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discovery-d2-phr

Discovery D2: PHR research arc + unorthodox recombination framing

Metadata

Statusdone
Assignedagent-131
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-05-01T22:55:58.574782677+00:00
Started2026-05-01T22:59:40.761577559+00:00
Completed2026-05-01T23:03:24.998657662+00:00
Tagsgrant,urgent,v3,discovery, eval-scheduled
Eval score0.87
└ blocking impact0.95
└ completeness0.92
└ constraint fidelity0.85
└ coordination overhead0.88
└ correctness0.85
└ downstream usability0.92
└ efficiency0.86
└ intent fidelity0.84
└ style adherence0.91

Description

Description

Articulate the PHR (pseudo-homologous regions) research arc as an ONGOING program of work, anchored in Garrison Nature 2023, with named follow-up directions including 'unorthodox recombination' analysis and expansion to other contexts/species. Goal: v3.1 cites PHR research as a real ongoing program WorkGraph substrates, NOT as a constructed grant deliverable promising clinical results.

Addresses panel weakness W1 (no specific science deliverable) and gives back some of v2's PHR vivid set piece without v2's clinical-results hostage.

What to research

Use WebFetch / WebSearch / read CLAUDE.md.

  1. Garrison et al. Nature 2023 — the PHR paper. What did it establish? What questions did it leave open?
  2. Follow-up work on PHRs — preprints, conference talks, follow-up papers since 2023. What's the next phase?
  3. 'Unorthodox recombination' in pangenomes — Erik specifically called this out. What does this mean technically? What ongoing work addresses it? (Likely connects to graph-aware recombination analysis, structural variation in repetitive regions, or population-level recombination patterns observed in pangenome graphs.)
  4. Expansion of PHR analysis to other contexts — non-human vertebrate pangenomes? Plant pangenomes? Other species sets where the methodology applies?
  5. What WorkGraph substrates here — what's the coordination problem in PHR research that WorkGraph addresses (multi-team analysis, version control of variant calls, traceable provenance for candidate variants, etc.)?

What to produce

~/poietic.life/notes/v3-discovery-d2-phr-research-arc-20260501.md — under 1000 words.

Structure:

PHR research program: established

What Garrison Nature 2023 established (one paragraph). Cite paper.

PHR research program: ongoing follow-ups

Named directions in active development. Include 'unorthodox recombination' analysis with technical clarification of what that means.

PHR analysis expansion

Where does the methodology extend (other species, other genome regions, other clinical applications)?

WorkGraph's role as substrate

What coordination problem in PHR research does WorkGraph solve? Be specific (not 'reliability' as buzzword).

Recommended v3.1 framing

2-3 sentences ready to drop into v3 §17 / §19 / §43 that position PHR research as ongoing program work substrate by WorkGraph, NOT as a 36-month deliverable.

Constraints

  • Cite URLs for every factual claim. Garrison Nature 2023 must have its DOI cited.
  • No clinical promises. The v3.1 framing should NOT say WorkGraph will deliver clinical PHR results in 36 months.
  • 'Unorthodox recombination' should have a technical definition, not just a buzzword pass.
  • No em-dashes.

Validation

  • Garrison Nature 2023 cited with DOI
  • Unorthodox recombination defined technically
  • At least 2 named ongoing PHR follow-up directions
  • WorkGraph substrate role articulated concretely
  • Drop-in framing produced for v3.1 sections
  • Output at ~/poietic.life/notes/v3-discovery-d2-phr-research-arc-YYYYMMDD.md

Depends on

Required by

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