Architecture paper · v1.0 · 2026
Protean & Galen.
A scientific OS.
The Protean runtime documented as systems research. Bounded cognition, sealed cycles, public commitments on Base mainnet, and review-gated wet-lab handoff — twelve sections, four appendices, and an implementation status table that names — out loud — what is partial, flag-gated, or absent.
Authors: Protean Labs · License: CC-BY-NC-ND 4.0 (paper). The reproducibility bundle below contains the SHA-256 hashes, schema versions, and anchor metadata required to re-verify every commitment published with this work.
02—Figures
Companion
diagrams.
Runtime topology, the replay-validation gate, and the approval-pipeline state machine — reproduced inline so they can be linked, cited, and embedded without leaving this page.
Figure 01
Runtime topology
§3 · System Architecture
Figure 02
Replay validation flow
§4.4 · Replay Validation
Figure 03
Approval and remediation pipeline
§7.2 · Approval and Refusal
03—Implementation status
What is
shipped,
partial, absent.
Every section of the architecture paper maps to a row in this table. The runtime publishes its own implementation status alongside the paper — including the things that aren't built yet.
Implementation status
What is, what is not — said out loud.
paper §3.2 · table 1
| Subsystem | Status | Boundary |
|---|---|---|
| Cycle runner & snapshots | implemented | Full and cognition-only cycles write immutable cycle artifacts. |
| Runtime manifests | implemented | SHA-256 + bytes + rows + producer + validation pointers. |
| Public provenance graph | implemented | Redacted schema protean.scientific-object-graph.v1. |
| Object & edge IDs | implemented | Mainnet · UUPS proxy · canonical AccessControl (treasury holds admin). |
| Evidence index | implemented | SQLite + embeddings + lexical · blocks raw sequence queries. |
| Reranker | partial | Local cross-encoder · lexical fallback when unavailable. |
| Claim QA | implemented | Local NLI + heuristic fallback · evidence-relative, not proof. |
| Contradiction graph | partial | Builder + consumers implemented · not yet a default loop stage. |
| Scientific memory | implemented | Bounded consolidation · cannot mutate validators, scoring, or code. |
| Workflow DAG guard | flag-gated | Implemented but enforcement disabled by default. |
| Capability ontology | partial | Records + inspectors · not enforced by planner or wetlab map. |
| Wetlab coordination | review-only | Draft packets only · no provider execution, no payment, no submit. |
| Approval pipeline | implemented | HMAC receipts + allowlist + idempotency + telemetry. |
| External providers | partial | Remote escalation policy implemented · production-disabled. |
04—Reproducibility
Every claim,
re-checkable.
A reviewer with the public bundle can re-derive every commitment in this paper, re-verify every lineage edge against the on-chain registry, and confirm the published artifacts correspond bit-for-bit to what was actually written.
Schema
protean.public-export.v1
Hash algorithm
SHA-256
Anchor network
Base mainnet (8453)
Domain separator
PROTEAN_SCIENTIFIC_OBJECT_V2
Golden vectors
17 / 17 passing
Contract tests
30 / 30 passing
Citation
How to cite.
@misc{protean_architecture_paper_2026,
title = {Protean & Galen: a scientific operating system for autonomous peptide discovery},
author = {Protean Labs},
year = {2026},
url = {https://www.protean.sh/research/architecture-paper},
note = {Computational rankings are research prioritization, not biological proof.}
}Boundary
Computational rankings are research prioritization, not biological proof. Wet-lab validation and human scientific review remain the authoritative downstream layer.