Topics — What a work is about. Nucleation holds whatever reading the owner files here, whether or not an Anthology of the SOTA topic could also hold it; instruction for ML practice belongs to the anthology (ADR-048). The words are seeded from the clusters the reading-time triage of 2026-09-25 found, and grow by decision.
Natural sciences — physics, astronomy, planetary and earth science, chemistry, biology and medicine read outside any machine-learning claim.
191 of 2004 LIT documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| LIT-009 v3 | An 800 Myr-old Impact Shower on the Terrestrial Planets from the Breakup of the Eulalia Parent Body | Bottke et al. (2026), ARXIV-2606.05036. The paper builds a collisional-plus-dynamical source model. In its preferred Solution 5, the Eulalia parent body breaks up T = 865 Myr ago at a_c = 2.48 au next to the Jupiter 3:1 resonance. The model sends 6,995 D ≥ 2 km and 833 D ≥ 5 km fragments into the J3:1 (Table 1, before a ≈1.5× collisional correction). With impact probabilities per resonance entrant of 5.4×10⁻³ (Venus), 4.2×10⁻³ (Earth) and 0.6×10⁻³ (Mars), and the Moon at 1/20 of Earth, the expected largest impactor is D ≈ 8 km on Earth and Venus, 4.5 km on Mars and “>3 km” on the Moon. A Monte Carlo of 7 lunar projectiles puts the seven lunar craters dated 760–820 Ma “generally … within the 1σ” envelope. The authors conclude the breakup “can plausibly account for” the ~800 Ma lunar crater cluster, although on average the model’s projectiles are too small to make Copernicus. | Proposed — read in full 2026-09-25 (NOTE-002); a careful, well-sourced plausibility model for a hypothesised 800 Ma impact shower, and worth reading as the source model for it. It is unproven: its lunar dates are scaled from a single sample-dated crater (Copernicus), and only Solution 5, the most favourable, is carried forward. Whether the shower happened, which radiometric dating of samples from the other six ~800 Ma craters or a CI-like projectile signature at more than one of them would settle, is THEORY-1195, Proposed; the reading of the model is THEORY-499, Active. The Earth, Mars and Venus material in §7 is self-declared speculation. |
| LIT-010 v2 | Quantum Thermodynamics | Vinjanampathy & Anders (2015), ARXIV-1508.06099. A 2015–16 review with no new results, whose one synthesis (§5.2, §7) is that the field used four inequivalent notions of work: ensemble ⟨W⟩ = ∫tr[ρḢ]dt (Eq. 2), two-point-measurement W = E_m^(τ) − E_n^(0) (Eq. 24), ε-deterministic single-shot A^ε ≈ −kT ln(Z_Λ*/Z) (Eq. 49) and resource-theory w^max_ε = F^min_ε(ρ_S) − F(τ_S) (Eq. 50), of which only the last two coincide. It also judges that the field had “only made a small number of experimentally checkable predictions of new thermodynamic effects yet” (§7, p. 39). | Active — read in full 2026-09-25 (NOTE-011); still worth reading as a short, accessible tour of where quantum thermodynamics stood in 2015–16, especially §3 (fluctuation theorems derived in full) and §5 (single-shot and resource-theory second laws). It is a map of the field, not an authority. It is dated: nothing after early 2016. Some formulas are garbled as printed (Eq. 68, the operator-sum statement, the Diesel strokes), so cite the primary papers it points to rather than the review. |
| LIT-026 v2 | Comparative proteomic analysis of two wasps venom, Vespa tropica and Vespa affinis | Rungsa et al. (2016), DOI-10.1016/j.toxicon.2016.06.005. Venom from the great banded wasp (V. tropica) is more potent than venom from the banded tiger wasp (V. affinis): PD50 of 3 versus 12.5 µg/g. The authors attribute the difference to higher levels and activity of hyaluronidase (about 2.5× the proportion), phospholipase and dipeptidyl peptidase, since the two venoms’ protein profiles are otherwise similar. | Unavailable — seeded 2026-09-25 from the abstract; on 2026-10-14 a search for a lawful full text reached none, so it is not read and no NOTE is filed. OpenAlex lists the work as closed, with only the doi.org and PubMed locations and no repository copy. Unpaywall reports it closed with no open locations. Europe PMC holds it only as a subscription link, and it is not in PubMed Central. ScienceDirect (pii S0041010116301593) returned 403 and the Elsevier article API was rate-limited, so whether the journal’s open archive covers it is unknown. A title search found no author-posted copy: Khon Kaen University’s researcher pages list it as a citation only. It stays Unavailable until a copy is supplied. |
| LIT-029 v2 | Long-Term Cognitive and Neuropsychiatric Consequences of Repetitive Concussion and Head-Impact Exposure | McAllister & McCrea (2017), DOI-10.4085/1062-6050-52.1.14. This review concludes that most athletes’ symptoms recover within about 1–2 weeks of a concussion. Evidence that repetitive concussion or sub-concussive head impacts cause long-term cognitive decline, neuropsychiatric change or neurodegeneration (including CTE) is mixed and preliminary, with signals of vulnerability in subgroups (e.g., verbal memory). Settling it needs large prospective longitudinal studies with baselines and controls. | Active — read 2026-10-14 (NOTE-858) in full; worth reading as a 2017 statement of what was and was not known about repetitive concussion: recovery within 1–2 weeks for most athletes, and no prospective longitudinal study of long-term cognitive, psychiatric or neurodegenerative risk. Read it knowing that it is a narrative review by authors of several studies it reviews, that its figures are second-hand, and that it predates the prospective CARE consortium results it calls for. |
| LIT-034 v2 | The sound of an axon’s growth | Folz et al. (2018), ARXIV-1807.04799. The paper proposes that an axon can set its length from motor-generated oscillations without reading their frequency. Two Hill-type stages turn the period (which grows with length L) into a shape change and then into a change in the mean of a contractility signal R. Coupling growth-cone protrusion (v_g c_I) against R-driven contraction (v_s c_R) then gives a stable length: about 125 µm with sub-µm (< 1 %) oscillation for the Fig. 4a parameters. In part of parameter space the final length rises as kinesin influx J0 falls, or as dynein coupling J_O falls, qualitatively as in experiments. | Active — read in full 2026-09-25 (NOTE-067); A short, self-contained theory letter worth reading for its frequency-to-amplitude transduction argument (Eqs. 1–4) and the delay-equation length controller. It is a proof of mechanism, not a model fitted to axons: it has one parameter set, it never states the motor velocity v that converts its lengths into micrometres, and it proposes no experimental discriminator from gradient mechanisms. |
| LIT-036 v2 | Self-organization of primitive metabolic cycles due to non-reciprocal interactions | Ouazan-Reboul et al. (2023), ARXIV-2303.09832. For M chemotactic catalyst species in a closed cycle, where species m converts chemical m into chemical m+1, the linearised long-wavelength interaction matrix is circulant, so its eigenvalues are Re λ_ℓ = −(αρ0/D)(μ(p)−μ(s))[1−cos(2πℓ/M)] and Im λ_ℓ = (αρ0/D)(μ(s)+μ(p)) sin(2πℓ/M) (Eq. 5). The homogeneous state is unstable exactly when the species are self-attracting, μ(p) − μ(s) < 0 (Eq. 6). For even M the leading mode is real, with stoichiometry (1,−1,1,…), so same-parity species co-aggregate. For odd M the leading mode is a complex pair, and with chasing interactions this gives persistent “invasion–explosion” oscillations. The nonlinear phases were checked by Brownian dynamics at M = 5 and M = 6 only. | Active — read in full 2026-09-25 (NOTE-079); Worth reading as a clean, fully analytic example of how cyclic non-reciprocal coupling produces a circulant spectrum and an odd/even dichotomy. The origin-of-life framing is a proposal the paper does not test, and the authors concede in the peer-review file that the chemotactic mobilities of real prebiotic catalysts are unknown. |
| LIT-039 v2 | Rigorous renormalization group | Kupiainen (2023), DOI-10.1038/s41567-023-02233-x. A Comment, read in the author’s accepted manuscript. Rigorous RG iterates Wilson’s block-spin map on lattice Hamiltonians. Each step is controlled by a polymer (cluster) expansion that converges where fields are small and treats large fields as improbable. It proved Gaussian long-distance behaviour for massless 4D lattice φ⁴ and constructed the 2D Gross–Neveu model. Aizenman and Duminil-Copin showed continuum 4D φ⁴ is always Gaussian. The method is limited to near-Gaussian regimes. | Active — read 2026-10-14 (NOTE-821) in full, from the author’s accepted manuscript in the University of Helsinki repository; worth reading as a three-page orientation, by one of its principals, to what rigorous renormalization group is: Wilson’s block-spin step iterated, with each step made rigorous by cluster expansions that separate small and large fields, and what it proved (Gaussian long-distance behaviour of massless 4D lattice φ⁴; continuum 4D φ⁴ trivial; Gross–Neveu constructed). Read it knowing that it is a Comment with no proofs, that it speaks for the block-spin school, that it says nothing about learning, and that its claim that a non-perturbative formalism is missing is the author’s judgement. |
| LIT-041 v2 | The Work Capacity of Channels with Memory: Maximum Extractable Work in Percept-Action Loops | Fiderer et al. (2025), ARXIV-2504.06209. The paper models agent and environment as coupled finite hidden-Markov channels. It defines the environment’s work capacity C_work = max over agent models of ⟨H(A_t|M_t) − H(S_t|M_t)⟩_t (in k_BT ln 2 per round) and proves two things. First, for unifilar environments whose percepts ignore actions, the efficient agents are exactly the randomize-and-forget ∩ maximally-predictive ones, and C_work = log|A| − h(S). Second, one binary memoryless environment exists where predictive, max-entropy-action and efficient agents form three nonempty, pairwise-disjoint sets: every predictive agent extracts ≤ 0, uniform-random agents extract 1 − h(3/4) ≈ 0.189 bits, and the optimum is ½·log₂(3/4 + 1/√2) ≈ 0.272 bits, reached by a memoryless agent that plays action 0 with probability 1/√2. | Active — read in full 2026-09-25 (NOTE-032); worth reading for anyone working on the thermodynamics of prediction or agency. It gives a clean, fully proved extension of the tape-setting results (Boyd–Mandal–Crutchfield 2018) to feedback loops, and a sharp counterexample to “prediction is necessary for efficiency”. Read it knowing that the headline “trade-off” is shown by one existence example, that the example’s optimum simply forgets everything, and that Table I prints the memoryless-channel capacity with its sign flipped. |
| LIT-057 v2 | Effect of delay on the emergent stability patterns in generalized Lotka–Volterra ecological dynamics | Saeedian et al. (2021), ARXIV-2110.11914. The paper studies random delayed generalized Lotka–Volterra dynamics, ẋ_i = x_i(r_i + Σ_j b_ij x_j(t−τ)), with instantaneous interactions switched off (A = 0) in every delay result. A feasible, stable equilibrium loses stability by a Hopf bifurcation at τ_c = min over eig(J) of (1/|j|) arctan(Re j/Im j) (Eq. 14), where J = diag(−B⁻¹r)B, and this matches simulation (Fig. 5b; S = 100 is stable at τ = 12 and oscillates at τ = 18). In the oscillatory regime, at τ = 20 and 22 for S ≲ 70, community-level CV falls with S while mean species-level CV rises (Fig. 6). The paper reads this as a positive diversity–stability relation but tests it against no averaging null. | Proposed — read in full 2026-09-25 (NOTE-061); A modest, partly numerical preprint whose critical-delay formula is the standard linear delay result applied to a random community matrix. Its diversity–stability claim would be settled by comparing CV_c(S) against the √S averaging expected from weakly correlated oscillators (the “statistical inevitability” null of Tilman et al. 1998, which the paper cites as ref. 40), and by resolving whether the “divergent” phase is numerical or real. |
| LIT-059 v3 | The Strongest El Niño Ever | Hausfather (2026), https://www.theclimatebrink.com/p/the-strongest-el-nino-ever. Hausfather reports that the July 2026 runs of 14 seasonal models (667 members, model-weighted) put the median peak Niño 3.4 anomaly of the 2026-27 El Niño at 3.6 °C, against his computed record of 2.75 °C (2015-16). That gives about a 91% chance of a record, or about 77% on a relative index where 1982-83 holds the record at 2.69 °C. He cautions that no model has been verified at this intensity. - NOAA’s own series agree on the rankings but give lower record values: 2.67 monthly for 2015-16 and 2.6 in ONI. - Observations through mid-September 2026 are on a record-setting track: weekly Niño 3.4 +3.0 °C on 16 Sep, and monthly ERSSTv5 +2.17 in August. The event has not yet peaked, so the forecast cannot yet be verified. | Proposed — read in full 2026-09-25 (NOTE-031); This is a dated forecast. What settles it is the observed 2026-27 peak, i.e. monthly ERSSTv5 Niño 3.4 and RONI through about February 2027. The observations to mid-September are consistent with a record but do not yet reach 3.6 °C. |
| LIT-069 v2 | Surface optimization governs the local design of physical networks | Meng et al. (2026), DOI-10.1038/s41586-025-09784-4. The degree counts in Fig. 1d show k = 4 nodes making up 4.6–17.7% of branch points across the six datasets. The pooled 16.6% is 96% human-neuron nodes. Bifurcation angles also fail to peak at 2π/3. From this the authors infer that local branching minimises sleeve surface area under a minimum circumference w, not wire length. For a regular tetrahedron their numerical minimiser merges two bifurcations into a trifurcation at χ = w/r ≈ 0.83, and a thin branch sprouts orthogonally below ρ = w′/w ≈ 0.6. Per-dataset empirical thresholds are ρ_th = 0.52–0.92. The “exact mapping” to string-theory worldsheets covers only the unconstrained minimal-area problem. The SI says the implemented method yields surfaces that are only locally area-minimising (§5). | Proposed — read in full 2026-09-25 (NOTE-075); a promising and cleanly falsifiable hypothesis, but the evidence does not yet separate it from simpler accounts. Three things would settle it: recomputing the empirical P(λ) without the SI’s trifurcation-merging rule, running the actual surface minimiser (rather than a sigmoid fitted to one tetrahedron) on random terminal sets, and testing the branching-to-sprouting breakpoint against a no-breakpoint null. |
| LIT-074 v3 | What is polycrystalline water? | AlphaPhoenix (unverified), https://www.youtube.com/watch?v=g7ONBuVtz-w. unverified — Only the title and channel are reachable, so I can state no claim from the video. By its title it is a popular-science explainer about polycrystalline (multi-grain) ice or water. | Unavailable — seeded 2026-09-25 from the title and channel; on 2026-10-14 it is still not read and no NOTE is filed. It is a video, and a text-only client cannot watch a video, so only a transcript could serve. YouTube’s watch page redirected to a Google bot-check (‘sorry’) page with HTTP 429, so no caption track list, description or upload date was reached, and the unsigned timedtext endpoint returned an empty body. No lawful transcript was reached; this failed on access, not availability. A second attempt on 2026-10-14, at the owner’s direction that the transcript suffices, also failed on access, not availability: YouTube’s transcript API (youtube-transcript-api: IpBlocked), yt-dlp (“Sign in to confirm you’re not a bot”), the Invidious mirrors inv.nadeko.net, yewtu.be and invidious.nerdvpn.de (browser checks or protocol errors), the Piped API (the same LOGIN_REQUIRED bot check upstream) and a plain page fetch (navigation only). oEmbed confirms the title and the channel (AlphaPhoenix). A transcript the owner supplies would let it be read. It stays Unavailable until a transcript is supplied. |
| LIT-076 v2 | Performing all-atom molecular dynamics simulations of intrinsically disordered proteins with replica exchange solute tempering | Koneru et al. (2025), ARXIV-2505.01860. A how-to chapter for REST2 enhanced sampling of intrinsically disordered proteins in GROMACS 2022.5 with PLUMED 2.9.0, worked on the α-synuclein C-terminal fragment (residues 121–140) with the a99SB-disp force field and water. The example uses 10 replicas, a solute-temperature ladder from 300 K to 450 K, swap attempts every 1.6 ps, and a ≥ ~20 % acceptance target. Its load-bearing methodological point is that high swap acceptance “is not, in isolation, sufficient evidence of robust conformational sampling or convergence”. Convergence has to be judged by comparing demultiplexed replicas’ structural distributions, with blocking-analysis errors. | Active — read in full 2026-09-25 (NOTE-076); A practical, current protocol worth reading for anyone setting up REST2 on an IDP, especially the starting-structure advice and the demultiplexed-replica convergence checks. It is a tutorial, not a benchmark: it reports no quantitative results and makes no comparison with REST3, REHT or tREMD. It also has a few textual errors, listed below; the repository is the ground truth for the example. |
| LIT-077 v2 | What is quantum in quantum randomness? | Grangier & Auffèves (2018), ARXIV-1804.04807. The paper argues informally, with no equations anywhere in it, that an “elementary” system with a fixed finite number N of exclusive modalities, placed in contexts that can change, must behave unpredictably when the context changes: a return to C1 after C2 cannot be certain, or there would be N² > N joint modalities (p. 4). It asserts that adding one condition, that the context can change continuously, makes the N×N modality-transition matrix unistochastic, i.e. Born-rule, but defers that proof to refs [14, 15] (p. 5). The anti-reductionist conclusion follows from Postulate 0, which declares contexts non-contextual by definition, not from an argument against decoherence. | Active — read in full 2026-09-25 (NOTE-044); a short, equation-free position paper whose one argument of its own is an informal N = 2 reductio; read it for the position, and read the derivation it cites — Auffèves & Grangier, Sci. Rep. 2017 (arXiv 1610.06164) and arXiv 1801.01398, neither held here — for the result. |
| LIT-082 v2 | Unification of observational entropy with maximum entropy principles | Schindler et al. (2025), ARXIV-2503.15612. The paper defines S^τ_M(ρ) = S(τ) − D_M(ρ‖τ) = −Σ_x p_x log(p_x/V_x), with V_x = Tr(τM_x)e^{S(τ)} (Eqs. 10–12). It is bounded as S(τ) ≥ S^τ_M(ρ) ≥ S(ρ) when ρ obeys the constraint S(ρ;τ) ≤ S(τ) (Eqs. 17–18). It reduces to 24 listed entropies, and it removes traditional observational entropy’s infinite-dimensional pathologies whenever S(τ) < ∞ (§VIII.7). Its “second laws” are bounds D_M(ρ̄‖τ) ≤ ε on the time-averaged state, split as equilibration plus prior-fit (Eq. 27). The paper proves the first term small in two regimes (Eqs. 28–29) and the second only under the ETH (Eq. 31). It states that in its own numerical examples the smallness “was [not] proved here analytically” (p. 12). | Active — read in full 2026-09-25 (NOTE-043); worth reading as the reference definition of prior-generalised observational entropy and for its catalogue of special cases (§V, Table II). The unification is definitional and its bounds are correct. The second-law programme is a framework plus partial sufficient conditions, not a proved second law for any concrete system. |
| LIT-108 v3 | Philosophy of Mathematics and Natural Science | Weyl (1949), DOI-10.1515/9781400833337. Philosophy of mathematics and philosophy of physics are intertwined, with advances in philosophy led by scientific discovery. Weyl’s two-part treatment (mathematics, then natural science), drawing on Descartes, Galileo, Hume, Kant, Leibniz and Newton, is a classic mathematician-physicist’s statement of that view. | Unavailable — seeded from the abstract on 2026-09-26; a close reading was attempted the same day and found the book in copyright with no open copy: every Internet Archive scan (the 1949, 1959 and 1963 printings) is lending-only, and the De Gruyter e-book is paywalled. It stays Unavailable until a copy is supplied. |
| LIT-110 v3 | Unknotting reciprocal causation between organism and environment | Baedke et al. (2021), DOI-10.1007/s10539-021-09815-0. The paper gives an epistemic, not a metaphysical, tool for organism–environment reciprocal causation. The loop is “unrolled” into two ordered series of states, O_n and E_n, joined by interventionist (Woodward) causal arrows, and an experienced-environment node Ex_n is added as the interface. Its authors argue that this one diagram keeps an epistemically set organism–environment boundary and maps constitutive, mediational, relational, relocational and physical niche construction onto shared causal patterns. They support this with worked cases, including two multi-species ones (bumblebee–eggplant; rumen microbes–ruminant host). | Active — read in full 2026-09-26 (NOTE-111); worth reading as the clearest statement of the “keep the boundary, unroll the loop” position in the niche-construction reciprocity debate, and as the natural counterpart to Hazelwood (LIT-156); its model is illustrative, not formalized or tested, and the formalization it promises is deferred to later work. |
| LIT-114 v2 | Philosophy of Statistical Mechanics | Frigg & Werndl (2023), https://plato.stanford.edu/entries/statphys-statmech/. The entry argues that statistical mechanics has no canonical formalism but three umbrellas — Boltzmannian SM, the Boltzmann Equation and Gibbsian SM — and that every live account of the approach to equilibrium (ergodic, typicality, Mentaculus, long-run residence time, coarse-graining, interventionist, epistemic) survives Loschmidt’s and Zermelo’s objections only by giving up strict irreversibility or adding something outside the isolated dynamics; it closes on the unresolved “schism” that physicists compute in GSM while philosophers explain in BSM. | Active — read in full 2026-09-26 (NOTE-103); worth reading as the current authoritative map of the foundations of SM, with the caveat that it is written by two partisans who present their own long-run residence time account (§4.7) and their “BSM fundamental, GSM effective” view (§6.7) alongside the rivals. |
| LIT-127 v2 | Hutchinson’s ecological niche for individuals | Takola & Schielzeth (2022), DOI-10.1007/s10539-022-09849-y. The paper defines the individualized (ecological) niche as the environmental conditions under which a particular individual has an expected lifetime reproductive success of ≥ 1, counting each offspring as 0.5 per parent in outcrossers. The authors split it into five sub-concepts: realized (A), potential (B), time-slice (C), prospective (D) and trajectory-based (E), plus a “fundamental individualized niche” set aside as practically interchangeable with the potential niche. The individual niche has n + s dimensions, adding intraspecific axes such as density and morph frequency. Its boundary is the expected-LRS isocline of 1, which is estimable only by marginalizing fitness functions across individuals. The authors themselves call the concept “mostly of a metaphorical value”. | Active — read in full 2026-09-26 (NOTE-170); worth reading as the clearest structuring of the “individualized niche” vocabulary, and as the individual-level complement to Trappes (LIT-169); it is a behavioural-ecology position essay, and its own admission that the potential niche is unobservable and estimable only from population-level marginalization limits it to a framework rather than a measurement result. |
| LIT-141 v3 | Emergence: from physics to biology, sociology, and computer science | McKenzie (2025), ARXIV-2508.08548. Sole-authored survey by a condensed-matter physicist. It takes novelty (a property the parts lack) as the defining mark of emergence and sets it against twelve other characteristics in §2. The six “objective” ones are discontinuities, order, modification of parts, universality, diversity and mesoscale modularity. The six “subjective” ones are self-organisation, unpredictability, irreducibility, contextuality/downward causation, complexity and intra-stratum closure. Case studies from the Ising model to Schelling segregation and LLMs show that each can come apart from novelty: novelty without discontinuity (Kondo, Fermi liquids, spin ice), without unpredictability (BKT, spin ice), and with reduction (Butterfield). §22 sides with weak emergence and argues that strong-emergence claims from molecular structure are weak. | Active — read in full 2026-09-26 (NOTE-124); worth reading as a hub reference and example catalogue on emergence from physics outward, with unusually concrete case studies and a sceptical physicist’s §15 on molecular structure. It is a survey and a position, not a proof. Its definitional framework is stipulated and its logical relations between characteristics are left open by its own account (§24). |
| LIT-156 v4 | An Emerging Dilemma for Reciprocal Causation | Hazelwood (2023), DOI-10.1017/psa.2023.124. Hazelwood defines RC as “the process of natural selection is both a cause and effect of processes such as niche construction” and EC as “natural selection is an emergent causal process”. He argues they are incompatible. Emergence here is Wilson’s synchronic dependence plus autonomy, cashed out as Pence’s composition. If EC holds, niche construction partly composes selection, so the two fail Woodward’s independent-fixability condition and cannot stand in a causal relation. If EC fails, selection is either non-causal (statisticalism) or individual-level, which is incoherent because relative fitness needs a population (Millstein, Sober). EES proponents should drop RC but can keep niche construction as a genuine cause of the evolutionary product. | Active — read in full 2026-09-26 (NOTE-137); worth reading as a tight, well-sourced argument that brings the reciprocal-causation debate into the composition, exclusion and interventionism literature. Its force depends on accepting a process/product split for selection and a compositional reading of realization, both argued briefly and flagged as contestable. |
