] 2026 | Paper | The Golden Compass and the Lunar Flux: William Blake, Bimetallic Meta-stability, and the Architecture of Value | Zenodo | 10.5281/zenodo.19335196 [005] 2026 | Paper | Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) | Zenodo | 10.5281/zenodo.18364119 [006] 2026 | Series | Personal YouTube — 200+ livestreams: drawings, Synergetics, paper discussions | YouTube | https://www.youtube.com/@danielarifriedman/playlists [007] 2026 | Paper | The Doors of Perception are the Threshold of Prediction: Active Inference and William Blake's Theory of Seeing | Zenodo | 10.5281/zenodo.18600041 [008] 2025 | Presentation | 5th Applied Active Inference Symposium — Abstract Book | Presentation | 10.5281/zenodo.17555266 [009] 2025 | Paper | Adaptive Basic Income (AuBI): Integrating AI, Decentralized Infrastructure, and Active Inference | Zenodo | 10.5281/zenodo.17228945 [010] 2025 | Paper | CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling | Zenodo | 10.5281/zenodo.15170907 [011] 2025 | Paper | Computational Complexity and Energetics of the Ant Stack | Zenodo | 10.5281/zenodo.17238736 [012] 2025 | Paper | EvoJump: Stochastic Modeling of Evolutionary Ontogenetic Trajectories | Zenodo | 10.5281/zenodo.17229924 [013] 2025 | Paper | Increasing the Accessibility and Applicability of Active Inference | Zenodo | 10.5281/zenodo.15061667 [014] 2025 | Paper | MDKV: A Multitrack Markdown Container for Structured, Portable Documents | Zenodo | 10.5281/zenodo.16790554 [015] 2025 | Paper | Markdown Decision Process: A Framework for Probabilistic Document Analysis | Zenodo | 10.5281/zenodo.17244386 [016] 2025 | Paper | On Cognitive Art & Science: Toward Wholeness From Both Sides | Zenodo | 10.5281/zenodo.16740439 [017] 2025 | Paper | On Time | Zenodo | 10.5281/zenodo.15168381 [018] 2025 | Paper | QuadMath: An Analytical Review of 4D and Quadray Coordinates | Zenodo | 10.5281/zenodo.16887800 [019] 2025 | Paper | ResNei: Solution Design Document | Zenodo | 10.5281/zenodo.15389682 [020] 2025 | Paper | Symergetics: Symbolic Synergetics for Rational Arithmetic | Zenodo | 10.5281/zenodo.17114389 [021] 2025 | Paper | Synthesis of Agent and Niche | Zenodo | 10.5281/zenodo.17235137 [022] 2025 | Presentation | Systems Processes, Active Inference, and Beyond | Presentation | 10.5281/zenodo.17138223 [023] 2025 | Paper | Temporal Depth in a Coherent Self and in Depersonalization | Frontiers in Psychology | 10.3389/fpsyg.2025.1585315 [024] 2025 | Paper | The Active Inference Institute & Active Inference Ecosystem (v3, 2025 snapshot) | Zenodo | 10.5281/zenodo.17982447 [025] 2025 | Paper | The Ant Stack | Zenodo | 10.5281/zenodo.16782756 [026] 2025 | Paper | The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes | ArXiv | 10.48550/arXiv.2505.17500 [027] 2025 | Paper | Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics in Meditative States | Entropy | 10.3390/e27050459 [028] 2025 | Paper | Towards a Science of Consciousness and Social Complexity... For Ants | Book Chapter | https://www.editorafi.org/ebook/c128-colonias-formigas-conscientes [029] 2024 | Paper | Aligning Active Inference Ontology to SUMO | Zenodo | 10.5281/zenodo.11459322 [030] 2024 | Presentation | BioFirm Development at Applied Active Inference Symposium 2024 | Presentation | 10.5281/zenodo.14861595 [031] 2024 | Paper | Bridging gaps in image meme research: A multidisciplinary paradigm | JASIST | 10.1002/asi.24900 [032] 2024 | Paper | Chemical and transcriptomic diversity do not correlate with ascending levels of social complexity in Blattodea | Ecology & Evolution | 10.1002/ece3.70063 [033] 2024 | Paper | Comments on National Digital Twins R&D Strategic Plan | Zenodo | 10.5281/zenodo.13273681 [034] 2024 | Paper | Enhancing Population-based Search with Active Inference | ArXiv | 10.48550/arXiv.2408.09548 [035] 2024 | Paper | FarmWorks: Decentralized AI Agents for Personalized Solutions | Zenodo | 10.5281/zenodo.13754585 [036] 2024 | Paper | Federated inference and belief sharing | Neuroscience & Biobehavioral Reviews | 10.1016/j.neubiorev.2023.105500 [037] 2024 | Paper | Four-fold Fields of Quantum Dreams | Zenodo | 10.5281/zenodo.10798145 [038] 2024 | Presentation | MathArt Stream #8: William Blake and Active Inference | Presentation | 10.5281/zenodo.13711301 [039] 2024 | Presentation | Sensemaking Federation: Exploring the Frontiers of Digital Innovation | Presentation | 10.5281/zenodo.14574046 [040] 2024 | Paper | Shared Protentions in Multi-Agent Active Inference | Entropy | 10.3390/e26040303 [041] 2024 | Paper | The Active Inference Institute & Active Inference Ecosystem (v2, 2024 snapshot) | Zenodo | 10.5281/zenodo.14108992 [042] 2024 | Paper | Way Finding in the Infinite Imaginarium | Zenodo | 10.5281/zenodo.10601082 [043] 2024 | Paper | Why Paleolithic Rockstars were both enigmatic and sporadic | Physics of Life Reviews | 10.1016/j.plrev.2024.04.010 [044] 2024 | Paper | Writing on Curio Cards for the "On NFT" book | Taschen | https://www.worldcat.org/isbn/978-3-8365-9970-2 [045] 2023 | Paper | A guided tour through the spaces of particular "minds" | Physics of Life Reviews | 10.1016/j.plrev.2023.11.001 [046] 2023 | Paper | A single-pheromone model accounts for empirical patterns of ant colony foraging | Cognitive Systems Research | 10.1016/j.cogsys.2023.02.005 [047] 2023 | Paper | A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees | Zenodo | 10.5281/zenodo.10400744 [048] 2023 | Paper | A variational synthesis of evolutionary and developmental dynamics | Entropy | 10.3390/e25070964 [049] 2023 | Paper | ATLAS: A Question Oriented Approach to Pattern Languages in Knowledge Management | Zenodo | 10.5281/zenodo.10296601 [050] 2023 | Paper | An Account of Active Inference Modeling | Zenodo | 10.5281/zenodo.8415313 [051] 2023 | Paper | Cognitive Sovereignty & Active Inference in the State of Exception | Zenodo | 10.5281/zenodo.10038232 [052] 2023 | Paper | Comments on AI Accountability Policy to NTIA | NTIA | 10.5281/zenodo.8025957 [053] 2023 | Paper | Distributed Science — The Scientific Process as Multi-Scale Active Inference | OSF | 10.31219/osf.io/dnw5k [054] 2023 | Paper | Enhanced NSF Postdoctoral Reporting via Synthetic Intelligence Language Processing | Zenodo | 10.5281/zenodo.10160656 [055] 2023 | Paper | Experimental Entomology in the Age of Video | JoVE | 10.3791/65002 [056] 2023 | Paper | Generalized Notation Notation for Active Inference Models | Zenodo | 10.5281/zenodo.7803328 [057] 2023 | Paper | Generative Research Teams: Active Inference Compositions for Research and Meta-Science | Zenodo | 10.5281/zenodo.8164667 [058] 2023 | Presentation | Of Ants & Aging | Presentation | 10.5281/zenodo.7855582 [059] 2023 | Paper | Open Access science needs Open Science Sensemaking (OSSm) | MetaArXiv | 10.31222/osf.io/9nb3u [060] 2023 | Presentation | Postdoc review (2020–2023) | Presentation | 10.5281/zenodo.8377988 [061] 2023 | Paper | The Active Inference Institute and Active Inference Ecosystem (v1) | Zenodo | 10.5281/zenodo.8266281 [062] 2023 | Paper | The P3IF: Properties, Processes, and Perspectives Inter-Framework | Zenodo | 10.5281/zenodo.10034512 [063] 2023 | Paper | To comment or not to comment | Physics of Life Reviews | 10.1016/j.plrev.2023.06.002 [064] 2023 | Course | Transcript of Chris Fields, "Physics as Information Processing" course | Zenodo | 10.5281/zenodo.10447642 [065] 2023 | Paper | William Blake & Buckminster Fuller: Lives in Juxtaposition | Zenodo | 10.5281/zenodo.7514368 [066] 2022 | Paper | An Active Inference Ontology for Decentralized Science | Zenodo | 10.5281/zenodo.6320574 [067] 2022 | Paper | Catechism for Towards Active Diffusion | Zenodo | 10.5281/zenodo.7443848 [068] 2022 | Paper | From Users to (Sense)Makers: Stigmergic Social Annotation | Hypertext '22 | 10.48550/arXiv.2205.06345 [069] 2022 | Paper | On free will or the lack thereof (interview with Robert Sapolsky) | ALIUS Bulletin | 10.5281/zenodo.7394901 [070] 2022 | Paper | Predictive Processing Interpretation of the Mirror Test | Zenodo | 10.5281/zenodo.7377256 [071] 2022 | Book | Structuring the Information Commons: Open Standards and Cognitive Security | COGSEC.org | https://cogsec.org [072] 2022 | Paper | Systems Modeling and Cognitive Audits for Hypercert Ecosystems | Zenodo | 10.5281/zenodo.7626769 [073] 2022 | Paper | The Free Energy Principle & Active Inference: a Systematic Literature Analysis | Zenodo | 10.5281/zenodo.7449368 [074] 2022 | Paper | TrustFinder: Recommendations for Community-Based Trust Systems | Zenodo | 10.5281/zenodo.7093837 [075] 2021 | Paper | Active Inferants: An Active Inference Framework for Ant Colony Behavior | Frontiers in Behavioral Neuroscience | 10.3389/fnbeh.2021.647732 [076] 2021 | Paper | Active Inference in Modeling Conflict | Zenodo | 10.5281/zenodo.5759807 [077] 2021 | Paper | Digital Rhetorical Ecosystem Analysis: Sensemaking of Digital Memetic Discourse | Zenodo | 10.5281/zenodo.5573947 [078] 2021 | Playbook | Innovator's Digital Playbook | Web | https://innovatorsdigitalplaybook.com/ [079] 2021 | Book | Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier | COGSEC.org | https://cogsec.org [080] 2021 | Paper | Narrative Information Management | Zenodo | 10.5281/zenodo.5573287 [081] 2021 | Playbook | The Facilitator's Catechism Playbook | Zenodo | 10.5281/zenodo.4579414 [082] 2020 | Paper | Active Inference & Behavior Engineering for Teams | Zenodo | 10.5281/zenodo.4021163 [083] 2020 | Course | Communication for Remote Teams | Udemy | https://www.udemy.com/course/communication-for-remote-teams/ [084] 2020 | Paper | Distributed physiology and the molecular basis of social life in eusocial insects | Hormones & Behavior | 10.1016/j.yhbeh.2020.104757 [085] 2020 | Paper | Emergent Teams for Complex Threats | Zenodo | 10.5281/zenodo.3986085 [086] 2020 | Paper | Gene expression variation in the brains of harvester ant foragers is associated with collective behavior | Communications Biology | 10.1038/s42003-020-0813-8 [087] 2020 | Course | How to use Keybase for remote teams | Udemy | https://www.udemy.com/course/keybase-for-remote-teams/ [088] 2020 | Paper | Measurement of natural variation of neurotransmitter tissue content in red harvester ant brains | Analytical & Bioanalytical Chemistry | 10.1007/s00216-019-02355-3 [089] 2020 | Book | The Great Preset: Remote Teams and Operational Art | COGSEC.org | https://cogsec.org [090] 2020 | Paper | The Innovator's Catechism | Zenodo | 10.5281/zenodo.4383230 [091] 2020 | Paper | The neuroscience of decision making (interview with Timothy Hanks) | ALIUS Bulletin | 10.34700/8pg4-0h12 [092] 2019 | Paper | Dennett Explained (interview with Daniel Dennett) | ALIUS Bulletin | 10.34700/7gkw-zh08 [093] 2019 | Paper | PhD: Behavioral, Physiological, and Transcriptomic Variation Among Colonies of Pogonomyrmex barbatus | Stanford University | http://purl.stanford.edu/pb813wm1484 [094] 2019 | Paper | The ant colony as a test for scientific theories of consciousness | Synthese | 10.1007/s11229-019-02130-y [095] 2019 | Paper | The physiology of forager hydration and variation among harvester ant colonies | Scientific Reports | 10.1038/s41598-019-41586-3 [096] 2018 | Paper | Foraging behavior and locomotion of the invasive Argentine ant from winter aggregations | PLoS One | 10.1371/journal.pone.0202117 [097] 2018 | Presentation | MVEE: A Framework for Evolutionary Studies | Presentation | 10.5281/zenodo.13999298 [098] 2018 | Paper | Of woodlice and men: A Bayesian account of cognition, life and consciousness (with Karl Friston) | ALIUS