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In
Interact with Research
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, a selection of the work in
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is summarized and augmented through through the use of Large Language Models (LLM).
For a video overview of my postdoc research, and more context on the use of LLM to
Interact with Research
⁠
, see the
video to the right
⁠
.
⁠
Interact with Research
⁠
is an experiment and work in progress, there is (always) more to come!
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⁠
⁠
The Context, Contributions, and Implications columns are outputs from using GPT4 with
Perplexity.ai
⁠
.
Each paper PDF was uploaded to Perplexity, then prompted with the prompt at right.
The “Perplexity” link allows you to continue the conversation with that specific paper! 🐜🐜🐜🐜...
⁠
Research Summaries & Conversations
⁠
are sorted by Working Area, then by year within area.
Click the arrow next to a topic in “Working Area” to collapse the list.


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 sentences 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).

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Contributions
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Biology
4
15
2
Kallick_2015_Ehrlichia.pdf
“Could Ehrlichial Infection Cause Some of the Changes Associated with Leukemia, Myelodysplastic Diseases and Autoimmune Disorders, and Offer Antibiotic Treatment Options?”
Leukemia, myelodysplastic diseases, and autoimmune disorders are medical conditions with largely unknown etiologies. Ehrlichia/Anaplasma (EA) are a group of intracellular obligate parasitic bacteria that infect leukocytes and have been recognized as human pathogens for various medical conditions.
These bacteria can alter the DNA of their host cell during division, potentially disrupting the normal development and function of immune cells.
The hypothesis presented in the attached paper suggests that EA infection may be associated with or cause some of the changes observed in leukemia, myelodysplastic diseases, and autoimmune disorders.
The paper presents three case studies of leukemia patients with direct or indirect evidence of EA infection. Two of these patients, who were moribund and had exhausted all other treatments, were treated with therapeutic doses of Rifampin, an antibiotic known to be effective against EA.
Although they did not survive, their condition improved dramatically for a time, suggesting that Rifampin provided some therapeutic benefit.
The third case involved a patient with polycythemia vera, a myelodysplastic disease that sometimes progresses to leukemia. PCR analysis indicated the presence of a previously unknown EA in this patient.
These cases provide preliminary evidence of a potential connection between leukemia and EA infection.
The results presented in the paper warrant further investigation into the possible association between EA infection and leukemia, myelodysplastic diseases, and autoimmune disorders. If a causal link is established, it could open up new treatment options, such as antibiotic therapy, for these conditions.
The paper also highlights the need for more extensive study of serology and DNA to determine if there are enough cases to establish a connection between these diseases and EA infection.
The accumulating evidence discussed in the paper offers hope for a significant change in mortality rates from leukemia and other autoimmune syndromes, as well as the potential for new treatment strategies based on targeting EA infection.
Marcus_Crypto-Jews_2015.pdf
“Commentary: Portuguese crypto-Jews: the genetic heritage of a complex history”
The history of Portuguese crypto-Jews is complex, involving the secret adherence to Judaism while publicly professing another faith. This phenomenon emerged after the 15th-century decree of expulsion and the establishment of the Inquisition in Portugal, which led to the exile or assimilation of most Portuguese Jews into the general population, with the exception of a few crypto-Jewish communities.
The study of the genetic heritage of these communities has been an ongoing effort, with researchers using Y chromosome and mitochondrial genotype data to explore their genetic identity.
In their paper, Nogueiro et al. (2015) analyzed Y chromosome and mitochondrial genotype data from contemporary Iberian and non-Iberian human populations to explore the genetic identity of Portuguese crypto-Jews.
They reviewed Y chromosome and mtDNA population genetic data from previous studies and reanalyzed data from two Portuguese Jewish populations. The study detected a shared female lineage (HV0b) between the communities of Belmonte and Bragança, suggesting a genetic connection between these populations.
However, the authors acknowledged that the inference of a genetic profile for Portuguese Jews was not possible from the study of self-defined Sephardic Jews.
The study by Nogueiro et al. (2015) provides insights into the genetic heritage of Portuguese crypto-Jews, but it also raises questions about the strength of the matrilineal (mtDNA) and patrilineal (Y chromosomal) data used in the analysis.
The data reviewed in the paper are ambiguous regarding the inference of Jewish ancestry and do not identify diagnostic patrilineal or matrilineal markers.
Furthermore, the authors suggest that the data may support a history of "complex mating strategies" in Jewish populations but fail to test this hypothesis against models of even simple demographic histories or admixture events 1 . As a result, the study's findings should be interpreted with caution, and more research is needed to better understand the genetic heritage and demographic history of Portuguese crypto-Jews.
16
1
Friedman_nuclear_structure_2016.pdf
"Influence of Nuclear Structure on the formation of radiation-induced lethal lesions"
Ionizing radiation can cause lethal chromosome rearrangements, such as rings or dicentrics, by fragmenting nuclear DNA. The linear quadratic relationship between dose and cell survival has been used to interpret the generation of lethal lesions due to damage occurring in two separate chromosomes simultaneously (a component) or as potentially repairable separate events (b component).
However, the influence of DNA organization on the generation of such lesions is not well understood. Recent advances in genomic analysis have provided a more detailed spatial description of the genome, which can help in understanding the formation of lethal chromosome aberrations.
The paper "Influence of nuclear structure on the formation of radiation-induced lethal lesions" by Daniel A. Friedman, Lauren Tait, and Andrew T. M. Vaughan discusses the generation of lethal lesions by synthesizing existing knowledge with new insights from spatial proximity data obtained through high-throughput sequencing of chromosome conformation capture experiments.
The authors propose that the linear DNA strand is organized as a fractal globule, generating multiple sites of contact that may facilitate deletions or inversions if the points of contact are damaged. Additionally, they suggest that transcriptionally active euchromatin occupies a physically identifiable space separate from inactive areas and is preferentially susceptible to free radical attack after irradiation.
The findings of this paper have the potential to improve our understanding of the formation of lethal chromosome aberrations that kill irradiated cells.
By analyzing the factors that control chromosome proximity through high-throughput spatial analysis, researchers can better describe the impact of nuclear structure on the formation of radiation-induced lethal lesions.
This knowledge can inform future work and research in the field of radiation biology, potentially leading to improved radiation therapy strategies and a better understanding of the underlying mechanisms of radiation-induced cell death.
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1
entropy-25-00964.pdf
A variational synthesis of evolutionary and developmental dynamics
Evolutionary biology has long been focused on understanding the processes of natural selection, heredity, and variation. However, the gene-centric view of evolution has left a gap in understanding the connection between genetic and phenotypic processes.
The modern synthesis and the selfish gene hypothesis provide a gene-centric view of evolution, but they do not fully integrate phenotypic processes that impact organisms in developmental time.
To address this gap, researchers have been working on integrating phylogenetic (evolutionary) and ontogenetic (developmental) processes into a unified framework
The paper "A Variational Synthesis of Evolutionary and Developmental Dynamics" by Friston et al. introduces a variational formulation of natural selection that unifies slow phylogenetic processes with fast phenotypic processes.
The main result is a formulation of adaptive fitness as a path integral of phenotypic fitness. In this view, a phenotype actively infers the state of its econiche under a generative model, whose parameters are learned via natural (Bayesian model) selection.
The variational synthesis features some unexpected aspects, such as the necessity to consider populations of distinct natural kinds that influence each other.
The variational synthesis provides a mathematical framework that unifies slow, multi-generational (phylogenetic) processes with single-lifetime, phenotypic (developmental and behavioral) processes. This multiscale account highlights the circular causality that arises from the implicit separation of timescales.
The framework can potentially be applied to both biological and non-biological systems, provided their fitness depends on events during a lifetime and influences dynamics over a generational scale.
The paper sets the stage for future work that will use the variational synthesis to consider established and current evolutionary theories, as well as to address specific questions about evolutionary or developmental dynamics using analytic or numerical methods.
Active Inference
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Friston_Friedman_Fortier_2018_of_woodlice_and_men.pdf
“Of woodlice and men: A Bayesian account of cognition, life and consciousness”
The free energy principle is a theoretical framework that aims to unify the psychological, neural, and biological nature of living beings. It was first conceived by Karl Friston when he observed woodlice in his garden and realized that their scurrying behavior was a simple explanation for biotic self-organization.
The principle has since been developed into a comprehensive framework that encompasses Bayesian brain hypothesis, predictive coding, and other related concepts.
The paper "Of woodlice and men: A Bayesian account of cognition, life and consciousness" is an interview with Karl Friston, the founder of the free energy principle.
In the interview, Friston discusses the origins of the free energy principle, its development, and its implications for understanding cognition, life, and consciousness. He explains how the free energy principle is a normative principle that cannot be falsified, but can be used to evaluate whether measurable systems conform to it.
The paper also explores the relationship between the free energy principle, predictive coding, and the Bayesian brain hypothesis, as well as the implications of these frameworks for understanding various aspects of cognition, perception, and consciousness.
The free energy principle has significant implications for our understanding of cognition, life, and consciousness. It provides a unifying framework for studying the brain and behavior, suggesting that living organisms minimize surprise or uncertainty by continuously updating their internal models of the world.
This framework has been applied to various fields, such as neuroscience, psychology, and artificial intelligence, leading to new insights and directions for future research.
Additionally, the free energy principle has been used to explain various phenomena, such as perception, action, learning, and decision-making, as well as the emergence of consciousness and self-awareness.
20
1
AIN1_Act_Inf_Narratives_v1.pdf
Active Inference & Behavior Engineering for Teams
Communication is essential in both natural and designed teams, as it facilitates the organization and function of complex multi-agent systems.
The Free Energy Principle (FEP) and Active Inference (ActInf) frameworks have been applied to various domains, such as narratives, ontologies, and extended cognition in multiscale biological systems.
Remote Teams (RT) are of particular interest due to the observability of all states and updates in digital systems, making them suitable for theoretical study and direct applications of the ActInf framework.
The paper explores communication in located teams and all-online Remote Teams (RT) using the ActInf framework.
It combines the FEP-ActInf-Narrative nexus with the applied approach of Systems Engineering (SE) to formalize the processes of RT formation and lifecycle management.
The paper addresses various questions related to coherence, narrative, identity function of communication, methods for teams, multi-scale Active Inference frameworks, epistemic values, narrative reliability, and personal behavior engineering using ONFT in team communication.
The paper's findings have implications for the design and management of Remote Teams, as well as the development of Ontologies, Narratives, Formal documents, and Tools (ONFT) for RT within the ActInf framework.
By understanding and optimizing communication patterns in RTs, organizations can improve team performance, collaboration, and overall productivity.
The insights gained from this research can also inform future work in the areas of team behavior, communication, and the application of Active Inference frameworks to other complex systems.
22
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v3_ActInf-DeSci-AEOS-2022.pdf
An Active Inference Ontology for Decentralized Science: from Situated Sensemaking to the Epistemic Commons
The scientific community has been grappling with challenges such as the reproducibility crisis, p-hacking, and fake peer reviews, which have raised concerns about the credibility and reliability of scientific research.
Transdisciplinary research has emerged as a potential solution to address these issues, but it faces its own set of challenges, including the need for effective collaboration and communication among researchers from diverse fields.
The rise of decentralized technologies, such as blockchain and Web3, has opened up new possibilities for addressing these challenges by enabling secure, transparent, and decentralized systems for managing and sharing scientific knowledge.
The paper "An Active Inference Ontology for Decentralized Science: from Situated Sensemaking to the Epistemic Commons" introduces the Active Entity Ontology for Science (AEOS), a novel framework that combines active inference principles with decentralized technologies to create a more transparent, collaborative, and efficient scientific ecosystem.