| LIT-157 v3 | Reproducees, reproducers, and Darwinian individuals | Bourrat (2025), DOI-10.1007/s11229-024-04880-w. Bourrat builds a nested vocabulary. A reproducee is a B that comes after A, is caused by A, and is of A’s relevant class. A reproducer is a reproducee with reproductive autonomy, meaning it can reproduce across a range of backgrounds. A Darwinian individual is a reproducer with high reproductive causal control, meaning heredity survives as the parent’s description is made finer. On that vocabulary, genes of multicellular organisms are, like hearts, mere reproducees, but with high control. Material overlap is necessary for reproducers, which are whole life cycles, and unnecessary for reproducees, so Griesemer and Godfrey-Smith partly talk past each other. Both quantities get an information-theoretic recipe (conditional MI after Bertschinger et al. 2008 for autonomy; interventional MI across grains, Griffiths et al.’s INF, for control), and neither is computed. | Active — read in full 2026-09-26 (NOTE-100); worth reading as the clearest statement of the reproduced/reproducing distinction and a tidy, well-scoped settlement of the material-overlap dispute. Its value is conceptual. Its two measures are recipes that are never computed, and the autonomy recipe does not match its own verbal definition. |
| LIT-160 v2 | Units and Levels of Selection | Lloyd (2005), https://plato.stanford.edu/ENTRIES/selection-units/. Lloyd’s own four-question anatomy of “unit of selection”: interactor, reproducer (formerly replicator), manifestor of adaptation, and beneficiary. She combines it with a split between two multilevel schools, Wrightian “Evolutionary Change” and Fisherian “Adaptationist/KS”. She uses the two to argue for a verdict, not merely to map the debates. The verdict is that most rejections of group, species and holobiont selection come from demanding that an interactor also be a manifestor of engineering adaptation. By her account, genic pluralism, the ETI models and Godfrey-Smith’s Darwinian populations each fuse roles that should be kept apart. The support is argument plus citation of Wade, Goodnight and others. The entry reports no new results of its own. | Active — read in full 2026-09-26 (NOTE-184); worth reading as the authoritative statement of the interactor / reproducer / manifestor / beneficiary distinction and as a dense map of the units-of-selection literature to 2023. It has to be read as one side’s case. It is not a neutral survey: it argues for the Evolutionary Change school, and it criticises by name several authors this record holds or cites. |
| LIT-169 v2 | Defining the niche for niche construction: evolutionary and ecological niches | Trappes (2021), DOI-10.1007/s10539-021-09805-2. Trappes compares NCT’s evolutionary niche with the ecological niche. The evolutionary niche is the sum of selection pressures on a population (Odling-Smee, Laland & Feldman 2003), read “externally” as the environmental factors that produce fitness differences. The ecological niche is the conditions that permit continued existence; for a population, mean absolute fitness ≥ 1. Even at their closest, against the realized population niche, the two differ in extension. Habitat degradation is in the evolutionary niche but not the ecological one, and commensalism and non-limiting resources are in the ecological niche but not the evolutionary one. So NCT’s niche is not the “simple translation” of Hutchinson’s niche its proponents claim, and the evolutionary significance of niche construction must be shown case by case rather than following from the definition. | Active — read in full 2026-09-26 (NOTE-155); worth reading as a short, clean conceptual analysis that turns “persistence versus fitness differences” into a precise wedge between two fields’ uses of “niche”; its empirical cases are admittedly thin (the CO2 case is offered as “possible”), and it analyses only the 2003 book’s niche concept. |
| LIT-175 v3 | Evidence in Medicine and Evidence-Based Medicine | Worrall (2007), DOI-10.1111/j.1747-9991.2007.00106.x. Worrall argues that the EBM evidence hierarchy has no sound general rationale for giving randomisation extra epistemic weight, even though it lets high-quality RCTs “trump any number of observational studies”. He examines five standard arguments. Four fail: (a) Fisher’s significance-test logic, (b) control of unknown confounders, (d) that observational studies “exaggerate” effects, and (e) probabilistic causality. The fifth, (c) selection bias, is a “cast-iron argument”, but it supports only taking allocation out of the clinicians’ hands, and randomisation is one way to do that. What matters is balance on plausible confounders, a placebo or active control and blinding. Whether balance comes from randomising or from matching “seems epistemically unimportant”, and historically controlled trials can give strong evidence for large effects. | Active — read in full 2026-09-26 (NOTE-126); worth reading as the fullest single statement of the philosophical case against the special epistemic standing of randomisation. It is clearly argued and well documented, and it explicitly concedes the selection-bias argument. It is a partisan position piece, and its defenders-of-randomisation opponents (Pocock, Elbourne, Papineau) are summarised, not engaged at length. |
| LIT-180 v3 | Symmetry and Conservation Laws | Wigner (1964), DOI-10.1073/pnas.51.5.956. Wigner argues that invariance principles stand to the laws of nature as laws stand to events — they give structure to the laws — and distinguishes geometrical invariances (formulated on events; yielding energy/momentum/angular-momentum conservation, most directly in quantum kinematics) from dynamical ones such as gauge invariance and, he holds, general covariance, which are tied to specific interactions. | Unfetched — seeded from the abstract and a skim on 2026-09-26 (the skim read a Wayback copy of the PNAS scan); a close reading was attempted the same day and could not fetch the paper: the Wayback Machine reset its connections, Europe PMC refused the PDF, and PMC returned a challenge page. The paper is open in the PNAS archive, so this is an access failure, not a paywall. It stays Unfetched until it can be fetched. Free copy: doi:10.1073/pnas.51.5.956 (the PNAS open archive; also PMC300191). |
| LIT-188 v5 | Scaffolding individuality: coordination, cooperation, collaboration and community | Griesemer & Shavit (2023), DOI-10.1098/rstb.2021.0398. The paper sets out an idealized three-stage sequence of interaction types, which it calls a “first and rough sketch” (§1). Stage 1 is coordination in collections (pairwise, “aggregative” interactions of co-located individuals). Stage 2 is cooperation in conexuses (a connected web of binary interactions whose benefits can still be counted per member). Stage 3 is collaboration in communities: heterogeneous multi-way interactions around a shared goal, in which generatively entrenched “core” interactions give organizational closure. Table 1 puts the transition to a new level of individuality between stages 2 and 3 only. The paper asserts, rather than argues, that this describes evolutionary transitions non-circularly and that individuality is a special case of collectivity. Its one argued conclusion is hedged: community-level inheritance “seem[s] likely to evolve in tandem” with community-level individuality (§3). | Proposed — read in full 2026-09-26 (NOTE-173); a short programmatic sketch, and the authors call it one. It is worth knowing as the compact statement of Griesemer’s scaffolding, reproducer and generative-entrenchment view applied to human social transitions. Its headline claims (non-circularity; individuality as a special case of collectivity) appear only in the abstract. Two things would settle it: the model of community “reliability” and endogenization the authors promise in §2 (“We hope to explore such models in future work”), or an application of the 3Cs to a worked case, such as the companion Neolithic paper (LIT-1935, registered unread), that separates collection, conexus and community by measurable criteria. Re-read 2026-11-01 (NOTE-173, version 3). |
| LIT-201 v2 | Alternative formulations of multilevel selection | Damuth & Heisler (1988), DOI-10.1007/BF00647962. Multilevel selection comes in two formulations — MLS1, the effects of group membership on individual fitness, and MLS2, groups’ own tendencies to go extinct or found new groups — which answer different questions about one process, and much of the group-selection and species-selection dispute comes from running them together. | Unavailable — seeded from the abstract on 2026-09-26; a close reading was attempted the same day and found the article paywalled at Springer, with no open, repository or author copy. It stays Unavailable until a copy is supplied. |
| LIT-205 v2 | One equation to rule them all: a philosophical analysis of the Price equation | Luque (2016), DOI-10.1007/s10539-016-9538-y. Luque argues that the Price equation, Δz̄ = Cov(w, z) + E(wΔz) (eq. 1, p. 7), is a Kuhnian “generalization-sketch”, like f = ma. It is not a model, has no predictive power on its own, and becomes empirical only when a specific model interprets it. On that reading the critics’ charges (van Veelen 2005; van Veelen et al. 2012; Nowak & Highfield 2011) that it is “a tautology” and “lacks predictive power” are either false or ask too much, and he recommends that evolutionary biologists adopt it as their unifying framework. | Active — read in full 2026-09-26 (NOTE-101); worth reading as a clear statement of the generalization-sketch reading of the Price equation and as a map of its extensions up to 2015 (Tables 2–3). The philosophical argument is thin in places, notably the Gödel-based case that it is “not a tautology”, so it should be read as one side of the dispute and not as a settlement of it. |
| LIT-210 v2 | Philosophy of Microbiology | O’Malley & Parke (2020), https://plato.stanford.edu/entries/microbiology/. O’Malley & Parke argue in four steps that philosophy should attend to microbes. Microbes do most of the planet’s biological work and underlie every major transition. Microbiology founded medicine, molecular biology and genomics. Microbes are unusually good material models, including for phenomena once defined by animals (predation, ageing, kin recognition, cognition). Microbiome research bears on individuality and causation. They are sceptical about the strongest microbiome claims. Whether host and microbiome form one unit of selection is “still disputed”. Claims that microbiomes change the “self” are “usually expressed in very vague language”. The 2026 revision adds that Asgard-archaea phylogenies may make eukaryogenesis “first and foremost a story about diversification within Archaea” rather than a transition in individuality. | Active — read in full 2026-09-26 (NOTE-159); worth reading as a short, current (April 2026) orientation to where microbes change philosophy of biology, with a useful deflationary check on microbiome-and-self claims. It is a survey with no thesis beyond “pay attention to microbes”; for individuality it points onward to the Biological Individuals (LIT-168) and Units and Levels of Selection (LIT-160) entries. |
| LIT-211 v3 | What Lives? A meta-analysis of diverse opinions on the definition of life | Bender et al. (2025), ARXIV-2505.15849. Three LLMs (Claude 3.7 Sonnet, GPT-4o, Llama 3.3 70B), each run 3 times on both orderings of every pair, rated 68 hand-solicited definitions of life on a −1 to 1 “correlation” rubric. The averaged matrix, cut by complete-linkage clustering at an elbow, gives 8 clusters, 45/68 of them (66%) in “Cognitive Autonomy” (n=24) and “Dissipative Self-Organizing Systems” (n=21). The clusters are weak: the repo’s own saved statistics give an overall silhouette of 0.079, and cross-model agreement is an unadjusted Rand index of 71–79% against a chance level of about 62–74%. The headline that life is “a continuous semantic landscape” is not tested against any alternative. | Active — read in full 2026-09-26 (NOTE-109); worth reading as a dataset: 68 signed, three-sentence definitions of life from named researchers, with a manual thematic coding (Table 1). Its computational conclusions are weakly supported and are better read as illustrations than as findings. |
| LIT-301 v3 | Every Thing Must Go: Metaphysics Naturalized | Ladyman et al. (2007), DOI-10.1093/acprof:oso/9780199276196.001.0001. Argues for a naturalized metaphysics constrained by physics, defending ontic structural realism and a ‘rainforest realism’ of real patterns (building on Dennett 1991) with no self-subsistent individuals (per standard description). | Unavailable — seeded 2026-09-29 from metadata and published descriptions, not read: registered because the owner’s prior-art novelty map cites it. A close reading was attempted on 2026-09-29 and no legitimate full text could be reached; it stays Unavailable until a copy is supplied. |
| LIT-308 v2 | Stochastic Thermodynamics of Learning | Goldt & Seifert (2017), DOI-10.1103/PhysRevLett.118.010601. For a perceptron whose weights follow overdamped Langevin dynamics and whose predicted labels are fast two-state processes, the information learnt about fixed random labels is bounded by the weights’ total entropy production: Σ_μ I(σ_T^μ:σ^μ) ≤ Σ_n [ΔS(ω_n) + ΔQ_n] (Eq. 16, k_B = T = 1). This defines a learning efficiency η ≤ 1. The cost side includes the change in the weights’ own Shannon entropy, and in the paper’s toy model η → 0.99 as the heat ΔQ → 0 (slow driving). So the bound is not a heat floor of k_BT ln 2 per bit learnt. | Active — read in full 2026-09-29 (NOTE-296); worth reading as the founding letter of the “stochastic thermodynamics of learning” line, and as the precise statement of what learning costs in that framework: entropy production, of which heat is only one part. Read the main-text claim “for arbitrary learning algorithm … at all times” alongside its supplement. The derivation uses a γ ≫ 1 (fast-label) limit and a weight-independence step that holds for batch but is not argued for online learning. |
| LIT-321 v3 | Local Quantum Physics: Fields, Particles, Algebras (2nd ed.) | Haag (1996), DOI-10.1007/978-3-642-61458-3. Per publisher description: a monograph on algebraic (local) quantum field theory, treating physics through nets of local observable algebras, including the theory of superselection sectors and charges. | Unavailable — seeded 2026-09-29 from metadata and published descriptions, not read: registered because the owner’s prior-art novelty map cites it. A close reading was attempted on 2026-09-29 and no legitimate full text could be reached; it stays Unavailable until a copy is supplied. |
| LIT-327 v2 | Thermodynamics of Prediction | Still et al. (2012), DOI-10.1103/PhysRevLett.109.120604. For a system driven by a stochastic signal through a fixed Markov kernel, the average work dissipated as the signal steps x_t → x_{t+1} equals, in units of k_BT, the system’s instantaneous nonpredictive information, I[s_t;x_t] − I[s_t;x_{t+1}] (Eq. 14). Summed over a protocol, this total “nostalgia” lower-bounds dissipation and excess work (Eq. 18), and it adds to Landauer’s bound: −β⟨Q⟩ ≥ I_e + I_mem − I_pred (Eq. 21). All three are averages over paths and protocols. None of them is a per-operation or per-bit floor on the cost of storing or using predictive information. | Active — read in full 2026-09-29 (NOTE-295); worth reading as the short, exact source of “memory that does not predict costs dissipation” and of the nostalgia-augmented Landauer bound. Read it knowing three things. The bound prices only the nonpredictive part of memory. The nonnegativity of the per-step nostalgia needs a Markov drive, which the paper does not say. And nothing in it supplies a k_BT ln 2 floor per judgment. |
| LIT-328 v3 | Irreversibility and Heat Generation in the Computing Process | Landauer (1961), DOI-10.1147/rd.53.0183. Argues that logically irreversible operations (e.g. erasure) in computation must dissipate at least about kT ln 2 of heat per bit, tying the thermodynamic cost of computing to information loss. | Unavailable — seeded 2026-09-29 from metadata and published descriptions, not read: registered because the owner’s prior-art novelty map cites it. A close reading was attempted on 2026-09-29 and no legitimate full text could be reached; it stays Unavailable until a copy is supplied. |
| LIT-339 v2 | The intrinsic parity of elementary particles | Wick et al. (1952), DOI-10.1103/PhysRev.88.101. The paper defines a superselection rule: a decomposition of Hilbert space into orthogonal subspaces A, B, C, … between which there are no spontaneous transitions and no measurable quantities with non-zero matrix elements. Relative phases across subspaces, and hence relative parities, are then unobservable. It proves such a rule between integer and half-integer angular momentum, from time reversal with U_AKU_AK = +1 and U_BKU_BK = −1. It postulates, without conclusive evidence, a charge superselection rule. The consequence is that “all Hermitean operators represent measurable quantities” must be abandoned. | Active — read in full 2026-09-29 (NOTE-304); worth reading as the origin of the superselection concept and its first argued instance (univalence). It is short, and its definition is still the one used. The algebraic form (sectors as the centre of the observable algebra) is later work; Haag’s book, LIT-321, is the place for that. |
| LIT-360 v2 | Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon | Bennett (2002), arXiv:physics/0210005. Bennett states Landauer’s principle as a consequence of the Second Law. A logically irreversible step, meaning erasure or a merge of control flow, must export at least the lost entropy (k ln 2 per bit) to non-information-bearing degrees of freedom. That export need not take the form of heat (p. 1). Logically reversible operations, including copying onto a blank register and measurement, have no minimum cost. He calls “an intrinsic cost of order kT for every elementary act of information processing” a 20th-century “misconception” (pp. 5–6). Erasing random data can itself be thermodynamically reversible; the waste comes from applying a many-to-one operation to known data (pp. 1, 4). | Active — read in full 2026-09-29 (NOTE-310); Worth reading as a short, first-hand statement, by the principle’s main defender, of what Landauer’s principle requires (logical irreversibility) and what it does not (any cost for acquiring, copying or evaluating information). It is the best reachable stand-in for the unreachable LIT-328. Read it knowing that it is an argued position paper, not a derivation. On the Earman–Norton “unnecessary or insufficient” dilemma Bennett concedes the point “with some justice” (p. 5) and defends the principle only as pedagogy. |
| LIT-361 v2 | Superselection Rules for Philosophers | Earman (2008), DOI-10.1007/s10670-008-9124-z. A supplemental reading for the owner’s prior-art novelty map, where an earlier reading found the map’s citation wrong or unreachable. | Unavailable — seeded 2026-09-29 as a supplemental reading for the owner’s prior-art novelty map; a close reading was attempted and no legitimate full text could be reached |
| LIT-388 | The nature of feelings: evolutionary and neurobiological origins | Damasio & Carvalho (2013), Nature Reviews Neuroscience 14:143–152. Feelings are mental experiences of body states, and they report homeostatic value: a valenced read-out of interoceptive maps that lets an organism learn and anticipate what restores or threatens its physiology. The first integrated whole-body maps are in the upper brainstem (parabrachial nucleus, periaqueductal grey, deep superior colliculus); the insula refines feeling but is not needed for it, since a patient with both insulae destroyed still feels pain, pleasure, hunger and compassion. The authors propose, without evidence of their own, that feeling starts in unmyelinated interoceptive fibres open to ions and ligands along their length. | Active — read in full 2026-10-01 (NOTE-330); worth reading as the shortest statement of Damasio’s account of feeling as the felt read-out of homeostatic body maps, with its two empirical planks: patients whose insulae are destroyed still feel, and the upper brainstem is where whole-body interoceptive maps first assemble. It is an Opinion piece with no new data. The systems-level case rests on lesion and stimulation evidence it cites; the cellular proposal (unmyelinated interoceptive fibres and ephaptic coupling as the root of sentience) is offered as a hypothesis and stays one. |
| LIT-424 v2 | From Bacteria to Bach and Back: The Evolution of Minds | Dennett (2017), W. W. Norton. Per its publisher, the book shows “step by step, how a comprehending mind could in fact have arisen from a mindless process of natural selection”, with the decisive shift the sharing of memes, which produced “thinking tools” powerful enough that minds “create and comprehend”. Its contents run from the origin of reasons and “two strange inversions of reasoning”, through information, “brains made of brains”, words, memes and the origins of language, to consciousness as “an evolved user-illusion” and “the age of post-intelligent design”. Unread: registered from the description and the catalogue’s contents note. | Unavailable — registered 2026-10-02 from the publisher’s description and the catalogue record’s contents note, not read: no lawful full text could be reached. The Internet Archive scan is lending-only, Norton posts no excerpt beyond its description, and Dennett posted no draft chapters that I could find. It stays Unavailable until a copy is supplied. The claim the record wants from it, competence without comprehension, is not stated in the description or the contents, so nothing here places it. |
| LIT-439 | The Computational Boundary of a “Self”: Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition | Levin (2019), Frontiers in Psychology 10:2688. Proposes “Scale-Free Cognition”: an Individual or Self is the set of parts that pursue a goal together, bounded by the farthest events in space and time it can measure and try to change (its “cognitive light cone”). Selves scale up from homeostatic loops through memory and anticipation, and cells merge into larger Selves by sharing bioelectric state through gap junctions; cancer is the boundary shrinking back to one cell. Because every level that pursues its own goal is a Self, most living systems hold many nested, coexisting Selves, “not one, as implied by Integrated Information Theory”. Levin’s “Self” is a goal-pursuing collective, an agent and an individual in this record’s terms; the essay gives no account of a self as subject. A hypothesis essay: no model and no new data. | Active — read in full 2026-10-02 (NOTE-341); worth reading as the composition-side statement that agency is nested by default: a Self is whatever set of parts pursues a goal together, so cells, organs, organisms and swarms are Selves at once, each bounded by its “cognitive light cone”. It is a hypothesis-and-theory essay with no model, no measurement procedure for the light cone and no data of its own. Its one sentence against IIT’s single-Self picture is asserted in a bracket, not argued, and its consciousness claims are confined to a closing speculation. |
| LIT-495 v2 | The Biology of Moral Systems | Alexander (1987), DOI-10.4324/9780203700976 (the 2017 Routledge reissue). By the publisher’s account, moral questions arise from conflicts of interest, and moral systems use confluences of interest at lower levels of organization to manage conflicts at higher ones; they are “systems of indirect reciprocity”, run on reputation, and morality arose within groups for unity in intergroup competition. Unread: filed from the publisher’s description and chapter titles. | Unavailable — filed 2026-10-02 from the publisher’s description and the chapter list, not read: no lawful full text was reachable. The 1987 Aldine de Gruyter edition is lending-only at the Internet Archive (access-restricted, printdisabled), and the 2017 Routledge reissue is paywalled. A complete scan posted on a course blog was found and not used, since posting a whole in-copyright book is not a lawful copy. What the book argues is known here only from the publisher’s description and from Nowak 2006 (LIT-501), which cites it for the claim that indirect reciprocity leads to morality; both are labelled as theirs. It stays Unavailable until a copy is supplied. |
| LIT-497 v2 | The Genetical Evolution of Social Behaviour. I | Hamilton (1964), J. Theor. Biol. 7:1–16. A one-locus model in which an individual’s genotype affects relatives’ fitness. Weighting each effect by Wright’s coefficient of relationship r gives “inclusive fitness”, which tends to be maximized as classical fitness is. An action that costs the actor is favoured only if the benefit to a relative exceeds 1/r times the cost: more than two brothers, four half-brothers or eight first cousins (§5). The increase of mean inclusive fitness is proved only for giving traits; the model is not about morality. | Active — read in full 2026-10-02 (NOTE-401); worth reading as the source of inclusive fitness and of the rule the moral-psychology literature calls Hamilton’s rule. It is a population-genetic model with non-overlapping generations, random mating and weak selection, and its rule appears as −k > 1/r (§5), not in the later rb > c form. It proves that mean inclusive fitness increases only for genes whose total effect on others is non-negative (giving traits); for harming traits it shows only that selection points uphill. It says nothing about morality: it is the kin domain of morality-as-cooperation in its biological form, read as biology. |
