:orphan:

.. include:: /_templates/include-file/page-prefix.rst

.. note:: **Prompt B: ResearchCity Key Papers exhibit pages (19 PDFs) --- 2026m04d14.**
   Tier 1b priority for Matheo paper series launch.
   Estimated: 1 full session (long papers, but many details extractable from filenames).
   Prepared by Claude Opus 4.6.

****************************************************************************************************
Prompt B: ResearchCity Key Papers --- Exhibit Pages for 19 Published Scientific Papers
****************************************************************************************************

| **VVN:** ``dv_ClaOp46_ExhB_2026m04d14``
| **Scope:** ``dusty-deep-data/loewe-researchcity-key-papers/`` --- 19 PDFs
| **Existing:** No exhibit pages exist for this folder
| **Session estimate:** 1 full session


Purpose
=========

Create exhibit pages for 19 published scientific papers that establish
LLoL's scientific credentials. The Matheo papers make claims rooted in
evolutionary systems biology, Evolvix, population genetics, and
computational biology. Readers who want to check if LLoL has the
scientific background to make these claims will look for peer-reviewed
evidence. Without landing pages, these 19 papers are dark to search
engines.

Key papers for the Matheo series:

- **Ehlert-Loewe 2014** --- lazy updating in simulations implies core
  algorithm for Jubilee measuring (directly relevant to Jubilee System claims)
- **Loewe 2009, 2016** --- evolutionary systems biology framework
  (the scientific methodology behind the modeling claims)
- **Loewe et al. 2017** --- Evolvix naming philosophy, code2brain,
  semantic rot (directly relevant to POST system and language design)
- **Loewe 2002 dissertation** --- 444-page thesis (the deepest scientific root)
- **Loewe 1991** --- Jugend forscht study (earliest scientific work, age ~17)


Step 1: Read Procedure and Context
=====================================

Read these files in order:

1. ``.claude/CLAUDE.md`` --- Language Rules, EDEN, date format, all conventions.

2. **The generation procedure (your template and rules):**
   ``source/good-news-pack/vv/mmv3/llog/procedure-for-exhibit-page-generation.rst``

   Follow the per-file procedure, template, and conventions exactly.

3. **An existing exhibit page for quality reference:**
   ``source/good-news-pack/vv/mmv3/supporting-doc/sd1/index.rst``

   Match this quality level. Academic papers should get the same treatment
   as supporting documents: Abstract, Broader Significance, audience table,
   Key Concepts, Document Information, Related Documents.

4. **The mmv3 master index (for toctree registration):**
   ``source/good-news-pack/vv/mmv3/index.rst``


Step 2: The 19 Papers
========================

All PDFs live in ``source/_file/pdf/gnp/mmv3/dusty-deep-data/loewe-researchcity-key-papers/``.
Listed chronologically by publication year (from filenames):