AEOS provides a structured approach to model scientific entities, processes, and relationships, facilitating the integration of diverse scientific knowledge sources and fostering interdisciplinary collaboration.
The paper also presents several examples of how AEOS can be applied to various scientific contexts, demonstrating its potential to address the challenges faced by the scientific community.
The development and adoption of AEOS could have far-reaching implications for the future of scientific research.
By leveraging decentralized technologies and active inference principles, AEOS has the potential to enhance the transparency, reproducibility, and credibility of scientific findings, ultimately contributing to a more robust and reliable body of scientific knowledge.
Furthermore, AEOS could foster interdisciplinary collaboration and facilitate the integration of diverse knowledge sources, enabling researchers to tackle complex, real-world problems more effectively.
As the scientific community continues to explore and adopt decentralized technologies, future research could focus on refining and expanding the AEOS framework, as well as developing practical tools and applications that leverage its capabilities to address the challenges faced by modern science.
Predictive Processing Interpretation of the Mirror Test.pdf
Predictive Processing Interpretation of the Mirror Test and Implications of a Reflection Prediction for Human Cognition
The mirror test, developed by Gordon Gallup Jr. in 1970, has been used as a behavioral measure of mirror self-recognition in various species.
Predictive processing models suggest that individuals build internal predictive models of the external world and seek to minimize the extent to which their predictions differ from reality.
In the context of the mirror test, Apps and Tsakiris have explained how mirror self-recognition may be understood as the result of an individual successfully learning to predict their own reflection in the mirror .
The paper "Predictive Processing Interpretation of the Mirror Test and Implications of a Reflection Prediction for Human Cognition" applies a predictive processing interpretation to the results of the mirror test, offering a novel perspective on mirror self-recognition and self-directed behavior.
The authors hypothesize that a "reflection prediction" may help explain how humans locate themselves relative to a mirror, imitate others, and are self-aware from a social perspective.
They also suggest that atypical reflection predictions or atypical use of a reflection prediction may help to explain instances where these traits are atypical in certain individuals.
The predictive processing interpretation of the mirror test has several implications for understanding human cognition and future research.
First, it provides a new perspective on mirror self-recognition and self-directed behavior, suggesting that both species that learn to ignore their reflection and those that display self-directed behavior are capable of mirror self-recognition.
Second, it highlights the importance of considering reflection prediction errors and their potential impact on atypical mirror self-recognition and other cognitive traits.
Lastly, it opens up new avenues for research on the role of reflection prediction in various aspects of human cognition, such as mirror proprioception, imitation, and self-awareness from a social perspective.
Active Diffusion Catechism.pdf
Catechism for: "Towards Active Diffusion: A Tale of Multiple (den)Cities"
Active Inference (ActInf) and Diffusion Models (DM) are two research areas that have gained significant attention in recent years.
ActInf is a framework that describes perception and action through the lens of Bayesian statistics, where autonomous entities perform inference over the causes of their sensory input and adjust their internal representations, or beliefs, about themselves and their environment.
On the other hand, DMs are deep learning architectures used to create stochastic representations of input data and to remove noise, producing clean outputs.
These models have been successful in learning representations of high-dimensional, complex data and are finding diverse applications in synthetic data generation.
The paper "Towards Active Diffusion: A Tale of Multiple (den)Cities" aims to explore the connections between ActInf and DMs, specifically in the context of decision making and planning under the Free Energy Principle.
The authors combine both theoretical and applied approaches to elucidate the connection between DMs used in contemporary Artificial Intelligence research and ActInf generative models from the cognitive sciences.
They investigate how DMs can be used to represent internal beliefs about an agent's environment and their role in decision making and planning, such that outputs can be strategic rather than stochastically parroting the syntax of strategy.
This research has multiple implications in areas where ActInf and DM models are currently being applied, such as behavioral neuroscience and multimedia creation, as well as in emerging areas like Autonomous Cognitive Agents using Active Diffusion.
By exploring the connections between these two research areas, the authors aim to bridge the gap between the continuous and discrete time formulation of generative models in active inference, enabling work at the intersection of contemporary Artificial Intelligence and ActInf research.
This project could potentially lead to the development of novel techniques and applications in various domains, opening up new avenues for future work and research.
KnightCordesFriedman_2022_ActInf_FEP_Literature_v1.pdf
The Free Energy Principle & Active Inference: a Systematic Literature Analysis
The Free Energy Principle (FEP) and Active Inference (ActInf) are recent advancements in the mathematical descriptions of learning and decision-making, building upon predictive processing and variational inference by incorporating both perception and action into reducing overall uncertainty.
Over the last 20 years, FEP and ActInf have evolved significantly, developing a broad range of discourse. This scientific discourse is notable for its range of topics and seemingly rapid rate of increase.
In rapidly-changing fields, failures to develop educational and research materials can hamper the growth, accessibility, rigor, and ultimately the value of a scientific development .
The paper "The Free Energy Principle & Active Inference: a Systematic Literature Analysis" by Knight, Cordes, and Friedman performs a literature analysis of publications using the terms "Free Energy Principle" or "Active Inference," with an emphasis on works written by Karl J Friston.
The authors manually annotated a subset of papers with accessible full texts and performed automated analyses related to the terms in the Active Inference Institute's Active Inference Ontology.
The initial analysis, at the scale of thousands of citations and hundreds of annotated papers, is presented as a first step towards the development of systems that could facilitate integration of manual and artificial contributions, feature richer interfaces for use in learning and research, and address field-specific local questions and provide transferable approaches.
The analysis in this paper provides valuable insights into the development and trends of FEP and ActInf literature.
The results can help researchers engage with the latest developments in the field, avoid wasting time on older iterations, and identify problems that have already been solved.
The paper also highlights the need for further development of educational and research materials to support the growth and accessibility of FEP and ActInf.
Future work could expand the scope of relevant works, integrate multiple forms of annotation and participation, and address broader questions in the history and philosophy of science.
AII _ Blockference _ Protocol Labs Research RFP.pdf
Systems Modeling and Cognitive Audits for Hypercert Ecosystems
Decentralized Science (DeSci) aims to create a more open and collaborative scientific ecosystem by leveraging blockchain technology and other decentralized systems.
In this context, Hypercerts were introduced as a new primitive for public goods funding.
Developed by the Active Inference Institute, the Active Entity Ontology for Science (AEOS) is a framework that describes how entities of different types develop and interact within and across system scales, such as in DeSci projects.
The Active Blockference project combines cadCAD, a complex systems modeling framework, with pymdp, an active inference Markov Decision Process engine, to study theoretical and applied Active Inference.
The paper "Systems Modeling and Cognitive Audits for Hypercert Ecosystems" proposes to develop the Hypercert ecosystem by creating an AEOS specification and Active Blockference implementation for Hypercerts.
The authors aim to develop tooling, use cases, and educational resources that enable a cognitive audit of Hypercert protocols, facilitating trust and reliability in the system.
This implementation would allow anticipatory design and real-time analysis of Hypercert ecosystems at a granularity required for high-reliability systems design .
The development of Hypercerts and the AEOS implementation has the potential to transform the funding landscape in DeSci by providing a more flexible, utility-driven, and mature ecosystem.
By enabling cognitive audits, the Hypercert development stack can enhance trust and reliability in projects, maximizing their value. The AEOS implementation can also demonstrate areas where Hypercerts may be superior to other funding mechanisms and identify areas for improvement.
This research has the potential to impact various Web3 communities interested in formalizing their approach to community design, token engineering, and overall value creation.
Future work and research directions include refining the Hypercert concept, developing the rigor and efficacy of the Hypercert ecosystem, and exploring the cognitive, micro-economic, behavioral, and decision-making processes in Hypercert ecosystems.
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GNN_v1_April5_2023_Smekal_Friedman.pdf
Generalized Notation Notation for Active Inference Models
Active Inference, on the other hand, is a unifying theoretical framework that combines perception, action, and learning in a coherent manner.
Despite the potential value of models within this framework, the widespread adoption of Active Inference has been hindered by the lack of a standardized method for effectively representing and communicating them.
The paper "Generalized Notation Notation for Active Inference Models" by Smekal and Friedman introduces Generalized Notation Notation (GNN), a novel approach to generative model representation that facilitates communication, understanding, and application of Active Inference across various domains.
GNN complements the Active Inference Ontology as a flexible and expressive language for education and modeling, by providing a standardized method for describing cognitive models.
The authors present GNN, provide a step-by-step example of what GNN looks like in practice, and explore "the Triple Play", a pragmatic approach to expressing GNN in linguistic, visual, and executable cognitive models.
The introduction of GNN has several implications for the field of cognitive modeling and Active Inference. By providing a standardized method for describing cognitive models, GNN aims to facilitate interdisciplinary research and application, ultimately promoting the advancement of the field.
The "Triple Play" approach allows for the expression of GNN in various modalities, making it more accessible and understandable to different audiences.
Furthermore, the development of GNN can inspire further exploration and development of hierarchical cognitive models and Active Inference, leading to new insights and applications in various domains.
Future research directions may include better integration with natural language processing, formal semiotic methods, and the development of new GNN dialects and case systems.
ToCommentOrNotToComment_Tickles_Friedman_2023.pdf
To comment or not to comment, that is the question!: Comment on “To copy or not to copy?...” by Héctor M. Manrique and Michael J. Walker
The paper "To Copy or Not to Copy" by Héctor M. Manrique and Michael J. Walker is a follow-up to their previous work, "Snakes and Ladders in Paleoanthropology: From cognitive surprise to skillfulness a million years ago".
The research focuses on the cognitive processes underlying the ability to copy innovative behavior in humans and non-human primates. The authors explore this topic through the lens of Active Inference and the Free Energy Principle, which provide a framework for understanding how organisms minimize surprise and maximize evidence for their internal models.
Manrique and Walker introduce the concept of the "Zone of Bounded Surprisal" (ZBS) to explain the limitations in the ability of non-human primates to overcome cognitive surprisal and accurately copy innovative behavior.
They argue that the brains of non-human primates lack efficient neuronal networks for translating observed behavior into precise copying, which is crucial for the social transmission of technologies, cumulative learning, and culture.
The authors also emphasize the importance of working memory capacity in enabling cognitive versatility and recursive thinking, which are essential for overcoming surprisal and copying innovative behavior.
The findings of this research have far-reaching implications, as they challenge conventional views on the cognitive capacities of non-human primates and shed light on the evolutionary adaptations that enabled early humans to develop complex technological cultures.
The paper also raises important questions about the distinction between training (sequential learning) and learning (parallel dynamic updating), and how these processes are influenced by the timing and context of observed behavior.
Future research in this area could further explore the role of Active Inference and the Free Energy Principle in shaping the cognitive processes underlying the ability to copy innovative behavior, as well as the broader implications of these findings for understanding the evolution of human culture and technology.
Active Blockference _ IWAI 2022 Poster.pdf
Active Blockference: cadCAD with Active Inference for cognitive systems modeling
Active Inference is an integrated framework for modeling perception, cognition, and action in different types and scales of entities. It has been applied to various domains, including cognitive systems modeling, cyberphysical systems, and complex systems simulation.
The cadCAD (complex adaptive dynamics Computer-Aided Design) simulation framework is a powerful tool for modeling complex systems, providing features such as reproducible simulation, execution order specification, and parameter sweeps.
The Active Inference Institute has been working on projects that combine these two approaches, such as the Active Blockference project .
The paper "Active Blockference: cadCAD with Active Inference for cognitive systems modeling" presents a toolkit that connects the active inference approach and parameters from pymdp with the cadCAD simulation framework.