| LIT-498 | The Evolution of Cooperation | Axelrod & Hamilton (1981), DOI-10.1126/science.7466396. In an iterated Prisoner’s Dilemma with probability w of meeting again, TIT FOR TAT won two computer tournaments (14 and 62 entries) and an ecological simulation, and no strategy can do better against it when w ≥ max((T−R)/(T−P), (T−R)/(R−S)). ALL D is always stable; reciprocity can still enter through kinship or a cluster, after which a nice stable strategy resists clusters. Applications range from cleaner fish to disease and nondisjunction. | Active — read in full 2026-10-02 (NOTE-411); worth reading as the formal statement of how reciprocity can start, spread and hold: tit-for-tat is robust in Axelrod’s tournaments, cannot be bettered by any mutant when the continuation probability w is high enough, and can enter an all-defect population through kinship or clustering. “Evolutionarily stable” is stronger than what is proved: the proof shows no strategy does better than TIT FOR TAT, and always-cooperate does as well, which Boyd & Lorberbaum (1987) later turned into a proof that no pure strategy is evolutionarily stable in the repeated game. It grounds the exchange domain of morality-as-cooperation; it is not about morality. |
| LIT-501 | Five Rules for the Evolution of Cooperation | Nowak (2006), DOI-10.1126/science.1133755. Five mechanisms let natural selection favour cooperators who pay c to give b: kin selection (r > c/b), direct reciprocity (w > c/b), indirect reciprocity (q > c/b), network reciprocity (b/c > k) and group selection (b/c > 1 + n/m). Each is cast as a 2×2 game, from which conditions for cooperators to be evolutionarily stable, risk-dominant or advantageous follow. Punishment is said not to be a mechanism. Cooperation is proposed as a third principle of evolution. | Active — read in full 2026-10-02 (NOTE-409), main text only; the online supplement with the derivations was not read. Worth reading as the standard short map of mechanisms for the evolution of cooperation (kin selection, direct, indirect and network reciprocity, group selection), each reduced to a benefit-to-cost threshold from a 2×2 game. Every mechanism is modelled with the donation game, so it covers altruism only: mutualism, coordination and conflict resolution, four of morality-as-cooperation’s seven domains, are outside it. Its one sentence on morality credits indirect reciprocity with “the evolution of morality”, citing Alexander (1987). |
| LIT-503 | Morality as Cooperation: A Problem-Centred Approach | Curry (2016), DOI-10.1007/978-3-319-19671-8_2. Morality is “a collection of biological and cultural solutions to the problems of cooperation and conflict recurrent in human social life”. Nonzero-sum game theory yields seven problems (kin, coordination, exchange, hawkish and dovish contest displays, division, possession) and hence seven moral domains, illustrated but not tested. The chapter predicts that non-cooperative behaviour is morally neutral everywhere, and that MFT’s purity domain has no connection to cooperation. | Proposed — read in full 2026-10-02 (NOTE-408); the founding statement of morality-as-cooperation and the place its predictions are stated most sharply, including the one its own tests have not run: that behaviour unrelated to cooperation will be morally neutral, and that no culture’s morality will be about “aesthetics or nutrition” (p. 40). It reports no data. The seven domains are derived from game theory and then illustrated with quotations from philosophers and ethnographers, so the chapter shows the taxonomy is coherent, not that it is the right one. It would be settled by the test LIT-047 lacks: blind coding of all moralized content in one sample, asking whether non-cooperative domains are moralized. |
| LIT-505 | The Logic of Animal Conflict | Maynard Smith & Price (1973), DOI-10.1038/246015a0. Why do animals with dangerous weapons fight conventionally? A simulation of five strategies (Mouse, Hawk, Bully, Retaliator, Prober-Retaliator) shows Hawk is not an evolutionarily stable strategy while Retaliator nearly is, so “limited war” can be favoured by individual selection. In a pure war of attrition no fixed persistence is stable; the ESS is an exponential mixture. There is no Hawk–Dove game and no ownership asymmetry here. | Active — read in full 2026-10-02 (NOTE-404); worth reading as the paper that introduced the evolutionarily stable strategy and showed that “limited war” in animal contests can be favoured by individual selection. It is not the source of the Hawk–Dove game or of owner–intruder conventions, though morality-as-cooperation cites it for both: its strategies are Mouse, Hawk, Bully, Retaliator and Prober-Retaliator, its contestants are symmetric, and its “Retaliator is an ESS” ties with Mouse, so it fails the paper’s own second ESS condition. What it does ground for MAC’s contest domains is restraint backed by retaliation, and, informally, retreat before a visibly superior opponent and honest signals of formidability. |
| LIT-506 v2 | The Genetical Evolution of Social Behaviour. II | Hamilton (1964), J. Theor. Biol. 7:17–52. Part I’s model is generalized, “unrigorously”, into two principles: an animal values a neighbour’s fitness against its own by their relationship, and its social discriminations evolve to make relationship more determinate. They are applied to alarm calls, clones and colonies, the haplodiploid hypothesis for hymenopteran sociality, multiple mating, fights between relatives, sibling competition and seed provisioning. Evidence is anecdotal, and the author reports where it runs against him. | Active — read in full 2026-10-02 (NOTE-410); worth reading as the place inclusive fitness is turned into two general principles (valuing neighbours by relatedness; evolving discrimination that makes relatedness determinate) and tried on warning behaviour, social insects, clones, fights and parental care. The principles are offered as an “unrigorous” generalization of Part I, and the evidence is anecdotal and, by the author’s account, partly contrary. Its §6 on fights is the one place in Hamilton’s pair that touches contests: relatives should fight less, a kin-weighted version of the restraint Maynard Smith and Price derived without kinship. |
| LIT-508 | A mutualistic approach to morality: The evolution of fairness by partner choice | Baumard, André & Sperber (2013), DOI-10.1017/S0140525X11002202. When individuals can choose partners and have equal outside options, a split that gives one side less than it could get elsewhere is not stable, so partner choice selects for sharing the gains of cooperation in proportion to contribution. Competition to be chosen then favours a genuine, non-instrumental sense of fairness. Economic-game results (entitlement effects, merit-based division, need-based mutual aid, proportionate punishment) are reinterpreted as fairness, not altruism. Morality is defined as fairness; kin care and group loyalty are not intrinsically moral. | Active — read in full 2026-10-02 (NOTE-407), with all 28 open peer commentaries and the authors’ Response; worth reading as the strongest single-mechanism cooperative theory of morality and as the parent of moral disciplining (LIT-101). It is a cooperation theory that cuts the other way from morality-as-cooperation: partner choice selects one moral sense, fairness, and kin care and group loyalty are not intrinsically moral. Its evidence is a reinterpretation of others’ economic-game results, and its central formal claim is cited from the authors’ separate model. The commentaries (Graham, Ramlakhan & Brook, Machery & Stich, Sachdeva et al., Atran) press the purity, harm and scope objections, and the Response answers them two ways because the authors disagree among themselves. |
| LIT-510 | The Evolution of Reciprocal Altruism | Trivers (1971), DOI-10.1086/406755. Altruism between non-relatives can be selected if acts cost the giver less than they benefit the recipient, the same partners meet repeatedly and symmetrically, and altruists stop helping those who fail to reciprocate. Cleaner-fish hosts fit; bird alarm calls are explained instead by self-interest. In humans, friendship, moralistic aggression, gratitude, sympathy, guilt, suspicion and their sham versions are proposed as adaptations that regulate exchange, and rules of conduct as a multiparty extension. | Active — read in full 2026-10-02 (NOTE-402); worth reading as the source of reciprocal altruism and, for this record above all, of the first adaptive account of moral emotions: moralistic aggression, gratitude, sympathy, guilt and the detection of sham versions of each, with “norms of reciprocal conduct” as a later step. The formal part is slight (a verbal model and Hamilton’s communicated Prisoner’s Dilemma sketch); the human psychology is hypothesis supported by the social-psychology literature of the 1960s. It grounds the exchange domain of morality-as-cooperation and gives that domain its emotions. |
| LIT-514 v3 | Moral Origins: The Evolution of Virtue, Altruism, and Shame | Boehm (2012), Basic Books. By the publisher’s account, the moral sense is “a sophisticated defense mechanism”: group punishment of bullies, thieves, free riders and psychopaths over six million years made social selection favour altruists and bred conscience, virtue and shame. The chapter list adds a “selection-by-reputation hypothesis” and its test. Unread: filed from the description and chapter list. | Unavailable — filed 2026-10-02 from the publisher’s description and the chapter list, not read: no lawful full text was reachable. The book is lending-only at the Internet Archive (item moraloriginsevol0000boeh) and sold by Basic Books. What it argues is known here only from the publisher’s description, labelled as such. It stays Unavailable until a copy is supplied. |
| LIT-515 | Statistical physics of self-replication | England (2012; J. Chem. Phys. 2013), arXiv:1209.1179. For a system in a heat bath obeying detailed balance, a transition between coarse-grained ensembles I → II obeys β⟨ΔQ⟩ + ln π(II→I) + ΔS_int ≥ 0 (Eq. 6), a second law stated for macrostates. Applied to self-replication, the reverse probability is small when the copy is durable and made fast, so the heat released per copy is bounded below by about 2n ln(n τ_decay/τ_div) − ΔS_int (Eq. 8). The author’s estimates put E. coli within a factor of three of this bound and a self-replicating RNA near it. The “self” in self-replication is an observer’s classification of microstates, not a physical given. | Active — read in full 2026-10-02 (NOTE-419), from arXiv v1, the only arXiv version; the published J. Chem. Phys. text was not reached. Worth reading as the founding paper of the “dissipation-driven” programme and as a clean worked use of a macrostate fluctuation relation: the heat a replicator must release is bounded below by how fast it copies and how durable the copy is, not by the copying itself. The general bound (Eq. 6) is a coarse-grained second law and is sound; the numbers for E. coli and RNA rest on an argued, not derived, upper bound on the reverse probability (Eq. 7). It draws no line between living and non-living replicators, and says so: “self” is a classification an observer supplies. |
| LIT-516 | Time, Structure and Fluctuations | Prigogine (1977), Nobel Lecture, reprinted in Science 201:777 (1978). Near equilibrium the second-order excess entropy δ²S is a Lyapounov function, so fluctuations die out, and in the “strictly” linear regime the steady state minimizes entropy production. Far from equilibrium the sign of the excess entropy production ΣδJδX is no longer fixed. Given autocatalytic steps (necessary, not sufficient) the thermodynamic branch can go unstable, and fluctuations are amplified into “dissipative structures”: Bénard convection, the Brusselator’s limit cycle and “Turing bifurcation”. A closing programme derives irreversibility from a non-unitary transformation of the Liouville dynamics. | Active — read in full 2026-10-02 (NOTE-424); worth reading as Prigogine’s own short statement of the dissipative-structure programme, and as the place where its scope limits are stated in his words. A dissipative structure is a state beyond an instability of the “thermodynamic branch”, “a giant fluctuation stabilized by exchanges of energy with the outside world”. The minimum-entropy-production theorem is valid only in the “strictly” linear regime with constant phenomenological coefficients. Far from equilibrium the only general criterion offered is a sufficient one for stability (non-negative excess entropy production). Its §§6–7 programme of a non-unitary “entropy operator” is a sketch whose demonstrated link to macroscopic thermodynamics is, by its own account, “at least in the linear region”. |
| LIT-517 | Nonequilibrium Equality for Free Energy Differences | Jarzynski (1997), DOI-10.1103/PhysRevLett.78.2690. For a classical system that starts in canonical equilibrium and is switched from Hamiltonian H_0 to H_1 at any finite rate, the average of e^{−βW} over repetitions equals e^{−βΔF} (Eq. 2), whatever the path and the switching time. The proof is exact for an isolated system and for Nosé–Hoover thermostats, and needs weak coupling for a physical reservoir. Thermodynamic integration and the Zwanzig perturbation formula are its slow and fast limits, and ⟨W⟩ ≥ ΔF follows by Jensen. | Active — read in full 2026-10-02 (NOTE-417); worth reading as the four-page origin of the nonequilibrium work relation ⟨e^{−βW}⟩ = e^{−βΔF}: an equality, independent of path and switching rate, that turns irreversible work measurements into an equilibrium free-energy difference and gives ⟨W⟩ ≥ ΔF as a corollary by Jensen. Read it knowing two things. The physical-reservoir proof rests on weak coupling (Eq. 9 → 10), which the author states; and its usefulness is limited by the author’s own estimate to work fluctuations of order k_BT, so nanoscale systems or simulations. |
| LIT-518 | Statistical Physics of Adaptation | Perunov, Marsland & England (2014; Phys. Rev. X 2016), arXiv:1412.1875. Starting from a fluctuation relation between coarse-grained macrostates, the paper writes the log-odds of two outcomes of a driven system as an internal-entropy term, a reversal-probability term and Ψ − Φ, the mean heat minus a fluctuation correction (Eq. 8). Holding the first two fixed, the more likely outcome is the one whose formation absorbed and dissipated work from the drive more reliably. It calls such outcomes “adapted” and argues the tendency needs no self-replication. Two single-particle hopping models illustrate the dissipation and fluctuation terms (Eqs. 10–13); the many-body case is a plausibility argument. | Active — read in full 2026-10-02 (NOTE-416), from arXiv v1, the only arXiv version; the published Physical Review X text was not reached. Worth reading as the origin of “dissipative adaptation”: the claim that driven matter tends towards states whose formation absorbed and dissipated work reliably, with no replication needed. Read it as a heuristic argument with two toy models, not a theorem. Its exact content is a rearranged macrostate fluctuation relation; the step to “adaptation” holds two terms fixed that it does not show can be held fixed in a many-body system, and the simulation it reports was not shown. It deliberately erases the line between living and non-living organization. |
| LIT-519 | Nonequilibrium thermodynamics and maximum entropy production in the Earth system | Kleidon (2009), DOI-10.1007/s00114-009-0509-x. A review of MEP in the Earth system. MEP is the proposed principle that a system with enough degrees of freedom adopts the steady state of maximum entropy production. It selects among steady states, where Prigogine’s principle only describes relaxation toward one. Box models show the flux–force trade-off that gives an MEP state. The review estimates the Earth’s entropy budget, which is dominated by absorption of sunlight. It surveys MEP fits for atmosphere, ocean, mantle, hydrology and biota, and proposes that life drives the planet toward MEP, a thermodynamic reading of Gaia. The author grants that MEP is not established. | Active — read in full 2026-10-02 (NOTE-423); worth reading as the clearest statement of the maximum-entropy-production (MEP) programme in Earth-system science by its main advocate: what MEP claims, how it differs from Prigogine’s minimum principle (minimum entropy production describes relaxation toward a steady state; MEP selects among possible steady states), an order-of-magnitude entropy budget of the Earth, a survey of climate, ocean, mantle and biotic MEP applications, and the extension to life and Gaia. Read it as advocacy that is candid about its footing: the author calls MEP “proposed” and says “no one would argue that MEP is well established”. Chosen over the Kleidon–Lorenz 2005 book, which has no lawful open text. |
| LIT-520 v2 | Maximum entropy production principle in physics, chemistry and biology | Martyushev & Seleznev (2006), DOI-10.1016/j.physrep.2005.12.001. A 45-page Physics Reports review of the maximum entropy production principle (MEPP) across physics, chemistry and biology. Kleidon (2009) cites it as the review of MEP’s physical foundation. Semantic Scholar’s machine-generated summary says it analyses the principle’s thermodynamic and statistical basis, including its relation to the second law and to Prigogine’s principle. Unread: no text or abstract reached. | Unavailable — seeded 2026-10-02 from Crossref metadata and citing works, not read: no lawful full text or publisher abstract could be reached (Physics Reports, closed; Semantic Scholar and OpenAlex list no open copy, and the abstract is elided by the publisher). Filed because it is the main survey of the maximum-entropy-production principle and of its relation to Prigogine’s minimum principle; it stays Unavailable until a copy is supplied. |
| LIT-521 | Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states | Dewar (2003), DOI-10.1088/0305-4470/36/3/303. It applies Jaynes’s maximum-entropy inference to the microscopic paths of an open system in a stationary state. Under fixed initial densities and boundary fluxes plus local conservation, the path distribution is p_Γ ∝ exp(A_Γ), with A_Γ carrying τσ_Γ/2k_B (Eq. 14). A fluctuation theorem and ⟨σ⟩ ≥ 0 follow (Eqs. 18–21). Then, in a mean-field approximation and assuming the number of paths increases with irreversible action, maximizing path entropy over the remaining multipliers is maximizing mean entropy production (MaxEP, Eq. 24). A Landau–Ginzburg argument claims self-organized criticality as slow driving goes to zero. | Active — read in full 2026-10-02 (NOTE-426); worth reading as the founding attempt to derive the maximum-entropy-production principle (MaxEP) from Jaynes’s maximum-entropy inference over microscopic paths, and as the source most later MEP work, Kleidon’s included, cites for MEP’s theoretical foundation. Read it as a programme, not a proof. The path distribution p_Γ ∝ exp(A_Γ) and its fluctuation theorem follow from the stated constraints. The MaxEP step needs a mean-field approximation and an assumption that the number of paths grows with their irreversible action, which is stated, not argued. The self-organized-criticality corollary is a mean-field artefact by Grinstein and Linsker’s analysis (LIT-525), which this reading confirms. |
| LIT-522 | Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences | Crooks (1999), DOI-10.1103/PhysRevE.60.2721. For finite classical systems with stochastic, Markovian, microscopically reversible dynamics, the entropy production ω of a forward process and of its time reverse satisfy P_F(+ω)/P_R(−ω) = e^{ω} for any finite time, provided ω is odd under reversal. That holds for processes that start and end in equilibrium, where ω = β(W − ΔF), and for time-symmetric nonequilibrium steady states. The Jarzynski equality follows in one line, and for long times the theorem gives a heat fluctuation theorem and a Gaussian with variance twice the mean. | Active — read in full 2026-10-02 (NOTE-413); worth reading as the short paper that turned the entropy-production fluctuation theorem into a finite-time, trajectory-level statement for stochastic, microscopically reversible dynamics, P_F(+ω)/P_R(−ω) = e^{ω}, and derived the Jarzynski equality from it in a line. It also defines the trajectory entropy production ω = ln ρ(x_{−τ}) − ln ρ(x_{+τ}) − βQ that the record’s stochastic-thermodynamics papers inherit. Read it knowing that its conditions are stated exactly (finite classical system, constant-intensive-parameter baths, Markovian microscopically reversible dynamics, ω odd under time reversal), and that the steady-state version is formally exact but, by the author’s own account, of little practical use. |
| LIT-523 | Stochastic thermodynamics, fluctuation theorems and molecular machines | Seifert (2012), DOI-10.1088/0034-4885/75/12/126001. A 105-page review of stochastic thermodynamics. Work, heat and a stochastic system entropy s = −ln p(x(τ),τ) are defined along single trajectories of Markovian systems coupled to baths, and every known integral, detailed and Crooks fluctuation theorem is derived from one master theorem by choosing a conjugate dynamics. Further results: dissipation bounds forward–reverse distinguishability (⟨w⟩ − ΔF ≥ D[p‖p_eq]), Sagawa–Ueda feedback relations, a NESS fluctuation–dissipation theorem in terms of entropy production, and a cycle-based theory of efficiency at maximum power for molecular machines. | Active — read 2026-10-02 (NOTE-420; §§5, 8.3–8.4, 9.2 and 11 skimmed); worth reading as the systematic reference for stochastic thermodynamics as of 2012: first law, heat and stochastic entropy along single trajectories of Markovian systems coupled to baths, every known fluctuation theorem derived from one master theorem with a conjugate dynamics, dissipation as distinguishability of forward and reverse paths, Sagawa–Ueda feedback, the NESS fluctuation–dissipation theorem and efficiency of molecular machines. It is the framework in which the record’s thermodynamics-of-prediction and thermodynamics-of-learning results (LIT-327, LIT-308) are stated. Read it as a review: the derivations are its own and concise, the case studies are reported. |
| LIT-524 v2 | Self-Organization in Nonequilibrium Systems: From Dissipative Structures to Order through Fluctuations | Nicolis & Prigogine (1977), Wiley-Interscience. The Brussels school’s monograph on self-organization far from equilibrium, from the thermodynamics and bifurcation theory of dissipative structures to their stochastic theory (“order through fluctuations”). The Nobel lecture cites its ch. VII for the Brusselator and the book for its catalogue of chemical and biological examples. Unread: filed from catalogue records only. | Unavailable — filed 2026-10-02 from library catalogue records; no lawful full text was reachable (the book is in copyright, the Internet Archive scan is a lending-only copy, HathiTrust is search-only, and no publisher description or table of contents was found), so it is not read and no NOTE is filed. It is the Brussels school’s book-length treatment of dissipative structures and “order through fluctuations”, and the source the Nobel lecture (LIT-516) gives for the Brusselator; what it contains beyond that is not recorded here. |
| LIT-525 | Comments on a derivation and application of the ‘maximum entropy production’ principle | Grinstein & Linsker (2007), DOI-10.1088/1751-8113/40/31/N01. A Comment with two points. (1) Dewar’s 2005 derivation of MaxEP needs a quadratic approximation to p(f) near f = F to hold for all f. With the fluctuation theorem, that forces A(F) to be constant, i.e. linear constitutive relations. So the “orthogonality condition” behind both maximum and minimum entropy production fails far from equilibrium, as an exact spin-chain model shows. (2) Dewar’s 2003 SOC result is an artefact. Keeping the quartic term gives a finite flux variance at F_ext = 0. | Active — read in full 2026-10-02 (NOTE-422); worth reading as the short, exact critique of Dewar’s information-theoretic derivation of maximum entropy production. It shows that the 2005 derivation’s key step holds only where the constitutive relations are linear, so MaxEP far from equilibrium is not established by it, and that the 2003 claim that MaxEP yields self-organized criticality is an artefact of a mean-field expansion. Read from the authors’ submitted manuscript (Zenodo); the version of record was not seen. Its first point is checked here only on its own worked example, since Dewar 2005 itself could not be read. |
