# Full Text: Postdoc review (2020-2023) ~ September 25, 2023 > Extracted from `2023_PostdocReview.pdf` --- ## Page 1 2020-2023 Postdoc review Daniel Ari Friedman September 25, 2023 ## Page 2 .0 – Background & Context .1 – Working Areas a. Biology b. Entomology c. Active Inference d. Cognitive Security e. Meta-Science f. Philosophy & Arts .2 – Review, Livechats & Onwards Roadmap. ## Page 3 Background & Context .0 ## Page 4 Oct. 2023 2014 July 2019 Oct. 2020 ????????????? ????????????? ## Page 5 NSF: 2010290 - October 2020 to October 2023 Postdoctoral Research Fellowships in Biology (PRFB) https://www.nsf.gov/pubs/2023/nsf23620/nsf23620.htm Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes Through this Competitive Area, BIO aims to stimulate creative integration of diverse subdisciplines of biology using combinations of observational, experimental, theoretical, and computational approaches to discover underlying principles operating across hierarchical levels of life, from biomolecules to organisms to ecosystems. Research activities under this Competitive Area should lead to new understanding of how higher-order structures and functions of biological systems result from the interactions of heterogeneous biological components, as shaped by the environment and evolutionary processes furthering predictive capability of how key properties and mechanisms of living systems emerge from the interactions of genomes, environments, and phenotypes. This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2020, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. This research investigates the ecology and evolution of the Hymenoptera, the order of insects containing species such as ants, bees, wasps, and sawflies. The work contributes to our scientific understanding of how genetics, epigenetics, behavior, and ecology are related over developmental and ecological time scales, in the context of a well-studied and biodiverse clade of insects. This project addresses fundamental questions in biology including: How did colony living (eusociality) arise in ants and bees from their solitary ancestors? How do colony traits originate and become elaborate? How are the hormonal and neurobiological underpinnings of colony traits linked to genetic and ecological variation among species? How might these insights from eusocial colony evolution help humans design resilient distributed systems, for example to respond to disasters, manage socially-spread pathogens, and improve the security of cyberphysical systems? The Fellow will also actively engage in science communication, mentoring, and outreach programs, with a special emphasis on local underserved communities, team-based remote education, and transdisciplinary approaches such as Complexity Science. Eusocial (colony-living) insect species display variation within populations and among species in ecologically-important colony traits such as behavior (e.g. collective foraging, search, offense/defense) and reproductive strategies. Tissue-specific gene expression patterns can influence colony traits such as collective behavior in a non-linear fashion through altering colony-level physiological processes. Previous approaches to studying the evolution of eusocial insect colony traits have been of limited phylogenetic scope, have not considered the role of tissue-specific gene expression in colony-level physiological processes, or only considered genes with single-copy orthologs present in all species considered. This project will integrate multiple biological techniques (phylogenomics, transcriptomics, chemical profiling, ecological niche modeling) to investigate the evolutionary and functional roles of lineage-specific genes, complex gene families, and tissue-specific expression patterns in Hymenoptera. More broadly, the theoretical models and bioinformatic pipelines developed in this research will generalize far beyond the Hymenoptera, and provide avenues for integrative synthesis across taxa. The Fellow will be co-trained by Prof. Brian Johnson (University of California, Davis) and Prof. Tim Linksvayer (University of Pennsylvania), and will work to increase participation, inclusion, reproducibility, and transparency in science. https://www.nsf.gov/awardsearch/showAward?AWD_ID=2010290 Insects as/and Complex Biological Systems & Broader Impacts Prof. Brian Johnson Prof. Tim Linksvayer ## Page 6 *[Page 6 appears to be blank or image-only]* ## Page 7 Working Areas.1 Not covered in this stream: ● Things I’ve forgotten ● Works in progress or review ● Private, Secret, & Silent work ● Local Davis engagements & activities ~# of works 20-23 ## Page 8 # of publications by year per Working Area 20… ## Page 9 CognitiveSecurity.us For this presentation, I used GPT4 via Perplexity.ai to upload each paper and ask the following prompt -------------------------------------------------------------------- Please deeply analyze the attached paper and do all needed background research in order to be a professional expert in the area. Then, output 3 semantically-crystalline paragraphs of 2-6 sentence which to a human reader will elegantly convey the paper’s: - CONTEXT (the broader background of the work, which does not mention the paper’s contribution/approach at all) - CONTRIBUTIONS (specifically what the paper uniquely did, developed, and introduced) - IMPLICATIONS (the causal consequences of the paper in our complex world, and directions for future work and research). -------------------------------------- The next part of this stream will be over at the Coda website https://cognitivesecurity.us/ I will quickly describe each of the works carried out and how it related to the primary Working Area. You can pause the video to read the GPT4 Context, Contributions, Implications, which I will scroll over. You can visit the website and click the Perplexity link to “continue the conversation” and interact with the work! Following the overview section, I will cover 10 highlights. The highlights are sorted by working area, not relevance. ## Page 10 Biology ## Page 11 A Variational Synthesis of Evolutionary and Developmental Dynamics https://www.mdpi.com/1099-4300/25/7/964 