Research

Our work combines project incubation, working groups, and collaborative research across academic, civic, and industry partners.

Programs and Initiatives

Data x Direction

Examining how data science practices and tools intersect with ethical decision-making, human-centered AI, and governance frameworks.

Developmental AI

Open-source computational biology, neuroscience, and AI research training

From Here to There: Strategy and Mentorship for Innovators

Exploring emerging narratives, directionality, and the future of human experience

DigiNEST

Digital Narratives and Emerging Story Technologies (DigiNEST). A discussion series exploring how digital tools reshape narrative, authorship, and agency.

Joint Open Source Summer Cohort

A collaborative summer cohort across OREL, DevoWorm, and JOPRO — open-source contribution, instruction, and professional development, anchored by Google Summer of Code.

SMN @ OREL

Originally "Saturday Morning NeuroSim", Orthogonal Research and Education Lab weekly public session is a unique space for projects from across the lab network.

Open-source Sustainability

A multi-year initiative investigating the long-term health and sustainability of open-source communities through agent-based modeling, active inference, and cybernetic approaches.

CFRG

The Cognition Futures Reading Group explores concepts, methods, and opportunities in diverse intelligences (natural and artificial), phenomenology, and contemporary discussions on minds

Inactive

Cybernetics Discussion Series

Since the 1940s, cybernetics has had its own summers and winters. We explore theory, applications, and history of cybernetics & related fields.

Inactive

Projects

Towards an Ontological Taxonomy of Information Affordances

Theory and case study converted into heuristic prompts and appropriate tool routing towards relevant external representations of information

Cognitive ScienceEmbodied IntelligencePhenomenologyPsychology

Ethical Policy Analyzer

Towards standardizing and increased transparency in ESG reporting

Data EthicsArtificial Intelligence

Field Guide to Futures Ecosystem

Cartography of next-generation foresight organizations

FuturesResearch Management

Vizualizating Experience of Mental Health Models

Examining cultural bias in dominant mental health frameworks

Mental HealthPsychology

JOPRO & the New Learning Ecosystem

Contextual, developmental, and trajectory-aware learning in interdisciplinary spaces

EducationLeadershipProfessional DevelopmentResearch Management

Permanent Crisis / Kuhn Update

Temporal collapse of Kuhn's model of scientific revolutions

PhilosophyResearch Management

Something In The Way

Ethnography of 21st century directionlessness

Digital HumanitiesEducationEthnographyPhenomenologyPhilosophyPsychology

Steelmanning the Problem Space

Methodology for rigorous collaborative problem definition

Research ManagementPhilosophy

Reimagining Cybernetics

Artificial IntelligenceComplexityEmbodied Intelligence

Hegemonic Bias of Mental Health Conventions

Examining cultural bias in dominant mental health frameworks

Mental HealthPsychology

LLAMOSC: LLM Agent-Based Modeling for Open Source Communities

A framework that pairs Large Language Models with agent-based modeling to simulate and sustain open-source communities.

Artificial Intelligence

Mind/Brain Analogies & Technological Development

Historical and cross-cultural investigation of how societies analogize the mind, and how those analogies track technological change

Cognitive SciencePhilosophyHistory of Science

Spatial Cognition & Virtual Reality

Exploring how virtual environments reshape spatial cognition, cognitive mapping, and philosophical questions about realism

Cognitive ScienceEmbodied IntelligenceNeuroscience

Cognition Futures Paper Series

Affordance perception as a common currency of embodied intelligence

Cognitive ScienceEmbodied IntelligencePhenomenology

D-GNNs: developing DevoGraph for computational developmental biology

BiologyComputer VisionDevelopmental Biology

Developomental-AI

Dev-AI: Developmental approaches and components squared with machine learning and computation