The authors developed general grid-world simulations that can be adapted to arbitrarily complex discrete state-spaces.
Example exploratory simulations have been used to model the behavior of single and multiple agents in a distributed grid-world setting.
The p_actinf function runs the core action-perception loop through which the generative model interacts with its environment. Active Blockference enables the application of the Active Inference framework for designing, simulating, and evaluating different entity types in cyberphysical systems.
The Active Blockference project has several implications and directions for future work.
First, there is a need to extend and improve the available toolbox, documentation, and graphical user interface.
Second, enabling high-dimensional cognitive analysis of complex, cyberphysical systems is a crucial next step.
The project is hosted as an open-source initiative at the Active Inference Institute, and contributions from researchers and developers are welcome.
By combining Active Inference with cadCAD, the project has the potential to advance the understanding and modeling of cognitive systems in complex environments, opening up new avenues for research and practical applications.
GenerativeResearchTeams_7_19_2023.pdf
Generative Research Teams: Active Inference Compositions For Research and Meta-Science
Scientific research teams face a challenging landscape marked by rapid technological advancements, an explosion of data, and escalating complexity of scientific problems.
Traditional research teams, composed solely of human members, may struggle to effectively navigate this intricate landscape.
The integration of computational entities and the application of advanced cognitive models is emerging as a promising solution to these formidable challenges.
The paper "Generative Research Teams: Active Inference Compositions For Research and Meta-Science" by Daniel Friedman and Jakub Smékal introduces the concept of Generative Research Teams (GRT), which are a synthesis of human, computational, and informational entities that employ Active Inference, systems engineering, and cognitive security to explore research topics.
The primary novel contributions of this paper include the exploration of augmented architectures, the integration of Active Inference as a cognitive kernel into GRTs with shared intelligence, and the application of cognitive models for enhanced research processes.
The development and implementation of GRTs have significant implications for the future of scientific research.
By leveraging the unique strengths of both human and computational entities, GRTs can enhance their problem-solving capabilities, adapt more quickly to changes in the research landscape, and produce more impactful outcomes.
This approach also raises important ethical considerations related to data privacy, algorithmic bias, and the potential impacts of research findings on society.
Future research directions include the empirical modeling of GRTs using Active Inference and the exploration of advanced GRTs capable of navigating uncertain landscapes and producing impactful outcomes.
ActiveInference_Institute-Ecosystem_2023_v1-1.pdf
The Active Inference Institute and Active Inference Ecosystem
Active inference is a unifying computational framework for understanding perception, action, and learning in biological and artificial systems. It is based on the free energy principle, which posits that biological systems maintain their existence by minimizing the difference between their internal models of the world and the sensory data they receive.
This framework has been applied to various fields, including neuroscience, robotics, psychology, and artificial intelligence.
The Active Inference Institute is an online open-science organization dedicated to learning, researching, and applying active inference across disciplines.
The paper "ActiveInference_Institute-Ecosystem_2023_v1-1" 1 presents the Active Inference Institute's ecosystem, which aims to bridge the gap between research and practice in active inference. The Institute organizes education, research, and communications to advance the progress and public awareness of frontier knowledge in active inference and related topics.
They employ a participatory open science approach, focusing on accessibility and service to the epistemic community.
The Active Inference Journal, a project of the Institute, aims to increase the accessibility and quality of livestream transcripts.
The Active Inference Institute's work has significant implications for the broader scientific community and various application domains. By promoting open science and interdisciplinary collaboration, the Institute fosters the development of new insights and applications of active inference.
This can lead to advances in artificial intelligence, robotics, and our understanding of complex biological systems.
Future research directions include exploring the applicability of active inference to different types of social organizations, developing new computational models and tools, and investigating the potential of active inference in addressing psychiatric disorders.
An Account of Active Inference Modeling v1.pdf
An Account of Active Inference Modeling
Active Inference is a burgeoning field in computational neuroscience that seeks to develop generative models of ecosystems of shared intelligence by accounting for cognitive systems and phenomena. This approach is likened to accounting rather than calculation, memorization, or inference itself, as the generative model performs the inference.
The field is grounded in a first-principles scale-free approach, rather than a highly-specific scheme for cognitive systems, allowing for a more holistic and integrated understanding of cognition, including action and perception.
Active Inference is often used in conjunction with representations such as those found in textbooks or in works like Friston 2019. However, it is important to note that these representations do not necessarily encapsulate complex cognitive phenomena like affect or narrative reflexivity
The paper "An Account of Active Inference Modeling" introduces the concept of Active AccountAnts and Active InferAnts, which represent the roles of the generative modeler and the generative model respectively in the Active Inference process.
The paper draws an analogy between financial accounting and cognitive accounting, suggesting that the connection between the two may go beyond the pedagogical or analogical.
The paper also introduces the concept of the cognitive Tetrahedra, a model that represents Internal, External, Sensory, and Active states.
This model is used in Active Inference to account for cognition in a holistic manner.
The paper also suggests that the outcome of Active Inference Research-Application work is both organic-aesthetic and analytic-synthetic, as generative models can be crafted and/or interpreted as an intra-active art-science in P-adic time
The paper's approach to Active Inference has significant implications for the field of computational neuroscience and beyond. By likening the development of generative models to accounting, the paper provides a novel perspective on how we understand and model cognitive systems and phenomena.
This approach could potentially lead to more holistic and integrated models of cognition. The analogy between financial and cognitive accounting also opens up new avenues for interdisciplinary research and collaboration. Furthermore, the introduction of the cognitive
Tetrahedra provides a new tool for researchers to model and understand cognition in a comprehensive manner.
The paper also suggests that future work in Active Inference could explore the organic-aesthetic and analytic-synthetic outcomes of Research-Application work, potentially leading to new insights into the nature of generative models and their applications
CognitiveSovereignty_ActiveInference_StateOf_Exception_v1-1.pdf
Cognitive Sovereignty & Active Inference in the State of Exception
This paper provides an analysis of Giorgio Agamben's book Homo Sacer through the lens of Active Inference. Agamben's work explores the relationship between bare life and political existence in Western politics and metaphysics, arguing that politics is founded on the inclusive exclusion of bare life, where natural biological life is politicized only through its exclusion as an exception.
The paper also draws on Thomas Kuhn's theory of revolutionary science, which describes the process of paradigm shifts in scientific knowledge and practice.
The paper situates these concepts within the context of cognitive sovereignty, a term that refers to the enacted policy selection of the cognitive sovereign, which establishes what counts as valid knowledge and action.
The paper makes several unique contributions to the understanding of cognitive sovereignty, politics, and science. It connects Agamben’s framing of the political state of exception with Kuhn's theory of revolutionary science, asserting that realized epistemic agency is grounded in the enacted policy selection of the cognitive sovereign.
The paper also introduces the concept of Active Inference, a theoretical framework for scientific inference, as a tool to enhance our understanding of sovereignty, agency, and the state of exception.
The author draws several concordances between Active Inference and Homo Sacer, discussing the state of exception in terms of affordances, bare life in terms of variational free energy, and sovereign agency in terms of expected free energy.
The paper also provides pseudocode of an “Active Stateference” entity, offering an initial accounting of Homo Sacer from the Active Inference perspective

The implications of this paper are far-reaching, particularly in the fields of cognitive science, political science, and philosophy. The paper's exploration of cognitive sovereignty and active inference provides a novel perspective on the dynamics of power, knowledge, and sovereignty in politics and science.
The author uses Active Inference to analyze the state of exception, bare life, and sovereign agency opens up new avenues for understanding and modeling cognitive ecosystems. The paper also suggests that the Active Inference framework could be used to enhance our understanding of the relationships among cognitive sovereignty, political sovereignty, and scientific discovery.
Future research could further explore these connections and apply the Active Inference framework to other areas of study
Entomology
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Jasper_2014_HoneyBeeGeneExpression.pdf
"Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey Bees"
The genetic basis of phenotypic novelty is a major unresolved question in evolutionary biology.
The field of evolutionary developmental biology (evo-devo) has shown that changes to regulatory regions are the dominant mode of genetic change in early development.
However, it is unclear whether this extends to the evolution of novel phenotypes in adult organisms.
Honey bees serve as an ideal model system for this question, as they have evolved many novel traits for social functions missing from their solitary ancestors
The study conducted ten RNA-Seq experiments across both novel and conserved tissues in honey bees to determine the extent to which postdevelopmental novelty is based on changes to the coding regions of genes.
The researchers discovered that positively selected tissue-specific genes of high expression underlie novelty by conferring specialized cellular functions.
These genes are often, but not always, taxonomically restricted genes (TRGs).
They also found that positively selected genes, whether TRGs or conserved genes, are the least connected genes within gene expression networks
The findings of this study suggest that the evo-devo paradigm is limited, and the evolution of novelty in adult organisms follows additional rules.
Specifically, genes with low network connectedness (TRGs and tissue-specific conserved genes) underlie novel phenotypes by rapidly changing coding sequence to perform new specialized functions.
This work has implications for understanding the genetic mechanisms governing different evolutionary contexts of novelty and could guide future research in the field of evolutionary biology
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Ingram_2016_Circadian_foraging.pdf
“Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task”
The foraging gene has been widely studied in various species, including insects, due to its association with behavioral plasticity and task allocation among social insect workers.
In social insects, workers of similar genotypes adopt different behavioral phenotypes, making them an ideal framework for studying the molecular mechanisms underlying behavioral plasticity. P
revious studies have focused on laboratory settings, but field studies involving the genetic regulation of task allocation are rare.
The study by Ingram et al. (2016) aimed to investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and experimentally test how exposure to light affects foraging expression in brood workers and foragers.
The study found that the regulation of the foraging gene in harvester ants occurs at two time scales: levels of foraging mRNA are associated with ontogenetic changes over weeks in worker age, location, and task, and there are significant daily oscillations in foraging expression in foragers.
The results showed that gene expression changes in foragers occur across a scale of hours, and the level of expression is predicted by activity rhythms, with foragers having high levels of foraging mRNA during daylight hours when they are most active outside the nests.
In the experimental study, complex interactions in foraging expression were found between task behavior and light exposure, with oscillations occurring in foragers following experimental exposure to 13 L:11 D (LD) conditions, but not in brood workers under similar conditions.
The findings of this study have several implications for future research and understanding of the foraging gene's role in behavioral plasticity and task allocation in social insects. First, the results underscore the importance of assaying temporal patterns in behavioral gene expression, as daily fluctuations in foraging gene expression were observed in harvester ants .
Second, the study highlights the context-dependent regulation of the foraging gene, which is associated with both ontogenetic and daily behavioral plasticity in field colonies of harvester ants.
Further research could investigate the molecular pathways affected by circadian circuitry and how these pathways are related to behavior in social insects. Additionally, future studies could examine the spatial distribution of the foraging protein in the brain and its potential role in task transitions in harvester ant workers.
Friedman_Gordon_2016_Ant_Genetics_review.pdf
“Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior”
Ants exhibit a wide range of morphological, physiological, and behavioral diversity, which has been the subject of numerous studies.
Ant genomes are characterized by high rates of gene turnover, particularly in gene families related to olfactory communication, such as the synthesis of cuticular hydrocarbons and the perception of environmental semiochemicals.
Despite the growing body of research on ant genetics, few studies have directly investigated the genetics of ant behavior.
The paper "Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior" by D.A. Friedman and D.M. Gordon explores the genetics of ant behavior, focusing on gene expression, epigenetics, and quantitative genetic approaches.
The study highlights the extreme rates of gene turnover in ant genomes, especially in gene families related to olfactory communication.
