Goal
Propose a showcase experiment that Jay Shendure and the Seattle Hub for Synthetic Biology would plausibly greenlight: using in vivo barcoding to follow adaptive-immune clones from vaccine priming through memory formation and heterologous challenge. The deliverable must be concrete enough to function as a pilot-ready protocol, not just a concept note, and must include a domain check from an immunology co-persona aligned to Sue Kaech's memory-T-cell perspective.
Acceptance Criteria
☐ A four-round debate artifact exists for the Shendure × adaptive-immunity experiment.
☐ The final synthesis specifies the barcoding library, delivery vehicle, reporter, timepoints, sequencing depth, challenge model, and readouts.
☐ The synthesis includes a 3-month pilot plan and explicit persona greenlights from Jay Shendure and Sue Kaech.
☐ Feasibility is scored at or above 0.5 and the proposal cites at least one Shendure/Seattle Hub platform reference.
Approach
Review the task prompt, recent Jay Shendure persona commits, and the current analysis artifact structure in this checkout.
Design a technically conservative but still distinctly Seattle-Hub-style lineage-recording experiment centered on vaccine-induced CD8 memory, where Kaech-style immunology review is strongest.
Write a four-round debate and a structured synthesis artifact with enough operational detail to support a real pilot.
Record the work in this spec and commit the new experiment package.Dependencies
afc78b0c-2e9f-4dac-91c2-43ef1ef0c0bd — Jay Shendure persona content exists in recent commits and was used as context even though the file is absent from this checkout.
Dependents
- Future Allen-experiment tasks can reuse this artifact as a template for persona-gated showcase experiment proposals.
Work Log
2026-04-24 19:55 PT — Codex
- Started staleness review from the current worktree at
8ae0c20e4; confirmed no existing in-tree artifact covers this Seattle Hub adaptive-immunity proposal.
- Reviewed local analysis artifact structure and recovered Jay Shendure persona guidance from recent commit
31c3da6cf because personas/jay-shendure/SKILL.md is not present in this checkout.
- Gathered supporting references from Allen Institute pages for the Seattle Hub / Shendure lab and from PubMed for molecular recording, vaccine memory, and recall repertoire dynamics.
- Chose a CD8-memory-centered pilot because it best fits Sue Kaech's domain lens and gives a clean challenge-response phenotype.
- Creating a new analysis package with debate + synthesis plus this missing spec file.