Bulletin | 10.34700/h460-nz89 [099] 2018 | Paper | Partner Pen Play in Parallel (PPPiP): A New Paradigm for Relationship Improvement | Arts | 10.3390/arts7030039 [100] 2018 | Paper | The Role of Dopamine in Collective Regulation of Foraging in Harvester Ants | iScience | 10.1016/j.isci.2018.09.001 [101] 2017 | Paper | The MutAnts are here | Cell | 10.1016/j.cell.2017.07.046 [102] 2017 | Paper | Two lineages that need each other | Molecular Ecology | 10.1111/mec.13964 [103] 2016 | Paper | Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior | Annual Review of Neuroscience | 10.1146/annurev-neuro-070815-013927 [104] 2016 | Paper | Context-dependent expression of the foraging gene in field colonies of ants | Proceedings of the Royal Society B | 10.1098/rspb.2016.0841 [105] 2016 | Paper | Influence of Nuclear Structure on formation of radiation-induced lethal lesions | Int. J. Radiation Biology | 10.3109/09553002.2016.1144941 [106] 2015 | Paper | Commentary: Portuguese crypto-Jews: the genetic heritage of a complex history | Frontiers in Genetics | 10.3389/fgene.2015.00261 [107] 2015 | Paper | Could Ehrlichial Infection Cause Some Changes Associated with Leukemia? | Medical Hypotheses | 10.1016/j.mehy.2015.09.015 [108] 2015 | Paper | Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey Bees | Molecular Biology & Evolution | 10.1093/molbev/msu292 [109] 2026 | Paper | Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology | Zenodo | 10.5281/zenodo.19574118 [110] 2026 | Paper | A Living Meta-Analysis Architecture for Active Inference: Assertion Extraction, Nanopublications, and Hypothesis Scoring | Active Inference Journal | 10.5281/zenodo.19897664 [111] 2026 | Paper | Dynamic Attentional Agents in Focused Attention Meditation: Hierarchical Computational Modeling of Expert-Novice Differences | CSCIS vol 2857, Springer | 10.1007/978-3-032-16955-6_11 [112] 2026 | Paper | Compositional Approaches to Linguistic Case for Cognitive Modeling | Active Inference Journal | 10.5281/zenodo.19695260 [113] 2026 | Paper | Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics | Active Inference Journal | 10.5281/zenodo.19699234 [114] 2020 | Paper | The Facilitator's Catechism | Zenodo | 10.5281/zenodo.4203765 [115] 2026 | Paper | The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision | Zenodo | 10.5281/zenodo.20144984 [116] 2026 | Paper | Crescent City in Living Waves: Space, Time, People, and Minds on the Southern Cascadian Coast | Zenodo | 10.5281/zenodo.20286171 [117] 2026 | Book | Introduction to Biology: A Generative Approach | Zenodo | 10.5281/zenodo.20286478 [118] 2025 | Paper | CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling | Zenodo | 10.5281/zenodo.15231156 [119] 2026 | Paper | Policy Entanglement in Active Inference | Zenodo | 10.5281/zenodo.20419186 [120] 2026 | Paper | Bounded AutoResearch for a Tiny Reproducible Machine-Learning Task | Zenodo | 10.5281/zenodo.20417017 [121] 2026 | Paper | Convergence Analysis of Gradient Descent Optimization | Zenodo | 10.5281/zenodo.20417137 [122] 2026 | Paper | Editorial Quality at Scale: A Reproducible Prose-Review Pipeline | Zenodo | 10.5281/zenodo.20417105 [123] 2026 | Paper | A template/ approach to Reproducible Generative Research | Zenodo | 10.5281/zenodo.20419084 [124] 2026 | Paper | Active Inference Multi-Track Exemplar | Zenodo | 10.5281/zenodo.20417022 SOFTWARE (17) ------------- docxology/MetaInformAnt | Python | https://github.com/docxology/MetaInformAnt | Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond | paper: papers/2021_ActiveInferants/ docxology/ActiveInferAnts | Python | https://github.com/docxology/ActiveInferAnts | Active Inference for ants — multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy | paper: papers/2021_ActiveInferants/ docxology/active_inference | Python | https://github.com/docxology/active_inference | Active Inference for, with, and by Generative AI — Python implementations of free-energy-minimizing agents integrated with modern AI tooling | paper: papers/2020_BehaviorEngineering/ docxology/ant_stack | Python | https://github.com/docxology/ant_stack | The Ant Stack — layered computational model of collective ant-colony intelligence | paper: papers/2025_AntStack/ docxology/ento_linguistics | Python | https://github.com/docxology/ento_linguistics | Ento-Linguistics corpus pipeline — term extraction, terminology networks, semantic entropy, CACE scoring | paper: papers/2026_EntoLinguistics/ docxology/cognitive_case_diagrams | TeX | https://github.com/docxology/cognitive_case_diagrams | Compositional linguistic case for cognitive modeling — categorical case systems, DisCoCat/DisCoCirc diagrams, tests and figures for the Active Inference Journal manuscript | paper: papers/2026_CognitiveCaseDiagrams/ docxology/biology_textbook | Python | https://github.com/docxology/biology_textbook | Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo | paper: papers/2026_BiologyTextbook/ | zenodo: https://doi.org/10.5281/zenodo.20286478 docxology/enactive_inference_model | Python | https://github.com/docxology/enactive_inference_model | Three-level hierarchical enactive inference model of mental action — focused-attention meditation with expert/novice profiles; reproducible simulations and figures | paper: papers/2025_Thoughtseeds/ docxology/EvoJump | Python | https://github.com/docxology/EvoJump | Comprehensive Framework for Evolutionary Ontogenetic Analysis — modeling developmental trajectories and evolutionary dynamics | paper: papers/2025_EvoJump/ docxology/markdown_decision_process | Python | https://github.com/docxology/markdown_decision_process | Framework for Probabilistic Document Analysis — Markov Decision Process over Markdown artifacts for structured document reasoning | paper: papers/2025_MarkdownDecisionProcess/ docxology/mdkv | Python | https://github.com/docxology/mdkv | MKV-like key-value format and methods for Markdown — structured metadata embedding in plain-text documents | paper: papers/2025_MDKV/ docxology/p3if | Python | https://github.com/docxology/p3if | Properties, Processes, and Perspectives Inter-Framework (P3IF) — multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security | paper: papers/2023_P3IF/ docxology/blake_jiang | Python | https://github.com/docxology/blake_jiang | William Blake, Professor Jiang, and the Architecture of Intelligence — AI-augmented scholarly response to Game Theory #24 with Blake, Jiang, and Active Inference framing | paper: papers/2026_BlakeJiang/ ActiveInferenceInstitute/GeneralizedNotationNotation | Python | https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation | GNN — formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB · Zenodo software | zenodo: https://doi.org/10.5281/zenodo.19600217 ActiveInferenceInstitute/fep_lean | Python | https://github.com/ActiveInferenceInstitute/fep_lean | Lean 4 / Mathlib4 formalization of FEP-related mathematics — 50-topic sorry-free catalog, Hermes/OpenGauss LLM drafting, zero-mock verification, manuscript pipeline · · Zenodo | paper: papers/2026_FEPLean/ | zenodo: https://doi.org/10.5281/zenodo.19699234 ActiveInferenceInstitute/Journal-Utilities | HTML | https://github.com/ActiveInferenceInstitute/Journal-Utilities | Transcription, processing, and publishing pipelines for the Active Inference Journal — Whisper-based download, transcription, RAG/knowledge-graph, and export utilities · Zenodo release | zenodo: https://doi.org/10.5281/zenodo.18686966 ActiveInferenceInstitute/CEREBRUM | Python | https://github.com/ActiveInferenceInstitute/CEREBRUM | Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling — grammatical case framework for compositional cognitive models · Zenodo | paper: papers/2025_CEREBRUM2/ | zenodo: https://doi.org/10.5281/zenodo.15231156 CONFERENCES, POSTERS, SEMINARS, WORKSHOPS ----------------------------------------- 2025 | Talk | Queens College, CUNY, Biology | Inference about Foraging and Foraging as Inference | Sources: Queens College Biology: https://www.qc.cuny.edu/academics/bio/ 2025 | Talk | Enduring Patterns, Emerging Futures: Celebrating Dr. Len Troncale | Systems Processes, Active Inference, and Beyond | 2025-09-17 | Sources: Zenodo presentation: https://doi.org/10.5281/zenodo.17138223 2024 | Workshop | ISSS 2024 | ...And Eternity in an hour of Systems Science Education and Knowledge Engineering | Sources: ISSS: https://isss.org/world/ 2022 | Talk | Entomology Society of America, Pacific Branch | Tissue-specific gene expression meta-analysis in honey bees (Apis mellifera) | 2022-04-10 | Sources: Entomological Society of America: https://entsoc.org/events 2021 | Talk | Cognitio 2021 | Thinking like a State: Active inference and the deep roots of complex societies | Avel Guenin-Carlut, Daniel Friedman, and Virginia Bleu Knight. | Sources: Cognitio: https://cognitio.uqam.ca/ 2021 | Talk | ACM-CI 2021 | Introducing Active Inference as An Integrative Principle in The Study of Collective Intelligence | Avel Guenin-Carlut and Daniel Friedman. | Sources: ACM Collective Intelligence: https://ci.acm.org/ 2020 | Talk | IIBM, Chile | Active Inference for Communicating Systems | Invited online seminar. 2020-11-03 | Sources: IIBM: https://www.iibm.cl/ 2019 | Talk | Essig Brunch Seminar Series | Invited seminar, Department of Animal Behavior, University of California, Davis | 2019-04-05 | Sources: UC Davis Entomology: https://entomology.ucdavis.edu/ 2018 | Talk | Stanford University Mass Spectrometry Research Symposium | Invited seminar, SUMS-RAS | 2018-10-04 | Sources: Stanford Mass Spectrometry: https://mass-spec.stanford.edu/ 2018 | Talk | Essig Entomology Brunch | Invited seminar, University of California, Berkeley | 2018-02-06 | Sources: Essig Museum: https://essig.berkeley.edu/ 2017 | Poster | Entomology 2017 | The role of dopamine in the regulation of foraging in the red harvester ant | Sources: Entomological Society of America: https://entsoc.org/events/annual-meeting 2017 | Poster | ASMS 2017 | Quantitative LC-MS/MS analysis of dopamine in single ant brain samples | KM Krasinska, DA Friedman, DM Gordon, AS Chien. | Sources: ASMS Annual Conference: https://www.asms.org/conferences/annual-conference 2015 | Poster | Biology and Genetics of Social Insects, CSHL 2015 | Transcriptomic analysis of the regulation of foraging in harvester ants | DA Friedman, A Pilko, DM Gordon. | Sources: Cold Spring Harbor Meetings: https://meetings.cshl.edu/ 2014 | Poster | Drosophila Research Conference 2014 | Evolution of sex comb enhancers in the HOX gene Scr | DA Friedman, T Orenic, C McCullough, E Eksi, OY Barmina, A Kopp. | Sources: GSA Drosophila Conference: https://genetics-gsa.org/drosophila/ 2012 | Talk | UC Davis Undergraduate Research Conference | Visualizing the Integration of Sensory Neurons into a Sex-Specific Central Nervous System Circuit in 3-D | DA Friedman. | Sources: UC Davis Undergraduate Research Center: https://urc.ucdavis.edu/ SCIENCE ENGAGEMENT, OUTREACH, QUOTES, ARTICLES ---------------------------------------------- 2026 | Video conversation on another channel | S3E10 The FEP: A Tool for Understanding and Modelling Complex Systems | Sources: BathmikeC podcast: https://bathmikec.podbean.com/e/s3e10-the-fep-a-tool-for-understanding-and-modelling-complex-systems/ 2025 | Video conversation on another channel | (DIA 1/SESSAO 1) Lancamento do Livro: As Colonias de Formigas Sao Conscientes? | Sources: YouTube: https://www.youtube.com/watch?v=BJ-PAt3cqf4 2024 | Video conversation on another channel | From Ants to Active Inference with Daniel Ari Friedman | Love and Philosophy, Andrea Hiott | Sources: YouTube: https://www.youtube.com/watch?v=x_VPw1K55BM 2023 | Video conversation on another channel | Active Inference and The Free Energy Principle with Daniel Friedman | No Way Out podcast | Sources: YouTube: https://www.youtube.com/watch?v=pYleeDb-B5E 2022 | Video conversation on another channel | What Ant Behavior Reveals About Complexity Science with Daniel Friedman | Making Sense of Complexity | Sources: YouTube: https://youtu.be/lQr98-sG8r0; YouTube episode: https://www.youtube.com/watch?v=4qsyV38qfTw 2016 | Blurb | Blurb in Science magazine about what ants can teach human city planners | Sources: Science: https://www.science.org/doi/abs/10.1126/science.aag1520 2025 | Profile or Interview | No Signal 006: Daniel Ari Friedman and Jakub Smekal || Active Inference | Sources: No Signal: https://kernel0x.substack.com/p/no-signal-006-daniel-ari-friedman PROFESSIONAL PARTICIPATION, ENGAGEMENT, AND SERVICE --------------------------------------------------- 2022-2024 | ISSS | Board of Directors | Vice-President for Communication and Systems Education on the International Society for the Systems Sciences Board. | Sources: ISSS: https://www.isss.org/home/ 2021-2023 | JoVE | Academia | Co-editor, Field and Laboratory Methods for Modern Entomology. | Sources: JoVE methods collection: https://www.jove.com/methods-collections/567/field-and-laboratory-methods-for-modern-entomology 2021 | Cybernetics Society | Membership | Member (MCybS), Cybernetics Society. | Sources: Cybernetics Society: http://cybsoc.org/ 2020-ongoing | Active Inference Institute | Community | Active Inference Institute co-founder. | Sources: Active Inference Institute: https://www.activeinference.institute/ 2020-2023 | Davis Complexity Group | Community | Davis Complexity Group. | Sources: verification: https://danielarifriedman.com/resume/verify.html 2018-2021 | ALIUS | Membership | ALIUS Research Group contributor, editor, and co-organizer. | Sources: ALIUS Research Group: https://www.aliusresearch.org/ 2017-2021 | ESA | Membership | Entomological Society of America. | Sources: Entomological Society of America: https://www.entsoc.org/ 2017-2019 | Stanford | Academia | NeuroChoice group, Stanford Neurosciences Institute. | Sources: NeuroChoice: https://neurochoice.stanford.edu/purpose 2016-2019 | Stanford Complexity Group | Community | Stanford Complexity Group. | Sources: Stanford: https://www.stanford.edu/; verification: https://danielarifriedman.com/resume/verify.html 2015 | Santa Fe Institute | Workshop | Santa Fe Institute Complex Systems Summer School, one-month residential program. | Sources: Santa Fe Institute CSSS: https://www.santafe.edu/engage/learn/programs/sfi-complex-systems-summer-school 2014-2018 | Gordon Lab | Field work | Five summers of ant fieldwork during PhD under Prof. Deborah Gordon at Southwestern Research Station, Arizona. | Sources: Southwestern Research Station: https://www.amnh.org/research/southwestern-research-station 2014 | Stanford | Field work | Summer field ecology class with Stanford Prof. Rodolfo Dirzo at Las Tuxtlas tropical research station, Mexico. | Sources: Los Tuxtlas Biological Station: https://www.ibiologia.unam.mx/eblt/ 2014 | NIMBioS | Workshop | Summer workshop on Evolutionary and Quantitative Genetics at NIMBioS, University of Tennessee, Knoxville. | Sources: NIMBioS: http://www.nimbios.org/tutorials/TT_eqg 2014 | Science | Field work | Drosophila work with Dr. Michael Lang in Arizona. | Sources: Drosophila Evolution: https://droseu.net/drosophila-evolution/ 2014-ongoing | Science | Academia | Invited peer reviewer for 1-10 articles per year across different journals. | Sources: Science: https://www.science.org/ 2014-2023 | IUSSI | Membership | International Union for the Study of Social Insects. | Sources: IUSSI: https://iussi.org/