It also reveals transcriptomic and epigenetic differences between reproductive and sterile females, males and females, and workers with different body sizes.
The paper emphasizes the need for further investigation into the feedback between individual-level physiological changes and socially mediated responses to environmental conditions in ants.
The findings of this paper have significant implications for understanding the genetic basis of ant behavior and the evolution of social insects. By identifying genes and gene families associated with ant behavior, researchers can gain insights into the molecular mechanisms underlying the complex social organization of ant colonies.
This knowledge can also inform future studies on the evolution of sociality in insects and contribute to the development of novel strategies for pest control.
Furthermore, the paper highlights the importance of considering the interplay between genetics, behavior, and environmental factors in the study of ant behavior and suggests potential directions for future research in this area.
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FriedmanGordonLuo_MutAnts_2017.pdf
“The MutAnts are here”
Ant colonies are fascinating examples of collective behavior in nature. Genomic, epigenomic, and transcriptomic analyses have started to reveal the molecular underpinnings of physiology and behavior in various ant species.
However, without the ability to perform genetic manipulations, most hypotheses regarding ant genetics are based on correlative evidence and phylogenetic inference.
Eusocial insects, such as ants, rely heavily on olfactory cues to organize their collective behavior. The Orco gene, which encodes a key olfactory co-receptor, plays a crucial role in ants' ability to perceive olfactory stimuli.
In a groundbreaking study, researchers Trible et al. (2017) and Yan et al. (2017) successfully performed CRISPR/Cas9-mediated knockout of the Orco gene in two different ant species: the clonal raider ant (Ooceraea biroi) and Jerdon's jumping ant (Harpegnathos saltator).
This development opened a new window into exploring how social insects use olfactory cues to organize their collective behavior. In both ant species, homozygous Orco loss-of-function individuals displayed similar patterns of altered behavior and decreased reproductive performance, supporting the hypothesized centrality of Orco in mediating the perception of olfactory stimuli in ants.
The successful use of CRISPR/Cas9-mediated gene knockout in ants marks a significant milestone in the field of eusocial insect genetics.
This advancement enables researchers to investigate the role of genomic changes, such as the expansion of the Or gene family, in the adaptation of ants to diverse environments.
Future research can explore how ecological heterogeneity has been facilitated by neurophysiological and epigenetic plasticity in ants, shedding light on the evolution of the world's most ecologically dominant invertebrate societies
Molecular Ecology - 2017 - Gordon - Two lineages that need each other.pdf
“Two lineages that need each other"
In social insects like ants and bees, diploid females can develop into either reproductive or worker castes.
In honeybees, this fate is determined by the larval food supply, with larvae fed royal jelly becoming reproductives and others becoming workers.
A similar system was discovered in harvester ants of the genus Pogonomyrmex, where two interdependent lineages exist.
Mating between a reproductive and a male of the same lineage produces daughter reproductives, while mating between a female reproductive and a male of the other lineage produces daughter workers.
These two lineages rely on each other for colony survival, as colonies cannot produce offspring without reproductives and cannot maintain reproductives without workers.
The paper by Gordon and Friedman discusses a study by Romiguier et al., which used RNA sequencing to demonstrate a similar dependent-lineage system in another harvester ant genus, Messor.
This discovery raises several evolutionary questions, such as the relationship between this process and hybridization, and whether the origins of such systems are related to hybridization among related species.
The paper also highlights the ecological implications of the dependent-lineage system, as queens must mate with at least one male of each lineage to produce a viable colony with both reproductives and workers.
The dependent-lineage system in ants has potential consequences for the understanding of complex evolutionary processes and ecological factors.
The discovery of this system in multiple harvester ant genera suggests that it may be widespread among the thousands of ant species, and further research using high-throughput sequencing techniques could reveal more examples of this system in other genera and subfamilies.
Additionally, understanding the factors that drive the evolution of such diverse systems in ants could provide insights into the genetic and ecological mechanisms that shape the development and maintenance of complex social structures in other organisms.
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Friedman_2018_Dopamine_Foraging_Pogo.pdf
“The Role of Dopamine in the Collective Regulation of Foraging in Harvester Ants”
Red harvester ants (Pogonomyrmex barbatus) are known for their ability to adjust their foraging behavior in response to changes in humidity. These ants forage for seeds in the desert, where they face the challenge of balancing food accumulation and water loss.
Colonies of red harvester ants exhibit significant variation in how they regulate their collective foraging activity in response to humidity, which is an ecologically important trait.
The regulation of foraging activity in these ants is a distributed process based on local interactions, such as olfactory encounters between outgoing and returning foragers
The study investigated the molecular basis of the variation in collective foraging behavior among red harvester ant colonies.
The researchers used transcriptomic, physiological, and pharmacological experiments to analyze the differences in forager brain tissue among colonies.
They found that colony foraging activity was associated with differential expression of transcripts related to biogenic amine and neurohormonal metabolism and signaling.
Furthermore, pharmacological increases in forager brain dopamine titer led to significant increases in foraging activity. Interestingly, colonies that were naturally more sensitive to humidity were more responsive to the stimulatory effect of exogenous dopamine
The findings of this study suggest that neurophysiological variation among red harvester ant colonies, particularly in dopamine signaling, may underlie the heritable molecular variation that influences the collective regulation of foraging.
This research contributes to our understanding of the molecular mechanisms that drive variation in collective behavior among social insect colonies.
Future work could explore the role of other biogenic amines in the regulation of foraging in harvester ants and investigate the specific behavioral mechanisms through which dopamine affects a forager's decision to leave the nest.
Burford_2018_Argentine_Foraging.pdf
“Foraging behavior and locomotion of the invasive Argentine ant from winter aggregations”
The invasive Argentine ant (Linepithema humile) is native to South America and has spread to various regions worldwide, including Mediterranean climates.
These ants thrive in environments with hot, dry summers and colder, wet winters. They are known for their aggressive foraging behavior and have been reported to cause significant harm to native species and ecosystems.
However, the foraging behavior and locomotion of Argentine ants during winter have rarely been studied.
The study by Burford et al. examined the foraging behavior of three distinct Argentine ant colonies in northern California during winter.
They found that the colonies foraged most between 10 and 15°C, regardless of the maximum daily temperature.
Worker walking speed was positively associated with temperature (range 6–24°C) and negatively associated with humidity (range 25–93%RH).
All colonies foraged during all day and night hours in a predictable daily cycle, with a correlation between the rate of incoming and outgoing foragers.
Foraging activity was unrelated to the activity of a competing native ant species, Prenolepis imparis, which was present in low abundance, and ceased only during heavy rain when ants left foraging trails and aggregated in small sheltered areas on trees.
The findings of this study have implications for understanding the behavior and ecological impact of invasive Argentine ants during winter. The ants' foraging behavior and locomotion in response to temperature and humidity may provide insights into their ability to adapt and thrive in various environments.
Additionally, the study highlights the importance of considering the effects of invasive species like Argentine ants on native species and ecosystems when developing conservation and management strategies.
Future research could focus on exploring the interactions between Argentine ants and native species in different environments and developing effective control methods to mitigate their negative impacts.
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Friedman-Søvik2021_Article_TheAntColonyAsATestForConsciousness.pdf
The ant colony as a test for scientific theories of consciousness
The study of consciousness remains one of the major unsolved mysteries in both science and philosophy. Without an agreed-upon definition or a convenient system to test theories of consciousness, a confusing heterogeneity of theories has proliferated.
In an attempt to clarify this complicated discourse, the paper "The ant colony as a test for scientific theories of consciousness" by Daniel A. Friedman and Eirik Søvik introduces the Ant Colony Test (ACT) as a rigorous reverse test for consciousness.
The authors propose using social insect colonies, particularly ants and bees, as a model system for studying consciousness due to their fulfilling many prerequisites for conscious awareness met by humans and honey bee workers.
The paper uniquely develops the concept of the Ant Colony Test (ACT) as a reverse test for theories of consciousness, providing internal and external calibration of different frameworks.
The authors argue that social insect colonies can serve as a tractable and non-human model system for studying consciousness, as they fulfill many of the prerequisites for conscious awareness met by humans and honey bee workers.
The paper also discusses the notion of forward tests versus reverse tests, analogous to the normal and revolutionary phases of the scientific process, and how contemporary theories of consciousness are forward tests.
The Ant Colony Test (ACT) has significant implications for the study of consciousness. By providing a rigorous reverse test for theories of consciousness, the ACT can help calibrate and evaluate different frameworks, leading to a better understanding of the nature of consciousness.
Furthermore, the use of social insect colonies as a model system allows for ethically performing clarifying experiments about consciousness, as these colonies can be manipulated, divided, or drugged without the ethical concerns associated with human subjects.
The ACT has the potential to provide valuable insights into the nature of consciousness and guide future research in this complex field.
Friedman_2019_Pogo_Humidity.pdf
The physiology of forager hydration and variation among harvester ant (Pogonomyrmex barbatus) colonies in collective foraging
Desert ants, such as the red harvester ant (Pogonomyrmex barbatus), face significant desiccation stress when foraging outside their nests due to their high surface area to volume ratios and exposure to harsh conditions.
These ants obtain water through the oxidation of fats from seeds they eat and lose water primarily through cuticular evapotranspiration.
To manage the tradeoff between water loss and obtaining food and water, foraging activity is regulated through interactions among workers inside the nest.
Previous studies have shown that colonies that forage less in dry conditions and show more stable foraging in humid conditions are more likely to produce offspring colonies.
The paper "The physiology of forager hydration and variation among harvester ant (Pogonomyrmex barbatus) colonies in collective foraging behavior" by Friedman, Greene, and Gordon presents field experiments that demonstrate hydrated P. barbatus foragers made more foraging trips than unhydrated nestmates. The positive effect of hydration on foraging activity is stronger as the risk of desiccation increases.
Desiccation tests showed that foragers of colonies that reduce foraging in dry conditions are more sensitive to water loss, losing water and motor coordination more rapidly in desiccating conditions, than foragers of colonies that do not reduce foraging in dry conditions.
Surprisingly, foragers that are more sensitive to water loss are from colonies more likely to produce offspring colonies, possibly because these colonies conserve water with a more cautious response to desiccation risk.
This study highlights the importance of understanding the relationship between ant hydration and foraging behavior in the context of colony survival and reproduction.
The findings suggest that variation among ant colonies in worker physiology and response to ambient conditions may contribute to ecologically significant differences among colonies in collective behavior.
Future research could focus on further exploring the mechanisms behind the relationship between hydration status and foraging decisions, as well as investigating how these relationships may be influenced by other environmental factors and colony characteristics.
Additionally, understanding the role of hydration in the regulation of foraging activity could potentially inform the development of strategies for managing ant populations in various ecological contexts.
Friedman_2019_PhD_Dissertation_Overview.pdf
Behavioral, Physiological, and Transcriptomic Variation Among Colonies of the Red Harvester Ant (Pogonomyrmex barbatus)
Social insects, such as ants, exhibit complex collective behaviors that arise from the interactions of individual nestmates.
These behaviors have evolved in response to specific ecological contexts and are regulated by neurophysiological mechanisms. The red harvester ant (Pogonomyrmex barbatus) is a species that thrives in harsh desert environments and displays adaptive foraging behaviors in response to dry conditions.
Previous research has shown that colonies of P. barbatus vary in how they regulate foraging activity in dry conditions, with some colonies reducing foraging while others do not.
This variation in behavior is associated with differences in reproductive success and is thought to be heritable
In his dissertation, Daniel Ari Friedman investigates the physiological differences among colonies of the red harvester ant and how these differences are associated with colony-level behavioral differences and the evolution of collective behavior.
