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: full
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/
2006-2010 | High School | Crystal Springs Uplands School | Hillsborough, CA, USA
  - Crystal Springs Uplands School.
  - Sources: Crystal Springs Uplands School: https://www.crystal.org/

EXPERIENCE
----------
2026-ongoing | Community Organization | Del Norte Triplicate | Typographical Editor
  - Typographical editing for The Triplicate newspaper of Del Norte County and Crescent City.
  - Sources: The Triplicate: https://www.triplicate.com/
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
2025-2026 | Startup | Stealth Startup | Operator
  - Systems modeling and related work to be public later.
  - Sources: verification: https://danielarifriedman.com/resume/verify.html
2023-2024 | Startup | Stealth Startup | Co-founder, Operator
  - Stealth Active Inference startup.
  - Sources: verification: https://danielarifriedman.com/resume/verify.html
2019-2023 | Startup | Remotor | Co-founder, Researcher
  - Education, online event planning, and consulting for remote teams.
  - Sources: verification: https://danielarifriedman.com/resume/verify.html
2017-2019 | Startup | fm.analytics | Co-founder, Researcher
  - Predictive analytics and dashboard visualizations with Prof. Glenn Magerman at KU Leuven.
  - Sources: verification: https://danielarifriedman.com/resume/verify.html
2017-2019 | Startup | Cryptoptera | Co-founder, Researcher
  - Three-person cryptocurrency research group.
  - Sources: 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/
2014-2019 | Pedicab | Pedicab People Movers | Operator
  - Operated a pedicab/rickshaw at events including music festivals in California and downtown areas
  in Davis and San Jose.
  - Sources: verification: https://danielarifriedman.com/resume/verify.html
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/
2014 | UC Davis service awards
  - Campus Community Service Silver Award and Stanley and Jacqueline Schilling Award for Service.
  - Sources: UC Davis: https://www.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 (82)
-------------
docxology/template | Python | https://github.com/docxology/template | Multi-project research template with 10-stage CI/CD pipeline, Ruff linting, multi-Python-version testing, issue/PR templates, and security scanning
docxology/QuadCraft | JavaScript | https://github.com/docxology/QuadCraft | Minecraft variant built on tetrahedral geometry — voxels replaced by Quadray-coordinate tetrahedra, exploring Buckminster Fuller's synergetics in an interactive 3D world
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/codomyrmex | Python | https://github.com/docxology/codomyrmex | AI-native modular coding workspace — 128 modules, 600 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration
docxology/cognitive-engine | Python | https://github.com/docxology/cognitive-engine | Hybrid neuro-symbolic AI combining fractal symbolic representations with probabilistic neural models for enhanced reasoning; includes Unipixel fractal building blocks and PEFF ethical reasoning
docxology/opentir | Python | https://github.com/docxology/opentir | Comprehensive toolkit analyzing 250+ Palantir open-source repositories (6.2M+ lines of code) — automated discovery, multi-language analysis, dependency mapping, statistical profiling, and professional visualizations
docxology/timeline_generator | TypeScript | https://github.com/docxology/timeline_generator | Networked Life Encoding — interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network
docxology/FORMINDEX | Rich Text Format | https://github.com/docxology/FORMINDEX | Analysis and tooling around FORMIS, the world's largest ant-literature database; bibliometric mining and structured index generation
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/crescent-city | TypeScript | https://github.com/docxology/crescent-city | End-to-end pipeline for ingesting, parsing, and querying the Crescent City, CA municipal code; TypeScript-based legal-text processing
docxology/ivm-xyz | Python | https://github.com/docxology/ivm-xyz | Python library for 3D and 4D Quadray/IVM (Isotropic Vector Matrix) geometry — coordinate conversion, volume calculations, and polyhedral operations
docxology/Markov_Blanket_Detection | Python | https://github.com/docxology/Markov_Blanket_Detection | Dynamic Markov Blanket Detection (DMBD) — PyTorch-accelerated framework for identifying causal relationships in complex systems; static and temporal modes with cognitive-structure labeling