Artificial IntelligenceComplexityEmbodied Intelligence

Embodied Neurophenomenology

First-person experience, embodiment, and the structure of consciousness

Cognitive ScienceEmbodied IntelligenceNeurosciencePhenomenologyPsychology

FrontierMap

Mapping concept trajectories and field landmarks for emerging researchers

Artificial IntelligenceEducationResearch Management

PhASiC

Physical Intelligence, Augmentation Systems, and Complexity

Artificial IntelligenceComplexityEmbodied Intelligence

Allostatic Kinds

A taxonomy of permutations of subject-object directionality in causation

Agential ModelingAllostatic KindsCognitive Science

DevoTG: Dynamic Graph Neural Networks for Modeling C. elegans Development

Dynamic graph neural networks for modeling the temporal development of the C. elegans embryo.

BiologyArtificial IntelligenceDevelopmental Biology
Completed

NDP-HNN: Modelling Neural Developmental Programs of C. elegans Using Growing Hypergraph Neural Networks

Growing hypergraph neural networks for modeling the neural developmental programs of C. elegans.

BiologyArtificial IntelligenceDevelopmental Biology
Completed

SustainHub: Adaptive Agent-Based Model for Open-Source Community Sustainability

An adaptive agent-based model for studying and supporting the sustainability of open-source communities.

ComplexityArtificial Intelligence
Completed

Exploring Open Source Sustainability via Agent-based Modeling

Agent-based modeling approaches to understanding the long-term sustainability of open-source communities.

ComplexityArtificial Intelligence
Completed

Virtual Reality for Distributed Research

Virtual reality tools and environments to support distributed, collaborative research.

RoboticsArtificial Intelligence
Completed

D-GNNs: DevoGraph for Computational Developmental Biology

Graph neural networks for modeling developmental biological processes

BiologyArtificial Intelligence
Completed

Agent-based Collective Cognition for Open Source Communities

Agent-based models of collective cognition applied to open-source community dynamics.

ComplexityArtificial Intelligence
Completed

Digital Microsphere

Building the Digital Microsphere for modeling early embryonic development.

BiologyDevelopmental BiologyComputer Vision
Completed

Ethical Regulators for Open Source Communities

Applying the ethical regulator theorem to the governance of open-source communities.

ComplexityArtificial Intelligence
Completed

GNNs as Developmental Networks

Treating graph neural networks as models of biological developmental networks.

BiologyArtificial IntelligenceDevelopmental Biology
Completed

Modeling Axolotl Embryos

Computational modeling of axolotl embryo development within the Digital Microsphere effort.

BiologyDevelopmental BiologyArtificial Intelligence
Completed

Reinforcement Learning and Collective Cognition for Open Source Communities

Reinforcement learning approaches to collective cognition in open-source communities.

ComplexityArtificial Intelligence
Completed

Sustainability Auditing Tool (SAT)

A web-based auditing platform for evaluating the long-term sustainability and community health of open-source projects.

Completed

Improving DevoLearn

Extending and improving the DevoLearn library for computational developmental biology.

BiologyArtificial IntelligenceDevelopmental Biology
Completed

BraGenBrain

Braitenberg Vehicles Genetic Algorithms Simulation of Neural Development

Embodied IntelligenceArtificial IntelligenceBiologyComplexityRobotics
Completed

OpenDevoCell Integration

Integrating and extending the OpenDevoCell platform for cell-level developmental analysis.

BiologyDevelopmental BiologyComputer Vision
Completed

Pre-trained Models for Developmental Neuroscience

Developing pre-trained machine learning models for developmental neuroscience tasks.

BiologyArtificial IntelligenceDevelopmental Biology
Completed

Modeling Neural Development with Braitenberg Vehicles

Evolving embodied neural networks in Braitenberg vehicles to study brain development and connectome motifs

Embodied IntelligenceArtificial IntelligenceBiologyComplexityRobotics
Completed

Semantic Segmentation of the Embryogenetic Process

Semantic segmentation of microscopy data capturing the embryogenetic process.

BiologyComputer VisionDevelopmental Biology
Completed

Contextual Geometric Structures

Modeling contextual geometric structures for representing information and cognition.