| LIT-526 | Life as we know it | Friston (2013), J. R. Soc. Interface 10(86):20130475. Any ergodic random dynamical system whose states split into internal, sensory, active and external sets with a Markov blanket has internal and active states whose flow can be written as a gradient descent on a variational free energy of the blanket and internal states (Lemma 2.1, Eqs. 2.5–2.8). They therefore “appear” to do Bayesian inference about external states and to bound their own entropy. A simulated “primordial soup” of 128 coupled Lorenz subsystems forms a blanket-enclosed cluster whose internal states predict external motion (5 of 82 above a time-reversed null) and which disperses when blanket or internal states are lesioned. The paper says a candle flame cannot have a Markov blanket, and concedes that the universe holds countless blankets, conjecturing that minimum-entropy blankets mark life. | Active — read in full 2026-10-02 (NOTE-421), from the published text (the author’s posted PDF of the journal version and the PMC full text). Worth reading as the founding statement of the Markov-blanket formulation of the free energy principle applied to life, and as the one text in the record that names a candle flame and says it is not lifelike. Read it as a redescription, not a derivation: its “heuristic proof” shows that the flow of an ergodic system with a Markov blanket can be written as a gradient flow on a variational free energy, by choosing the variational density to equal the posterior. The free energy is variational, not thermodynamic; no heat or entropy production is computed. The simulation is one run, analysed with a blanket chosen by spectral clustering. |
| LIT-527 | Pattern formation outside of equilibrium | Cross & Hohenberg (1993), DOI-10.1103/RevModPhys.65.851. A 262-page review classifying non-equilibrium patterns by the linear instability of a uniform state: type I_s (finite wave-number, stationary: convection rolls, Turing patterns), III_o (uniform oscillation: the stirred BZ reaction) and I_o (travelling waves). Near threshold, universal amplitude equations describe them, and phase equations describe them further above it. It finds no general variational principle for non-equilibrium steady states, only perturbative ones near threshold. | Active — skimmed 2026-10-02 (NOTE-418), about 30 of 262 pages read closely; worth reading as the physicists’ standard account of pattern formation away from equilibrium, and as the sober counterweight to the dissipative-structure programme. It treats Rayleigh–Bénard convection, Turing patterns and the BZ reaction in one framework, classifying patterns by the linear instability of a uniform state and describing them near onset by universal amplitude equations. Its conclusion finds “no evidence for the existence of any global minimization principles controlling the structure, except as a perturbative statement near threshold”, and quotes Glansdorff and Prigogine conceding as much. |
| LIT-528 | Energy flow and the organization of life | Morowitz & Smith (2006 working paper; Complexity 2007). Life may be forced into existence by abiotic free-energy sources, as lightning and hurricanes are channels that relieve electric and thermal potentials. Core anabolism, the reductive citric-acid cycle and the cascade built on it, is read as a relaxation channel for geochemical redox and phosphate energy. Jaynes-style entropy maximization with current-dependent entropies (not entropy-production principles) is offered as the framework, and the emergence of life as a “collapse”, a phase transition of a metastable abiotic earth. Selection on metabolism comes before replication. No quantitative model is given; the authors say the claim is undemonstrated. | Active — read in full 2026-10-02 (NOTE-425), from the Santa Fe Institute working paper (2006-08-029, dated 7 August 2006), not the Complexity version of record. Filed in place of Morowitz’s 1968 book Energy Flow in Biology, which could not be read: every Internet Archive scan of it is lending-only. Worth reading as a short statement of the “life was inevitable” view by Morowitz and Smith: core metabolism, the reductive citric-acid cycle, is a channel geochemistry was forced to open to relieve free-energy stresses, as lightning relieves a charge separation. It is an essay. It says itself that the claim “has not been quantitatively demonstrated”, and its evidence is the structure of core metabolism read in that light. It puts life on a continuum with lightning and hurricanes and draws no principled line. |
| LIT-530 v2 | What Is Life? The Physical Aspect of the Living Cell | Schrödinger (1944), Cambridge University Press. Lectures given at Trinity College Dublin in February 1943, published as a short book for the lay reader. It asks how events inside a living organism can be accounted for by physics and chemistry. It treats the gene as an “aperiodic crystal” carrying a code-script, defended through the Delbrück model, and in chapter 6 says an organism keeps its order by drawing “order from order” and by feeding on negative entropy from its surroundings. Unread: registered from the publisher’s description and contents; the text itself was not reached. | Unavailable — registered 2026-10-02 from the publisher’s description, the Cambridge Core contents and chapter excerpts, and library catalogue records, not read: no lawful full text could be reached. The book is in copyright with Cambridge University Press. Every Internet Archive scan of a Cambridge or Macmillan printing is lending-only, and the freely downloadable PDFs that turn up (course sites, personal uploads, Internet Archive “opensource” uploads) are unauthorized copies of the Canto edition, so I did not open them. Chapter 6, the negative-entropy chapter, is unread beyond the publisher’s one-paragraph excerpt. |
| LIT-531 | Belousov-Zhabotinsky reaction | Zhabotinsky (2007), Scholarpedia 2(9):1435. BZ reactions are metal-ion-catalysed oxidations of organic reductants by bromate in acid. The core loop is autocatalytic oxidation of the catalyst via HBrO₂, switched off by bromide, which the oxidized catalyst regenerates from bromomalonic acid. Closed, stirred, it can run “up to several thousand” cycles; only in a continuous-flow reactor do oscillations continue indefinitely, and there bursting and chaos appear. Unstirred thin layers support target and spiral waves (Zaikin & Zhabotinsky 1970). The Oregonator is qualitatively right and quantitatively not. | Active — read in full 2026-10-02 (NOTE-414); worth reading as the short, authoritative account of the Belousov–Zhabotinsky reaction by the chemist who named half of it: discovery, the core mechanism (autocatalytic HBrO₂ inhibited by Br⁻), the Oregonator and its known defects, closed versus open-reactor dynamics, and target and spiral waves. Chosen over Zaikin & Zhabotinsky (1970) because it is openly readable and covers the 1970 waves paper; it is a short encyclopedia review with no new results. |
| LIT-532 v2 | Inadequacy of entropy and entropy derivatives in characterizing the steady state | Landauer (1975), DOI-10.1103/PhysRevA.12.636. Per its abstract: in a bistable system the kinetics of transitions between the two locally stable states can be changed without changing the behaviour near either state, so no quantity that characterises only the vicinity of the states can determine which is more probable. Separately, even a monostable linear circuit’s steady state need not be one of minimum entropy production. Unread: filed from the abstract. | Unavailable — seeded 2026-10-02 from its abstract and Crossref metadata, not read: no lawful full text could be reached (Physical Review A, closed; Semantic Scholar and OpenAlex list no open copy). Filed because it is the classic objection to entropy-based characterisations of nonequilibrium steady states, Prigogine’s minimum principle among them; it stays Unavailable until a copy is supplied. |
| LIT-533 | Life as a manifestation of the second law of thermodynamics | Schneider & Kay (1994), Math. Comput. Modelling 19(6–8):25–48. A “restated second law”: systems moved from equilibrium “utilize all avenues available to counter the applied gradients”. Bénard convection and a vortex draining a bottle are read as structures that destroy gradients faster. Life is “another means of dissipating the solar induced gradient” (living systems as “sophisticated mini-tornados, with a memory”), and ecosystems develop to degrade more incoming exergy. A stressed marsh shows smaller flows and fewer cycles; airborne thermal scans show mature forests cooler (degrading 90% of net solar radiation against a quarry’s 62%). The second law is “necessary but not sufficient” for life. | Active — read in full 2026-10-02 (NOTE-415), from the authors’ own formatted text (copyright line “James J. Kay and Eric Schneider, 1992”), not the journal’s typeset version. Worth reading as the canonical statement of the “gradient-dissipation” view of life: living systems and ecosystems are dissipative structures that develop so as to degrade the solar gradient more completely, and the second law is “a necessary but not sufficient cause for life”. Read the thermodynamics as a programme, not a derivation. The “restated second law” is offered as a corollary of Kestin’s stability result but not derived from it. The ecological evidence is one stressed-versus-control marsh pair and a few thermal-scanner and satellite comparisons, all correlational. It draws no line between living and non-living dissipative structures beyond “memory” (DNA). |
| LIT-534 v2 | Order Out of Chaos: Man’s New Dialogue with Nature | Prigogine & Stengers (1984), Bantam; based on their La nouvelle alliance. A book for general readers that sets the science of complexity and irreversibility against classical dynamics. By its contents: the rise and limits of Newtonian science and its philosophical reception (Diderot, Kant, Hegel, Bergson, Whitehead); thermodynamics from Carnot to Boltzmann’s order principle; linear and far-from-equilibrium thermodynamics, bifurcations and order through fluctuations; and the rediscovery of time in physics. Unread: filed from catalogue records only. | Unavailable — filed 2026-10-02 from library catalogue records and a partial contents note; no lawful full text was reachable (the book is in copyright, the Internet Archive scans of the Bantam and Flamingo printings are lending-only, HathiTrust is search-only), so it is not read and no NOTE is filed. It is the popular and philosophical statement of the programme whose technical core is the Nobel lecture (LIT-516); what it argues, beyond its contents, is not recorded here. |
| LIT-535 | The Chemical Basis of Morphogenesis | Turing (1952), DOI-10.1098/rstb.1952.0012. Chemicals (“morphogens”) that react and diffuse through tissue can turn a stable homogeneous state unstable, with random disturbances setting which pattern grows. On a ring of cells the linearized onset takes six forms. The most important is stationary waves of finite “chemical wave-length”, which (9.4a, b) allow for two morphogens only if they diffuse at different rates. A 20-cell example computed on the Manchester computer gives a three-lobed pattern. Hydra tentacles, whorled leaves, dappling and gastrulation are suggested applications, not tested ones. | Active — read in full 2026-10-02 (NOTE-427); worth reading as the founding paper of reaction–diffusion pattern formation and the origin of what the Brussels school later called the “Turing bifurcation”. A homogeneous, stable steady state of reacting and diffusing chemicals can be destabilized by diffusion itself and settle into a stationary pattern with an intrinsic “chemical wave-length”. The analysis is linear and near onset by design, every biological application is offered as suggestion, and the paper says outright that its patterns are “dynamic equilibria” fed by “a continual supply of free energy”, which places them among dissipative structures before the term existed. |
| LIT-536 v4 | Biological Autonomy: A Philosophical and Theoretical Enquiry | Moreno & Mossio (2015), Springer, History, Philosophy and Theory of the Life Sciences 12. The book argues that biology should revolve around autonomy, not only natural selection: organisms are organized systems that self-produce and self-maintain as integrated wholes, set their own goals and norms, and promote the conditions of their existence through interaction with their environment. Chapters treat constraints and organisational closure, emergence and inter-level causation, teleology and function, agency, evolution, organisms and levels of autonomy, and cognition. Only the Introduction is read (NOTE-1437): there the authors make closure of constraints the core of biological organisation, say it differs fundamentally from the self-organisation of dissipative structures, and announce that it grounds teleology, normativity and function; the chapters that argue this are unread. | Unfetched — registered 2026-10-02 from the publisher’s description and the chapter list. The book is not open access at Springer. Its only free copy, the authors’ HAL deposit (hal-01151449, hal.science/hal-01151449/document, CC BY-NC 4.0, deposited 13 May 2015), is not the whole book, as this note earlier said: it holds the front matter (Hooker’s Foreword and the contents), the Introduction (pp. xix–xxxiv), the references and the index, and no chapter. The Introduction was read in full on 2026-10-30 (NOTE-1437, Skimmed, because only the Introduction was read). For chapters 1–8 no fuller lawful copy was found: on 2026-10-30 OpenAlex listed the HAL deposit as the book’s only open copy, and the publisher’s chapters are paywalled. HAL also served its anti-bot page to a direct fetch on 2026-10-02 and again on 2026-10-30; the deposit was read from a copy retrieved earlier the same day. It stays Unfetched for the chapters. |
| LIT-537 v2 | Thermodynamic Theory of Structure, Stability and Fluctuations | Glansdorff & Prigogine (1971), Wiley-Interscience. The monograph of the Brussels thermodynamic stability theory. By the Nobel lecture’s citations, it treats local equilibrium (ch. II), the second-order excess entropy δ²S as a Lyapounov function near equilibrium (ch. V), and the excess-entropy-production criterion far from equilibrium, including convection (ch. VII). Unread: filed from catalogue records only. | Unavailable — filed 2026-10-02 from library catalogue records; no lawful full text was reachable (the book is in copyright, the Internet Archive scan is a lending-only copy, HathiTrust is search-only, and no publisher description or table of contents was found), so it is not read and no NOTE is filed. It is the monograph in which Glansdorff and Prigogine set out the thermodynamic stability theory that the Nobel lecture (LIT-516) summarizes; what it contains beyond what the lecture and Cross & Hohenberg cite from it is not recorded here. |
| LIT-548 v2 | The Need for a New Medical Model: A Challenge for Biomedicine | Engel (1977), Science 196(4286):129–136. The paper that named the biopsychosocial model. Its abstract says the dominant biomedical model of disease “leaves no room within its framework for the social, psychological, and behavioral dimensions of illness”, and proposes a biopsychosocial model as “a blueprint for research, a framework for teaching, and a design for action in the real world of health care”. Unread: registered from its PubMed abstract and Crossref; no lawful full text was reachable. | Unavailable — registered 2026-10-03 from its PubMed record and Crossref, not read. Not open access: Unpaywall lists no open copy of the Science article or of any of its five reprints (Dimensions of Behavior 1978, Holistic Medicine 1989, Family Systems Medicine 1992, The Health Psychology Reader 2002, Psychodynamic Psychiatry 2012), and Europe PMC holds the abstract only. science.org answered both the article page and the PDF with a Cloudflare “Just a moment” challenge, which I did not try to get past. The copies a web search turns up are on a private practitioner’s site and on document-sharing sites, neither an author nor an institutional deposit, so I did not open them. A reader with Science or AAAS access, or a library copy of any reprint, can read it lawfully; a reading would move this to Active. No shorter open work by Engel stating the same model was found (his 1980 American Journal of Psychiatry follow-up, “The clinical application of the biopsychosocial model”, DOI 10.1176/ajp.137.5.535, is closed in Unpaywall, and psychiatryonline.org answered it with HTTP 403 and a challenge page). |
| LIT-566 | Defining Agency: Individuality, Normativity, Asymmetry, and Spatio-temporality in Action | Barandiaran, Di Paolo & Rohde (2009), Adaptive Behavior 17(5):367–386. Three conditions are jointly necessary and sufficient for minimal agency: the system defines its own individuality, it is the active source of modulations of its coupling with the environment (interactional asymmetry), and it regulates that coupling by norms it generates (normativity). Generatively, an agent is an open autonomous system (a precarious network of mutually enabling processes) that adaptively modulates its coupling so as to maintain some of its constituent processes. Minimal life satisfies this; life is sufficient for agency but not necessary. | Active — read in full 2026-10-03 (NOTE-458), from the authors’ own deposit of the accepted text. Worth reading as the standard organizational definition of minimal agency, and as the clearest statement that an agent is not the same thing as an individual. Individuality is one of three conditions, with interactional asymmetry and normativity; it is a precondition for the other two and is not sufficient for agency. The generative definition: an agent is an autonomous organization that adaptively regulates its coupling with its environment and contributes to sustaining itself as a consequence. The paper rejects statistical and energetic measures of asymmetry as sufficient, and says systems optimising an externally fixed function should not be treated as models of agency. |
| LIT-570 | An Organizational Account of Biological Functions | Mossio, Saborido & Moreno (2009), BJPS 60(4):813–841. A trait has a function iff it contributes to the maintenance of a self-maintaining organization, is produced and maintained under that organization’s constraints, and the organization is differentiated. Closure grounds teleology and normativity in the current system, unifying etiological and dispositional accounts. Flames, Bénard cells and hurricanes have closure but no functions, because each makes a single undifferentiated contribution to its own maintenance. | Active — read in full 2026-10-03 (NOTE-444), from the HAL deposit of the submitted version. Worth reading as the organizational account of function and as the place where the organizational school says plainly that a candle flame has closure. Functions are contributions to a differentiated self-maintaining organization by traits that organization produces and maintains. Closure alone grounds teleology and norms but is shared by flames, Bénard cells and hurricanes; organizational differentiation is what functions need. Reproduction is admitted to be a problem and left to a sketch. |
| LIT-582 | Biological organisation as closure of constraints | Montévil & Mossio (2015), J. Theor. Biol. 372:179–191. Two causal regimes act in organisms: processes (thermodynamic changes) and constraints, which act on processes while being conserved at the relevant time scale. Closure is mutual dependence among constraints: each is produced by a process another constraint constrains, and each helps produce another. Closure mixes slow and fast dependence, grounds functions, and is proposed as a boundary criterion. A volume-sweeping count of dependencies, the tendency to closure, separates symbionts that share an encompassing closure, and separated nested closures mark levels of organisation. | Active — read in full 2026-10-03 (NOTE-468), from the authors’ HAL deposit of the accepted text. Worth reading as the paper statement of the central claim of Biological Autonomy (LIT-536): biological organisation is closure of constraints. A constraint is defined by a symmetry: it acts on a process at a time scale at which it is itself conserved. Closure is a set of constraints each of which depends directly on another in the set and generates another, and cannot be split into two closed sets. The paper offers closure as a boundary criterion and gives a preliminary measure, the tendency to closure, for drawing boundaries between interacting organisms. It does not claim closure defines an organism. |
| LIT-588 v3 | A theoretical model of phase transitions in human hand movements | Haken, Kelso & Bunz (1985), Biological Cybernetics 51(5):347–356. Models the involuntary switch from anti-phase to in-phase finger or hand movement as movement frequency rises: relative phase φ is the order parameter, φ̇ = −∂V/∂φ with V = −a cos φ − b cos 2φ, both patterns are stable while |b| > |a|/4 and only in-phase below it, and hysteresis follows. The φ equation is derived from two self-sustained oscillators whose coupling must be nonlinear, with amplitude falling as frequency rises acting as the control. A theory paper: its data are Kelso’s earlier experiments, summarized. | Active — read 2026-10-30 (NOTE-1424) in full, from the publisher’s scan posted on Kelso’s lab page at Florida Atlantic University (https://ccs.fau.edu/hbblab/pdfs/1985_Haken_Kelso_Bunz_Biol_Cyb.pdf); worth reading as the paper that states the HKB model: relative phase as order parameter, the potential V = −a cos φ − b cos 2φ with anti-phase lost when b/a falls below 1/4, and its derivation from two nonlinearly coupled limit-cycle oscillators. Read it knowing that it is a theory paper with one numerical simulation and no new data: the switch and the hysteresis it models are summarized from Kelso’s earlier experiments, and critical fluctuations and critical slowing are named as future work, not reported. |
| LIT-601 | The Haken–Kelso–Bunz (HKB) model: from matter to movement to mind | Kelso (2021), Biological Cybernetics 115(4):305–322, a 60th-anniversary retrospective. HKB models bimanual coordination by the relative phase φ, with dφ/dt = −a sin φ − 2b sin 2φ and potential V = −a cos φ − b cos 2φ: both in-phase and anti-phase are stable for b/a > 1/4, and anti-phase loses stability below it, as observed when movement frequency rises. Noise, symmetry breaking (Δω) and metastability extend it; with Kuramoto’s model it becomes a generalized HKB for many agents. The same dynamics is reported within a body, between people and with machines, and in brain activity. | Active — read in full 2026-10-03 (NOTE-467), from the free-to-read publisher PDF. Filed in place of Kelso’s book Dynamic Patterns (LIT-578) and as the read account of the paywalled Haken–Kelso–Bunz paper (LIT-588), both Deferred. Worth reading as Kelso’s own short statement of coordination dynamics: the HKB order-parameter equation for relative phase, its stochastic and symmetry-breaking extensions, metastability as relative coordination, the generalized HKB–Kuramoto model, and the claim that one coordination dynamics holds within and between people. It is a retrospective by an author of the model, not a review, and it says so. |
| LIT-627 v2 | At the crossroad of the search for spontaneous radiation and the Orch OR consciousness theory | Derakhshani, Diósi, Laubenstein, Piscicchia & Curceanu (2022), Physics of Life Reviews 42:8–14. By its abstract: a critical analysis of Orch OR against new bounds on the spontaneous radiation that the simplest gravity-related dynamical collapse model predicts, concluding that Orch OR built on that simplest version is “highly implausible in all the cases analyzed”. Unread: registered from the abstract and the reference list. | Unavailable — registered 2026-10-03 from the abstract, keywords and reference list, not read. The article is closed access at Elsevier. Unpaywall, OpenAlex and Europe PMC list no open copy; there is no arXiv version (searched by title, abstract phrase and author pairs); Diósi’s publication list gives the DOI but, unlike his other 2022 papers, no PDF; ScienceDirect returned a bot challenge and CORE a redirect challenge, so I stopped. A human reader with library access, or a copy requested from the authors, would move this to Active. |
| LIT-628 | Homeostatic feelings and the biology of consciousness | Damasio & Damasio (2022), Brain 145(7):2231–2235, an Essay. Consciousness occurs when mind contents are spontaneously identified as belonging to their organism, and a continuous flow of homeostatic feelings (hunger, pain, well-being, plain feelings of existence) supplies that identification and “lends” consciousness to exteroceptive images. Feelings are hybrid: interoceptive pathways are unmyelinated, partly non-synaptic and unprotected by a blood–brain barrier, so the body and its neural map interact directly. Posterior brainstem lesions abolish consciousness where large cortical ones may not; consciousness needs “a partnership of nervous systems with the bodies they serve”. | Active — skimmed 2026-10-03 (NOTE-507): every section was covered, but through a fetch tool that returned section-by-section accounts with short quotes, not a verbatim copy, so the quotes are unchecked; worth reading as the shortest complete statement of the Damasios’ claim that consciousness is the spontaneous identification of mind contents as one’s own, supplied by a continuous flow of homeostatic feelings, which are hybrid: in interoception the map and the body it maps interact and “commingle”. It is a five-page Essay with no data. Its evidence is clinical and cited (brainstem coma versus cortical lesions, general anaesthesia), and its mechanism is the cellular contrast in Table 1: unmyelinated, non-synaptic, barrier-free interoceptive pathways. |