docxology/QuadMath | TeX | https://github.com/docxology/QuadMath | Mathematical exposition of Quadray coordinate systems (4-vector tetrahedral coordinates); LaTeX documentation and computation library
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/AgenticMesh | Python | https://github.com/docxology/AgenticMesh | Active Inference & Agentic Mesh — modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles
docxology/curriculum | HTML | https://github.com/docxology/curriculum | Curriculum development framework for interdisciplinary education in Active Inference, biology, and computational science
docxology/lean_niche | Python | https://github.com/docxology/lean_niche | Lean/minimal niche-construction modeling — formal computational representations of ecological niche dynamics
docxology/literature | Python | https://github.com/docxology/literature | Literature collection and analysis tools for structured ingestion, annotation, and exploration of scientific publications
docxology/obsidian-construction-from-text | Python | https://github.com/docxology/obsidian-construction-from-text | Automated Obsidian vault construction from unstructured text — NLP pipelines to generate bidirectionally-linked knowledge graphs
docxology/qr_live_protocol | Python | https://github.com/docxology/qr_live_protocol | QR code-based live protocol system for real-time data exchange and interactive session management
docxology/ultralink-docx | HTML | https://github.com/docxology/ultralink-docx | UltraLink document format tooling — linking, rendering, and transformation utilities for rich hyperlinked documents
docxology/cognitive | Python | https://github.com/docxology/cognitive | Cognitive Ecosystem Modeling Framework — Active Inference agents with Obsidian-compatible knowledge management, bidirectional graph validation, belief updating, and network visualization
docxology/active_torchference | Python | https://github.com/docxology/active_torchference | PyTorch-based Active Inference implementations — GPU-accelerated variational inference and free energy minimization
docxology/ant-pheromone | Python | https://github.com/docxology/ant-pheromone | Computational simulation of ant pheromone trail dynamics and stigmergic communication
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/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference | Julia | https://github.com/docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference | Active Inference-driven autonomous drone navigation in Microsoft AirSim simulation environment
docxology/biol-1 | HTML | https://github.com/docxology/biol-1 | BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content
docxology/biol-8 | HTML | https://github.com/docxology/biol-8 | BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content
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/cascadia | Python | https://github.com/docxology/cascadia | Cascadia bioregion modeling and data analysis tools
docxology/course | Python | https://github.com/docxology/course | Course materials framework for structured interdisciplinary learning modules
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/flick | Python | https://github.com/docxology/flick | Lightweight Python tooling for rapid data flicking and processing pipelines
docxology/fuller-obsidian | unspecified | https://github.com/docxology/fuller-obsidian | Obsidian vault dedicated to R. Buckminster Fuller's ideas — synergetics, geodesics, and design science
docxology/godel_ivm | Python | https://github.com/docxology/godel_ivm | Gödel numbering meets the IVM (Isotropic Vector Matrix) — formal encoding of geometric objects as prime products
docxology/goference | Go | https://github.com/docxology/goference | Active Goference — production-ready Go framework for Active Inference autonomous agents; genuine variational inference, free energy minimization, POMDP policy planning via gonum
docxology/hhs-opendata | Python | https://github.com/docxology/hhs-opendata | Analysis of HHS (Department of Health and Human Services) open data — policy analytics and public-health data pipelines
docxology/infra-calc | JavaScript | https://github.com/docxology/infra-calc | Infrastructure calculator for estimating resource requirements and costs in multi-agent and AI systems