The study comprises four main chapters:
"The Role of Dopamine in the Collective Regulation of Foraging in Harvester Ants" explores the differences in gene expression and biogenic amine metabolism among colonies with varying foraging behaviors. The study demonstrates that dopamine plays a significant role in regulating foraging activity.
"The Physiology of Forager Hydration and Variation among Harvester Ant (Pogonomyrmex barbatus) Colonies in Collective Foraging Behavior" examines the relationship between colony foraging behavior, colony reproductive success, and forager desiccation physiology. The study shows that hydrated foragers go on significantly more foraging trips than their unhydrated nestmates.
"Forager Brain Gene Expression Patterns and the Evolution of Colony Behavior in Red Harvester Ants" uses RNA-seq on single forager brains to investigate how variation in gene expression within and among colonies is associated with colony traits and the degree of protein coding sequence constraint over evolutionary time.
"The Effect of Dopamine and Hydration on Individual Red Harvester Ant Foraging Activity" characterizes how heterogeneity among nestmates in foraging activity is related to the effect of hydration and dopamine treatment on increasing overall foraging trips.
Friedman's research provides valuable insights into the neurophysiological basis of variation among red harvester ant colonies in foraging behavior.
The findings have implications for understanding the evolution of collective behavior in social insects and the role of neurophysiological mechanisms in regulating individual and colony-level behaviors.
Future research could further explore the genetic and environmental factors that contribute to the observed variation in foraging behavior among colonies, as well as the potential applications of these findings in the development of distributed systems and swarm intelligence algorithms
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Friedman_DistributedPhysiology_2020.pdf
Distributed physiology and the molecular basis of social life in eusocial insects
Eusocial insects, such as ants, bees, and termites, exhibit complex social structures and behaviors, with individuals in a colony performing specialized tasks. These insects have evolved a unique form of physiology, known as distributed physiology, where key physiological processes are regulated at the colony level rather than within individual organisms. This decentralized physiological system has led to the development of novel mechanisms related to pheromone detection, hormone signaling, and neural signaling pathways that influence nestmate and colony traits
The paper "Distributed physiology and the molecular basis of social life in eusocial insects" by Friedman et al. explores the functional genomic, physiological, and behavioral aspects of eusocial insects in the context of distributed physiology.
The authors highlight functional genomic work that investigates how nestmate-level and colony-level traits arise and are influenced by interactions among physiologically-specialized nestmates of various developmental stages.
They also discuss similarities and differences between nestmate-level (organismal) and colony-level (superorganismal) physiological processes, and propose specific hypotheses regarding the physiology of eusocial taxa
1
.
The study of distributed physiology in eusocial insects has important implications for understanding the evolution of complex social systems and the molecular mechanisms underlying these systems.
By examining the traits of eusocial insects, researchers can gain insights into the genetic, evolutionary, and physiological aspects of their social behaviors and colony-level traits.
This knowledge can potentially be applied to other areas of biology, such as the study of human social behavior and the development of novel strategies for pest control.
Furthermore, the research on eusocial insects can contribute to a better understanding of the evolution of eusociality and collective behavior in natural systems
Friedman_York_PogoGeneExpress_2020.pdf
Gene expression variation in the brains of harvester ant foragers is associated with collective behavior
The collective behavior of social insects, such as ants and bees, arises from the responses of individuals to interactions with others and their environment. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success.
Biogenic amine neurotransmitters, such as dopamine and serotonin, influence ant worker behavior through their role in modulating sensory sensitivity to stimuli.
Previous studies on ant neurophysiology have primarily been conducted in controlled indoor conditions.
Friedman et al. extended these studies to examine how differences among colonies in forager neurophysiology are associated with variation in colony behavior in natural conditions.
They collected actively foraging ants from nine P. barbatus colonies that varied in two traits: sensitivity of foraging activity to humidity and forager brain dopamine-to-serotonin ratio.
Using RNA-seq, they found that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with the two colony traits.
The study suggests that natural selection may shape colony foraging behavior by acting on variation among colonies in gene expression.
The findings provide insights into the role of gene expression in individual forager brains in relation to phenotypic variation across colonies in a natural setting.
This research contributes to the understanding of the molecular basis of collective behavior in social insects and could potentially inform future studies on the evolution and regulation of social behavior in other species.
Shin2020_Article_MeasurementOfNeurotransmitters.pdf
Measurement of natural variation of neurotransmitter tissue content in red harvester ant brains among different colonies.
Red harvester ants (Pogonomyrmex barbatus) are known to regulate their foraging activity based on food availability and local conditions.
The variation in foraging behavior among different colonies is thought to be linked to biogenic amine signaling and metabolism.
However, measurements of differences in neurotransmitters among ant colonies in a natural environment have not been made before.
Understanding the natural variation in neurotransmitter content in ant brains can provide valuable insights into the neurophysiological basis of the evolution of collective behavior.
The paper "Measurement of natural variation of neurotransmitter tissue content in red harvester ant brains among different colonies" by Mimi Shin, Daniel A. Friedman, Deborah M. Gordon, and B. Jill Venton presents a novel method for quantifying tissue content of four biogenic amines (dopamine, serotonin, octopamine, and tyramine) in single forager brains from nine red harvester ant colonies collected in the field.
The researchers used capillary electrophoresis coupled with fast-scan cyclic voltammetry (CE-FSCV) to separate and detect the amines in individual ant brains.
This study is the first to demonstrate that CE-FSCV is a useful method for investigating natural variation in neurotransmitter content in single ant brains.
The findings of this study have significant implications for understanding the neurophysiological basis of the evolution of collective behavior in ants.
The results showed that there was less variation in neurotransmitter content within a colony than among colonies, suggesting that the neurotransmitter content of each colony might change with environmental conditions.
This research opens up new avenues for future studies correlating tissue content with colony behavior, such as foraging. Additionally, the CE-FSCV method developed in this study could be applied to other insect species and contexts, further expanding our knowledge of the role of neurotransmitters in the regulation of collective behavior.
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Friedman_2021_InferAnts.pdf
Active Inferants: An Active Inference Framework for Ant Colony Behavior
Ant colonies exhibit complex collective behaviors, such as foraging, that emerge from the interactions among individual ants and their environment.
These behaviors can be studied using computational models that simulate the decision-making processes of ants.
Active inference is a multiscale approach to behavioral modeling that has been applied across various settings in theoretical biology and ethology.
The study of ant colonies within the eco-evo-devo framework emphasizes ecological context, subunit sensitivity to interactions, and emergent properties of groups 1 .
The paper "Active Inferants: An Active Inference Framework for Ant Colony Behavior" by Friedman et al. introduces an active inference model of ant colony foraging behavior and implements it in a series of in silico experiments.
The authors focus on stigmergic regulation of colony foraging, where accumulated traces left in the environment by agents are used to direct the behavior of their conspecifics.
They specify and simulate a Markov decision process (MDP) model for ant colony foraging, investigating the well-known alternating T-maze paradigm from laboratory ant colony behavioral experiments.
The model demonstrates the ability to recover basic colony phenomena such as trail formation after food location discovery.
The active inference framework presented in the paper can be extended to study various aspects of ant colony behavior, such as temporal variability, learning and memory, multiple types of pheromone, abiotic factors, and interaction patterns among nestmates at different developmental stages.
This approach can help researchers understand the complex dynamics of ant colonies and their interactions with the environment, as well as inform the design of artificial systems inspired by ant colony behaviors, such as swarm robotics and optimization algorithms.
The model can also serve as a foundation for future research on the evolution of multiscale foraging processes in ant colonies and other Bayesian agents, exploring how these complex systems solve various challenging problems with limited and local information.
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Saund_Friedman_2023.pdf
A single-pheromone model accounts for empirical patterns of ant colony foraging previously modeled using two pheromones
Ants are known for their complex social behavior and efficient foraging strategies. In a 2009 study, Dussutour et al. proposed that big-headed ants (Pheidole megacephala) use two distinct attractant pheromones during foraging: one for exploration and another for food gathering. This two-pheromone model (2PM) was based on laboratory experiments using a Y-maze apparatus, where ants chose between different branches with varying food availability and pheromone history.
The attached paper by Saund and Friedman challenges the 2PM by presenting an alternative one-pheromone model (1PM) that can also account for the observed experimental results.
The 1PM assumes that ants deposit a single attractant pheromone during both exploration and food gathering, with a higher amount deposited when returning from a found resource.
The model incorporates nonlinear amplification of pheromone concentrations and a preference function based on the absolute difference in perceived pheromone concentration between branches.
The authors show that the 1PM can explain the main experimental observations previously attributed to the 2PM, suggesting that it is plausible but unnecessary to hypothesize two distinct pheromones for these ants.
The 1PM offers a more parsimonious and biologically plausible explanation for the observed foraging patterns in Pheidole megace
The findings of this paper highlight the importance of considering alternative models when interpreting animal behavior and sensory-cognitive mechanisms.
Friedman_JoVe_2023.pdf
Experimental Entomology in the Age of Video
Entomology, the study of insects, has evolved over thousands of years of human-insect interactions. Insects play crucial ecological roles and are present across nearly all terrestrial surfaces, making theoretical and applied entomology central research domains for the 21st century and beyond.
Recent technological advancements, such as the widespread accessibility to video creation, are transforming the processes of education, research, and governance in entomology
The paper "Experimental Entomology in the Age of Video" by Friedman, Wexler, and Alvarado discusses several modern entomological methods and their applications.
The authors summarize protocols associated with contemporary entomology, aiming to communicate recent methodological developments to facilitate their adoption.
The paper covers various scientific methods used to study the morphology, physiology, and behavior of ants and bees, addressing challenges in laboratory and field manipulation, observation of nestmates, long generation times, and scaling up experiments to the colony level.
The authors also highlight the potential of video presentation to increase the adoptability, proficiency, and reproducibility of these methods, which can benefit researchers globally.
The advancements in entomological methods presented in the paper have broad implications for entomologists, agriculturalists, and researchers in related fields.
The adoption of these methods can lead to more effective studies and improved empirical data, which can be useful for applying complexity science techniques (e.g., agent-based modeling, stigmergy, multi-scale systems analysis) to insects and beyond.
Future work could expand the scope of species studied, leverage ecological databases to identify niches and species for method application, and explore emerging technologies such as augmented reality, interspecies communication, robotics, and cognitive modeling of insect-based cyberphysical systems.
DAF_Ants_Aging_4_22_2023.pdf
Of Ants & Aging
In the context of aging, the presentation discusses various questions related to the reasons behind aging in ants and humans, similarities and differences in aging mechanisms across different species, and the progress made in reversing aging.
The presentation also explores the motivations and definitions of ants and aging, as well as the reasons behind biological aging using Tinbergen's 4 Questions
The contributions of the paper include a discussion of the similarities and differences in aging mechanisms between ants and humans, highlighting the potential for universal mechanisms or those shared by a majority of taxa and set up early in the evolution of multicellular organisms.
The paper also presents a roadmap for further research, including motivations and definitions, reasons behind biological aging, and discussions on maps, territories, and decisions.
The implications of the paper suggest that understanding the aging process in ants may provide insights into the aging process in humans and other species.
The paper highlights the need for further research in this area, particularly in understanding the causal consequences of aging and the potential directions for future work and research.
By studying the aging process in ants, researchers may uncover new information about the mechanisms behind aging and potentially develop strategies for promoting healthy aging in humans
COGSEC
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GreatPreset_Friedman_Cordes_2020.pdf
The Great Preset: Remote Teams and Operational Art
In recent years, remote work has become increasingly prevalent, with teams and organizations adapting to new ways of collaborating and communicating across distances.