| LIT-645 | Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures | Babcock et al. (2024), J. Phys. Chem. B 128(17):4035–4046, ARXIV-2302.01469. Modelling tryptophan 1La transition dipoles in tubulin architectures with a radiative non-Hermitian Hamiltonian in the single-excitation limit, the authors predict strongly superradiant states (up to about 4000 times the single-tryptophan rate in a centriole, about 7000 extrapolated for large axon-like bundles) and a thermal quantum yield that rises with network size and survives static disorder of room-temperature size. Steady-state spectroscopy of taxol-stabilised porcine microtubules in buffer gives a tryptophan quantum yield of 17.6 ± 2.1% against 10.6 ± 0.6% for tubulin dimers, which they read as superradiance. Lifetimes, and so radiative rates, were not measured. | Active — read in full 2026-10-03 (NOTE-509); worth reading as the measured, room-temperature part of the case for collective quantum optical states in microtubules: a radiative-Hamiltonian model of up to more than 10⁵ tryptophan transition dipoles in microtubules, centrioles and axon-like bundles predicts superradiant states and a quantum yield that grows with network size, and steady-state spectroscopy finds the tryptophan quantum yield of microtubules (17.6 ± 2.1%) above that of free tubulin dimers (10.6 ± 0.6%). No lifetimes were measured, so the radiative rate itself was not, and the paper says nothing about consciousness, objective reduction or Orch OR. |
| LIT-709 | Conceptualization of the Holobiont Paradigm as It Pertains to Corals | Goulet, Erill, Ascunce, Finley & Javan (2020), Frontiers in Physiology 11:566968, a review. A coral is a consortium: the animal plus the Symbiodiniaceae, bacteria, archaea, fungi and viruses in its body, mucus and skeleton, and neighbours are excluded by definition. Membership can change, so one colony may be a different holobiont at different times. Traits such as thermal tolerance belong to the host–symbiont combination: not every Durusdinium is heat tolerant, and a novel anemone–alga pairing gave higher oxygen flux under heat than both natural ones. Measuring both partners shows different routes to the same bleaching outcome. Whether the holobiont is the unit of selection is asked, not answered. | Active — read in full 2026-10-04 (NOTE-555); worth reading as a short, explicit statement of why a coral should be studied as a composite of host and microbes rather than as an animal with passengers. It is a mini-review with no data of its own (about 3,700 words), and its strongest point is conceptual: traits such as thermal tolerance belong to host–symbiont combinations, not to either partner. The physiological evidence it cites is thin and partly not from corals: its one demonstration that a combination is “not necessarily the sum of its parts” is an oxygen-flux experiment in the sea anemone Exaiptasia. It poses, and does not answer, whether the coral holobiont is a unit of selection. |
| LIT-710 | Signaling cascades and the importance of moonlight in coral broadcast mass spawning | Kaniewska, Alon, Karako-Lampert, Hoegh-Guldberg & Levy (2015), eLife 4:e09991. Acropora millepora colonies from Heron Island, held in outdoor tanks for the eight days before the 2011 spawning night, spawned with the reef under ambient night light (21:30–22:30). They did not spawn that night under added light after sunset (N = 5) or under darkness (N = 5). 184 transcripts varied only on the spawning day, rose around gamete release in ambient colonies, did not change in dark ones and changed early in lit ones. Spawning-night genes were enriched for G-protein-coupled signalling; the proposed melanopsin and neuropeptide cascade is untested. | Active — read in full 2026-10-04 (NOTE-557); worth reading as the record’s one experiment in which an environmental cue is manipulated and a collective biological timing event fails. Colonies of Acropora millepora held in outdoor tanks spawned with the reef only under natural night light. Colonies given artificial light after sunset, and colonies kept dark, did not spawn that night (N = 6, 5, 5). A second experiment found that blue, green and white nocturnal light delayed spawning by 6–8 h or 2 nights and red light did not. The signalling cascade (melanopsin-like opsins, neuropeptide G-protein-coupled receptors) is a model proposed from transcript changes and is not tested. The study shows each colony tracking a shared cue; it does not test coordination between colonies. |
| LIT-711 | Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change | Hughes et al. (2007), Current Biology 17(4):360–365. A replicated fish-exclusion experiment at Orpheus Island, Great Barrier Reef, begun in 2000 after the 1998 mass bleaching: four roofless 5 × 5 m cages, four partial cages and four open plots, over 30 months. Excluding large and medium fishes produced a phase shift to Sargassum-dominated macroalgae. Coral recovery was suppressed, through about two-thirds lower recruitment and more than double the mortality of surviving colonies. In the controls, coral cover nearly doubled to 20%, mainly by recruitment of taxa that bleaching had removed locally. Reopened cages lost their macroalgae within 30 days. | Active — read in full 2026-10-04 (NOTE-558), main text and methods; the supplement was out of reach. Worth reading as the controlled experiment behind the claim that reef recovery after bleaching depends on an ecological interaction, not only on surviving corals. On an inshore Great Barrier Reef crest after the 1998 bleaching, roofless cages kept large and medium fishes out of four 25 m² plots for 30 months. Macroalgae rose to a mean of 56% cover in the cages against 4.1% and 1.7% in partial cages and open plots. Coral cover in the cages rose only from 6.0% to 7.7%, against 19.2% and 20.2%, because recruitment was about two-thirds lower and mortality of established colonies more than double. It is one site with four replicates per treatment. The cages excluded all large and medium fishes, not herbivores alone, and the macroalgal state vanished within 30 days of reopening them. |
| LIT-712 | Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont | Boilard, Dubé, Gruet, Mercière, Hernandez-Agreda & Derome (2020), Microorganisms 8(11):1682, a review. Bleaching, the breakdown of the coral–dinoflagellate symbiosis, is redefined as a succession of three holobiont dysbiosis stages: (i) the microbiota buffers the stress and keeps essential functions; (ii) the algal partners are reorganised by shuffling or switching, with or without transient bleaching; (iii) the stress exceeds both buffers, symbionts are lost for good, opportunists invade and the coral dies, and at reef scale algae take over. The stages are a proposal, with no criteria to tell them apart, and the authors concede that microbial shifts are not shown to cause bleaching. | Active — read in full 2026-10-04 (NOTE-556); worth reading as the statement of the “adaptive dysbiosis” account of coral bleaching, which treats bleaching as three successive holobiont states: microbial buffering, reorganisation of the algal partners by shuffling or switching, and an irreversible breakdown ending in death. It is a review with no data of its own, and the account is a proposal. Its own text says that bacterial shifts during bleaching cannot yet be read as cause or consequence, so the title’s “microbial dysbiosis” claims more than the body supports. |
| LIT-740 | Cancer across the tree of life: cooperation and cheating in multicellularity | Aktipis et al. (2015), Phil. Trans. R. Soc. B 370:20140219. Multicellularity rests on five kinds of cellular cooperation, and cancer is cheating on them. Surveying cancer-like growth across the independent origins of complex multicellularity, the authors find division-of-labour cheating in every form, and resource and environment cheating so far only in animals and plants. Complex multicellularity is a cheater detection and suppression system. | Active — read 2026-10-05 (NOTE-562): in full, from the open-access deposit in PubMed Central (CC BY 4.0). Worth reading as a survey of cancer-like growth across the independent origins of multicellularity, read as cheating on five foundations of cooperation: proliferation inhibition, controlled cell death, division of labour, resource allocation and maintenance of the extracellular environment. Cheating on division of labour is reported in every form of multicellularity, and complex multicellularity is described as a cheater detection and suppression system. Limits: a literature review with no model or new data; absences may reflect lack of study, and animals’ apparent susceptibility may reflect sampling. |
| LIT-819 | Getting to the Bottom of Noether’s Theorem | Baez (2020; chapter 2022), ARXIV-2006.14741. In Poisson algebras, complex *-algebras and Banach–Lie algebras, “a generates symmetries of b iff b generates symmetries of a” follows from the antisymmetry of the bracket and uniqueness of solutions; for a bilinear bracket, antisymmetry is the self-conservation principle {a, a} = 0. The nontrivial content is a map from observables to generators: in complex quantum mechanics multiplication by i, and in a unital JB-algebra Alfsen and Shultz’s dynamical correspondence, whose second condition Baez links to “inverse temperature is imaginary time”. | Active — read 2026-10-09 (NOTE-630); worth reading as an account of what Noether’s theorem, in its Hamiltonian form, actually assumes: given unique solutions of the flow equations, “a generates symmetries of b iff b generates symmetries of a” reduces to the antisymmetry of a bilinear bracket, which is equivalent to each observable conserving itself. The content lies in identifying observables with generators; in quantum theory that identification is multiplication by i, and Alfsen and Shultz’s dynamical correspondence recovers it from a JB-algebra under the self-conservation principle and a second condition that Baez reads as “inverse temperature is imaginary time”. The paper proves nothing new, by its own statement. |
| LIT-852 | A sensor of oxidative stress confers virulence via response memory in Acinetobacter baumannii | Ngo et al. (2026), bioRxiv 10.64898/2026.04.08.717352 (preprint, not peer reviewed). Reports that the PmrB sensor of the PmrA/PmrB two-component system in Acinetobacter baumannii detects sublethal oxidative stress via four periplasmic histidine residues coordinating a nickel cofactor; PmrA then activates iron-sulfur repair, a ferritin, a catalase and a peroxidase. The sensor is claimed to stay active 30—90 min after the stimulus is removed (a “response memory”), priming cross-protection against lethal peroxide and antimicrobial peptides, and the histidine box is reported necessary for virulence in mice and for hypervirulence in a clinical carbapenem-resistant isolate. | Active — read 2026-10-09 (NOTE-656) from the bioRxiv full-text PDF of the v1 preprint. An unrefereed preprint: worth keeping as a clean biological instance of the memory from a temporary signal'' pattern that THEORY-136 sets the evidential bar for, and as a self-contained worked example of a two-component signalling system (PmrA/PmrB) that is claimed to sense oxidative stress through a histidine box with a nickel cofactor, to hold a redox-gated conformational switch, and to retain a 30--90 minute response memory” after the stimulus is removed. Read for what it shows, not for what a manuscript might use it for; its central memory and virulence claims rest on this single unreviewed study. |
| LIT-853 | A heritable iron memory enables decision-making in Escherichia coli | Bhattacharyya, Bhattarai, Pfannenstiel, Wilkins, Singh and Harshey (2023), PNAS 120(48):e2309082120. In single-cell swarm assays (over 10,000 plates), an E. coli cell’s swarming potential is shared by its fourth-generation descendants and lost by the seventh; it tracks the cell’s iron status (low iron, better swarmer), iron starvation or forced uptake lengthens it, and a three-state switching model fits the lineages only with a fixed holding delay before switching. The iron–swarming link is correlational and measured through a Fur-repressed promoter, not iron itself. | Active — read 2026-10-09 (NOTE-657); worth reading as an experimental case of a non-genetic, multigenerational state in single bacteria: a cell’s swarming potential is shared by its descendants for about four generations and gone by seven, and it tracks the cell’s iron status as reported by a Fur-repressed promoter (Spearman r = 0.71 between reporter signal and swarm diameter over 96 sorted cells; 0.15 and 0.05 in the controls). The state is not a bistable switch: an ODE of three swarming classes fits the lineage data only when each founding cell holds its class for a fixed delay (about three or four generations) before switching at constant rates. The “memory”, “decision-making” and “conditioning” of the title and text are figurative; the iron link rests on a promoter reporter and on correlation, and the model fixes five parameters on two time points. |
| LIT-854 | Irreversibility in bacterial regulatory networks | Zhao, Wytock, Reynolds and Motter (2024), Science Advances 10(35):eado3232. In Boolean models of the E. coli transcriptional regulatory network, a transient single-gene knockout or overexpression often moves the network to a different attractor, so one genotype can hold several heritable expression states without epigenetic marks. The genes able to do this are those upstream of, or inside, strongly connected components with positive circuits, and the more weighted paths to them the likelier. A prediction from a model ensemble, with no direct experiment. | Active — read 2026-10-09 (NOTE-655); worth reading as a whole-network test of whether transcriptional regulation alone can make a bacterium’s state history-dependent. In an ensemble of sign-consistent Boolean rules on the 87-gene core of the largest E. coli regulatory subnetwork (RegulonDB), 51 genes admit a transient knockout or overexpression that leaves the network in a different attractor; every such gene reaches a strongly connected component containing a positive circuit, and the probability grows roughly as a power of the weighted number of paths to one. Model only: the paper runs no transient-perturbation experiment. Its one comparison with data, against strains evolved after a permanent crp knockout, mostly tests the sign structure of the network, and its link to irreversibility is weak (P = 0.03 on small counts). |
| LIT-872 | Hyperbolic geometry of the olfactory space | Zhou, Smith & Sharpee (2018), Science Advances 4(8):eaaq1458. In four natural odour sources the rank order of correlations between compound concentrations has the clique-topology signature of points near the surface of a 3D hyperbolic ball and not of a uniform Euclidean cube, and human perceptual descriptions of 127 odorants have that of a full 3D hyperbolic ball. Pleasantness, boiling point and acidity read out as linear axes of the fitted fruit-odour space. The hierarchy that motivates the hyperbolic model is argued from biochemistry, not recovered from the data. | Active — read 2026-10-09 (NOTE-672); worth reading as the first application of clique topology to stimulus statistics rather than neural data, and as the Sharpee lab’s first claim of a hyperbolic geometry in biology. For four natural odour sources (strawberry, tomato, blueberry, mouse urine; 45–78 compounds over 50–101 samples), the rank order of absolute concentration correlations gives Betti curves that match points sampled near the surface of a 3D hyperbolic ball (R_max = 7, R_min = 0.9 R_max, the same for all four) and reject uniform Euclidean cubes of any dimension tried. Human descriptor profiles for 127 odorants (Dravnieks) match a full 3D hyperbolic ball and no Euclidean cube. Linear axes for pleasantness, boiling point and acidity are found in the fitted fruit-odour space. The tree that motivates the hyperbolic model is argued, not recovered: compounds do not cluster by chemical class, and the only null geometry is a uniform Euclidean cube. |
| LIT-873 v2 | Mutual information, neural networks and the renormalization group | Koch-Janusz and Ringel (2017; Nature Physics 14, 578–582, 2018). Defines the relevant degrees of freedom of a spatial block as the coarse variable that maximizes mutual information with the environment beyond a buffer, and learns it with restricted Boltzmann machines from Monte Carlo samples (the RSMI algorithm). It recovers Kadanoff block spins in the 2D Ising model and the electric-field variables of the dimer model, ignores decoupled noise, and, iterated, gives the Ising flow and ν ≈ 1.0 ± 0.15; a distribution-fitting RBM does none of this. The link to a short-ranged effective Hamiltonian is proved only in 1D. | Active — read 2026-10-09 (NOTE-674); worth reading as the paper that turns “the relevant degrees of freedom” of real-space renormalization into an objective that can be optimized: a block’s coarse variable is chosen to maximize its mutual information with the system beyond a buffer around the block. Trained on Monte Carlo samples alone, the network rediscovers Kadanoff’s block spin for the 2D Ising model, finds the low-momentum electric fields of the 2D dimer model while ignoring a strongly patterned but decoupled noise, and, iterated, reproduces the Ising flow away from T_c (located to about 1%) with ν ≈ 1.0 ± 0.15. An RBM trained instead to fit the data distribution latches on to the noise. The equivalence of the objective with a short-ranged effective Hamiltonian is argued, and shown only for 1D and quasi-1D chains; in 2D the evidence is the two models, whose answers were known beforehand. |
| LIT-878 v2 | Statistical Physics through the Lens of Real-Space Mutual Information | Gökmen, Ringel, Huber and Koch-Janusz (2021; Phys. Rev. Lett. 127, 240603). Replaces the RBM estimator of LIT-873 with a neural InfoNCE lower bound co-trained with a convolutional coarse-graining filter (RSMI-NE), and uses the optimal filters at a single buffer size, not an iterated flow, as lattice forms of the most relevant operators. On the interacting dimer model they are the columnar and plaquette order parameters below T_BKT and the electric fields at high T; the maximal information marks the phases; one fitted scaling dimension (1.00037 against 1) is given. The optimality theorem is cited, not proved here. | Active — read 2026-10-09 (NOTE-681); worth reading as the paper that turns the real-space mutual-information principle of LIT-873 from an iterated coarse-graining into a single-shot extraction of operators: with the mutual information estimated by a neural InfoNCE bound and the coarse-graining a convolutional filter trained against it, the filters that best compress what a block shares with its distant environment are, across the whole phase diagram of the interacting dimer model, the columnar and plaquette order parameters below the BKT transition and the electric fields at high temperature, and the plaquette filter’s correlator gives a scaling dimension of 1.00037 against the predicted 1. The maximal information itself, log 4 in the ordered phase and decaying algebraically with the buffer in the critical one, traces the phase diagram. The theorem that the optimal filters are the most relevant operators is cited to another paper, and the model’s operators were known beforehand. |
| LIT-881 v2 | Optimal Renormalization Group Transformation from Information Theory | Lenggenhager, Gökmen, Ringel, Huber and Koch-Janusz (2018; Phys. Rev. X 10, 011037, 2020). Proves that a block coarse-graining keeping all the mutual information the block shares with the system beyond a buffer makes the coarse measure factorize across the block, so a finite-range Hamiltonian gains no range (1D; D dimensions under an extra assumption) and 1D disorder gains no correlations across it. For blocks of two spins of the 1D clean and dilute random Ising chain, where that condition is not met, couplings beyond nearest neighbour and disorder correlations shrink as more information is kept, vanishing at decimation. Encoding into a single binary spin explains why decimation wins in 1D and majority rule in a 2D toy model. | Active — read 2026-10-09 (NOTE-682); worth reading as the theory written for the RSMI algorithm of LIT-873: it proves that a coarse-graining which keeps all the information a block shares with the system beyond a buffer factorizes the coarse measure across that block, so a finite-range Hamiltonian does not gain range (in 1D; in D dimensions under an extra per-block assumption) and, for 1D disorder, no correlations are generated across the block. The full-capture condition is not met by the coarse-grainings it then studies: in its own 1D Ising example decimation keeps about half of the block’s information, and the decay of next-nearest-neighbour and four-spin couplings, and of disorder correlations, as information grows is shown numerically for blocks of two spins. Its other result is information-theoretic: a single binary block spin loses information by encoding, which is why decimation beats majority rule in 1D and majority rule wins in a 2D toy model. |
| LIT-882 | An exact mapping between the Variational Renormalization Group and Deep Learning | Mehta and Schwab (2014), arXiv preprint, never published in a journal. Identifies Kadanoff’s variational RG kernel with an RBM’s energy by T = −E + H, under which the coarse-grained Hamiltonian is the RBM’s hidden-marginal Hamiltonian for any parameters and an exact RG step is a perfect fit of the data. Illustrates it with a hand-built decimation network for the 1D Ising chain and a four-layer stacked RBM trained on 2D Ising samples near T_c, whose receptive fields are local and grow with depth. It concedes that, short of exactness, RG and RBM training use different variational schemes; LIT-873 shows the difference matters. | Active — read 2026-10-09 (NOTE-683); worth reading as the paper that first put deep restricted Boltzmann machines and Kadanoff’s variational renormalization group side by side, and as the position Koch-Janusz and Ringel (LIT-873) argue against. Its “exact mapping” is an identification: setting the RG kernel T = −E + H makes the coarse-grained Hamiltonian equal the RBM’s hidden-marginal Hamiltonian for every parameter value, and makes an exact RG step the same thing as a perfect fit of the data distribution. Away from that point the paper itself says the two procedures use different variational approximations, so the mapping does not show that training an RBM performs RG. The evidence that it does is a hand-built 1D decimation network and qualitative receptive fields of a stacked RBM on 2D Ising samples; no flow, fixed point or exponent is computed. |
| LIT-885 | Relevance in the Renormalization Group and in Information Theory | Gordon, Banerjee, Koch-Janusz and Ringel (2020; Phys. Rev. Lett. 126, 240601, 2021). On a cylinder, with block and environment as slabs separated by a buffer of length L_B, the information-bottleneck encoder just past its first transition depends on the block only through the boundary weak value of the leading transfer-matrix eigenvector, the lowest-dimension primary at large circumference, and the transition is at β_c = (λ0/λ1)^(2L_B). Checked on a three-site critical Ising cylinder. With a large enough alphabet the encoder respects the data’s symmetry near that transition; a small one can break it. | Active — read 2026-10-09 (NOTE-690); worth reading as the theorem the real-space mutual-information programme (LIT-873, LIT-881, LIT-878) cites for its claim that the optimal coarse-graining picks out the most relevant operators. What it proves is narrower than that claim: for a short-range lattice model on a cylinder, with the block and the environment taken as whole slabs of the cylinder separated by a buffer, the information-bottleneck encoder just past its first transition depends on the block only through the boundary weak value of the leading transfer-matrix eigenvector, and the transition sits at β_c = (λ0/λ1)^(2L_B); for large circumference that eigenvector is the lowest-dimension primary. The planar block-in-a-shell geometry the algorithms use, the fixed-alphabet β → ∞ limit that is RSMI, and the regime beyond the first transition are not covered. A second result: past the first transition, with a large enough alphabet and no fine-tuning, the optimal encoder carries a representation of the data’s symmetry, and a two-symbol example with Z4 symmetry breaks it. |
| LIT-887 v2 | Why does deep and cheap learning work so well? | Lin, Tegmark and Rolnick (2016; Journal of Statistical Physics 168, 1223–1247, 2017). Argues that networks are cheap because physical data have low-order, local, symmetric Hamiltonians, and deep because data come from Markov generative hierarchies whose minimal sufficient statistics compose. Proves that a single hidden layer needs exactly 2^n neurons to multiply n inputs, against about 4n in a deep tree, and gives linear no-flattening examples. Holds that RG is supervised feature extraction, not unsupervised learning; arXiv v1–v2 carried a counterexample against LIT-882 that hit a typo in its Eq. 8, and was dropped later. | Active — read 2026-10-09 (NOTE-688); worth reading as the third position in the dispute over whether deep learning performs renormalization, and for two results that stand on their own. On the dispute it holds that RG is “essentially a feature extractor for supervised learning”: a coarse-graining is a renormalization only once the variables to keep are specified, and fitting the data distribution does not specify them. That holds, and it agrees with what LIT-882 concedes and LIT-873 shows; its sharper form was in an appendix of arXiv v1 and v2 only, dropped from v3 on and from the journal text, showing that a matched partition function does not give a matched distribution and (v2) that the exact trace condition is met by hidden variables that do not interact with the system at all. Its conclusion that RG has “little to do” with unsupervised learning is too strong: LIT-873 gets the relevant variables without labels, from the far environment. On its own merits: a two-variable product needs four neurons and an n-variable product needs exactly 2^n in one hidden layer against about 4n in a deep tree (proved, in a Taylor-matching sense, with weights that grow without bound); the minimal sufficient statistics of a Markov generative hierarchy compose level by level (proved, and nearly immediate); that physics favours low-order, local, symmetric Hamiltonians, and that this is why cheap networks work, is argued, not shown. |