Artificial IntelligenceComplexity
Completed

Developmental Networks and XML Frameworks for the C. elegans Embryo

Developmental network models and XML data frameworks for the C. elegans embryo.

BiologyDevelopmental Biology
Completed

Image Processing with ImageJ (Segmentation of High-Resolution Images)

ImageJ-based processing and segmentation of high-resolution developmental microscopy images.

BiologyComputer VisionDevelopmental Biology
Completed

Publications

Paper 2026

A 'good' regulator may provide a world model for intelligent systems

Philosophical Transactions of the Royal Society A DOI
Preprint 2026

Landscape of Futurists: Toward a Cartography of Next-Generation Foresight Organizations

History of Science
Preprint 2025

The Augmentation of Intelligent Agents for Human-Machine Superperformance

OSF Preprints
Review 2024

Alicea reviews 'The Open Dynamics of Braitenberg Vehicles' by Hotton and Yoshimi

CogNet / MIT Press
Cognitive ScienceEmbodied IntelligenceArtificial Intelligence
Presentation 2024

Developmental Neurosimulation as a Route to Embodied Morphogenetic-inspired Intelligence

Embodied Intelligence 2024 (Self-Organized Systems track)
Embodied IntelligenceDevelopmental BiologyNeuroscienceRobotics
Presentation 2024

"The Mind as a '___'": Past, Present, and Futures of Analogies of Mind & Brain and its Relationship to Technological Development

Embodied Intelligence 2024
Cognitive SciencePhilosophyHistory of ScienceEmbodied Intelligence
Presentation 2024

Navigating Reality: Exploring Spatial Cognition, Virtual Environments, and Philosophical Implications

Embodied Intelligence 2024 (Morphological Computation track)
Cognitive ScienceNeuroscienceEmbodied IntelligencePhilosophy
Paper 2024

The Augmentation of Intelligent Agents for Human-Machine Superperformance

Studies in Computational Intelligence, 1243, 44–51
Preprint 2024

A Brief History of Cybernetic Imperatives and Behavior

PsyArXiv DOI
Paper 2024

Continual Developmental Neurosimulation Using Embodied Computational Agents

IOP Conference Series: Materials Science and Engineering, 1321, 012013
Paper 2024

An Ensemble Approach to the Origin of Life

Origin of Life via Archaea, Chapter 8 DOI
Presentation 2024

LLAMOSC Framework: LLM/ABM Hybrid Models

OREL Medium
Paper 2024

The Molecular Basis of Differentiation Wave Activity in Embryogenesis

BioSystems, 105272
Preprint 2024

A Primer on Gibsonian Information

arXiv:2403.18829
Presentation 2023

Landscapes and Learning Objectives: FrontierMap and the Challenges of Imbuing Contextual Nuance into Research Practices

Hyperdigital Designs, University of Cambridge
EducationResearch Management
Presentation 2023

Key Concepts in Tech Careers and Tech Ethics in 2023

ACM NYCWiC 2023
EthicsGenerative AILaw PolicyOpen Source
Paper 2023

Open-source Community Sustainability using Agent-based Models

Cognitive ScienceEmbodied IntelligenceArtificial Intelligence
Paper 2023

AI and Equality: a Multidisciplinary Approach to Confronting AI Bias

Artificial IntelligenceEthicsLaw Policy
Paper 2023

Alicea reviews "The Open Dynamics of Braitenberg Vehicles" by Hotton and Yoshimi

Agential ModelingArtificial IntelligenceCognitive ScienceEmbodied Intelligence
Paper 2023

Embodied Cognitive Morphogenesis as a Route to Intelligent Systems

Royal Society Interface Focus, 20220067
Preprint 2023

Hypergraphs Demonstrate Anastomoses During Divergent Integration

arXiv:2311.17067
Presentation 2023

Updates from the OpenWorm Project: Incorporating NeuroPAL Data and ASH Neuron Electrophysiological Recordings