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/service | Python | https://github.com/docxology/service | Service-layer infrastructure and API tooling for Python-based research applications
docxology/snake | Python | https://github.com/docxology/snake | Classic snake game implemented in Python — used for testing multi-agent and reinforcement learning algorithms
docxology/steganographer | Rust | https://github.com/docxology/steganographer | High-performance Rust tool for embedding BLAKE3+Ed25519 cryptographic signatures and visible watermarks into live video/audio via LSB steganography; four Rust crates, 132 tests, GStreamer integration
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/
docxology/symergetics | Python | https://github.com/docxology/symergetics | Symbolic Synergetics — computer algebra and formal symbolic systems for Buckminster Fuller's synergetics mathematics
docxology/transformer | Python | https://github.com/docxology/transformer | Transformer architecture explorations — attention mechanisms and architectural variants for Active Inference research
ActiveInferenceInstitute/ActiveInferenceJournal | HTML | https://github.com/ActiveInferenceInstitute/ActiveInferenceJournal | Content hub for the Active Inference Journal — 500+ video transcripts, stream archives, and multimedia publishing infrastructure for the Institute's primary educational output
ActiveInferenceInstitute/ActiveBlockference | Jupyter | https://github.com/ActiveInferenceInstitute/ActiveBlockference | Active Inference agents in cadCAD block-based simulation — formal agent-based modeling using complex-systems simulation framework
ActiveInferenceInstitute/ActiveInferAnts | Python | https://github.com/ActiveInferenceInstitute/ActiveInferAnts | Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference
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/cognitive | Python | https://github.com/ActiveInferenceInstitute/cognitive | Cognitive modeling and simulation tools — multi-agent Active Inference environments, benchmarks, and visualization
ActiveInferenceInstitute/Active_Inference_Ontology | unspecified | https://github.com/ActiveInferenceInstitute/Active_Inference_Ontology | Formal OWL/RDF ontology for Active Inference — defines classes, properties, and axioms for free energy principle concepts
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/Symposium | Python | https://github.com/ActiveInferenceInstitute/Symposium | Applied Active Inference Symposium materials — talks, workshops, proceedings, and collaborative session artifacts from annual Applied AIF symposia
ActiveInferenceInstitute/ActiveInferenceCategoryTheory | unspecified | https://github.com/ActiveInferenceInstitute/ActiveInferenceCategoryTheory | Formal categorical foundations for Active Inference — string diagrams, functorial semantics, and compositional models using category theory
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
ActiveInferenceInstitute/GEO-INFER | HTML | https://github.com/ActiveInferenceInstitute/GEO-INFER | Geospatial Active Inference — applying free energy minimization to geographic systems, spatial planning, and bioregional intelligence
ActiveInferenceInstitute/AEOS | unspecified | https://github.com/ActiveInferenceInstitute/AEOS | Active Entity Ontology for Science — OWL ontology for representing active entities, their actions, and causal relationships in scientific models
ActiveInferenceInstitute/courses | HTML | https://github.com/ActiveInferenceInstitute/courses | Structured Active Inference learning courses — cohort-based curriculum materials, exercises, and collaborative learning artifacts
ActiveInferenceInstitute/Research-Discovery-Engine | HTML | https://github.com/ActiveInferenceInstitute/Research-Discovery-Engine | AI-driven research synthesis and navigation — semantic search, citation graph analysis, and cross-domain connection discovery across the Active Inference literature
ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook | Julia | https://github.com/ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook | Active Inference Textbook Study Group — code, exercises, and reading notes accompanying Parr, Pezzulo & Friston (2022)
ActiveInferenceInstitute/Biofirm | Python | https://github.com/ActiveInferenceInstitute/Biofirm | Bioregional Active Inference for organizational stewardship — applying free energy minimization to ecological and community governance systems