| LIT-889 v2 | Symmetries and phase diagrams with real-space mutual information neural estimation | Gökmen, Ringel, Huber and Koch-Janusz (2021; Phys. Rev. E 104, 064106), the long companion of LIT-878. Derives the RSMI-NE estimator in full and applies it to the 2D Ising model (1 bit below T_c, exponential decay with the buffer above it, boundary filters at T_c), the interacting dimer model and a 1D non-equilibrium chipping model. Its new object is the ensemble of optimal filters from independent runs: it maps an RSMI-degenerate subspace whose projections show broken and emergent (U(1)) symmetries, and PCA of it recovers the pristine operators. Every model’s answer was known beforehand. | Active — read 2026-10-09 (NOTE-692); worth reading as the long companion of LIT-878 and the place where the real-space mutual-information method is shown on more than one model and its outputs are read as an ensemble: the maximal information counts the ordered sectors (exactly 1 bit in the 2D Ising ferromagnet, 2 bits in the columnar dimer phase), decays exponentially with the buffer in the Ising paramagnet and algebraically at criticality, and the optimal Ising filter goes uniform, boundary and random across T_c; 500 independent runs per temperature map an RSMI-degenerate subspace of filters whose projections show the broken C4 and translation symmetries of the dimer model and, at high temperature, its emergent U(1), and PCA of the ensemble recovers the pristine operators from a window where they never appear alone. The number of coarse variables is chosen where the information stops growing. A non-equilibrium chipping model is a one-figure validation, and its formal status is said to be missing. |
| LIT-891 | Comment on “Why does deep and cheap learning work so well?” | Schwab and Mehta (2016), arXiv comment, never published elsewhere. Reply to the appendix counterexample of Lin and Tegmark’s arXiv v1 (LIT-887): agrees that preserving the free energy does not recover the distribution, calls the “if and only if” of LIT-882’s Eq. 8 a typo (the trace condition implies ΔF = 0, not conversely), and shows that the counterexample violates the trace condition, so the mapping’s exact step is untouched. It does not reach the later objection that the trace condition fails to select the coarse variables. | Active — read 2026-10-09 (NOTE-694); worth reading as Mehta and Schwab’s own statement of how far their mapping (LIT-882) reaches, made in reply to the counterexample in arXiv v1 of Lin and Tegmark (LIT-887). It concedes two things: that preserving the free energy does not recover the distribution (“we entirely agree with this statement and never claimed otherwise”), and that the “if and only if” of LIT-882’s Eq. 8 is a typo, since the trace condition implies ΔF = 0 but not conversely. It argues one: that exact variational RG means the trace condition Tr_h e^T = 1 for every v, which the counterexample violates (checked), so the mapping’s Eq. 22 is untouched. That reply is right against v1. It locates the mapping’s content at the trace condition alone, which is the scope THEORY-197 gives it, and it does not answer the point Lin and Tegmark added in their v2 a fortnight later, that the trace condition is also met by hidden variables that do not interact with the system (THEORY-202). The “typo” did work in LIT-882: its Section I derives the exactness condition from ΔF = 0 through the direction the comment withdraws. |
| LIT-892 v3 | Quantum mechanics near closed timelike lines | Deutsch (1991), Phys. Rev. D 44, 3197. The standard model of quantum systems near closed timelike curves: the state on the loop must be a fixed point of the interaction, as a density matrix, and such a fixed point always exists. Not read: registered to ground the record’s contrast between causal-loop consistency and contextuality. | Unavailable — filed 2026-10-10 from its Crossref record, not read: it is registered to ground one claim (CLAIM-141) on what it is standardly cited for, the density-matrix consistency condition for closed timelike curves. No NOTE is filed. It stays Unavailable until it is read, not on merit. Looked for on 2026-10-10: the publisher’s page (APS) refused the request, and the only full text found online is a scan of the journal article on a personal site (gwern.net) with no sign of the publisher’s permission, so it was not used. |
| LIT-903 | From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators | Han et al. (2021), Microbiome 9:162. A narrative review of how microbe-derived metabolites and proteins may regulate host appetite: SCFAs through FFAR2 to GLP-1 and PYY; bile acids through TGR5; indoles; ClpB as an α-MSH mimetic; and immunoglobulins against appetite peptides. Mostly rodent and in vitro evidence, by the authors’ own account. The human findings are associations, or prebiotic trials that conflict. | Active — read in full 2026-10-11 (NOTE-706) from the open-access text in Europe PMC (PMC8293578, CC BY). Worth reading as a map of the mechanisms by which gut microbes are proposed to reach host appetite (SCFAs, bile acids, tryptophan and indoles, bacterial protein mimics of host peptides such as ClpB for α-MSH), and for its own admission that the field “is mainly based on in vitro studies and rodent models”. The human evidence it cites is correlational, or comes from prebiotic and metabolite interventions that do not isolate microbes as the cause. |
| LIT-917 v3 | Disappearing Polymorphs | Dunitz & Bernstein (1995), Acc. Chem. Res. 28, 193. Cases where a crystal form that had been made reproducibly could no longer be made once a new, usually more stable, form had appeared, attributed to seeding by stray nuclei of the new form. Not read. | Unavailable — filed 2026-10-11 from its Crossref record, not read. Registered at the owner’s request for the nucleating-argument line, on what it is standardly cited for. No NOTE is filed, and it stays Unavailable until it is read, not on merit. Looked for on 2026-10-11: Unpaywall reports no open-access copy for the DOI, and Europe PMC holds no full text, so no lawful full text was found. |
| LIT-919 v2 | Nucleation | Vekilov (2010), Cryst. Growth Des. 10, 5007. For lysozyme, nucleation rates are about ten orders of magnitude below the classical prediction, and the paper places the error in the prefactor. It explains this by a solution–crystal spinodal, past which the barrier vanishes, and by two-step nucleation inside metastable dense-liquid clusters, where ordering is the slow step. The mechanism is inferred from a fitted model for one protein. | Active — read in full 2026-10-11 (NOTE-708), from the NIHPA author manuscript at PMC2995260; worth reading as the line’s one clear statement, in a single paper, of classical nucleation theory (n* = 64Ω²α³/Δμ³, ΔG* = 32Ω²α³/Δμ²), of where it fails, and of the two things the author puts beside it: a solution–crystal spinodal, past which the nucleus is one molecule and there is no barrier, and the two-step mechanism, in which crystals nucleate inside metastable dense-liquid clusters that form fast, so that ordering inside them is the slow step. Read the sections on the nucleus size and spinodal, the two-step rate law, and the rate-determining step. The quantitative case is one protein, lysozyme. For metastable clusters the mechanism is inferred from a fitted kinetic model, not observed, and the claim that substrates act on the prefactor rather than the barrier is argued, not measured. It complicates CLAIM-176: the physical threshold is a size that moves with supersaturation and vanishes near the spinodal, not a fixed count. |
| LIT-920 v2 | Studien über die Bildung und Umwandlung fester Körper. 1. Abhandlung: Übersättigung und Überkaltung | Ostwald (1897), Z. Phys. Chem. 22, 289. Measures how small a seed can be (about 10⁻⁹–10⁻¹² g) and shows that only the solid itself or a strictly isomorphous solid seeds; separates metastable states (change only on contact with the new phase) from labile ones (spontaneous change); and states the rule later called the rule of stages: on leaving a state spontaneously, the form reached is the nearest in free energy, not the most stable. Offered as a frequent rule, not a law. | Active — read in full 2026-10-11 (NOTE-709), in German, from the public-domain scan of the volume at the Internet Archive; worth reading as the primary source of the rule later called the rule of stages, and of the metastable/labile distinction. Read §§26–41 (pp. 301–313): the definitions on p. 302, the rule on pp. 306–307 (“nicht der … stabilste …, sondern der nächstliegende”), and the conditional on p. 308 that a metastable intermediate stays until seeded unless it is labile with respect to the next form. Ostwald offers it “not as a law” but as “a frequently applicable rule” (p. 308), from a handful of cases and an analogy with the liquid–vapour isotherm, and absorbs exceptions by assuming unseen intermediates, a move he calls questionable (p. 309). Most of the paper measures seeds: only the solid or a strictly isomorphous solid seeds, down to about 10⁻⁹–10⁻¹² g. It supports the narrowed form of CLAIM-181 within the metastable zone, gives CLAIM-176 no support for a count threshold, and does not support reading the thesis sequence as successive metastable forms. |
| LIT-923 v2 | Synergetics: An Introduction. Nonequilibrium Phase Transitions and Self-Organization in Physics, Chemistry and Biology | Haken (1977), Synergetics, Springer. Near an instability, a few slowly varying order parameters come to govern the many fast degrees of freedom of a system (the slaving principle). One formalism is applied to lasers, fluid convection, chemical reactions and biology. Not read. | Unavailable — filed 2026-10-11 from its Crossref record, not read. Registered at the owner’s request for the nucleating-argument line, on what it is standardly cited for. No NOTE is filed, and it stays Unavailable until it is read, not on merit. Looked for on 2026-10-11: Unpaywall reports no open-access copy for the DOI, and Europe PMC holds no full text, so no lawful full text was found. |
| LIT-924 v3 | Principles of Crystal Nucleation and Growth | De Yoreo & Vekilov (2003), Rev. Mineral. Geochem. 54, 57. A review of classical nucleation theory and of crystal growth at surfaces: the critical nucleus, the barrier set by surface against bulk free energy, and how both depend on supersaturation. Not read. | Unavailable — filed 2026-10-11 from its Crossref record, not read. Registered at the owner’s request for the nucleating-argument line, on what it is standardly cited for. No NOTE is filed, and it stays Unavailable until it is read, not on merit. Looked for on 2026-10-11: Unpaywall reports no open-access copy for the DOI, and Europe PMC holds no full text, so no lawful full text was found. |
| LIT-925 v3 | Diffusion-Limited Aggregation, a Kinetic Critical Phenomenon | Witten & Sander (1981), Phys. Rev. Lett. 47, 1400. The diffusion- limited aggregation model: particles random-walk in one at a time and stick on contact, building a branched, fractal cluster. It is the minimal model of growth that branches because tips screen the interior. Not read. | Unavailable — filed 2026-10-11 from its Crossref record, not read. Registered at the owner’s request for the nucleating-argument line, on what it is standardly cited for. No NOTE is filed, and it stays Unavailable until it is read, not on merit. Looked for on 2026-10-11: Unpaywall reports no open-access copy for the DOI, and Europe PMC holds no full text, so no lawful full text was found. |
| LIT-926 v3 | The two-step mechanism of nucleation of crystals in solution | Vekilov (2010), Nanoscale 2, 2346. The two-step mechanism: crystals nucleate inside metastable clusters of dense liquid, which form first, rather than directly from the solution. Proposed for proteins and small molecules, to explain nucleation rates far below the classical prediction. Not read. | Unavailable — filed 2026-10-11 from its Crossref record, not read. Registered at the owner’s request for the nucleating-argument line, on what it is standardly cited for. No NOTE is filed, and it stays Unavailable until it is read, not on merit. Looked for on 2026-10-11: Unpaywall reports no open-access copy for the DOI, and Europe PMC holds no full text, so no lawful full text was found. |
| LIT-927 v3 | Instabilities and pattern formation in crystal growth | Langer (1980), Rev. Mod. Phys. 52, 1. The standard review of morphological instability in crystal growth: why a growing front far from equilibrium loses its flat shape and branches into dendrites, and what selects the pattern that results. Not read. | Unavailable — filed 2026-10-11 from its Crossref record, not read. Registered at the owner’s request for the nucleating-argument line, on what it is standardly cited for. No NOTE is filed, and it stays Unavailable until it is read, not on merit. Looked for on 2026-10-11: Unpaywall reports no open-access copy for the DOI, and Europe PMC holds no full text, so no lawful full text was found. |
| LIT-929 v2 | Generalized Stability Theory. Part II: Nonautonomous Operators | Farrell & Ioannou (1996), J. Atmos. Sci. 53, 2041. For a time-dependent operator A(t) there are no modes; the propagator’s singular vectors, the Lyapunov exponents and the Lyapunov vectors take their place. Its main result: an operator stable or neutral at every instant can be asymptotically unstable when it varies in time, only if it is non-normal, and random variation destabilizes generically, needing less variation the more non-normal and less damped the mean operator. Examples: a switched oscillator, random neutral matrices, the Lorenz system and a three-layer baroclinic model. | Active — read 2026-10-14 (NOTE-842) in full; worth reading for its main result: a time-dependent linear operator that is stable, or neutral, at every instant can be asymptotically unstable, only if it is non-normal, and random variation of the operator does this generically, with less variation needed the more non-normal and less damped the mean operator. Read it knowing that genericity is cited to stochastic stability theory rather than proved, that its examples are low-dimensional, and that in its deterministic examples variation much faster than the transient growth destabilizes nothing. Filed from it: THEORY-325. |
| LIT-931 v2 | Generalized Stability Theory. Part I: Autonomous Operators | Farrell & Ioannou (1996), J. Atmos. Sci. 53, 2025. For du/dt = Au with A non-normal, the eigenvalues fix only the t → ∞ behaviour. Growth over time t is the top singular value of e^{At}, set at t → 0 by the numerical abscissa, the top eigenvalue of (A + A†)/2. Systems with every mode damped amplify perturbations by large factors before decaying, and their forced and white-noise responses exceed the equivalent normal response. Worked in a 2 × 2 example and damped Eady models. | Active — read 2026-10-14 (NOTE-831) in full; worth reading as the compact statement of non-modal stability for a fixed linear operator: growth over a finite time is the top singular value of the propagator, the eigenvalues govern only the long-run limit, and forced and stochastic responses exceed those of the normal system with the same spectrum. Read it knowing that it is a synthesis of earlier results with worked atmospheric models, that non-normality is relative to the chosen norm, and that it is linear and autonomous. Filed from it, with LIT-932: THEORY-323. |
| LIT-932 v2 | Hydrodynamic Stability Without Eigenvalues | Trefethen et al. (1993), Science 261, 578. Plane Couette and Poiseuille flow become turbulent at Reynolds numbers where eigenvalue analysis says they are stable. Their linearized operators are far from normal: with every mode decaying, perturbations grow transiently by O(R) and resonate by O(R²), and an operator perturbation of O(R⁻²) makes them eigenvalue-unstable. Pseudospectra, not eigenvalues, show it. That nonlinear mixing then carries the amplified disturbance into turbulence is conjectured, from a 2 × 2 model with threshold O(R⁻³). | Active — read 2026-10-14 (NOTE-839) in full; worth reading as the short statement of why eigenvalue analysis fails for shear flows: the linearized Couette and Poiseuille operators are far from normal, so perturbations grow transiently by O(R), resonate by O(R²), and an operator perturbation of O(R⁻²) destabilizes, all read off the pseudospectra. Read it knowing that the transient growth results are credited to earlier work, and that its account of transition, linear growth plus energy-neutral nonlinear mixing with threshold O(R^γ), γ < −1, is a conjecture from a 2 × 2 model. Filed from it: THEORY-304, and with LIT-931, THEORY-323. |
| LIT-947 v2 | Unravelling the Flow of Information in a Nonequilibrium Process in the Presence of Hydrodynamic Interactions | Das et al. (2025). Two colloidal particles in optical traps are coupled by the fluid through a symmetric tensor, and the trap of one is moved by recorded Ornstein–Uhlenbeck noise. Mutual information, time-delayed mutual information and transfer entropy, estimated from experimental and simulated trajectories, recover drive → driven particle → other particle. They show backflow between the particles at the measured drive strengths, and one-way flow at strong drive in simulation only. Stronger coupling lowers the information the driven particle shares with the drive and raises what the particles share, in parallel with a reported trend of irreversibility under coarse-graining. Without drive the particles are statistically independent. | Active — read 2026-10-14 (NOTE-788) in full; worth reading as a clean experimental benchmark for directional information measures: two colloids, symmetrically coupled by the fluid, one trap moved by recorded noise, with transfer entropy and time-delayed mutual information recovering drive → driven → other particle. Read it knowing that the drive acts on one particle and is recorded, so the measures locate where a drive enters; they do not tell a shared drive from coupling, and the direction they report changes with drive strength while the coupling stays symmetric. Held for QUESTION-063 as a limit on what such measures can see, in THEORY-275. |
| LIT-1148 v2 | Functional information and the emergence of biocomplexity | Hazen, Griffin, Carothers & Szostak (2007). Functional information is −log2 of the fraction of all configurations, uniformly weighted, that reach at least a given degree of a specified function. In random Avida genomes its curve against degree of function is stepped, which the authors attribute to distinct classes of solutions; letter strings and GTP aptamers illustrate it. | Active — read 2026-10-29 (NOTE-1402) in full, from the publisher’s version in PubMed Central (PMC1876432, HTML, equations read from their images); worth reading as the general statement of functional information, −log2 of the fraction of all configurations that reach a stated degree of a stated function, with its stepped curves in random Avida genomes. Read it knowing that the measure is relative to one function and to a uniform weighting of configurations, explicitly not to what selection produces, that it says nothing about history or identity, and that its letter example is off by a bit (37, not 36). |
| LIT-1239 v2 | Localness of energy cascade in hydrodynamic turbulence. I. Smooth coarse graining | Eyink & Aluie (2009). Builds an exact decomposition of kinetic energy into band-pass contributions from smooth, graded filters on a geometric sequence of scales, with band budgets whose fluxes telescope, and carries over Eyink’s (2005) bounds: if velocity increments scale with exponents strictly between 0 and 1, the mean energy flux across a scale ℓ takes from scales above Δ or below δ at most a power of the scale ratio, 2/3 at K41 scaling. The bounds are sketched here and proved in the 2005 paper. A heuristic decorrelation argument and one 512³ simulation account for Kraichnan’s faster 4/3 decay of the signed contributions. | Active — read 2026-10-20 (NOTE-969) in full, from arXiv:0909.2386v1; worth reading for its exact band-pass decomposition of kinetic energy with smooth filters (a multiscale Germano identity, in which each band’s energy changes by the flux in minus the flux out), for a compact statement of when and why the energy flux across a scale is local in scale (THEORY-754), and for the account of why the rigorous 2/3 exponent is weaker than Kraichnan’s 4/3. Read it knowing that the rigorous bounds are proved in Eyink (2005), LIT-1252, and only sketched here; that they are conditional on a scaling hypothesis for velocity increments (exponents strictly between 0 and 1) and a non-zero mean flux, neither proved for Navier–Stokes; that the 4/3 argument is heuristic and its one simulation brackets rather than confirms it; that the band decomposition’s non-negativity holds only after integration for the kernels it needs; and that locality here is in scale, for one field, and says nothing about units. |
| LIT-1243 v2 | Scaling of information in turbulence | Granero-Belinchón, Roux & Garnier (2016). On one Modane wind-tunnel velocity record, estimates with k-nearest-neighbour estimators the conditional entropy of a sample given samples a lag τ earlier (the “entropy rate”) as a function of τ. Slopes −1/3 (inertial) and −1 (dissipative) are S₂’s scaling through a Gaussian formula the data obey. Entropy rates conditioned on the sign of the increment differ, which the paper reads, without warrant, as an information-theoretic proof of the energy cascade. | Active — read 2026-10-20 (NOTE-970) in full; worth reading for a clean demonstration that a scale-dependent information measure of a near-Gaussian turbulent signal reduces to the second-order structure function (THEORY-750), and as a worked example of why entropy rates cannot carry the direction of the cascade (THEORY-748). Read it knowing that its “information” is a lag-dependent conditional entropy of the velocity, not a quantity distributed over or transferred between scales; that its claim to “prove the existence of an energy cascade” with information theory does not follow, since one-point skewness alone gives unequal sign-conditioned entropy rates; and that no result ties an information quantity to the energy balance. |
| LIT-1245 v2 | Optimal prediction and the Mori–Zwanzig representation of irreversible processes | Chorin, Hald & Kupferman (2000). For any flow with an invariant measure, writes the resolved variables’ exact evolution as Zwanzig’s generalized Langevin equation, with conditional expectation as the projection: a Markovian term E[LA|A], a memory integral and a noise with zero conditional mean. First-order optimal prediction is the Markovian term alone. In a perturbative nonlinear Schrödinger example, keeping the memory recovers the decay of the conditional mean that the Markovian scheme misses. | Active — read 2026-10-20 (NOTE-989) in full, from the authors’ PostScript copy on Chorin’s Berkeley page; worth reading for the generalized Langevin identity of the resolved variables, with conditional expectation under an invariant measure as the projection (Markovian term R(A) = E[LA|A], memory K(s, A) = E[LS⊥ˢF|A], noise S⊥ᵗF with zero conditional mean), for first-order optimal prediction as its Markovian part, and for the renormalized Hamiltonian −log∫e^{−H} in the canonical case. Read it knowing that its claim that no m-equation Markovian model beats first-order optimal prediction in mean square holds only for the instantaneous rate, that it states no fluctuation–dissipation relation and no criterion for when memory may be dropped, and that its one demonstration (m = 0, perturbative, kernels cut off at a time chosen to give a reasonable decay) shows the decay of the mean but not a faithful mean after t ≈ 2. |
| LIT-1248 v3 | Onsager’s conjecture on the energy conservation for solutions of Euler’s equation | Constantin, E & Titi (1994). Proves the positive half of Onsager’s conjecture: a weak solution of the incompressible Euler equations on the periodic box with u ∈ L³(0,T; B^α_{3,∞}) ∩ C([0,T]; L²) and α > 1/3 conserves energy, because the coarse-grained energy flux across scale ε is O(ε^(3α−1)). Hölder regularity above 1/3 is a special case. It says nothing about solutions below 1/3. | Active — read 2026-10-20 (NOTE-982) in full, from the authors’ manuscript (the url:); worth reading for a complete one-page proof that a weak solution of incompressible Euler with L³-averaged increments scaling as |y|^α, α > 1/3, conserves energy (THEORY-749), and for its mechanism: the energy flux into scales below a mollification scale ε is a commutator of size ε^(3α−1). Read it knowing that it is the positive half of Onsager’s conjecture only and shows nothing about rougher fields: that dissipative solutions exist below 1/3 is Isett (2018) and others, and some rough solutions conserve energy anyway; that its “physical interpretation” (ε̄ = 0) passes to Navier–Stokes and to ensemble averages without proof; that the endpoint 1/3 is not covered; and that the manuscript misprints the exponents in the middle line of its final estimate and integrates (2) over R³ for the box D, neither affecting the result. |
