Symbiont

Bio-Inspired Trust and Orchestration Protocol

Version 0.1 | December 2025

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Abstract

Symbiont is a decentralized trust and orchestration protocol inspired by biological network optimization systems. Drawing from the adaptive behavior of Physarum polycephalum (slime mold) and mycorrhizal fungal networks, Symbiont enables multi-agent systems to establish trust, detect adversarial behavior, and intelligently route tasks without central authority.

graph TB
    subgraph "Biological Inspiration"
        BIO1[Physarum polycephalum<br/>Slime Mold]
        BIO2[Mycorrhizal Networks<br/>Forest Fungi]
        BIO3[Plant Defense<br/>Signaling]
    end

    subgraph "Symbiont Protocol"
        CONN[Connection<br/>Dynamics]
        TRUST[Trust<br/>Computation]
        DEF[Defense<br/>Signaling]
        CORE[Core Protocol]
        ORCH[Intelligent<br/>Orchestration]
    end

    BIO1 -->|Network Optimization| CONN
    BIO2 -->|Resource Exchange| TRUST
    BIO3 -->|Threat Response| DEF

    CONN --> CORE
    TRUST --> CORE
    DEF --> CORE
    CORE --> ORCH

    style BIO1 fill:#7d9f85
    style BIO2 fill:#7d9f85
    style BIO3 fill:#7d9f85
    style CORE fill:#b8956b
    style ORCH fill:#6b8fa3

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Key Features

Feature	Description
Emergent Trust	Trust emerges from interaction patterns, not central authority
Adaptive Connections	Connections strengthen through positive reciprocity (like slime mold tubes)
Collective Defense	Defense signals propagate through trusted connections
Adversary Detection	Behavioral analysis identifies strategic adversaries
Intelligent Routing	Workflows route to the most trusted, capable nodes

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The Core Equation

At the heart of Symbiont lies the Physarum Equation, which governs how connection strengths evolve:

$$\frac{dw}{dt} = \gamma \cdot |Q|^\mu \cdot \sigma(r) \cdot \psi(q) \cdot \phi(\tau) - \alpha \cdot w - D$$

graph LR
    subgraph "Inputs"
        Q[Q: Interaction<br/>Volume]
        R[r: Reciprocity]
        QS[q: Quality]
        T[τ: Tone]
    end

    subgraph "Transforms"
        Q --> FLOW[Flow Factor]
        R --> SIG[Reciprocity Sigmoid]
        QS --> QMULT[Quality Multiplier]
        T --> TMULT[Tone Multiplier]
    end

    subgraph "Output"
        FLOW --> PHI[Φ: Reinforcement]
        SIG --> PHI
        QMULT --> PHI
        TMULT --> PHI
        PHI --> W[Δw: Weight Change]
    end

    style PHI fill:#b8956b
    style W fill:#7d9f85

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Symbol	Description	Range
w	Connection weight	[0, 1]
Q	Interaction volume (flow)	[0, ∞)
r	Reciprocity score	(-∞, +∞)
q	Quality score	[0, 1]
τ	Tone score	[-1, 1]
D	Defense dampening	[0, ∞)

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Documentation

Documentation Legend

Complete documentation is available in the /docs directory:

Foundational Concepts

Document	Description	Audience
Introduction	High-level overview and motivation	All readers
Biological Foundations	The science behind the protocol	Students, researchers
Core Principles	Seven design principles and philosophy	All readers
Glossary	Terminology, symbols, and constants	Quick reference

System Architecture

Document	Description	Audience
Architecture Overview	System design, layers, and components	Developers, architects
Node Architecture	Individual node structure and lifecycle	Implementers
Network Topology	Network structure, evolution, properties	System designers
Data Flow	How information moves through the system	All technical readers

Protocol Specification

Document	Description	Audience
The Physarum Equation	Core mathematical dynamics	Researchers, advanced developers
Trust Computation	How trust emerges and is calculated	All technical readers
Reciprocity System	Exchange balance tracking	Implementers
Defense Signaling	Threat detection and propagation	Security-focused readers
Convergence Protocol	How agents reach consensus	Distributed systems developers
State Machines	Node, defense, connection state transitions	Implementers

Tutorials

Document	Description	Audience
Getting Started	Installation and first simulation	New users
Running Simulations	Advanced simulation and metrics	Experimenters
Understanding Trust	Interactive trust calculation walkthrough	Students
Building Workflows	Creating multi-agent workflows	Developers

API Reference

Document	Description	Audience
Core Types	Type definitions and structures	Implementers
Constants	Protocol parameters and ranges	Configuration
Mathematical Functions	Helper functions and implementations	Implementers
Node API	Node interface and methods	Developers

Master Specifications

Document	Description	Audience
Master Reference	Complete protocol specification	All readers
Language-Agnostic Spec	Implementation guide for any language	Implementers
Complete Specification	Full technical specification	Advanced readers