ActiveInferenceInstitute/Start | Python | https://github.com/ActiveInferenceInstitute/Start | Institute onboarding hub — getting-started guides, contributor pathways, project index, and orientation materials for new participants
ActiveInferenceInstitute/Knowledge-Engineering | Jupyter | https://github.com/ActiveInferenceInstitute/Knowledge-Engineering | Knowledge engineering tools and workflows — ontology alignment, concept mapping, and structured knowledge-base construction for Active Inference
ActiveInferenceInstitute/ActInf_RxInfer | unspecified | https://github.com/ActiveInferenceInstitute/ActInf_RxInfer | Active Inference with RxInfer.jl — Julia-based reactive message passing for efficient Bayesian inference in Active Inference models
ActiveInferenceInstitute/pymcp | Python | https://github.com/ActiveInferenceInstitute/pymcp | PyMCP — Model Context Protocol bridge for PyMDP, enabling Active Inference agents to interoperate with MCP-compatible AI tooling
ActiveInferenceInstitute/GEN24 | Jupyter | https://github.com/ActiveInferenceInstitute/GEN24 | GEN-24 working project — collaborative generative systems research from the 2024 active inference cohort
ActiveInferenceInstitute/NoOrg | HTML | https://github.com/ActiveInferenceInstitute/NoOrg | NoOrg is a Real Org — experimental organizational infrastructure and governance frameworks for decentralized scientific institutions
ActiveInferenceInstitute/ultralink | unspecified | https://github.com/ActiveInferenceInstitute/ultralink | UltraLink — framework for linking, rendering, and transforming richly cross-referenced documents across multiple output formats
ActiveInferenceInstitute/ActiveInferenceImplementations | Jupyter | https://github.com/ActiveInferenceInstitute/ActiveInferenceImplementations | Learning and exploring probabilistic inference — beginner-accessible Jupyter notebooks for Active Inference from first principles
ActiveInferenceInstitute/ATLAS | Python | https://github.com/ActiveInferenceInstitute/ATLAS | Question-Oriented Pattern Languages for Knowledge Management — structured templates for navigating complex scientific knowledge spaces
ActiveInferenceInstitute/Bots | unspecified | https://github.com/ActiveInferenceInstitute/Bots | Institute bot infrastructure — automation, notification, and community management bots for the Active Inference Institute's platforms
ActiveInferenceInstitute/Garden-of-Iris | Python | https://github.com/ActiveInferenceInstitute/Garden-of-Iris | Interactive visualization garden — generative art and data-visualization experiments exploring Active Inference dynamics
ActiveInferenceInstitute/gen25 | unspecified | https://github.com/ActiveInferenceInstitute/gen25 | GEN-25 working project — generative systems and collaborative research from the 2025 active inference cohort
ActiveInferenceInstitute/gnn | unspecified | https://github.com/ActiveInferenceInstitute/gnn | Generalized Notation Notation v2 — next-generation GNN specification with extended model classes and improved toolchain
ActiveInferenceInstitute/ISSS | Python | https://github.com/ActiveInferenceInstitute/ISSS | International Society for the Systems Sciences collaboration — joint research and educational materials bridging Active Inference and systems science
ActiveInferenceInstitute/topp | TeX | https://github.com/ActiveInferenceInstitute/topp | The Open Problems Project — curated registry of open scientific problems in Active Inference and the free energy principle

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/
2024 | Panel | Funding the Commons | Funding AI public goods and keeping them public | Sources: Funding the Commons: https://fundingthecommons.io/
2024 | Panel | European Identity and Cloud Conference 2024 | Intelligence in the Age of LLMs | Sources: KuppingerCole EIC speaker: https://www.kuppingercole.com/events/eic2024/speakers/3516
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
2024 | Video conversation on another channel | Building Smarter AI: Active Inference and Nested Models | Bagaev, de Vries, Friedman, Pashea. | Sources: YouTube: https://youtu.be/u3w24FtAsKw
2024 | Video conversation on another channel | Interaction. In Search of Daniel Friedman's Deepest Value | Math4Wisdom | Sources: YouTube: https://www.youtube.com/watch?v=T05uLRbcloE
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
2023 | Video conversation on another channel | Episode 6: Daniel Friedman - Active Inference Institute - What is Active Inference? | Denise Holt | Sources: YouTube: https://www.youtube.com/watch?v=ZyFgRBp1KE0
