Does Siggia et al.'s 2025 PNAS work actually reconstruct Waddington landscapes directly from single-cell data?

The 2026-07-09 hop capture (10-inbox/raw/2026-07-09-hop-waddington-hopfield-landscape.md) cites an August 2025 PNAS paper (attributed to Eric Siggia et al.) as reconstructing Waddington-style developmental landscapes directly from single-cell data — evidence that the landscape-as-dynamical-system programme is still an active research seam in 2025–26, not a settled historical curiosity. The capture only ran a "confirmation check" (final-gate max_cosine 0.69) and did not read the paper, so the claim is currently unverified.

Why it matters: if confirmed, it extends the thread promoted at claim-hopfield-network-formalizes-waddington-epigenetic-landscape from a 2016 Hopfield-network formalization to a live 2025 single-cell method — and would be worth its own claim-note (does it use an energy/attractor formalism, and does it cite the Hopfield-network line at all?).

What would answer it: locate the actual 2025 PNAS paper (confirm authors, title, exact venue, and DOI — the "Siggia et al." attribution is the capture's, unverified), read the method, and record whether it reconstructs an explicit energy landscape from single-cell transcriptomes. If it does, promote a claim-note; if the attribution is wrong, correct the lead.

Progress log

• 2026-07-27 — Answered by claim-cislo-siggia-2025-fit-waddington-landscape-directly-to-single-cell-gene-expression (+ claim-cislo-siggia-2025-landscape-from-discretized-fokker-planck-on-sampled-data-points, claim-cislo-siggia-2025-validated-on-real-mesc-neural-tube-flow-and-rnaseq-data). Confirmed against the authors' own Tier-1 bioRxiv preprint: yes, the paper fits landscapes directly to single-cell data (flow cytometry + scRNA-seq) in gene-expression space, via a discretized Fokker–Planck path integral yielding fixed points, saddles, and basins of attraction. It uses an attractor/potential formalism but cites the Morse–Smale dynamical-systems lineage, NOT the Hopfield-network line — so the thread is live but the two formalization traditions do not meet here.