This shift has led to a growing interest in understanding how to effectively manage and operate remote teams.
In this context, "The Great Preset: Remote Teams & Operational Art" emerges as a valuable resource for those seeking to navigate the challenges and opportunities presented by remote work.
"The Great Preset: Remote Teams & Operational Art," edited by Daniel A. Friedman and Richard J. Cordes, offers insights and guidance on managing remote teams, drawing from various disciplines and perspectives.
The book introduces the concept of the Facilitator's Catechism, a framework for project management that covers administration, logistics, and communications.
It also discusses the implications of achieving project milestones, helping potential collaborators align on the impact and importance of their mission.
Furthermore, the book explores the historical development of remote work and the tools and techniques that have emerged to support it, in the context of modern cognitive security.
The insights and strategies presented in "The Great Preset: Remote Teams & Operational Art" have significant implications for organizations and individuals navigating the remote work landscape.
By applying the principles and practices outlined in the book, teams can enhance their communication, collaboration, and overall effectiveness in a remote setting.
Additionally, the book's exploration of the historical development of remote work and its associated tools can inform future research and development in this area.
As remote work continues to evolve and become more prevalent, the lessons and guidance offered in "The Great Preset" will remain relevant and valuable for those seeking to optimize their remote teams and operations.
The Innovators Catechism.pdf
The Innovator’s Catechism
Innovation teams, such as those formed in incubators, research accelerators, hackathon weekends, and within organizations, often face challenges in aligning their narrative, workflow, and objectives, which can lead to disintegration or failure to perform.
Operations orders (OPORDs), which have been used by the military to improve organizational efficacy and success, provide a structured approach to achieving goals and objectives.
The study of high reliability organizations (HROs), such as air traffic control, emergency services, and military operations, offers insights into how structured operational approaches like OPORDs can be applied to increase the reliability of innovation management.
The paper "The Innovator's Catechism" by Richard J. Cordes, Daniel A. Friedman, and Steven E. Phelan presents a catechism-styled operations order for use by early-stage innovation teams.
This operations order is built upon the "Facilitator's Catechism," an operations order for rapidly formed research teams, and acknowledges the unique information requirements for emergent and early-stage teams that are market-facing.
The Innovator's Catechism combines the Facilitator's Catechism approach with Blank's innovation pipeline concept to produce a series of structured questions that innovators can ask at each stage of the innovation pipeline, aiming to improve the reliability and effectiveness of innovation teams.
The Innovator's Catechism has the potential to impact innovation teams by providing a structured approach to aligning their goals, objectives, and communication, ultimately increasing their chances of success.
By addressing the unique challenges faced by early-stage innovation teams, this tool can help them navigate the complexities of their market-facing environment.
Future work and research could explore the effectiveness of the Innovator's Catechism in various contexts, such as remote teams, start-ups, and hackathons, and further refine the tool to better support the needs of innovation teams in different stages of development.
Reimagining Maps.pdf
Reimagining Maps
Geospatial mapping has evolved significantly with advancements in technology, data availability, and infrastructure. However, there are still challenges in the field, such as interoperability, skill gaps, user awareness, mapping uncertainty, threat actors, data volume, and accessibility.
As the world becomes more complex and interconnected, the need for innovative solutions in geospatial mapping is more important than ever.
In this context, the paper "Reimagining Maps" aims to explore the potential future of cartography through interdisciplinary synthesis, drawing from fields such as applied mathematics, engineering, and digital pedagogy.
The paper "Reimagining Maps" identifies three key contemporary challenge areas for geospatial mapping: rapid generation of relevant maps, informational compression and user experience, and security, governance, and trust of maps and data .
It proposes an interdisciplinary approach to address these challenges, considering the strengths, limitations, and objectives of diverse fields adjacent to cartography.
The paper also provides direction for future research activities, focusing on the development of integrative frameworks for geospatial intelligence production and user experiences involving rapid generation and customization of user-aware maps, signal processing techniques, role-based access systems, open source intelligence, next-generation analytics, and artificial intelligence in the loop with humans.
The paper's findings have significant implications for the future of geospatial mapping and related fields.
By addressing the identified challenges through interdisciplinary approaches, it is possible to develop more effective, flexible, and understandable maps that can better serve various users and facilitate modern action affordances.
Additionally, the paper highlights the importance of transparent, effective, and secure governance of datasets and map generators, as well as the need for rapid, contextual, and human-in-the-loop responses to disasters.
As a result, the insights provided in "Reimagining Maps" can guide future research and development in cartography, ultimately leading to more advanced and useful geospatial mapping solutions for a wide range of applications.
The Facilitators Catechismv2.pdf
The Facilitator's Catechism
The concept of sensemaking has been widely explored in various fields, including military psychology, neuroscience, and artificial intelligence.
Sensemaking refers to the process of creating meaning and understanding from complex and often ambiguous information. In recent years, there has been a growing interest in developing methods and tools to facilitate sensemaking in diverse contexts, such as combat situations, digital transformation, and active inference.
One such approach is the use of facilitation techniques, which aim to guide individuals and groups through the sensemaking process by fostering collaboration, communication, and critical thinking.
"The Facilitator's Catechism" is a paper that introduces a new operations order format called the Facilitator's Catechism, designed for use by process facilitators in military, intelligence, and civilian teams. This format is intended to help teams navigate complex situations and make sense of the information they encounter.
The paper discusses the origins and evolution of operations orders, as well as the key characteristics of survivability, contemporary and future requirements, and current limitations of extant operations orders.
The Facilitator's Catechism aims to address these limitations and provide a more effective and adaptable tool for sensemaking in various contexts.
The development and implementation of the Facilitator's Catechism have several implications for future work and research.
First, it offers a novel approach to sensemaking that can be applied in diverse fields, potentially improving decision-making and problem-solving processes.
Second, it encourages further exploration of facilitation techniques and their effectiveness in different contexts, which could lead to the development of new methods and tools for sensemaking.
Finally, the Facilitator's Catechism may serve as a foundation for interdisciplinary research, fostering collaboration between researchers in fields such as psychology, neuroscience, and artificial intelligence, ultimately contributing to a better understanding of the complex processes involved in sensemaking.
infinite_games_for_infinite_teams.pdf
Infinite Games for Infinite Teams
The rise of the internet and social media has led to an increasingly complex and interconnected world, where online narratives can have significant real-world implications.
The rapid spread of information, both true and false, has made it difficult for individuals and organizations to make sense of the vast amount of data available.
In this context, the concept of Complex Adaptive Systems (CAS) has emerged as a useful framework for understanding the dynamics of online narratives and culture production. CAS are systems composed of many interacting subunits, leading to properties such as anti-fragility, multiscale chaotic patterns, non-linear responses to stimuli, and evolvability.
The paper "Infinite Games for Infinite Teams" by DA Friedman and RJ Cordes explores the potential of using games and remote teams to address the challenges posed by the complex online narrative landscape.
The authors introduce the concept of Instantaneous Remote Teams (IRTs), which are rapidly formed online-native teams that can adapt and respond to the ever-changing information ecosystem.
They also discuss the idea of Infinite Games, which are open-ended and evolving games that can be played in the complex and uncertain "Gray Zone" of online narratives. The paper presents two visions for harnessing the power of Infinite Games for IRTs:
1) Formal Memetics, which involves the development of ontologies, controlled vocabularies, and taxonomies for memes and narratives, and
2) a case-management-like system for knowledge mapping, enabling a cooperative "Cadavre Exquis" role-playing game played by Infinite Teams.
The ideas presented in the paper have significant implications for the future of online narrative management and the development of tools and strategies to address the challenges posed by the complex information ecosystem.
By leveraging the power of games and remote teams, it may be possible to develop novel approaches to assess, design, and deploy online narratives in real-time, with a focus on cultural awareness, interlingual understanding, and human-in-the-loop systems.
Furthermore, the exploration of Infinite Games and IRTs could lead to new insights into the dynamics of online culture production and the potential for harnessing collective intelligence to address complex global challenges.
Future research in this area could draw from diverse fields such as wearable neurofeedback devices, video game strategy, and military science, as well as exploring the potential for large-scale, collaborative online games to facilitate solutions to emergent problems requiring crowd effort or rapid cultural transmission.
CordesFriedman2020_Emergent_Teams.pdf
Emergent Teams for Complex Threats
The paper "Emergent Teams for Complex Threats" by Richard J. Cordes and Daniel A. Friedman discusses the changing landscape of conflict management due to social and technological developments.
The introduction of nuclear weapons and the maintenance of large military budgets during peacetime in the latter half of the 20th century have altered the risk calculus of conflict among state and non-state actors.
As a result, centralized actors face new challenges such as ideological warfare and sustained low-intensity and gray zone conflicts, while decentralized participants have emerged and evolved. Nation-states now have to contend with potential novel, emergent hazards from a myriad of Complex Threat Surfaces in various environments.
The paper highlights the application of Complexity Science in analyzing Complex Threat Surfaces in military and civilian organizations, particularly High Reliability Organizations (HROs).
The paper uniquely focuses on the intersection of Complexity Science and Military Science by analyzing counterinsurgency and counterterrorism operations.
It emphasizes the importance of rapid reorganization, pooling collective expertise, and assembling novel organizational components as potential foundations for developing spontaneous expertise, actionable intelligence, and solutions to novel, emergent hazards.
The authors use the 2008 Mumbai attack as a case study to demonstrate how the rapid assembly of teams and successful counterinsurgency efforts are linked, and how Complexity Science can provide valuable insights into managing such threats.
The paper's findings have significant implications for future work and research in the field of conflict management and counterinsurgency operations.
By applying Complexity Science to analyze and understand the dynamics of complex threats, military and civilian organizations can develop more effective strategies and tactics to address novel, emergent hazards.
This approach can lead to the creation of more adaptive and resilient teams capable of responding to rapidly changing environments and threats.
Additionally, the paper highlights the need for further research at the intersection of information sharing system design, decentralized intelligence, and other related topics to enhance the effectiveness of counterinsurgency efforts in an increasingly complex world
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AIC v1_2.pdf
Active Inference in Modeling Conflict
The study of conflict and warfare has evolved over time, with models becoming increasingly abstract and context-informed.
Early quantitative models, such as the Lanchester model, employed mathematical tools like linear regressions and differential equations.
As research progressed, the understanding of human structures of information, cognition, organization, and interaction across various disciplines expanded, leading to more sophisticated models of conflict
The paper "Active Inference in Modeling Conflict" introduces the Active Inference Conflict (AIC) model, which builds upon the application of Active Inference (ActInf) to represent modern conflict and the BOLTS (Business, Operations, Legal, Technical, and Social) structures that interact within it.
The AIC model provides insights beyond simply projecting winners and losers in iterated games, shedding light on the nature of the BOLTS structures themselves and their objectives in reducing uncertainty in their niche
The AIC model has several implications for future research and technology development.
As human interactions increasingly depend on information landscapes, traditional institutions struggle to govern in non-physical domains.
The AIC model reveals that conflict can be viewed as a form of information generation for participating agents, with violent and non-violent interactions serving as means to reduce uncertainty.
This understanding can guide the development of new technologies and strategies to navigate and manage conflicts in the digital age, as well as inform future research on the evolution of conflict and its impact on human society
FaciliatorsCatechismPlaybook.pdf
The Facilitator's Catechism Playbook
In today's fast-paced and increasingly remote work environment, teams face challenges in synchronizing and ensuring that the right people have the right information at the right time.