1.  ``loewe-1991-study-jugend-forscht-electric-spark-productivity-miller-urey-chem-evolution-15page.pdf``
2.  ``loewe-2002-diss-evobioinf-asexual-genome-stability-global-computing-vv_2003m11d28-444page.pdf``
3.  ``loewe-2002-review-global-computing-compared-to-other-distributed-computing-12page.pdf``
4.  ``loewe-textor-scherer-2003-study-stationary-phase-mutation-rate-increases-in-e-coli-with-xtras-17page.pdf``
5.  ``loewe-charlesworth-2006-study-lognormal-deleterious-mutational-effects-fitness-6page.pdf``
6.  ``loewe-2006-study-in-silico-genomic-decay-in-human-mitochondrial-dna-due-to-mullers-ratchet-27page.pdf``
7.  ``loewe-charlesworth-2007-study-quantify-background-selection-in-single-genes-13page.pdf``
8.  ``loewe-2007-study-simple-global-computing-system-with-participant-choice-for-evolution-at-home-30page.pdf``
9.  ``loewe-hillston-2008-study-evosysbio-in-silico-distributions-mutational-effects-circadian-clock-20page.pdf``
10. ``loewe-2009-review-evosysbio-framework-for-evolutionary-systems-biology-34page.pdf``
11. ``loewe-moodie-hillston-2009-study-eptcs-biopepa-model-mapk-signal-transduction-cascade-15page.pdf``
12. ``loewe-moodie-hillston-2009-techreport-sgbntext2biopepa-mapk-signal-transduction-cascade-29page.pdf``
13. ``loewe-hill-2010-review-population-genetics-of-mutations-intro-15page.pdf``
14. ``loewe-2012-review-evosysbio-nested-adaptive-landscapes-distributions-mutational-effects-12page.pdf``
15. ``ehlert-loewe-2014-study-lazy-updating-simulations-imply-core-algorithm-for-jubilee-measuring-20page.pdf``
16. ``james-2014-study-reproducibility-challenges-in-supercomputing-xsede-final-report-16page.pdf``
17. ``loewe-2016-study-framework-definition-for-systems-in-evolutionary-systems-biology-22page.pdf``
18. ``loewe-et-al-2017-study-evolvix-best-names-code2brain-vs-semantic-rot-with-xtras-95page.pdf``
19. ``mcloone-et-al-2018-study-game-theory-stochastic-cooperation-snowdrift-game-14page.pdf``


Step 3: Page Strategy
=======================

Use **individual exhibit pages for all 19 papers.** These are peer-reviewed
published science --- each deserves its own landing page for SEO, credibility,
and cross-referencing from the Matheo papers.

**Context budget warning:** Several papers are very long (444pp dissertation,
95pp Evolvix naming, 34pp EvoSysBio review). Use the Read tool's ``pages``
parameter to read only the first 10--15 pages of each (title, abstract,
introduction, conclusion). Extract from the filename when the paper is too
long to fully read. The filename convention already encodes: authors, year,
type (study/review/diss/techreport), topic summary, page count.

**Create these files:**

- ``dusty-deep-data/index.rst`` --- folder index for all of dusty-deep-data
  (covering loewe-about-me-science/, loewe-about-me-spirituality/, and
  loewe-researchcity-key-papers/). For the two about-me subfolders, add
  brief placeholder entries noting they will get exhibit pages in a later
  session. For key-papers, list all 19 with links.

- ``dusty-deep-data/loewe-researchcity-key-papers/index.rst`` --- subfolder
  index listing all 19 papers chronologically.

- 19 individual exhibit pages, one per paper, named by short slug:
  ``dusty-deep-data/loewe-researchcity-key-papers/loewe-1991-jugend-forscht.rst``,
  ``dusty-deep-data/loewe-researchcity-key-papers/loewe-2002-diss.rst``, etc.

**For each paper, the exhibit page should include:**

- Standard template (meta, title, download box, WebP preview, AI markers)
- Abstract (from reading the PDF's abstract section)
- Broader Significance (how this paper relates to the LLoL/ZION project ---
  be honest about the connection; some papers are pure science with no
  direct link to the spiritual framework)
- Bibliographic Information table (authors, year, journal/venue, pages, DOI
  if visible in the PDF)
- Key Concepts (technical terms from the paper)
- Related Documents (cross-reference to other papers in this collection
  and to relevant Matheo papers once they exist)


Step 4: Structural Updates
============================

After creating all pages:

1. **Register** ``dusty-deep-data/index.rst`` in ``mmv3/index.rst`` toctree
   under a new toctree group. Use caption "Background & Evidence" or similar.

2. **Update** ``collection-overview.rst`` --- change Dusty Deep Data status.

3. **Run** ``make dev`` to check for warnings.


Step 5: Create LLog
======================

Create an append-only LLog at:
``source/good-news-pack/vv/mmv3/llog/llog_2026m04d14_researchcity-key-papers.rst``

Record: which papers were processed, any context budget issues, bibliographic
details extracted, and the concluding summary.