docxology

Maintain and extend the docxology public GitHub Pages static site (danielarifriedman.com)

We study a minimal Active Inference stack on toy models: a Bernoulli–Ising analytical oracle, a pymdp T-maze rollout, and a sheaf-indexed compose contract that binds 34 fragment tracks into 12 flat IMRAD sections. The methodological contribution is a...

<p>Synthetic Analytic Tradecraft (AGEINT, or Agentic Intelligence), is a local curriculum-and-assurance atlas for teaching bounded AI-agent support inside intelligence education by making the machinery of Synthetic Analytic Tradecraft visible on the ...

Use for Autopoietic Project Generation, a paired GitHub and Zenodo publication with DOI 10.5281/zenodo.21227869.

CogSecSkills is a defensive, harness-neutral agent-interface library that turns the human doctrine of cognitive security and analytic tradecraft into dependable, inspectable, agent-usable skills, distributed as an open repository from github.com/docx...

This paper presents a convergence study of fixed-step gradient descent on a convex quadratic, framed as the computational exemplar of the Research Project Template (https://github.com/docxology/template). The implementation lives in projects/template...

This paper describes a small, tested domain language for specifying controlled methods — the methods-paper exemplar of the Research Project Template (https://github.com/docxology/template). Unlike a results paper, this manuscript's subject is the met...

Use for DuckRabbit: Typed Multimodal Illusion Generator, a paired GitHub and Zenodo publication with DOI 10.5281/zenodo.21419693.

This paper documents template_prose_project, the prose-focused exemplar of the Research Project Template (https://github.com/docxology/template). It pairs the template's two-layer architecture with the prose analysis infrastructure (https://github.co...

Use for Entomological Law: A Field Map of Insects as Evidence, Threat, Property, Product, Patient, and Weapon, a paired GitHub and Zenodo publication with DOI 10.5281/zenodo.21137276.

Exploratory data analysis (EDA) is the most common entry point in applied research, yet it is also where reproducibility most often breaks down: logic accumulates in notebook cells that are never tested and quietly drift from the prose describing the...

Manual synthesis cannot keep pace with a fast-growing research literature, and ad-hoc reviews bind no evidence to a reproducible pipeline. We present a configurable, reproducible meta-analysis framework that takes a single search term and produces a ...

Use for Prior Cognitive Art, a paired GitHub and Zenodo publication with DOI 10.5281/zenodo.21316510.

This exemplar documents template_sia, a deterministic implementation of the Self-Improvement Agent (SIA) harness contract described in . The default pipeline replays fixture-backed generations for the mini_classify task; opt-in live mode runs bounded...

Use for The Shape Between: A Full-Page Illustrated Storybook Template, a paired GitHub and Zenodo publication with DOI 10.5281/zenodo.21176000.

How should you choose the judges, jurors, or reviewers who form a panel — and does that upstream choice change how well you can evaluate them without an answer key? A panel can be selected many ways — by competence, by a representative lottery (sorti...

The reproducibility crisis in computational research is fundamentally structural: research artifacts are scattered across disconnected tools—LaTeX editors, Jupyter notebooks, ad-hoc shell scripts—with no enforced mechanism to keep code, data, and man...

Use for template_pitch_deck: Reproducible, Validated Pitch-Deck Generation, a paired GitHub and Zenodo publication with DOI 10.5281/zenodo.21281509.

"A modular, fillable scaffold for book-length technical works: a data-driven manuscript (parts/chapters/labs/questions), a tested computational backbone, deterministic figures and Mermaid diagrams, and a content scaffold/validation engine. --- Associa..."

Hypothesis linking Ehrlichia/Anaplasma intracellular parasitic bacteria to leukemia and immune disorders, with clinical evidence for Rifampin treatment

A key question in evolutionary biology concerns how novel traits arise at the molecular level. Honey bees (Apis mellifera) have evolved numerous postdevelopmental novel traits, including royal jelly...

The behavioral repertoire and ecology of ant colonies emerge from the interactions among individuals, each with distinct genetic, epigenetic, and physiological states. Genetic approaches are beginning...

Previous work has found that workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulati...

Ionizing radiation causes DNA double-strand breaks and disrupts chromatin architecture, potentially leading to chromosomal aberrations and genomic instability. Chromosome conformation capture (3C) tec...

The development of CRISPR/Cas9-mediated gene knockout in two ant species opens a new window into exploring how social insects use olfactory cues to organize their collective behavior. In this issue of...

Dependent-lineage ant species challenge conventional assumptions about colony genetic structure and its relationship to colony-level behavior. In dependent-lineage species, queens must mate with males...

Argentine ants (Linepithema humile) are one of the world's most widespread invasive species, forming massive supercolonies spanning hundreds of kilometers. Here we examine the relationship between the...

Individual behavioral variation within colonies is shaped by neurochemical signaling. Dopamine is a key neuromodulator associated with locomotion, arousal, and reward across taxa. Here we investigate...

How can we formalize the evolution of heredity, environment, and phenotype through time and across biological levels? This presentation introduces the Multilevel Variational Ecology and Evolution (MVE...

Healthy romantic relationships contribute to human physical health and emotional well-being. Here we introduce Partner Pen Play in Parallel (PPPiP), the act of simultaneous improvisational drawing on...

In this interview, Karl Friston discusses the origins and implications of the Free Energy Principle (FEP), from childhood observations of woodlice to a comprehensive framework for understanding cognit...

Here we address the scientific study of consciousness by proposing the ant colony as a model system. We introduce the Ant Colony Test (ACT) as a rigorous reverse test for consciousness, showing that s...

Red harvester ant colonies must spend water to obtain water: colonies lose water as workers forage outside the nest, and gain water through seeds collected. Here we present field experiments showing t...

Behavior engineering applies structured approaches from systems engineering to the understanding and management of behavior at individual and collective scales. This paper proposes frameworks for conn...

Ant colonies regulate collective behavior through interactions among individual workers, creating colony-level physiological processes that are distributed across all individuals. We examine how this...

Historical and futures-oriented analysis of operations orders (OPORD) for organizational sensemaking, leading to a catechism-style OPORD format for process facilitators in military, intelligence, and civilian teams.

Gene expression differences among workers performing different tasks are a key mechanism underlying division of labor in social insects. Here we characterize transcriptomic profiles of foragers compar...

This essay examines what the Great Reset means from a cognitive security perspective, analyzing how global socioeconomic narratives shape public belief and behavior. Through the lens of Active Inferen...

Infinite Games for Infinite Teams was published by and in response to the DARPA Polyplexus Citizen Incubator: &ldquo;Inventing a Remote Culture to Deal with Pandemics&rdquo;, and was done so with the intent of discussing the questions outlined below....

Innovation teams formed in incubators, research accelerators, hackathon weekends, and within organizations need to quickly align on narrative, workflow, and objectives. Many of these teams fail due to...