High Reliability Organizations (HROs), such as special forces, aircraft carrier crews, and operating rooms, have developed and utilized Operations Orders (OPORDs) for thousands of years to manage complex tasks and maintain low failure rates.
One such OPORD format is the Facilitator's Catechism (FC), which is designed to address the needs of modern remote teams and improve organizational alignment, project comparability, reliability, and productivity.
The FC Playbook, produced by Daniel Ari Friedman, PhD, and R.J. Cordes, is based on the fourth chapter of the book "The Great Preset: Remote Teams and Operational Art".
The playbook provides a step-by-step guide on how to use the FC, which is an operations order formatted as a project management document.
The FC is built from battle-tested project management techniques used by national militaries and the Defense Advanced Research Projects Agency (DARPA). It aims to help remote teams increase alignment, project comparability, reliability, and productivity while reducing work-about-work.
The FC has the potential to greatly impact remote teams and organizations by providing a structured and adaptable framework for project management. It can be used and refined by teams across various sectors and stages, allowing for customization and integration with other project management tools and documentation.
By adopting the FC, teams can improve their ability to coordinate complex work across time zones, cultures, contexts, and perspectives, ultimately leading to better project outcomes and increased efficiency.
Future research and development in this area could focus on creating additional catechisms for specific use cases, as well as building tools that complement the use of catechisms, such as mapping them to various formats and connecting them to task tracking frameworks, project management systems, and CRM platforms.
NIE_21_Cordes_Friedman.pdf
Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier
Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier, edited by Richard J. Cordes and Daniel A. Friedman, is a collection of research papers that explore the challenges and opportunities in managing information and narratives in various domains.
The book is a product of the Cognitive Security and Education Forum (COGSEC) and aims to address the growing need for effective tools and methodologies to manage information in an increasingly complex and interconnected world.
The book is divided into four main sections, each focusing on a different aspect of narrative information management.
The first section, "Narrative Information Management," provides an integrative overview of the field and explores various disciplinary approaches to managing information.
The second section, "Digital Rhetorical Ecosystem Analysis," presents a model for analyzing online communication and addressing the ongoing epistemic crisis.
The third section, "Knowledge Management Archipelago," offers a literature meta-analysis of keywords and themes related to knowledge and information management.
The fourth section, "Active Inference in Modeling Conflict," proposes a new model for modeling conflict using active inference, a first-principles framework for action and perception.
The book's findings have significant implications for the future of information management, cognitive security, and interdisciplinary research.
By providing a comprehensive analysis of the challenges and opportunities in narrative information management, the book encourages further exploration and collaboration among researchers from various fields.
The proposed models and frameworks, such as the Digital Rhetorical Ecosystem model and the Active Inference Conflict model, offer new directions for future research and practical applications in managing information and addressing complex problems.
Additionally, the book highlights the importance of developing effective tools and methodologies to manage information in an increasingly complex and interconnected world, emphasizing the need for interdisciplinary collaboration and the synthesis of knowledge across various fields.
Innovators-Digital-Playbook.pdf
Innovator’s Digital Playbook
The Innovator's Digital Playbook, written by Monica H Kang, RJ Cordes, and Daniel Ari Friedman, addresses the challenges and opportunities of remote collaboration in the modern workplace.
The authors explore how online teams can be healthy, creative, and productive by focusing on trust, communication, and innovation.
The playbook is designed to help early- and mid-career professionals adapt to the changing landscape of work and improve their collaboration skills in the virtual and hybrid world
The playbook introduces a structured approach to remote collaboration, focusing on three main areas: mindset and approach when collaborating, igniting innovation as a group, and using the Innovator's Catechism (ICAT) as a tool for project documentation and team alignment.
The authors provide practical tips, questions, and guidelines to help teams build trust, set clear expectations, and foster innovation throughout the project lifecycle.
The Innovator's Catechism is a unique project documentation system that guides teams through the ideation, curation, and pitch phases, ensuring effective communication and alignment among team members
The Innovator's Digital Playbook has several implications for the future of work and research.
By providing a comprehensive guide to remote collaboration, it empowers professionals to adapt to the changing work environment and improve their skills in virtual and hybrid settings.
The playbook's emphasis on trust, communication, and innovation can lead to more effective and inclusive teamwork, ultimately resulting in better project outcomes.
Additionally, the Innovator's Catechism offers a valuable tool for project management and team alignment, which can be adapted and customized to suit various industries and team structures.
Overall, the playbook contributes to the growing body of knowledge on remote work and collaboration, providing actionable insights and strategies for professionals navigating the evolving workplace
ECOMEME v1.1.pdf
Digital Rhetorical Ecosystem Analysis: Sensemaking of Digital Memetic Discourse
Digital rhetoric, an emerging interdisciplinary field, focuses on the application of rhetorical theory to digital texts and performances, encompassing various forms of communication such as text, images, videos, and audio.
It draws from related fields like digital literacy, visual rhetoric, new media, human-computer interaction, and critical code studies.
The study of digital rhetoric involves the use of rhetorical strategies in the production and analysis of digital texts, identifying characteristics, affordances, and constraints of new media, and the formation of digital identities.
The integration of rhetorical and ecological approaches to studying digital discourse has gained traction in recent years, allowing researchers to trace multimedia rhetorical artifacts across platforms, media types, and languages.
The paper "Digital Rhetorical Ecosystem Analysis: Sensemaking of Digital Memetic Discourse" introduces a Digital Rhetorical Ecosystem three-tiered model (DRE3) to explain how memes impact public narratives and beliefs.
The study combines concepts from rhetoric, ecology, and complex systems analysis to develop this model.
The DRE3 model focuses on three key elements:
a) recognizing how parsimony and polysemy give image memes narrative power,
b) focusing on how image memes engage audiences through identity construction, and
c) applying "Rhetorical Ecosystem" mapping based on toolkit transfer and system design implications.
This approach aims to reveal how digital artifacts like image memes create, sustain, and disrupt public narratives and, thereby, socio-political dynamics.
The DRE3 model has significant implications for the design and development of systems for monitoring and analyzing digital discourse.
By understanding the dynamics of digital rhetorical ecosystems, researchers, policymakers, and educators can better comprehend the impact of digital artifacts on public narratives and beliefs. This knowledge can inform the development of tools and strategies to promote healthy digital discourse, counter misinformation, and foster critical thinking in online spaces.
Additionally, the DRE3 model can serve as a foundation for future research in digital rhetoric, leading to a deeper understanding of the complex interplay between digital artifacts, platforms, and socio-political dynamics.
NIM21 v1.1.pdf
Narrative Information Management
Narrative Information Management (NIM) is a concept that addresses the challenges of managing complex information across various domains, such as personal finance, ancestry research, hybrid cloud infrastructure security, neuroscience, and genomics.
NIM aims to facilitate the understanding, organization, and communication of information by leveraging narrative structures and techniques.
The need for NIM arises from the increasing complexity and volume of information in various fields, which can lead to cognitive overload and difficulties in decision-making.
By employing narrative techniques, NIM seeks to compress, synthesize, and manage information in a way that is more accessible and actionable for users.
The paper "Narrative Information Management" explores the application of NIM across multiple domains and identifies key features and insights that can be applied to improve information management.
The authors analyze the challenges, requirements, and ad hoc solutions related to managing narrative information in the aforementioned domains.
They identify several key aspects of NIM, such as managing information gaps, compression of information, case management, prescriptive information, synthesizing intelligence, and facilitating communication.
The paper highlights the need for more tool and methodology transfer between fields, as well as the importance of trust and structure in managing complex information.
The implications of the paper on NIM are far-reaching, as it suggests potential avenues for future research and development in information management across various domains.
By identifying common challenges and solutions, the paper encourages interdisciplinary collaboration and the sharing of tools and methodologies.
This could lead to the development of more effective and efficient information management systems, ultimately reducing cognitive overload and improving decision-making processes.
Furthermore, the insights provided by the paper can inform the design of new technologies and platforms that better support users in managing complex information.
By fostering a deeper understanding of narrative structures and techniques, NIM has the potential to transform the way we approach information management in our increasingly complex world.
C3PO.pdf
Collaborative Writing for Catechism-Based Teams
Asynchronous and remote collaborative writing projects in interdisciplinary teams can be highly productive and enjoyable, as they bring together diverse perspectives, personalities, and expertise to rapidly produce written deliverables.
However, such collaborations can also be challenging due to issues like managing deadlines, handling disputes, communication, staying on mission, and collective editing.
To address these challenges, a catechism-styled operations order and the use of a team facilitator can greatly improve the likelihood of success by ensuring alignment on protocol and etiquette among team members
The paper presents a set of procedures, processes, and protocols that can help interdisciplinary teams avoid derailment during collaborative writing projects or even before they begin.
These guidelines cover various stages of a project, including before the project starts, during the project, and after the project ends. They also provide recommendations on etiquette to ensure smooth collaboration and effective teamwork.
Some key aspects of the guidelines include reading the catechism, being aware of expectations, submitting resources, converging on a team writing approach, making distress calls, documenting changes, and asking for feedback.
The proposed procedures and protocols can have significant implications for interdisciplinary teams working on collaborative writing projects.
By following these guidelines, teams can prevent misunderstandings, stay on schedule, and increase the likelihood of producing high-quality deliverables.
Furthermore, these guidelines can help build a shared language and understanding among team members, fostering better collaboration and communication.
Future work and research in this area could focus on refining these guidelines, exploring their effectiveness in various contexts, and developing tools or platforms that facilitate the implementation of these protocols in collaborative writing projects
KnowledgeManagementArchipelago_1_0.pdf
Knowledge Management Archipelago
The findings of this paper suggest that there is an archipelago of partially connected "islands" in the knowledge management space.
The state of the literature indicates a need for synthesis across these domains and areas of expertise to benefit from each other's research and reduce the likelihood of redundant work.
Potential avenues for synthesis include restoring prominence to existing keywords, creating new keywords, encouraging interdisciplinary communities of practice, developing new tools, and raising awareness of the similarities and opportunities for synergy across fields.
These efforts could help improve knowledge sharing capabilities, foster interdisciplinary collaboration, and ultimately lead to better-performing systems in various sectors
The paper "The Knowledge Management Archipelago" presents an exploratory bibliometric analysis of various research areas that share concerns, approach, and scope in common with knowledge management.
The authors used search strings associated with selected areas of research to query Google Scholar in various combinations, quantifying and visualizing the results.
The analysis revealed variable couplings and differential prevalence of keywords, serving as a starting point for targeted analyses and next steps in understanding the connections and fragmentation within the KM literature
Knowledge management (KM) is a multidisciplinary field that has evolved over the past three decades, addressing challenges such as synthesizing, interpreting, and managing large streams of information.
In the age of the internet, these challenges are no longer confined to professional disciplines and are present in everyday life. The field shares concerns and approaches with various other areas of research, some of which preceded its formalization as a field.
This commonality and timelessness of concerns present a potential problem for KM, as it often seeks to address the creation of silos or "islands" in the knowledge base
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ECOMEME2-v1.0.pdf
Tracking Public Sensemaking through Rhetorical Annotation of Image Memes
Political polarization and declining trust in institutions have led to societal destabilization and radicalization.
Image memes play a significant role in public sensemaking, discourse, and the emergence of public beliefs. However, they are challenging to collect, classify, and analyze in aggregate due to their diverse formats and the complexity of their content.
As a result, there is a need for a deeper understanding of how beliefs emerge and crystallize, as well as improved connectivity in the work of interdisciplinary teams and organizations to reduce bias and partisanship in collection and analysis.
The paper "Tracking Public Sensemaking through Rhetorical Annotation of Image Memes" proposes a rhetorical annotation approach to analyze image memes, focusing on their communicative function as quasi-arguments in public discourse.
