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lit-review-synthesis

Lit review synthesis: integrate 14 topics into readable history; augment REFERENCES.bib

Metadata

Statusdone
Assignedagent-928
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Modelclaude:opus
Created2026-05-06T01:46:50.531320322+00:00
Started2026-05-06T13:46:36.364528213+00:00
Completed2026-05-06T13:58:35.788545119+00:00
Tagslit-review, synthesizer, paper-prep, eval-scheduled
Eval score0.74
└ hallucination rate0.35
└ requirement coverage0.70
└ semantic match0.85
└ specificity match0.65

Description

GOAL: integrate the 14 topical lit reviews under paper_prep/lit_review/topic_NN_.md into a single readable narrative history that lead-author Erik Garrison can read end-to-end to: (1) understand the full historical and conceptual context of this manuscript's claims; (2) field BoG questions confidently; (3) guide manuscript writing without getting confused. Produce an augmented bibliography combining all topic_NN_.bib files with the existing paper_prep/synthesis/REFERENCES.bib.

INPUTS:

  • paper_prep/lit_review/topic_01_.md … topic_14_.md (14 topical reviews)
  • paper_prep/lit_review/topic_01_.bib … topic_14_.bib (14 BibTeX files)
  • paper_prep/synthesis/REFERENCES.bib (existing 24-entry bibliography)
  • paper_prep/synthesis/ABSTRACT_nature.md (anchor; falls back to ABSTRACT_BoG.md)
  • paper_prep/synthesis/CROSSWALK.md (claim-to-substrate map)
  • end-to-end-report/report/12_literature.md (Andrea's literature/novelty ledger)

DELIVERABLES (under paper_prep/lit_review/):

  1. SYNTHESIS.md — narrative history, ~6,000-10,000 words, structured as: Foreword: how to read this document (1 paragraph) Part I — Cytogenetic and structural foundations (combines topics 01, 02, 04) Part II — The pseudohomology concept and its variants (combines topics 03, 05, 06, 13, 14) Part III — Mechanism: meiotic 3D and recombination (combines topics 07, 08, 09) Part IV — Methods: pangenomes and pedigrees (combines topics 10, 11, 12) Part V — How this paper sits in the field (synthesis: which claims are novel, which confirm prior work, what the abstract's thesis adds) Each part: chronological flow, claim-anchored citations to papers in REFERENCES_v2.bib, transitions between topics.
  2. CHRONOLOGY.md — timeline table: year | author(s) | brief description | claim(s) supported (C1-C8) | citation key.
  3. paper_prep/synthesis/REFERENCES_v2.bib — augmented BibTeX combining REFERENCES.bib + all 14 topic_NN_*.bib; deduplicated (same DOI / author+year / title), sorted alphabetically by citation key. Should grow from ~24 entries to ~120-200 entries.
  4. GAPS.md (short — 1 page max) — anything the synthesis flagged as missing, mis-cited, or open question. Optional.

ACCEPTANCE:

  • SYNTHESIS.md exists with all 5 parts; each part has chronological flow and explicit claim anchoring (C1-C8).
  • CHRONOLOGY.md has at least one row per major paper in REFERENCES_v2.bib.
  • REFERENCES_v2.bib has ≥120 deduplicated entries.
  • Single commit: "docs: lit review synthesis — readable history + augmented REFERENCES_v2.bib".
  • wg artifact records all 4 deliverables.

DO NOT modify any topic_NN_.md or topic_NN_.bib (read-only inputs).

Depends on

Required by

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