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Author SHA1 Message Date
84124de143 Manuscript revision and pending experiment work, snapshot before restructuring
Clarity pass over the main text (36-item audit), Discussion rewrite and cut,
acknowledgements, Souly et al. as ref 62, lettered SI panels, model section
moved under Results; plus the untracked curriculum/society/compose/smol
configs, runners, figures, stats and tests that the SI already cites.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
2026-09-13 16:54:09 +01:00
70c8c54434 Fig. 1: borderless cells in A; the Flaticon robot everywhere in B
Cells lose their borders (pastel fills float; not-tested/literature/open cells
go light gray, headers keep their frame); Fig. 1B's hand-drawn robots are
replaced by the same licensed Flaticon robot as the 1A headers, embedded
unsampled, with the capability dots kept. Both panels visually inspected
post-render (text visible, no overlaps) per the new standing rule in the
global CLAUDE.md: never ship a figure you have not seen.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:48:25 +01:00
60ef253c77 Fig. 1A: wrap the two long header subtitles inside their boxes
"RNN · MLP · VAE on a synthetic oracle;" and "LoRA specialists on Qwen 0.5B &
7B;" overflowed the box edge once the text column shifted left of the larger
icons; both now wrap to three short centred lines, with the block nudged up
so the guarantee line keeps its separation.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:44:30 +01:00
40ad268c6d Fig. 1A: double the icon size (56 px placed; taller header row to fit)
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:41:38 +01:00
438931d67b Fix icon resolution: imshow + interpolation="none" embeds icons unsampled
The OffsetImage path composites at figure dpi, so the icons were going into
the PDF as 39x39 bitmaps regardless of source resolution (pdfimages-verified;
this is why the SVG switch changed nothing visually). Placing them as
AxesImage with interpolation="none" embeds the full 1024 px rasterisation
with a scaling transform: 4719 ppi at the placed size, print-crisp.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:37:53 +01:00
c9c4d927ad Fig. 1A icons: committed SVGs rasterised at build time; CDN PNGs removed
The two Flaticon icons (licensed via GG's paid subscription) are now committed
as SVG source and rasterised at 2048 px by make_figs.py via rsvg-convert
(~6000 DPI at the placed size - print-lossless), keeping every figure a pure
function of the script plus committed sources. The 512 px CDN PNGs are gone;
a clear error names the librsvg dependency if rsvg-convert is missing.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:27:25 +01:00
9055fca792 Fig. 1A: pastel palette (green biology, two blues for AI) + Mendel peas and robot icons
Per GG: the biological model goes pastel green (nature), the two AI tiers
light and darker pastel blue; header text switches from white to the dark
shade of each hue (white is unreadable on pastel). A green-pea icon honours
Mendel in the biology header; a friendly robot marks the two AI headers.
Icons are Flaticon #2347052 and #10479785, used under GG's paid Flaticon
licence (noted in make_figs.py); header text is centred slightly left of a
dedicated icon slot so nothing collides. Caption colour sentence updated
(green vs blues).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:23:35 +01:00
2d8f661924 Paper-wide rename: the pop-gen construct is "the biological model"; "(exact)" dropped
"Model" now means an AI model everywhere; the Wright-Fisher construct is "the
biological model" throughout (19 occurrences): tier header, section title (now
"The biological model, and where trained learners depart from it"), Table 1
support column ("Exact" -> "Closed form"; "Analytic model" -> "Biological
model"), Results, Discussion, Methods ("Biological-model tier"), and all
figure captions. "Exact" survives only in technical noun phrases (exact-match
verifier, exact oracle, exact equilibrium, exact recovery); the abstract's
"exactly Wright-Fisher" is now "literally Wright-Fisher".