| LIT-1251 v2 | Turbulence: the filtering approach | Germano (1992). Develops algebraic relations among filtered fields and subgrid stresses at different filter widths, the basis of the Germano identity used in dynamic subgrid models. | Unavailable — filed 2026-10-19, not read. On 2026-10-20 a search for a lawful full text reached none. Cambridge Core’s page gives the abstract and offers the article only by purchase or institutional access; Crossref lists only a similarity-checking link and Cambridge’s terms. Unpaywall, OpenAlex and Semantic Scholar report it closed, with no repository copy. Germano’s institutional records hold no copy: Politecnico di Torino’s IRIS finds only a 2021 paper on the filtering approach, a different work, and the UNIMORE catalogue lists the same 2021 paper; Duke Scholars lists the citation with no file. arXiv has nothing by Germano under this title. A title search found no author-posted copy; the nearest was a CFD Online forum thread of readers asking each other for it. It stays Unavailable until a copy is supplied. No NOTE is filed. |
| LIT-1252 v2 | Locality of turbulent cascades | Eyink (2005). Treats locality of forward and inverse cascades, in three- and two-dimensional turbulence, in one coarse-graining framework, so that locality of transfer and its direction are separate properties. | Unavailable — filed 2026-10-19, not read. On 2026-10-20 a search for a lawful full text reached none. ScienceDirect returned a 403 bot-check page, and Unpaywall, OpenAlex and Semantic Scholar report it closed with no repository copy. Eyink’s Johns Hopkins pages (ams.jhu.edu/~eyink/, including publications.html), where he posts many of his papers, returned a Cloudflare block to both clients tried, and the Internet Archive refused the connection when tried for an archived copy of them. So whether Eyink posts this paper is unknown: the failure there is on access, not availability. An arXiv search of Eyink’s papers found no preprint of it, only later companions (Eyink & Aluie 2009, arXiv:0909.2386 and 0909.2451). A title search found only a ResearchGate record and citing papers. It stays Unavailable until a copy is supplied. No NOTE is filed. |
| LIT-1253 v3 | Optimal prediction with memory | Chorin, Hald & Kupferman (2002). Writes the resolved variables of an ODE with uncertain unresolved initial data as an exact generalized Langevin equation (Markovian term, memory, noise) under three projections, computes the memory from equilibrium correlation functions through a Volterra equation, and introduces the t-damping (t-model) equation, whose leading-order memory term dissipates the effective energy of separable Hamiltonian systems. On one 4-variable example the memory restores the decay of the conditional mean that the Markovian equation misses. No error bounds. | Active — read 2026-10-20 (NOTE-975) in full, from the published version on Chorin’s Berkeley page; worth reading for the exact generalized Langevin equation under three projections (conditional expectation, linear, finite-rank), for computing the memory kernel from equilibrium correlation functions through a Volterra equation, and for the t-damping (t-model) equation dΦ/dt = R̄(Φ) + tS(Φ) with its proof that, for separable Hamiltonians, it dissipates the effective energy (THEORY-752). Read it knowing that it has one 4-variable example, no error bound for any approximation, no Markovian augmentation by memory coordinates, that its abstract’s “close to the best possible estimate” holds on that example only to t ≈ 8, and that the t-model it calls a short-memory approximation treats the kernel as constant over the whole window. |
| LIT-1254 v2 | Information loss under coarse graining: A geometric approach | Raju, Machta & Sethna (2018). Follows the Fisher information metric of the bare parameters as the data are coarse-grained along an RG flow. Exactly: coarse-graining an exponential family loses the expected conditional covariance of its energy operators, and under an exact RG step with linear beta functions that loss is analytic, so the singular part of the metric survives; for diffusion the metric scales as n^(1−μ) by Hermite order, keeping only the drift. By a scaling argument: irrelevant directions contract as b^−(d−2λ). On its own scalings only directions with eigenvalue above d/2 keep their information, not every relevant one. | Active — read 2026-10-20 (NOTE-972) in full, from arXiv v2; worth reading for the identity that coarse-graining an exponential family loses exactly the expected conditional covariance of its energy operators, for its consequence under an exact RG step (the loss is the Hessian of an analytic constant, so the singular part of the Fisher metric survives; THEORY-742), and for the exact diffusion case, where the metric scales as n^(1−μ) by Hermite order. Read it knowing that “relevant directions are exactly maintained” is true only of the singular part, that on its own scalings the preserved directions are those with RG eigenvalue above d/2 rather than above 0, that the contraction of irrelevant directions (Eq. 21) is a scaling argument backed by the numerics of Machta et al. (2013) and not derived, that the drift is exactly preserved only at the Gaussian fixed point, and that no learning dynamics appear. |
| LIT-1255 v2 | A proof of Onsager’s conjecture | Isett (2016; Annals 2018). For every α < 1/3 it constructs a nonzero weak solution of the 3D incompressible Euler equations on R × T³, with velocity in C^α and pressure in C^{2α} in space and time, that is identically zero outside a finite time interval, so its kinetic energy is not constant. This is the negative half of Onsager’s conjecture; the positive half, conservation above 1/3, is Constantin, E and Titi’s. The construction iterates a Main Lemma that adds high-frequency corrections built from Mikado flows, after a new “gluing” step that rearranges the error so that it lives on short, separated time intervals and the corrections never interact. | Active — read 2026-10-20 (NOTE-974), skimmed, from arXiv:1608.08301v2: the introduction, the statement of the theorem, the Main Lemma and its three sublemmas, the gluing construction and the convex-integration ansatz, and the whole proof of the theorem from the Main Lemma; the long estimates of §§9–10 and 17 and the appendix were not checked. Worth reading for the negative half of Onsager’s conjecture: for every α < 1/3 there is a nonzero weak solution of the 3D incompressible Euler equations on the periodic box, Hölder-continuous with exponent α in space and time, that vanishes outside a finite time interval and so does not conserve energy (THEORY-763). With Constantin, E and Titi (LIT-1248) it fixes 1/3 as the threshold. Read it knowing that its solutions gain energy from zero and lose it again, so they are not dissipative (admissible) solutions, which came later (Buckmaster, De Lellis, Székelyhidi and Vicol 2019); that they are built by convex integration from the zero solution and so also show non-uniqueness, not that turbulent or vanishing-viscosity limits are of this kind; that the endpoint 1/3, two dimensions and finite-energy solutions on R³ are left open; and that the arXiv v2 copy read is a 2024 revision, not compared with the Annals text. |
| LIT-1257 v2 | Renormalization-Group Analysis of Turbulence | Smith & Woodruff (1998). Reviews renormalization-group methods in turbulence, including Yakhot and Orszag’s, and examines which of their approximations support a Wilsonian interpretation. | Unavailable — filed 2026-10-19, not read. On 2026-10-20 a search for a lawful full text reached none. Annual Reviews’ article page and PDF both returned a Cloudflare bot check (403); older volumes of the Annual Review of Fluid Mechanics are not free in any case. Unpaywall and OpenAlex report it closed. Semantic Scholar’s open-access link points to NASA technical report 19890013450, which on fetching is L. M. Smith’s 5-page Center for Turbulence Research annual research brief of 1988 under the same title, a different work. Smith’s University of Wisconsin page lists the review without a file, and arXiv has nothing by Woodruff under this title. A title search found a copy only on a file site that mirrors a shadow-library collection, which was not used. It stays Unavailable until a copy is supplied. No NOTE is filed. |
| LIT-1259 v2 | Non-Markovian closure models for large eddy simulations using the Mori-Zwanzig formalism | Parish & Duraisamy (2017; arXiv 2016). Derives subgrid closures for large-eddy simulation from the Mori–Zwanzig formalism by Stinis’s finite-memory approximation, which replaces the memory integral by auxiliary relaxation equations for the subgrid force: a finite Markovian augmentation of the resolved modes, with no error bound and a memory length fitted to DNS (Burgers: about 0.2 over the spectral radius of the resolved Jacobian) or preset. On Burgers, isotropic turbulence, the Taylor–Green vortex and channel flow it tracks filtered DNS about as well as dynamic Smagorinsky, and better on the transitional Taylor–Green vortex. | Active — read 2026-10-20 (NOTE-973) in full; worth reading for the clearest working example of a Mori–Zwanzig memory term turned into a finite Markovian augmentation (Stinis’s finite-memory closure: the resolved modes plus a relaxing subgrid-force field), tested against filtered DNS on Burgers and four Navier–Stokes flows. Read it knowing that the augmentation’s error is not bounded, the memory length is fitted or preset, the zero-variance projection makes the formalism a deterministic trajectory closure, “finite support” is exponential decay, and the comparisons are plots without error norms. THEORY-760 (Active) and THEORY-747 (Proposed) are filed from it. |
| LIT-1289 v2 | The L³-based strong Onsager theorem | Giri, Kwon & Novack (2023; Annals of Mathematics 2026). For every β < 1/3 there is a weak solution of the 3D incompressible Euler equations on T³ in C⁰([0, T]; B^β_{3,∞} ∩ L^{1/(1−3β)}) that satisfies the local energy inequality ∂_t(½|u|²) + div((½|u|² + p)u) = −D[u] ≤ 0 and strictly dissipates its total kinetic energy: the L³-based strong Onsager conjecture, previously known only for β < 1/7 (in Hölder spaces, De Lellis and Kwon). In the proof D[u] is exactly a prescribed smooth density, −e(t)e′(t)ρ₀(x₁, x₂)² with e(t) a decaying exponential and ρ₀ a pipe flow along e₃, so dissipation is strictly positive inside a periodic array of pipes and zero outside. The construction is an intermittent, L³-measured convex integration in which successive velocity increments overlap in frequency (“partial wavelet sums”), kept apart in space by multi-scale “Mikado bundles”, with an intermittent pressure that dominates every error pointwise. Section 3’s proofs are in a companion paper (Annals of PDE 10:19, 2024). | Active — read 2026-10-20 (NOTE-1022), skimmed, from arXiv:2305.18509v3: the introduction and its heuristics, the whole of Section 2 with the inductive Proposition 2.11 and the proof of Theorem 1.1 from it, the derivation of the new current errors (§5.1) and the closing of the relaxed local energy identity (§6.3, Lemma 6.10) were read; the estimates of Sections 3–6, the dodging lemmas of Section 4, the parameter choices of Section 7 and the appendix were paged through and not checked, and Section 3’s proofs are in a companion paper (Annals of PDE 2024) that the record does not hold. Worth reading for the local, L³-based version of the negative half of Onsager’s conjecture: for every β < 1/3 there is a weak solution of the 3D incompressible Euler equations on the periodic box in C⁰_t(B^β_{3,∞} ∩ L^{1/(1−3β)}) that satisfies the local energy inequality and whose total energy strictly decreases; and, from the proof rather than the theorem’s statement, for the fact that its Duchon–Robert dissipation is exactly the smooth, nonnegative density E(t, x) = −e(t)e′(t)ρ₀(x₁, x₂)² fixed at the iteration’s first step, positive in a periodic array of straight pipes and zero outside them (THEORY-772). So the coarse-grained energy flux into vanishing scales converges, as a distribution in space and time, to a one-signed density: one-way at every place and time in the limit, which Buckmaster, De Lellis, Székelyhidi and Vicol (LIT-1300) showed only for the whole box. Read it knowing that the solutions are not Hölder or even bounded (the strong Hölder version is open; the best Hölder result with the local inequality is β < 1/7, De Lellis and Kwon); that where and how fast energy is dissipated is an input of the construction, carried unchanged through every step, not something the dynamics selects; that the one-signed statement is about the limit ℓ → 0 tested against nonnegative functions, and nothing is said about the sign of the flux at any finite scale; that nothing ties these solutions to vanishing-viscosity limits, though the paper notes that the local inequality is what such limits would satisfy; and that the arXiv v3 copy read is the authors’ final version, not compared with the Annals text. |
| LIT-1295 v2 | A Contraction Theory Approach to Singularly Perturbed Systems | Del Vecchio & Slotine (IEEE TAC 2013; conference version CDC-ECC 2011). Revisits singular perturbation with nonlinear contraction theory. For ẋ = f(x, z, t), εż = g(x, z, ε) with g contracting in z, the fast state’s distance from the slow manifold z = γ(x) obeys an explicit global bound, decaying at rate λ_z/ε to a floor εχ_z(d + K)/λ_z (Lemma 2). With a contracting slow subsystem the slow state stays within an explicit O(ε) of the reduced trajectory for all t ≥ 0 (Theorem 3), and the result extends to three time scales and to retroactivity attenuation in a phosphorylation cycle. Theorem 3 as stated assumes only partial contraction of f in x; its proof needs, and a counterexample shows it requires, contraction of the reduced system. Metrics are constant throughout. | Active — read 2026-10-20 (NOTE-1020) in full, from the authors’ revised manuscript of 22 December 2011 on Del Vecchio’s MIT pages, with the CDC-ECC 2011 conference version (MIT DSpace) for comparison; worth reading for the contraction robustness lemma with its one-line proof (Lemma 1: a system contracting at rate λ in a constant metric Θ, disturbed by d with |d| ≤ d̄, stays within χe^{−λt}|Δ(0)| + χd̄/λ of an undisturbed trajectory), for an explicit, global, uniform-in-time bound on the distance of the fast state from the slow manifold (Lemma 2: χ_z e^{−λ_z t/ε}|z(0) − γ(x(0))| + εχ_z(d + K)/λ_z), and for an explicit O(ε) bound on the error of the quasi-steady-state (Markovian) reduction for all t ≥ 0 (Theorem 3), extended to three time scales and applied to retroactivity in a phosphorylation cycle. Read it knowing that Theorem 3 as stated is false: it assumes only that f is partially contracting in the slow state x, while its proof uses contraction of the reduced system ẋ = f(x, γ(x), t), and a two-variable example satisfying every stated hypothesis has a bistable reduced system and an O(1) error (NOTE-1020); with the reduced system assumed contracting, which the CDC version’s introduction says, the theorem and its proof are correct. Read it also knowing that its metrics are constant (state- and time-dependent metrics are mentioned, not used), that the bound d on |∂γ/∂x · f| is global and cannot hold for a linear system, though the proof needs it only along the trajectory, that the example’s contraction rate λ_z is printed as a max where it is a min, and that the copy read is the revised manuscript, not the version of record. |
| LIT-1299 v2 | Parameter Space Compression Underlies Emergent Theories and Predictive Models | Machta, Chachra, Transtrum & Sethna (Science 2013). Two physics models are not sloppy at their microscopic scale and become so when observed coarsely. In a 1-D hopping model the Fisher spectrum of the density at time t spreads as t^(3/2−k), ordered particle creation, drift, diffusion constant, then skew and higher moments. In Monte Carlo on a decimated 64×64 critical Ising model with 13 couplings and a field, the field and temperature eigenvalues stay put while the rest fall in bands drawn at b^(2y−d) per step. The rate is argued by scaling, not derived, and the Ising numbers have no error bars. The paper reads the resemblance to sloppy models from biology as a common cause of effective theories, which it does not show. | Active — read 2026-10-20 (NOTE-1018) in full, from arXiv:1303.6738v1 with its nine-page supplement; worth reading for the original numerics behind the claim that coarse-graining contracts irrelevant directions of the Fisher metric (Fig. 3: a 64×64 square-lattice Ising model at its critical point, 13 couplings and a field, up to six checkerboard decimations, in which the field and temperature eigenvalues stay put and the rest fall in bands drawn at b^(2y−d) per step for y = 0, −2, −4), for the supplement’s scaling argument for that rate (Eqs. 28–41), which already states that only directions with 2y ≥ d are carried by the singular part, and for the hopping model of diffusion, whose density at time t carries Fisher eigenvalues scaling as t^(3/2−k) (THEORY-774). Read it knowing that the Ising rates are read off a figure with no error bars, no fitted exponents and no second lattice size, and that the eigenvalues are assigned to y by drawn bands, with y = 0 not an operator of the 2D Ising model (THEORY-777, Proposed); that the derivation of the rate is the same scaling argument Raju, Machta and Sethna (2018) later repeat, and assumes the coarse metric is the Hessian of a coarse free energy in the bare couplings; that the Fig. 3 caption’s rate 2^(−d−y) contradicts the supplement and the figure, whose bands fall as 2^(y−d/2); that the diffusion model is not a coarse-graining of one data set, so its leading eigenvalues grow with t rather than staying put; that the main text’s “‘relevant’ directions in the RG are exactly those whose FIM eigenvalues do not contract” is contradicted by its own supplement for relevant directions with 0 < 2y < d; and that the closing claim that emergent theories are “due to” the sloppy hierarchy is not shown, since the paper traces both to the same separation of scales. |
| LIT-1300 v2 | Onsager’s conjecture for admissible weak solutions | Buckmaster, De Lellis, Székelyhidi & Vicol (2017; CPAM 2019). For every β < 1/3 and every smooth strictly positive e : [0, T] → R there is a weak solution of the 3D incompressible Euler equations on T³ × [0, T], in C^β in space and time, with ∫|v(x, t)|² dx = e(t) for every t. With e strictly decreasing these are dissipative (admissible in the sense of a non-increasing total energy), which Isett’s solutions were not. An h-principle (Theorem 1.3) adds that any smooth strict subsolution is a weak-* limit of such solutions. The proof modifies Isett’s: a gluing step whose Reynolds stress stays trace-free, then Mikado-flow perturbations placed in disjoint “squiggling” space-time regions that cover every time, so energy can be pumped in even where the stress vanishes. | Active — read 2026-10-20 (NOTE-1013) in full, from arXiv:1701.08678v1: worth reading for the admissible half of Onsager’s negative direction: for every β < 1/3 and every smooth, strictly positive energy profile e(t) on [0, T] there is a weak solution of the 3D incompressible Euler equations on the periodic box, Hölder-continuous with exponent β in space and time, whose energy ∫|v|² equals e(t) at every time; taking e strictly decreasing gives solutions whose kinetic energy strictly decreases, so the energy flux into vanishing scales is one-signed on every time interval (THEORY-776); and for a shorter, more self-contained proof of the 1/3 threshold than Isett’s (LIT-1255), with a trace-free glued stress and perturbations added everywhere in time so as to steer the energy. Read it knowing that “admissible” here means only that the total energy does not increase (the word appears in the title alone), not the local energy inequality, so the transfer is one-way for the whole box and may run backwards in places; that the same theorem gives solutions with increasing energy just as readily, so the direction is chosen by the prescribed profile and is not forced by the equations; that nothing is shown about vanishing-viscosity limits, about uniqueness or non-uniqueness for given initial data, or about the endpoint 1/3; that the h-principle (Theorem 1.3) rests on a result of Daneri and Székelyhidi stated without proof; and that the abstract’s “typical” is looser than the weak-* density that Theorem 1.3 proves. |
| LIT-1304 v2 | Discrete approach to stochastic parametrization and dimension reduction in nonlinear dynamics | Chorin & Lu (PNAS 2015). Proposes model reduction done entirely in discrete time: the resolved variables are advanced by a fixed numerical scheme plus a discrepancy sequence computed exactly from data, and the discrepancy is fitted as a NARMAX time series (autoregression in itself, lags of functions of the resolved variables, moving average in past innovations). Memory is thereby carried by finitely many lags. The connection to Mori–Zwanzig is drawn by analogy, not derived. On two-scale Lorenz 96 with ε = 0.5, a fit with one autoregressive lag, one or two exogenous lags and at most one moving-average term reproduces the statistics of x₁ better than a polynomial-plus-AR(1) closure, and at observation spacing 0.05 extends the lead time at anomaly correlation 0.6 from 2 to 4. Nothing is proved and no error bound is given. | Active — read 2026-10-20 (NOTE-1028) in full; worth reading for the fully discrete stochastic parametrization: fix a numerical integrator for the resolved equations, take the discrepancy z^{n+1} = (x^{n+1} − x^n)/δ − R_δ(x^n), which the data give without differentiation, and fit it as a NARMAX time series with x as exogenous input, so that memory of past x, past z and past innovations is carried by finitely many lags; for the conditional-likelihood (least-squares) fit; and for a Lorenz 96 test with no time-scale separation (ε = 0.5), where one or two lags reproduce the pdf, autocorrelation and cross-correlation of x₁ and, at δ = 0.05, double the forecast lead time over a polynomial-plus-AR(1) closure (THEORY-818). Read it knowing that the link to Mori–Zwanzig is motivation, not derivation: nothing shows that the fitted Φ approximates the MZ memory or that ξ is the MZ noise, which is orthogonal to the resolved variables but neither white nor independent; that “generalizes the MZ formalism” is an overstatement; that the model structure is found “by trial and error” and changes with δ; that nothing is proved, no error bound is given and no case is shown in which a finite discrete memory suffices exactly; and that the δ = 0.01 fit has a moving-average coefficient 0.9997, at the edge of invertibility. |
| LIT-1305 v2 | Nonuniqueness and existence of continuous, globally dissipative Euler flows | Isett (2017; Archive for Rational Mechanics and Analysis 2022). For every α < 1/15 there are weak solutions of the incompressible Euler equations on T³ (and T^d, d ≥ 3) in C^α_{t,x} that satisfy the local energy inequality ∂_t(|v|²/2) + ∇·((|v|²/2 + p)v) ≤ 0, strictly on an open time interval: the first continuous examples, and a first partial result on the strong Onsager conjecture. From one initial datum there is a Cantor family of them, with no isolated points, positive Hausdorff dimension in C_tL²_x and one common dissipation measure; the same holds for solutions with the local energy equality, and wild data are C⁰ dense. The scheme is a convex integration of “dissipative Euler–Reynolds flows” with one-directional transported plane waves, whose triad interactions cancel the unresolved energy flux current. In the proof the dissipation measure is a function of time alone, switched on only while the construction drains the solution to zero. | Active — read 2026-10-20 (NOTE-1027), skimmed, from arXiv:1710.11186v4: the introduction, Sections 2 and 3 (the dissipative Euler–Reynolds flow and the Main Lemma), Sections 4.1–4.5 (the shape of the construction, the coefficient equations and the energy increment), the opening of 4.10, Section 4.14, Section 5 and Section 6 in full were read; Sections 4.6–4.13, the estimates, were paged through and not checked. Worth reading for the first continuous, indeed C^α_{t,x} with α < 1/15, weak solutions of the 3D incompressible Euler equations that satisfy the local energy inequality with nonzero dissipation (Theorems 1 and 4); for nonuniqueness of such solutions from one initial datum, as a Cantor family with a common dissipation measure and positive Hausdorff dimension in C_tL²_x, and of energy-conserving ones (Theorems 4, 5 and 7); for C⁰ density of wild initial data (Theorem 8); for the notion of a dissipative Euler–Reynolds flow, whose relaxed local energy inequality carries an unresolved flux density and current; and, from the proof rather than any statement, for the fact that the dissipation measure is a function of time alone, equal at each time to the rate of loss of total energy and so spread uniformly over the torus (THEORY-821). Read it knowing that “globally dissipative” means the local energy inequality (not whole-box dissipation, and not strict); that the exponent 1/15 is far below 1/3 (De Lellis and Kwon later reached 1/7 in Hölder spaces, Giri, Kwon and Novack 1/3 in L³-based ones); that the dissipation happens only in a short final interval in which the construction drains the solution to zero, its timing an input; that the shared initial datum is produced by the construction, not prescribed; that the “probabilistic method” is a binary choice per stage, not a random construction; and that the Burgers example of §1.2.1 misstates two constants (−d/dt∫u₀² is 1/3, not 2/3, and the threshold (1/6)^{1/3} is sufficient but not sharp, which is (1/4)^{1/3}), without affecting its point. |