2022 | Video conversation on another channel | Artist of Curio Cards 24-26 Shares Incredible Journey through Art and Science | Jake Gallen | Sources: YouTube: https://youtu.be/X_F2YFJiUnY
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
2022 | Video conversation on another channel | What is Active Inference?...with Daniel Friedman | Inner Sense | Sources: YouTube: https://youtu.be/yHnm-zMqLvY
2022 | Video conversation on another channel | Great discussion with Daniel, OG Curio Card artist, cards 24, 25, 26 | ZeroG | Sources: YouTube: https://youtu.be/AHOGPsgJWmU
2022 | Video conversation on another channel | Daniel Friedman Interview - Adventures in NFTs #3 | World Crypto Network | Sources: YouTube: https://www.youtube.com/watch?v=mU_IwFsEpNg
2022 | Video conversation on another channel | Banging the Drum with Daniel Friedman | Nicholas Pacheco | Sources: YouTube: https://www.youtube.com/watch?v=fBuS4yItitw
2022 | Video conversation on another channel | KB7 Fireside: Scaling Principled Games | Kernel | Sources: YouTube: https://www.youtube.com/watch?v=vFOk8UR-UVQ
2022 | Video conversation on another channel | KBCast Episode 7: Kernel Block 5 Week 6 and special guest Daniel Ari Friedman | Active Inference Lab | Sources: YouTube: https://www.youtube.com/watch?v=R5zdTez8CPk
2021 | Video conversation on another channel | Daniel Friedman Interview - Adventures in NFTs #3 | World Crypto Network | Sources: YouTube: https://youtu.be/mU_IwFsEpNg
2020 | Video conversation on another channel | Interview with Monica Kang about Complexity Weekend, with co-founder Shaun Swanson and organizer JP Gonzales | Sources: YouTube: https://youtu.be/nEaG4xj6MCE
2021 | Blurb | Blurb in Science magazine inventing the word disinforge | Sources: Science: https://www.science.org/doi/10.1126/science.abg0904
2021 | Blurb | Complexity Weekend featured on InnovatorsBox blog, with quotes from Friedman and others | Sources: InnovatorsBox: https://blog.innovatorsbox.com/complexity-weekend/
2020 | Blurb | Blurb in Science magazine about rethinking time use for scientists | Sources: Science: https://www.science.org/
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
2013 | Blurb | Blurb in Science magazine about time travel | Sources: Science: https://www.science.org/
2017 | Lecture | Public lecture: Red Vic lecture series, San Francisco. History and philosophy of Art and Biology. | Sources: verification: https://danielarifriedman.com/resume/verify.html
2016 | Lecture | Public lecture: Red Vic lecture series, San Francisco. History and philosophy of self-organization, stigmergy, and eusocial insects. | Sources: verification: https://danielarifriedman.com/resume/verify.html
2021 | Quote | Quoted in Dopamine Nation by Dr. Anna Lembke, p. 75: The world is sensory rich and causal poor. | Sources: Dopamine Nation: https://www.penguinrandomhouse.com/books/624957/dopamine-nation-by-anna-lembke-md/
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
2022 | Profile or Interview | Daniel Friedman: Drawing Decentralized Beauty From Biology | Curio DAO | Sources: Curio DAO Mirror: https://mirror.xyz/0x8Fbf5c7Ca1295e892cC865500A8420C3316b889c/ztyis_d2IhlBUAb0LI4mCjJrvomZr939O1T71a5-R1Y
2021 | Profile or Interview | Written interview with RosyBVM | Sources: Rosy Conversation: https://rosybvm.com/2021/01/20/rosy-conversation-with-daniel-ari-friedman/
2019 | Radio | Radio Interview, KPOO 89.5 FM in San Francisco | Sources: KPOO: https://kpoo.com/

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 | IPA | Membership | Information Professional Association. | Sources: IPA: https://information-professionals.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
2019-2024 | Complexity Adventures | Community | Complexity Adventures co-founder. | Sources: Complexity Adventures: https://www.complexityadventures.com/
2018-2021 | ALIUS | Membership | ALIUS Research Group contributor, editor, and co-organizer. | Sources: ALIUS Research Group: https://www.aliusresearch.org/
2018-2019 | Wonderfest | Community | Wonderfest Science Envoy; science outreach and community training. | Sources: Wonderfest: https://wonderfest.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
2017-2018 | Stanford | Membership | Graduate student member of Arts Committee for Stanford Biology department. | Sources: Stanford Biology: https://biology.stanford.edu/