The authors recommend applying the Toulmin model of argument analysis to trace public argumentation performed by image meme circulation.
They also discuss the challenges of performing image meme collection and analysis within the context of emergent, interdisciplinary teams and provide requirements and recommendations for alleviating these challenges.
The paper's findings have significant implications for understanding the role of image memes in shaping public beliefs and discourse. By analyzing image memes through a rhetorical annotation approach, researchers can gain insights into their persuasive influence and the mechanisms through which they propagate misinformation and counter-narratives.
This knowledge can inform the development of targeted interventions and strategies to address the spread of misinformation and restore trust in institutions.
Additionally, the paper's recommendations for interdisciplinary teams and organizations can help improve the efficiency and effectiveness of image meme collection and analysis, ultimately contributing to a better understanding of the complex dynamics of public sensemaking in the digital age.
Future work and research could focus on developing computational systems for rhetorical annotation and analysis of image memes and exploring the ethical, legal, and privacy implications of collecting and analyzing social media information.
COGSEC2022-StructuringtheInformationCommons.pdf
Structuring the Information Commons: Open Standards and Cognitive Security
In the age of information, managing and structuring knowledge has become increasingly important. The concept of Narrative Information Management (NIM) has emerged as a way to facilitate the organization and sharing of information across various domains .
NIM focuses on the user experience, relevance, and relationships between different pieces of information, as well as the incentives and potential damage that user contributions may bring to the knowledge base.
The need for consensus, governance, and trust mechanisms in contributions is essential to prevent a tragedy of the commons, where valuable historical data becomes unusable due to a lack of proper management.
The book "Structuring the Information Commons: Open Standards and Cognitive Security" addresses the challenges and opportunities in NIM.
It introduces user experience (UX) design features that allow users to scope their information environment based on relevance, relationships, and degrees of separation between objects.
The book also discusses the importance of universal entity identifiers that enable users to rapidly develop surfaces of agreement, even when they do not agree on all facts or interpretations associated with content.
Furthermore, it emphasizes the need to consider consensus, governance, and trust mechanisms in contributions to prevent the tragedy of the commons in various domains, such as ancestry research and amateur genealogy.
The contributions of this book have significant implications for the future of information management and cognitive security.
By providing a framework for structuring and managing information, it enables more effective collaboration and knowledge sharing across different domains.
The book also highlights the importance of considering user incentives and potential damage to the knowledge base, which can inform the development of better governance and trust mechanisms in various fields.
Future research and work in this area can build upon the concepts and methodologies introduced in the book to further improve information management, cognitive security, and the overall user experience in accessing and sharing knowledge.
VIE-IG_1.pdf
TrustFinder: Recommendations for a Community-Based System for Finding Trusted Sources and Evaluating Claims
The rapid growth of digital information has led to the need for efficient systems to manage, synthesize, curate, and search through vast amounts of data.
In response, the paper "Narrative Information Management" identifies key features that such systems should possess, including managing information gaps, facilitating situational awareness, providing descriptive and explanatory information, and compressing complex information structures.
The paper also discusses the importance of understanding and addressing the cognitive aspects of information management, such as the role of emotions, anecdotes, and narratives in shaping people's understanding and decision-making processes.
"TrustFinder" is a novel system introduced in the paper that aims to address the challenges of managing and navigating digital information.
The system combines the contributions of Blue and Red contributors, who focus on evidence and logic, with those of Green contributors, who emphasize the evocation of emotion, anecdotes, and narrative.
By integrating these diverse perspectives, TrustFinder maps an emergent, stigmergic memetic landscape, linking disparate concepts from multimodal digital media and providing a unique form of situational awareness around a topic.
The paper also highlights the importance of addressing information gaps, facilitating situational awareness, and providing descriptive and explanatory information in the design and implementation of information management systems.
The development of TrustFinder has significant implications for the future of information management and cognitive security.
By combining diverse perspectives and approaches, TrustFinder offers a more comprehensive and nuanced understanding of complex information landscapes, which can inform decision-making processes and help users navigate the ever-growing digital world.
Future research in this area could explore ways to further refine and expand the system, incorporating additional perspectives and methodologies to enhance its effectiveness.
Additionally, the principles and techniques outlined in the paper could be applied to other domains, such as knowledge management, cognitive security, and the development of AI systems that can better understand and respond to the complexities of human cognition and behavior.
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ATLAS
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NTIA_6-11-23_IRSIRI-AII-PIVOT-COGSEC.pdf
Comments on AI Accountability Policy Submitted to NTIA Docket 2023-0005-0001 by IRSIRI, AII, PFH, and COGSEC
Artificial Intelligence (AI) technologies have been rapidly advancing, leading to increased concerns about their potential risks and ethical implications.
As a result, there have been numerous calls for regulation, ethical frameworks, and even full halts to continued research on AI.
However, due to the diverse nature of AI technologies and their applications, it is challenging to create a comprehensive regulatory framework that would not generate negative externalities or new conflicts.
Instead, focusing on specific sectors and use-cases, as well as addressing the underlying data and actors involved in AI systems, may provide a more practical approach to AI accountability
The paper submitted by the University of Washington APL Information Risk and Synthetic Intelligence Research Initiative (IRSIRI), Active Inference Institute (AII), Pivot for Humanity (PFH), and Cognitive Security and Education Forum (COGSEC) to the National Telecommunications and Information Administration (NTIA) provides recommendations for AI accountability policy.
The authors argue that blanket regulation of AI technologies is inappropriate and suggest focusing on facilitating professional regulation, data reference standards, and insurance.
They emphasize the importance of sector-specific approaches, addressing the challenges related to data sourcing and labeling, and considering insurance mechanisms to manage risks associated with AI systems
The paper's recommendations have significant implications for the future of AI regulation and policy.
By focusing on sector-specific approaches and addressing the underlying data and actors involved in AI systems, policymakers can create a more effective AI accountability ecosystem.
This approach can help reduce regulatory ambiguity, diversity in use-cases and agents, and ambiguity of harms and agents.
Furthermore, the development of professional regulation, data meta-standards, and insurance mechanisms can provide a foundation for addressing common risks shared by multiple stakeholders across various AI systems.
The paper also highlights the potential role of NTIA as a facilitating and convening authority in this process, given its mission and history
TAAB-P3IF_v1_10.5281_zenodo.10034512.pdf
The Properties, Processes, and Perspectives Inter-Framework (P3IF): Multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security
Requirements engineering frameworks have historically focused on technical and operational aspects of data security within individual organizations. However, the proliferation of interdisciplinary, multi-organizational systems has created a need for frameworks that can manage information risk across domains.
This paper explores how frameworks facilitate requirements engineering for complex information systems. It analyzes the relationships between common frameworks used today, revealing limitations in their ability to account for emerging interoperability needs.
The healthcare domain illustrates these challenges, as clinical and public health decisions depend on multi-step information flows vulnerable to misinformation. Securing the integrity of evidence-based decisions is critical, but differs from traditional cybersecurity perspectives. This context motivates the need for practical methods to blend insights from isolated frameworks.
This paper makes three key contributions.
First, it surveys requirements frameworks, analyzing their form, function, and evolution over time.
Second, it categorizes framework dimensions into Properties, Processes, and Perspectives, finding these encompass all attributes.
Third, it proposes the Properties, Processes, and Perspectives Inter-Framework (P3IF) as a modular abstraction layer.
Rather than replacing frameworks, P3IF enables multiplexing factors from different frameworks into customized combinations matched to emerging interdisciplinary contexts. This provides shared vocabulary and risk management without continual framework replacement.
The P3IF approach has several important implications. It allows frameworks to remain specialized while gaining interoperability, facilitating cross-domain collaboration.
Organizations can adaptively select relevant factors to manage new vulnerabilities at framework intersections. P3IF also expands considerations beyond cybersecurity to cognitive security, enhancing decision integrity across information pipelines.
Further work can explore P3IF applications, integrate additional frameworks, and study effectiveness in securing complex, distributed decisions. Overall, P3IF enables more comprehensive, evolving frameworks to meet modern interdisciplinary information system challenges.

Meta-Science
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PPPiP_2018_Mikhailova_Friedman.pdf
"Partner Pen Play in Parallel (PPPiP): A New PPPiParadigm for Relationship Improvement"
Healthy romantic relationships contribute to human physical health and emotional well-being. However, the rise of technology has introduced new challenges and opportunities for human intimacy.
Technologies that catalyze human sexuality, such as silicone sex toys and video-conferencing, are increasingly common, and disruptive sexological artifacts like sexbots are speculated to eventually compete directly with human-human sexuality.
The consequences of these evolutionary transitions in human sociosexual behavior are unknown at the individual or collective scale. In this context, researchers are exploring new strategies for relationship development that can adapt to the changing landscape of human intimacy.
The paper "Partner Pen Play in Parallel (PPPiP): A New PPPiParadigm for Relationship Improvement" by Alexandra Mikhailova and Daniel A. Friedman introduces PPPiP, the act of simultaneous improvisational drawing on paper without clinical supervision.
PPPiP combines the advantages of individuated artistic practice with established frameworks of improvisation and dyadic relationship interventions.
It is less clinically oriented, features fewer external constraints, and directly encourages the dynamic integration of artistic creation with relationship co-creation compared to traditional art therapy practices.
The paper provides interdisciplinary evidence from art therapy, sexology, affective neuroscience, and aesthetics to support PPPiP as a useful strategy for relationship development.
PPPiP has several potential implications for the future of relationship improvement and research. It offers a low-cost, non-gendered, and accessible technique that uses artistic creation as collective self-therapy.
By promoting joint attention, neural synchrony, partner improvisation, controlled novelty, and aesthetic benefits, PPPiP may enhance intimate relationships in a world increasingly influenced by technology.
Furthermore, PPPiP represents a transdisciplinary answer to the question of what we will carry from our sociosexual past towards a healthier textosexual future.
Future work and research can explore the effectiveness of PPPiP in various relationship contexts, its impact on mental health, and its potential integration with other therapeutic modalities.
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ALIUS_bulletin03-dennett_2019.pdf
Dennett Explained
Throughout his career, Professor Daniel Dennett has been known for integrating ideas from various fields, such as academic philosophy, artificial intelligence, and cognitive science, while engaging with unconventional thinkers like Julian Jaynes and J.J. Gibson.
Dennett has been influential in promoting interdisciplinary approaches to understanding consciousness and the mind, often challenging traditional views and incorporating empirical findings from neuroscience and psychology into his philosophical work.
In the attached interview, Dennett discusses his philosophical roots, thoughts on Freud, predictive processing, psychedelics, consciousness, and ancient Athens.
He emphasizes the importance of philosophers engaging with scientific research and contributing to the understanding of the mind, as well as the potential value of psychoactive drugs in scientific and therapeutic contexts.
Dennett's work has been instrumental in bridging the gap between philosophy and science, fostering cross-disciplinary collaboration, and inspiring new approaches to studying consciousness and cognition.
Dennett's work has far-reaching implications for the study of consciousness and the mind, as it encourages interdisciplinary collaboration and challenges traditional views in both philosophy and science.
His ideas have paved the way for new research directions, such as the predictive processing paradigm and the integration of Freudian concepts into contemporary theories of consciousness.
Furthermore, Dennett's emphasis on the importance of philosophers engaging with empirical research has contributed to a more holistic understanding of the mind and its underlying processes.
As a result, his work continues to inspire future research and collaboration across various fields, ultimately advancing our understanding of consciousness and cognition.
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Tamari_Friedman_et_al_2022.