Karl Friston, Daniel A. Friedman, Axel Constant. V. Bleu Knight, Chris Fields,Thomas Parr, and John O. Campbell Entropy 2023 Figure 1. Schematic (i.e., influence diagram) illustrating the sparse coupling among states that constitute a particular partition at two scales. Figure 2. Schematic showing the hierarchical relationship between particles at scales i and i + 1. ● Foundational work that provides a multiscale analytic framework based upon Active Inference & the Free Energy Principle. ● Reflecting discourse with the authors and others in ActInf Ecosystem since 2017, and setting directions for some time to come! ## Page 12 A single-pheromone model accounts for empirical patterns of ant colony foraging previously modeled using two pheromones https://www.sciencedirect.com/science/artic le/pii/S1389041723000207 Eric Saund, Daniel Ari Friedman Cognitive Systems Research 2023 • Big headed ants (Pheidole megacephala) are able to forage in a Y-maze for food. • Previously, investigators modeled P. megacephala with a two-pheromone model. • We account for empirical results of P. megacephala foraging with a one-pheromone model. • Our one-pheromone model recapitulates key patterns and is biologically plausible. • This work demonstrates principles of sensory-cognitive modeling and ant foraging. Dussotour’s experiment Fig. 3. Proposed pheromone measurement function M is a power-law amplification of the raw pheromone level ph, subtracting a small base level noise factor, B. Fig. 5. Modeling the branch preference function as a product of sigmoid squashing functions. Fig. 6. a. Simulated trajectories of pheromone amounts and measurements under the one-pheromone model. ## Page 13 Active Inference ## Page 14 Active Inferants: An Active Inference Framework for Ant Colony Behavior https://www.frontiersin.org/articles/10.3389/ fnbeh.2021.647732/full Daniel Ari Friedman, Alec Tschantz, Maxwell J. D. Ramstead, Karl Friston, Axel Constant Front. Behav. Neurosci. 2021 ● Above – Pheromone dynamics ● Left – Collective phenotypes ● Bottom – Generative model and T-maze simulation setup ● First Active Inference model of stigmergic collective behavior ● Sets up extensible framework for studying the diversity of Ant behaviors; foraging and beyond ● Early pre-pymdp collaboration that could already be updated ## Page 15 Active Inference in Modeling Conflict https://zenodo.org/record/5759807 Scott David, Richard J. Cordes, Daniel A. Friedman Zenodo 2021 ● Application of Active Inference to multiscale conflict/cooperation settings ● Foundation of further work on CogSec, OODA, (inter)organizational developments ● BOLTS (Business, Operational, Legal, Technical, and Social) ## Page 16 The Active Inference Institute and Active Inference Ecosystem (2023) https://zenodo.org/record/8266281 Active Inference Institute; Aguirre, Ander; Boik, John; Burian, Libor; Brown, Matthew; Cordes, RJ; David, Scott; Douglass, David S; Fernandez-Maquieira, Pablo; Friedman, Daniel A; Grimm, Holly; Guénin–Carlut, Avel; Iennaco, Maria Luiza; Knight, V Bleu; Mikhailova, Alexandra; Rahmjoo, Ali; Razi, Adeel; Smékal, Jakub; Tamari, Ronen; Tickles, Dean; Vyatkin, Alex 375+ livestreams on Active Inference 2020-2023 along with transcripts at the Active Inference Journal 2020-2023 ~30 Interns, SAB, BoD, and so many other nestmates! ## Page 17 Cognitive Security ## Page 18 COGSEC books 2020-2022 cogsec.org/research-initiatives-3 Ongoing initiative in 2023: ATLAS 2020 2021 2022 RJ Cordes https://coda.io/@aien/rj-cordes ## Page 19 Innovator’s Digital Playbook https://www.innovatorsdigitalplaybook.com/ Monica Kang, Richard J. Cordes, Daniel A. Friedman 2021 Monica Kang innovatorsbox.com Rethink Creativity & Rethink Facilitation https://www.youtube.com/watch?v=4f4rrMZ-Wyo https://www.youtube.com/watch?v=aMiremrUx3g ## Page 20 Beyond Research ## Page 21 Context ● CJ Fearnley passed away at end of 2022, with plans in play for Collaborating for Comprehensivity and related initiatives hosted by Shrikant Rangnekar at 52 Living Ideas. ● With others in the Trimtab Reading Group (Curt, Kirby, Richard, Struppi, Richard, Maurice, Luke, Brett, Lionel, Stephen, Luke, Jim, Nathan, Sean, Andrew, Jalen, and more!) we read many Fuller texts and wove other influences into the picture. William Blake & Buckminster Fuller: Lives in Juxtaposition (A study in Comprehensivity) https://zenodo.org/record/7519132 Daniel A. Friedman Zenodo 2023 ## Page 22 ● 230 total drawing livestreams (~150 during the last 3 years). Contributions Context ● Passionate about Art (drawing), Synergetics (geometry of nature/thinking), Research, other areas. 200+ livestreams on personal channel, including drawings, Synergetics, paper discussion and various other events Daniel A. Friedman, YouTube 2023 ● 17 Synergetics streams (all within last 3 years) ● 8 PaperStreams (all within last 3 years) ## Page 23 Kernel Community kernel.community/en/ complexityadventures.com/ https://www.aliusresearch.org/ https://www.isss.org/home/ Information- professionals.org/ Thanks Jason, Sid, and others for DeSchool! Education Knowledge Engineering Common Sense[makers] Ronen, Shahar, William, Lauren, Brad, Charles et al. StigPeople Apoideas Tucker et al. curio. cards block. science/ The mostly-unnamed colony ## Page 24 Review, Livechats & Onwards.2 If you are watching live, please add any comments/questions in the livechat & I will try to address everything I can. ## Page 25 *[Page 25 appears to be blank or image-only]* ## Page 26 Onwards! ● Continued thanks to Family, Friends, Nestmates, the Niche, and Beyond ● Every day was an opportunity, honor, blessing, and journey. ● I acknowledge contributions of so many over the years. ● I am & will be active in: ○ Research ○ Education ○ Service ● People can get involved with the listed open source projects and communities ● Get in touch with questions, comments, and offers. I expect and prefer to be your advocate, ally, & colleague. ● Read between and among the lines (Quantum Active Inference) && Unity is plural and at minimum two. ● There is much more to come! It is a rising and not a setting sun. --- *Extraction method: pymupdf*