2016-2019 | Stanford Complexity Group | Community | Stanford Complexity Group. | Sources: Stanford: https://www.stanford.edu/; verification: https://danielarifriedman.com/resume/verify.html
2016 | Stanford | Community | Science Teaching Through Art (STAR) outreach program; poster presentations and conversations about ants at local middle and high schools. | Sources: Stanford: https://www.stanford.edu/
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/
2014-2017 | Stanford | Community | Stanford Center for Evolutionary and Human Genomics outreach programs, including teaching genetics in local middle schools and hosting high school students at Stanford. | Sources: Stanford Center for Evolution and Human Genomics: https://cehg.stanford.edu/
2014-2017 | Stanford | Community | Stanford Bio Core Explorations hands-on lecture/workshop for undergraduates: Art and Biology. | Sources: Stanford Biology: https://biology.stanford.edu/
2013 | UC Davis | Community | Science mentoring at Woodland High School. | Sources: Woodland High School: https://whs.wjusd.org/
2012 | UC Davis | Community | Drums and percussion for UC Davis production of RENT. | Sources: UC Davis: https://www.ucdavis.edu/
2012-2013 | UC Davis | Community | Volunteer in emergency room at hospital in Sacramento, four hours per week for six months. | Sources: UC Davis Health: https://health.ucdavis.edu/
2011-2014 | UC Davis | Community | Chess Club at UC Davis President (2012-2014), organizing free outdoor chess at the farmer's market twice weekly for two years. | Sources: UC Davis Campus Recreation: https://campusrecreation.ucdavis.edu/

ART PORTFOLIO AND USES
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All | Art portfolio | Posting drawings to an online portfolio since 2009. | Sources: Flickr: http://flickr.com/photos/daniel_friedman/
2021 | Curio Cards | A full Curio Cards set sold at Christie's on October 1, 2021 for 393 ETH, approximately $1.2 million. | Sources: Christie's Curio Cards lot: https://www.christies.com/lot/lot-6337619
2021 | Curio Cards | Curio Cards collection stored in the Arctic World Archive with art and provenance data intended for long-duration preservation. | Sources: Top Dog Beach Club: https://topdogbeachclub.com/non-fungible-vault/
2021 | Curio Cards | Public auction and market history for Curio Cards includes major 2021 sales; verify venue-specific claims before reusing exact auction-house wording. | Sources: Sotheby's Curio Cards: https://metaverse.sothebys.com/natively-digital/lots/curio-cards-complete-set-1-30-plus-17b
2019 | Art used | Art used in the eBook Rebelling with Care: Exploring open technologies for commoning healthcare. | Sources: ResearchGate: https://www.researchgate.net/publication/335911369_Rebelling_with_Care_Exploring_open_technologies_for_commoning_healthcare
2019 | Art used | Art used in Slate.fr blog. | Sources: Slate France: https://www.slate.fr/story/173103/fecondation-spermatozoide-ovule-chevalier-belle-au-bois-dormant-mythe-sexisme-naturalisation-biologie?
2019 | Art used | Art used in degrowth blog. | Sources: Degrowth.info: https://www.degrowth.info/blog/on-strategies-for-socioecological-transformation
2018 | Art used | Art used in Medium post by Lorena Cabeza, August 23, 2018. | Sources: Medium: https://medium.com/@lorenacabeza/manifiesto-la-escritura-y-la-vida-10d4c254c0bf
2018 | Art used | Cover image of Probe magazine. | Sources: Probe Magazine: https://www.ssbprobe.com/decentraldogma-danielfriedman
2017 | Curio Cards | Early Ethereum art NFT project; art for Curio Cards 24, 25, and 26. | Sources: Curio Cards artist: https://curio.cards/artist/danielfriedman/; Curio Cards docs: https://docs.curio.cards/the-artists/daniel-friedman
2017 | Art used | Art used in Bas Haring blog. | Sources: Me Judice: https://www.mejudice.nl/artikelen/detail/mijn-economiemuseum-de-markt
2017 | Art used | Art used in Vice Motherboard blog. | Sources: VICE Motherboard: https://www.vice.com/en/article/jpaqk8/a-dollar25-million-book-heist-proves-the-printed-page-is-still-sacred
2016 | Art used | Featured in Genetics Society of America art blog. | Sources: Genes to Genomes: https://genestogenomes.org/gsa-art-daniel-friedman/
2016 | Art used | Art featured by Stanford Art of Neuroscience competition. | Sources: Stanford Scope: https://scopeblog.stanford.edu/2016/07/06/art-of-neuroscience-competition-highlights-beauty-of-the-brain/