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Project Structure

symbiont/
├── symbiont-core/          # Core protocol library
│   └── src/
│       ├── types.rs        # Core types (NodeId, Score, Weight)
│       ├── node.rs         # Node structure and behavior
│       ├── connection.rs   # Connection dynamics (Physarum)
│       ├── trust.rs        # Trust computation
│       ├── defense.rs      # Defense signaling
│       ├── routing.rs      # Task routing
│       ├── workflow.rs     # Workflow orchestration
│       ├── handoff.rs      # Task handoff protocol
│       ├── detection.rs    # Adversary detection
│       ├── convergence.rs  # Convergence protocol
│       ├── math.rs         # Mathematical functions
│       └── constants.rs    # Protocol constants
│
├── symbiont-sim/           # Simulation harness
│   └── src/
│       ├── network.rs      # Network simulation
│       ├── agents.rs       # Agent behavior models
│       ├── scenarios/      # Test scenarios
│       └── metrics.rs      # Metrics collection
│
├── symbiont-cli/           # Command-line interface
│   └── src/main.rs
│
└── docs/                   # Documentation
    ├── concepts/           # Foundational concepts
    ├── architecture/       # System architecture
    ├── protocol/           # Protocol specification
    ├── tutorials/          # Step-by-step guides
    ├── api/                # API reference
    └── master design docs/ # Master specifications

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Quick Start

Prerequisites

• Rust 1.70 or later
• Cargo package manager

Installation

# Clone the repository
git clone https://github.com/your-org/symbiont.git
cd symbiont

# Build all crates
cargo build --release

# Run tests
cargo test

Run Simulations

# Trust emergence in honest network
cargo run -p symbiont-cli -- simulate trust-emergence

# Strategic adversary injection
cargo run -p symbiont-cli -- simulate strategic --inject-at 100

# Workflow chain routing
cargo run -p symbiont-cli -- simulate workflow-chain

# With verbose output
cargo run -p symbiont-cli -- simulate trust-emergence -v

Available Scenarios

Scenario	Description
trust-emergence	Observe trust dynamics in honest network
strategic	Strategic adversary builds trust then defects
free-rider	Free riders take but don't contribute
sybil	Sybil cluster attack
workflow-chain	Sequential workflow routing
workflow-fan-out	Parallel workflow with merge

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Protocol Constants

Key parameters governing protocol behavior:

Constant	Symbol	Default	Description
Reinforcement Rate	γ	0.1	Rate of connection strengthening
Decay Rate	α	0.01	Natural connection weakening
Reciprocity Sensitivity	β	2.0	Sigmoid steepness
Memory Factor	λ	0.9	EMA weighting
Flow Exponent	μ	0.5	Sublinear flow scaling
Initial Weight	W_INIT	0.3	Starting connection weight
Minimum Weight	W_MIN	0.01	Connection removal threshold
Maximum Weight	W_MAX	1.0	Maximum connection strength

See Constants Reference for the complete list.

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Design Philosophy

graph TB
    subgraph "Core Principles"
        P1[Trust Through<br/>Interaction]
        P2[No Central<br/>Authority]
        P3[Behavioral<br/>Adaptation]
        P4[Reciprocity<br/>Balance]
        P5[Collective<br/>Defense]
        P6[Graceful<br/>Degradation]
        P7[Verifiable<br/>State]
    end

    P1 --> GOAL[Robust<br/>Decentralized<br/>Trust]
    P2 --> GOAL
    P3 --> GOAL
    P4 --> GOAL
    P5 --> GOAL
    P6 --> GOAL
    P7 --> GOAL

    style GOAL fill:#b8956b

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1. Trust Through Interaction — Trust emerges from consistent, high-quality, reciprocal interactions
2. No Central Authority — No master node, no oracle, no single point of failure
3. Behavioral Adaptation — Trust adapts to changing behavior over time
4. Reciprocity Balance — Sustainable relationships require balanced exchange
5. Collective Defense — The network defends itself through coordinated signaling
6. Graceful Degradation — The system continues functioning when components fail
7. Verifiable State — All state changes are traceable and cryptographically signed

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Contributing

See CONTRIBUTING.md for guidelines on contributing to this project.

Security

See SECURITY.md for security policy and reporting vulnerabilities.

License

This project is licensed under the MIT License - see the LICENSE file for details.

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References

1. Tero, A., et al. (2010). "Rules for Biologically Inspired Adaptive Network Design." Science, 327(5964), 439-442.

2. Simard, S. W. (2018). "Mycorrhizal Networks Facilitate Tree Communication, Learning, and Memory." In Memory and Learning in Plants. Springer.

3. Meyerson, D., Weick, K. E., & Kramer, R. M. (1996). "Swift Trust and Temporary Groups." In Trust in Organizations. Sage.

4. Heil, M., & Ton, J. (2008). "Long-distance signalling in plant defence." Trends in Plant Science, 13(6), 264-272.

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Symbiont v0.1 — Trust emerges from interaction. Orchestration emerges from trust.