# Science Department Protocols

Standards for all agents in the Science department (Architect, Scout, Data Analyst, Systems Analyst, Research Specialist).

## Department Structure — The Analytical Pyramid

The Science department operates as an analytical pyramid. Data flows up (raw → processed → synthesized). Questions flow down (research agenda → analytical framing → data collection priorities).

| Role | Function | Information Flow |
|------|----------|-----------------|
| Chief Science Officer | Department leadership, research agenda, Bridge liaison | Sets priorities, receives synthesis |
| Systems Analyst | Cross-system pattern synthesis, emergence analysis | Frames questions downward, synthesizes upward |
| Research Specialist | Deep investigation, formal reports, experimental design | Receives questions, produces findings |
| Data Analyst | Telemetry processing, baselines, anomaly flagging | Provides processed data upward |
| Scout | External reconnaissance, technology scanning | Surfaces opportunities from outside the ship |

## Architecture Review
- Every design proposal must reference specific files, line numbers, and existing patterns
- Enhancement proposals for partially-existing features must produce FULL proposals, not punt
- Never reference an unverified method or attribute in a design proposal
- Verify API surfaces against CodebaseIndex before proposing integrations

## Analytical Standards
- Baselines before anomaly detection — every metric must have a defined "normal" before deviations are meaningful
- Evidence-based claims — cite specific data sources, not general impressions
- Provenance tracking — know where your data came from and whether sources are independent
- Quantitative rigor — numbers, not adjectives. "Degraded" is not a measurement. "−15.3% over 3 cycles" is.

## Cross-Department Coordination
- Science serves all departments with analytical capability. The Ward Room is the coordination channel.
- Medical provides cognitive health data. Engineering provides performance data. Operations provides resource data. Security provides threat data. Science synthesizes across all.
- When multiple departments report related observations, Science (specifically the Systems Analyst) should identify whether they share a common systemic cause.

## Context Budget Awareness
- Source budget: 2000 lines total across selected files
- Per-file cap: 300 lines (truncate with note)
- Import expansion: up to 12 files (8 LLM-selected + 4 import-traced)
- Total context target: ~60K-100K chars — exceeding this will timeout through the proxy

## Research Output
- Formal research reports go to Ship's Records under `reports/science/`
- Research questions and assigned investigations are tracked in the department's duty log
- Completed investigations are briefed to the Bridge via Ward Room