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:08:58 +01:00
f1970728cf Fig. 1B: information-flow taglines under each panel
Space: "information is passed on, but not easily stored: it fades with the
conversation". Time: "information is inherited, evolutionarily selected, and
passed on again — from parent model to child model — where population
genetics applies". The contrast that justifies the transfer, stated where the
reader's eye lands.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 13:03:41 +01:00
3a41ee0c2e Fig. 1B polish: larger text, no overlaps, speech bubble says hi
Per GG: the "a society in time" label no longer collides with the gen-2
agent's capability dots (taller canvas, pedigree spread), the "inherit" label
clears the timeline (shortened; the caption carries "training on output"),
the cryptic "..." bubble now reads "hi!", and every text element is one to
two points larger.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 12:59:59 +01:00
b417a66c23 Fig. 1B: the conceptual cartoon — from a society in space to a society in time
The paper's key move drawn as a two-panel partner to the programme grid (now
Fig. 1A): on the left, the usual picture — contemporaries exchanging messages
(multi-agent systems, one moment on the clock); on the right, the same
ecosystem seen along its time axis — a pedigree in which a rare capability
(gold dot) is lost under single-parent inheritance, reassembled by merging
complementary parents, and re-supplied by grounding from a reality that can
say no (the globe). Friendly-robot glyphs, colour-coded capability dots;
build.py now stacks multiple PDFs per figure; the Introduction cites 1A and
1B in panel order.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 12:50:36 +01:00
16e9002773 Fig. 1 doubles as a map of the paper: per-cell figure/panel tags
Each filled cell now carries, in its bottom-right corner, the figure or table
where that result is reported (Fig. 2A ... Figs. 7E-F, 3C-D); the caption says
so. Building the mapping surfaced one imprecise citation: the bred-and-screened
seed-replication claim cited Fig. 3A, whose panel shows the soup/ties bars -
that result lives in SI Appendix Table S2, and the citation now says so.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 12:10:51 +01:00
d75c58474a Fig. 1: "not tested at this tier" -> "adds no discriminating test at this tier"
The old label read as an omission; the skipped middle-tier cells were a design
decision (the tier would replicate the exact theory, not test it), and the new
wording matches the fill principle the caption states.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 11:39:55 +01:00
e9fb28d8c4 Fig. 1: colour-separate theory from AI tiers; explain every empty cell
Category separation per GG: population genetics stays blue, both AI tiers move
to shades of orange, with a wider gutter between the theory column and the AI
pair. The grounding x LLM cell is upgraded from "not tested" to "established
at LLM scale in prior work (21, 30); not re-run here" (Shumailov's Nature
collapse result; Gerstgrasser's real-data rescue) - it was never a gap, it was
already settled. The caption now states the fill principle: each claim is
tested at the cheapest tier that can falsify it; a costlier tier is entered
only where it adds a discriminating test, and the LLM society is the one
genuinely open cell.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 11:35:59 +01:00
5cb49943db Fig. 1: rename first tier "Exact model" -> "Population genetics (exact)"
"Model" is reserved for AI models in this paper, so a tier named "Exact
model" read as a kind of AI model; the tier is the Wright-Fisher theory run
exactly. Caption and Introduction adjusted to match ("three tiers" rather
than "three tiers of model architecture"; "an exact population-genetic
simulator").

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 11:31:56 +01:00
e42fe497ff Fig. 1 revision: pop-gen definitions as row labels, title into the caption, solid header row
Row labels now teach the vocabulary (grounding = immigration, recombination =
sex, epistasis, the composed society, speciation = reproductive isolation),
each with a two-to-three-line definition in the left margin, replacing the
question taglines. The in-figure title/arrow is removed (the caption carries
it); the tier header row is now solid-colour with white text so the
model-nature band reads as a header rather than a content row.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 11:21:06 +01:00
0159e2839a New Fig. 1 (experimental-programme schematic); Table 2 to SI; figures in citation order; Fig. 2B legible labels
Replaces the results table with a pipeline figure: five questions x three
architecture tiers (exact Wright-Fisher simulator, trained networks, language
models), filled cells naming the experiments, dashed cells the honest gaps.
Table 1 (the dictionary) stays; Table 2 moves to SI Appendix Table S2. The
renumber surfaced a pre-existing citation-order violation (the LLM figure was
cited in the recombination section before Figs. 3-6), so figures are renumbered
to strict first-citation order (LLM tier is now Fig. 3). Fig. 2B: the montage's
baked-in raster labels are cropped away and replaced with vector row numbers
under a rotated "generation" header.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 11:12:33 +01:00
96902e87f0 figures: publication-ready — unified, lettered, codename-free
paper/pnas/make_figs.py re-plots every panel directly from the committed
results artifacts into six single-file figures (figs/fig1..fig6.pdf):
no experiment codenames or suptitles (interpretation moved to captions),
bold panel letters, plain-language axis labels and legend entries, one
consistent style (8pt, no top/right spines). Panels: fig1 A-B (grounding
equilibrium + MNIST montage with its baked-in title cropped), fig2 A-B
(blending cancellation + Fisher-Muller), fig3 A-D (outbreeding, directed
recombination, mating breadth champion + diversity), fig4 A-C (society
ablation trajectories), fig5 A-F (speciation: analytic curve + cliff,
MLP decomposition + conflict sweep, LLM coherence + duration null),
fig6 A-D (seed-replicated merging, 7B-hard routing vs averaging,
predictive-test scatter, predictor comparison). build.py now places the
single PDFs; captions rewritten per lettered panel; in-text panel refs
updated (5B->5C-D, 5C->5E-F); stale stacked copies removed. Document
20pp -> 18pp.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-07 09:09:46 +01:00