International C. elegans Conference, Glasgow, Scotland
Paper 2023

Our Virtual Lives and Digital Companionship: Opportunities and Challenges of Shared Experience in an Augmented Century

Digital HumanitiesEducationMental Health
Book Chapter 2023

The Psychophysical World of the Motile Diatom Bacillaria Paradoxa

Mathematics and Biology of Diatoms, Chapter 9 DOI
Paper 2023

Super-performance: sampling, planning, and ecological information

Studies in Computational Intelligence, 1130, 33–40
Paper 2022

Towards Sharing Cognitive Environments: Methodology and Theory

WeRobot 2022
Cognitive ScienceEmbodied IntelligenceAssistive TechnologyDisability StudiesPhenomenologyNeurotechnology
Paper 2022

Our Virtual Lives and Digital Companionship: Opportunities and Challenges of Shared Experience in an Augmented Century

WeRobot 2022
Digital HumanitiesEducationMental Health
Paper 2022

Braitenberg Vehicles as Developmental Neurosimulation

Artificial Life, 28(3), 1–27 DOI
Preprint 2022

DevoLearn: Machine Learning Models and Education that Enable Computational Developmental Biology

INCF / DevoLearn
Paper 2022

Flipping the Switch on Local Exploration: Genetic Algorithms with Reversals

Proceedings of the Conference on Intelligence Systems
Presentation 2022

Game Theory of Developmental Processes

Dynamics Days 2022, Atlanta, GA
Report 2022

Game Theory of Developmental Processes

ResearchGate
Paper 2022

Gibsonian Information: A New Approach to Quantitative Information

Studies in Computational Intelligence, 1032, 15–19
Paper 2022

Intelligence Offloading and the Neurosimulation of Developmental Agents

IOP Conference Series: Materials Science and Engineering, 1292, 012019 (International Workshop on Embodied Intelligence)
Paper 2022

Layers, Folds, and Semi-Neuronal Information Processing

Procedia Computer Science, 213, 443–452
Presentation 2022

Mathematics of DevoWorm

Find Your Inner Modeler V, University of Illinois–Chicago
Paper 2022

Meta-brain Models: Biologically-inspired Cognitive Agents

Proceedings of the Embodied Intelligence Workshop, 20
Presentation 2022

Research Methods in Cognition Studies & Phenomenology: Challenges and Opportunities

Neuromatch 5
Cognitive SciencePhenomenologyEmbodied Intelligence
Presentation 2022

Terminology & Taxonomy: of Agent-Environment Analyses & Recent Work at Orthogonal Research and Education Lab

International Conference on Embodied Intelligence 2022
Agential ModelingCognitive ScienceEmbodied Intelligence
Preprint 2021

Allostasis Machines: a model for understanding internal states and technological environments

PsyArXiv DOI
Agential ModelingAllostatic KindsCognitive Science
Paper 2021

Mapping Cyborg Cognition Futures: From Partitioned Pasts to a Symbiotic Century

Conference on Artificial Life (ALIFE 2021), Prague
Cognitive ScienceEmbodied IntelligenceArtificial Intelligence
Presentation 2021

Allostatic Kinds: Towards a Taxonomy of Permutations of Subject-Object Directionality in Causation

Agential ModelingAllostatic KindsCognitive Science
Paper 2021

Data-theoretical Synthesis of the Early Developmental Process

Neuroinformatics DOI
Presentation 2021

Neuromorphogenetic Patterns and the Theory of Deep Learning

NetNeuro Satellite, Networks Conference
Presentation 2021

The OpenWorm Project: Progress Update, Available Resources and Future Plans

International C. elegans Conference (Virtual)
Paper 2021

Periodicity in the Embryo: Emergence of Order in Space, Diffusion of Order in Time

BioSystems, 204, 104405
Paper 2021

Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria paradoxa Dynamic Morphology

Diatom Gliding Motility
Preprint 2020

Cultural, Emotional, and Associative Traits to Determine Literary Inclination

PsyArXiv DOI
Report 2020

Elementary Morphogenetic Cellular Automata for Modeling Developmental Phenotypes

ResearchGate
Paper 2020

Raising the Connectome: The Emergence of Neuronal Activity and Behavior in C. elegans

Frontiers in Cellular Neuroscience DOI
Paper 2019

AI and Equality: A Multidisciplinary Approach to Confronting AI Bias

ACM NYCWiC 2019
Artificial IntelligenceEthicsLaw Policy
Paper 2019

Cultural Affinity through Associative Machine Learning and Behavioral Computation

International Conference on Computing, Communication, Control and Automation (ICCUBEA) DOI
Presentation 2019

Meta-brain Computational Models for Representing Cultural Diversity

Brain.tc (Twitter conference)
Presentation 2019

A New Kind of Developmental Biology

Find Your Inner Modeler III, University of Alabama–Birmingham DOI
Paper 2018

Cell Differentiation Processes as Spatial Networks: Identifying Four-dimensional Structure in Embryogenesis

BioSystems, 173, 235–246
Report 2018

Data Repository for "Morphogenetic Processes as Data: Quantitative Structure in the Drosophila Eye Imaginal Disc"

Open Science Framework DOI
Report 2018

Embryo Networks and Connectomes in Caenorhabditis elegans

Open Science Framework DOI
Paper 2018

Morphogenetic Processes as Data: Quantitative Structure in the Drosophila Eye Imaginal Disc

BioSystems, 173, 256–265
Paper 2018

OpenWorm: Overview and Recent Advances in Integrative Biological Simulation of Caenorhabditis elegans

Philosophical Transactions of the Royal Society B, 373, 20170382 DOI
Paper 2018

Origins of the Embryo: Self-organization through Cybernetic Regulation

BioSystems, 173, 73–82
Paper 2017

The Emergent Connectome in Caenorhabditis elegans Embryogenesis

BioSystems, 173, 247–255
Preprint 2017

Morphognosis: The Shape of Knowledge in Space and Time

arXiv:1701.02272
Report 2016

Data from: Evolution in Eggs and Phases

Dryad DOI
Paper 2016

Evolution in Eggs and Phases: Experimental Evolution of Fecundity and Reproductive Timing in Caenorhabditis elegans

Royal Society Open Science, 3, 160496 DOI
Preprint 2016

Genotype-specific Developmental Plasticity Shapes the Timing and Robustness of Reproductive Capacity in Caenorhabditis elegans

bioRxiv DOI
Preprint 2016

Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages

bioRxiv DOI
Paper 2016

Morphozoic: Cellular Automata with Nested Neighborhoods as a Metamorphic Representation of Morphogenesis

Multi-Agent Based Simulations Applied to Biological and Environmental Systems, Chapter 3
Essay 2016

Playing Games with Ideas: When Epistemology Pays Off

Journal of Brief Ideas DOI
Paper 2016

Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos

Biology, 5(3), 33
Presentation 2015

DevoWorm: Raising the Worm on Datapoints, Trees, and Matrices

20th International C. elegans Conference, Los Angeles, CA
Report 2015

The Foundations of Control and Cognition: The Every Good Regulator Theorem

Figshare DOI
Presentation 2015

Network Architecture of Embryo Developmental Regulation

Network Frontiers Workshop, Northwestern University
Preprint 2014

Contextual and Structural Representations of Market-mediated Economic Value

arXiv:1403.7021
Preprint 2014

DevoWorm: Differentiation Waves and Computation in C. elegans Embryogenesis

bioRxiv DOI
Paper 2012

Contextual Geometric Structures: Modeling the Fundamental Components of Cultural Behavior

Proceedings of Artificial Life, 13, 147–154
Preprint 2011

Lagrangian Coherent Structures (LCS) May Describe Evolvable Frontiers in Natural Populations

arXiv:1101.6071