| LIT-1307 v2 | Data-driven model reduction, Wiener projections, and the Koopman-Mori-Zwanzig formalism | Lin & Lu (J. Comput. Phys. 2021). Writes data-driven model reduction for an invertible map with an invariant measure in Koopman-operator terms, derives the discrete Mori–Zwanzig equation from the Dyson formula, and introduces the Wiener projection: orthogonal projection onto the span of the entire past of chosen functions Ψ of the resolved variables. Under it the memory term vanishes, the reduced equation is the causal Wiener filter x_{n+1} = Σ_k Ψ(x_{n−k})h_k + ξ_{n+1}, and the residual is orthogonal to all of Ψ’s past. A rational approximation of the filter’s transfer function, called “uncontrolled” by the authors, turns it into a NARMAX-type recursion. That recursion is fitted by nonlinear least squares with a stability constraint and tested on Kuramoto–Sivashinsky and a stochastically forced Burgers equation. The Wiener projection is proved; the NARMAX derivation is heuristic and no error is bounded. | Active — read 2026-10-20 (NOTE-1029) in full; worth reading for the discrete-time Mori–Zwanzig identity derived from the Dyson formula in a few lines (Eq. 2.5–2.6), valid for any projection; for the Wiener projection, orthogonal projection onto the closed span of the whole past of chosen functions Ψ of the resolved variables, under which the Dyson formula collapses (Eq. 3.5), the memory term disappears into the projection, and the residual is orthogonal to all of Ψ’s past (Eq. 3.6b), not only to its present (THEORY-819); for the skew-product construction that brings randomly forced systems and bounded delays under the same formalism (§3.3); and for the cascade-of-quadratics parametrization that enforces stable memory during fitting (§4.1). Read it knowing that the step from the Wiener projection to NARMAX is a rational approximation the authors themselves call “uncontrolled” and “heuristic”, so no error bound and no convergence statement is proved; that the Wiener projection needs an invertible map and an invariant measure, and its claimed series representation (property (i)) needs more than the linear independence it states; that the KS and Burgers results are numerical, with orders chosen by trial for stability; that Appendix C says the noise term does not appreciably change the KS statistics or forecasts while §5.1 says that without it the models “do considerably worse at all tasks”; and that the record’s check shows the rational form is exact, with orders at most n − 1, for a scalar coarse variable of a stable linear Gaussian VAR(1), where the Wiener filter’s poles are the moving-average zeros, not the eliminated block’s eigenvalues. |
| LIT-1557 v3 | Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora | Nowack & Grossman (2012). In the amoeba Paulinella chromatophora, whose photosynthetic chromatophores arose about 60 million years ago, three photosystem I subunits encoded by genes transferred to the nucleus are made in the cytoplasm, traffic into the chromatophores, apparently via the Golgi, and assemble there with chromatophore-encoded subunits. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC3325729) and the publisher’s free PDF is at pnas.org/content/pnas/109/14/5340.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1558 v3 | Dominant contribution of Asgard archaea to eukaryogenesis | Tobiasson, Luo, Wolf & Koonin (2026). Hypothesis tests on constrained trees for widespread eukaryotic genes traced to the last eukaryotic common ancestor give Asgard archaea about half of all likelihood weight in the best-resolved families and the lead in nearly every functional system. The alphaproteobacterial contribution is small and centred on the mitochondrion (oxidative phosphorylation, Fe–S cluster assembly, mitochondrial translation). About a third of families point to other bacteria, scattered across functions, which the authors read as piecemeal gene transfer and not further symbioses. A test of stem lengths finds they do not track acquisition time. The authors infer a complex Asgard ancestor that took up the mitochondrion late. | Active — read in full 2026-10-27 (NOTE-1242) from the PubMed Central copy of the version of record (PMC12872458, open access); worth reading as the largest survey so far of where the last eukaryotic common ancestor’s genes came from, finding Asgard archaea the largest single source in nearly every functional system, the alphaproteobacterial share small and mitochondrial, and other bacteria diffuse (THEORY-1104), and for its test of the stem-length method, which it finds does not behave as a clock (THEORY-1101). Read it knowing that “dominant” means about half of likelihood weight among well-resolved families, not a count of genes; that the paper is itself mitochondrion-late; that its denial of further symbioses is read off the diffuseness of the bacterial signal, not shown; and that it rests on sparse, biased genome sampling, as the authors stress. |
| LIT-1559 v3 | Extreme genome reduction in symbiotic bacteria | McCutcheon & Moran (2011 online; 2012 issue). Review of bacterial symbionts with extraordinarily small genomes, from independent lineages: gene sets rivalling some organelles, lacking genes thought essential elsewhere, with fast protein evolution and abundant chaperones. The authors read these as highly degenerate genomes retaining only the most essential functions, many serving the host. | Unavailable — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1560 v3 | Protein import into bacterial endosymbionts and evolving organelles | Sørensen, Stiller, Kröninger & Nowack (2024 online; 2025 issue). Review of the evidence for protein import from host into bacterial endosymbionts, long taken to mark an organelle off from an endosymbiont. Import of hundreds of proteins is established in two systems, the Paulinella chromatophore and the nitroplast, where the imported proteins come mostly from the host’s own genes or from other bacteria, so gene transfer from the endosymbiont is not required. Elsewhere there are one to seven targeted proteins per system. Each system uses its own targeting signal, and the mechanisms are largely unknown. | Active — read in full 2026-10-27 (NOTE-1241) from the PubMed Central copy of the version of record (PMC12176269, open access); worth reading as the system-by-system statement of what is known about host proteins entering bacterial endosymbionts, import at scale in the Paulinella chromatophore and the nitroplast and single proteins elsewhere, for its point that gene transfer from the endosymbiont is not needed for an organelle (THEORY-1100), and for its ordered scenario of effectors, dependence and general import (THEORY-1107). Read it knowing that it is a review whose import-at-scale evidence is two proteomic studies, that most single-protein cases rest on antibody localization, that the scenario is offered as plausible on limited data, and that import mechanisms are almost entirely unknown. |
| LIT-1561 v3 | Gene ancestries reveal diverse microbial associations during eukaryogenesis | Bernabeu, Manzano-Morales, Marcet-Houben & Gabaldón (2026). A revised reconstruction of the last eukaryotic common ancestor’s proteome, with thresholds calibrated on the accepted partners, finds two further bacterial donors, Myxococcota (3.92% of the proteome) and Planctomycetota (2.24%), comparable to Alphaproteobacteria (3.99%) and Asgard archaea (3.28%). Stem lengths order the acquisitions as waves, with Planctomycetota before the mitochondrion. About 4.5% of families have viral sisters, mostly giant viruses, some carrying prokaryotic genes. The authors suggest early eukaryotes arose within complex microbial communities through a succession of associations, while conceding their data cannot say whether any donor was a symbiont. | Active — read in full 2026-10-27 (NOTE-1237) from the PubMed Central copy of the version of record (PMC13468126, open access); worth reading as the strongest current case that the last eukaryotic common ancestor received genes from bacterial donors besides the mitochondrial ancestor, Myxococcota and Planctomycetota, in shares comparable to the accepted partners’, and for its ordering of those acquisitions as waves (THEORY-1105). Read it knowing that its thresholds are calibrated on the accepted partners; that its key controls are in a supplement; that the ordering rests on stem lengths as a clock, which Tobiasson et al. dispute; and that the authors say their data cannot tell whether any donor was a symbiont. |
| LIT-1562 v3 | Nitrogen-fixing organelle in a marine alga | Coale et al. (2024). UCYN-A, a streamlined nitrogen-fixing cyanobacterium known as an endosymbiont of a marine alga, is integrated into the alga’s cell architecture and organellar division and imports proteins encoded by the algal genome, so the authors call it an early-stage nitrogen-fixing organelle, the “nitroplast”. | Unavailable — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1563 v3 | Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One | Van Leuven, Meister, Simon & McCutcheon (2014). In some cicadas of the genus Tettigades, the endosymbiont Hodgkinia has split into two cytologically distinct, metabolically interdependent lineages whose gene loss and retention are almost perfectly complementary, so a three-member symbiosis became four. The authors suggest nonadaptive forces can build organismal complexity. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S009286741401037X/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1564 v3 | Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes | Santana-Molina, Williams, Snel & Spang (2025). The last eukaryotic common ancestor had a complete central carbon metabolism of chimeric origin: six putative Asgard-archaeal enzymes, mainly in cytosolic glycolysis and the pentose phosphate pathway; seventeen alphaproteobacterial ones, mostly mitochondrial and ten in the TCA cycle; and others from various bacteria, with no third dominant donor. Gene loss, horizontal replacement and retargeting have remodelled it since, so that compartment no longer follows origin. The authors read the split as a trace of host–symbiont syntrophy, though the split is what any archaeal-host, bacterial-endosymbiont origin would leave. | Active — read in full 2026-10-27 (NOTE-1239) from the PubMed Central copy of the version of record (PMC11976288, open access); worth reading as a careful, enzyme-by-enzyme history of eukaryotic central carbon metabolism, showing Asgard contributions to cytosolic glycolysis and the pentose phosphate pathway, alphaproteobacterial ones mostly in the mitochondrial TCA cycle, other donors with none dominant, and extensive later replacement and retargeting (THEORY-1109). Read it knowing that it rests on 64 single-gene trees, several weakly supported and all in the supplement; that alphaproteobacterial contributions outnumber Asgard ones 17 to six; and that its support for syntrophy comes from a compartment split that any archaeal-host, bacterial-endosymbiont model predicts, so it does not discriminate syntrophy-first from complexity-first scenarios. |
| LIT-1565 v3 | An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs | McCutcheon & von Dohlen (2011). In the mealybug Planococcus citri, the gammaproteobacterium Moranella lives inside the betaproteobacterium Tremblaya. Their complete genomes show little overlap in nutrient-production genes, and several essential amino-acid pathways need a patchwork of gene products from Tremblaya, Moranella and possibly the insect. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC3169327) and the publisher’s free PDF is at cell.com/article/S096098221100724X/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1566 v3 | Dated gene duplications elucidate the evolutionary assembly of eukaryotes | Kay et al. (2026). A relaxed molecular clock dates 135 gene duplications on the two eukaryotic stem lineages, inside a species tree that puts the archaeal branch point at 3.05–2.79 billion years ago, the alphaproteobacterial one at 2.37–2.13 and LECA at 1.80–1.67. Taking the onset of duplications in genes from the mitochondrial partner, about 2.2 billion years ago, as the start of endosymbiosis, most host-side duplications (actin and tubulin, vesicle trafficking, nuclear-targeted paralogues) are older and most other bacterial duplications are younger. The authors reject mitochondrion-early scenarios, argue against serial endosymbiosis, and favour a complexified-archaean, late-mitochondrion sequence. The dates are maximum ages for paralogue functions, and the authors cannot order phagocytosis and the mitochondrion. | Active — read in full 2026-10-27 (NOTE-1234) from the PubMed Central copy of the version of record (PMC12872463, CC BY 4.0); worth reading as the first relaxed-clock dating of the duplications on both eukaryotic stem lineages, which puts most host-side duplications (cytoskeleton, trafficking, nuclear targeting) before the onset of duplications in genes from the mitochondrial partner at about 2.2 billion years ago, and most other bacterial duplications after it (THEORY-1099). Read it knowing that each date is a maximum age for its paralogues’ functions and many intervals reach below 2.2 billion years; that equating the onset of symbiont-gene duplication with endosymbiosis is argued, not tested; that the priors let archaeal duplications be older than any alphaproteobacterial one; and that the authors cannot order phagocytosis and the mitochondrion, though the abstract lists phagocytotic machinery among the features that came first. |
| LIT-1567 v3 | A Eukaryote without a Mitochondrial Organelle | Karnkowska et al. (2016). The genome of the oxymonad Monocercomonoides sp. lacks all hallmark mitochondrial proteins; the mitochondrial Fe–S cluster assembly pathway is replaced by a cytosolic SUF system acquired by lateral transfer from bacteria. Phylogeny places the loss as secondary, so the mitochondrion is not absolutely essential to a eukaryotic cell. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0960982216302639/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1568 v3 | The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss | Morris, Lenski & Zinser (2012). In free-living bacteria such as Prochlorococcus and Pelagibacter, loss of a costly, leaky function whose products are public goods is favoured at the individual level, and proceeds until production just suffices for the community, leaving the losers dependent on co-occurring helpers. Selection, not drift, makes the dependency. The one worked case is Prochlorococcus’s loss of catalase-peroxidase (katG). | Active — read in full 2026-10-27 (NOTE-1212) from the PubMed Central copy of the version of record (PMC3315703, CC BY-NC-SA); worth reading as the selection route to microbial dependency, in which losing a costly, leaky function is favoured until helpers just supply the community (THEORY-1048). Read it knowing that it is an opinion piece with one worked case (katG in Prochlorococcus) whose benefit is computed, not measured; that it is stated for free-living microbes and credits drift for endosymbiont reduction; that its equations assume linear responses; and that its other examples and the “shooting the moon” acceleration are suggestions. |
| LIT-1569 v3 | Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis | Husnik et al. (2013). Tremblaya’s extreme genomic degeneracy likely followed its acquiring Moranella; at least 22 expressed genes transferred to the mealybug genome from diverse bacteria complement missing symbiont genes, none of them from Tremblaya. The three-way symbiosis depends on genes from at least six lineages, a path to intimate endosymbiosis distinct from the organelles’. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0092867413006466/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1571 v3 | How do bacterial endosymbionts work with so few genes? | McCutcheon, Garber, Spencer & Warren (2024). An “Unsolved Mystery” essay on how radically reduced, compositionally biased endosymbiont gene sets function and interact with the host cell. Below about 400 kb endosymbionts lose the ability to build their own envelope, and below about 200 kb, the “tipping point”, translation-related genes erode. Host supply of membranes, transport and translation components is proposed, not shown. | Active — read in full 2026-10-27 (NOTE-1213) from the PubMed Central copy of the version of record (PMC11020763, CC BY); worth reading as the current statement of what endosymbionts with the smallest genomes lack, envelope biogenesis below about 400 kb and parts of translation below about 200 kb, and of the host’s presumed role in supplying them (THEORY-1049). Read it knowing that the thresholds come from a hand-picked matrix with draft genomes, that the composition analysis is called preliminary, and that every mechanism of host supply it names is a hypothesis. |
| LIT-1572 v3 | Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis | Husnik & McCutcheon (2016). Host and symbiont genomes from five mealybug species show Tremblaya from a single ancestral infection but the gammaproteobacterial symbionts inside it from multiple replacements by related lineages, while horizontally transferred genes on the host genome stay stable through the turnover. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC5027413), the bioRxiv preprint is at biorxiv.org/content/10.1101/042267v1, and the publisher’s PDF is at pnas.org/content/pnas/113/37/E5416.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1573 v3 | Accelerated evolution and Muller’s rachet in endosymbiotic bacteria | Moran (1996). Endosymbiont lineages, with small populations and no recombination, should accumulate mildly deleterious mutations. 16S rDNA of five independent endosymbiont clades evolves faster than in free-living relatives, and Buchnera coding genes show elevated nonsynonymous change and A+T-rich substitutions: Muller’s ratchet with mutational bias. | Unfetched — filed 2026-10-27, not read. Registered from the exchange of 2026-10-27, “Repository coverage assessment” (curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds the scanned article (PMC39726), and Europe PMC’s REST service lists its PDF at europepmc.org/articles/PMC39726?pdf=render. This client could not fetch it: both PMC and Europe PMC answered with a Cloudflare challenge page, and Europe PMC has no full-text XML for the scan. |
| LIT-1574 v3 | The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion | Karnkowska et al. (2019). The genome of Monocercomonoides exilis is as complex as other eukaryotes’ and less reduced than some other metamonads’; its nuclear machinery, cytoskeleton, endomembranes and biosynthetic pathways are canonical. The authors find two preadaptations for losing the mitochondrion: the SUF Fe–S system, which replaced the mitochondrial pathway in all examined relatives including some that kept a mitochondrion-related organelle, and the later loss of the glycine cleavage system and SHMT. Mitophagy went with the organelle, and no compensating change was found. | Active — read in full 2026-10-27 (NOTE-1243) from the PubMed Central copy of the version of record (PMC6759080, open access); worth reading as the account of what happened to the rest of a eukaryotic cell when its mitochondrion was lost, which is almost nothing, and of the two preadaptations that emptied the organelle of essential jobs before it went (THEORY-1098). Read it knowing that it is homology searches on a draft genome with most gene lists in supplementary tables, that “no compensating change” is an absence bounded by annotation, that the order of the preadaptations is inferred from relatives, not dated, and that a highly reduced mitosome below microscopic resolution is not excluded. |
| LIT-1585 v2 | Chance and necessity in the evolution of minimal metabolic networks | Pál et al. (2006). Repeatedly simulating successive gene loss on an in silico E. coli metabolic network, with the environment held fixed, gives minimal networks that vary in content by contingency alone but preserve a core metabolism. Simulating each symbiont’s environment predicts the gene content of Buchnera and Wigglesworthia with over 80% accuracy. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1586 v2 | Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas | Łukasik et al. (2018). A single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over four million years, giving complexes of two to six lineages per host. The lineages differ in abundance, size and gene content, and their losses imply extensive sharing of gene products. Together they encode nearly the ancestral gene set. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC5777040) and the publisher’s PDF is at pnas.org/content/pnas/115/2/E226.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1588 v2 | Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes | Timmis, Ayliffe, Huang & Martin (2004). The standard review of endosymbiotic gene transfer: DNA moves from mitochondria and plastids to the nucleus continually and at measurable rates, a minority of transfers become functional nuclear genes whose products are targeted back, and the process has shaped eukaryotic chromosomes. No abstract was seen. The summary is what the review is standardly cited for, and a reading should check it. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1590 v2 | Changes in Endosymbiont Complexity Drive Host-Level Compensatory Adaptations in Cicadas | Campbell et al. (2018). Where Hodgkinia has split into essential lineages of very uneven abundance, rare lineages risk loss at the transmission bottleneck from mother to egg, and a simulation shows the cells needed per egg rising steeply with complexity. Counts in eggs of four cicada species find Sulcia roughly constant and Hodgkinia up to about six times higher in Magicicada septendecim than in a single-lineage species, though only that species differs significantly. Every sampled egg carried every tracked lineage, and the transmission route looks unchanged. The authors read the raised titre as host compensation and a cost of fragmentation, and speculate that it could feed further splitting. | Active — read in full 2026-10-27 (NOTE-1235) from the PubMed Central copy of the version of record (PMC6234865, CC BY 4.0); worth reading as the record’s one documented case of a host compensating for its symbiont’s changes at transmission: cicadas whose Hodgkinia has split into many lineages send more Hodgkinia cells to each egg, not more Sulcia, and every sampled egg carried every tracked lineage (THEORY-1106). Read it knowing that the rise in titre is significant for one species, Magicicada septendecim, of four compared, with five or six eggs each and no phylogenetic control; that the six-lineage species does not differ significantly from single-lineage ones; that lineage presence was tracked by one or two marker genes; and that the order of cause, splitting before titre, is inferred. |
| LIT-1591 v2 | Isolation of an archaeon at the prokaryote–eukaryote interface | Imachi et al. (2020). After 12 years from sampling to culture, an Asgard archaeon related to Lokiarchaeota, Candidatus Prometheoarchaeum syntrophicum MK-D1, was obtained in stable co-culture with a methanogen. It is an anaerobic, extremely slow-growing small coccus that degrades amino acids only in syntrophy, passing hydrogen and formate to partners that can be exchanged, and it has long branching protrusions but no visible internal compartments. From its genome and other Asgard genomes the authors infer that the Asgard ancestor was a partner-dependent amino-acid degrader, and they propose the entangle–engulf–endogenize model of eukaryogenesis as a hypothesis. | Active — read in full 2026-10-27 (NOTE-1238) from the PubMed Central copy of the version of record (PMC7015854, CC BY 4.0); worth reading as the first physiology of an Asgard archaeon, a small, internally simple coccus with branching protrusions that grows only in syntrophy, handing hydrogen and formate to partners that can be exchanged, and for the authors’ inference that the Asgard ancestor was likewise partner-dependent (THEORY-1108). Read it knowing that the organism was grown only in co-culture, never alone; that it is the closest relative of eukaryotes among cultured organisms only; that the ancestral lifestyle is inferred from gene presence in metagenome-assembled genomes; that the entangle–engulf–endogenize model is, in the authors’ words, hypothetical and not definitive; and that the model is not the hydrogen hypothesis, since here the host makes the hydrogen. |
| LIT-1595 v2 | Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry | Pittis & Gabaldón (2016). For 1,078 protein families inferred in the last eukaryotic common ancestor, the branch to the closest prokaryotic relatives, corrected for each family’s rate, is shortest for families of alphaproteobacterial origin and mitochondrial location, longer for other bacterial families, which associate with endomembranes, and longest for archaeal families, which associate with the nucleus. The authors read this as late acquisition of the mitochondrion by a host whose genome already held genes of several bacterial origins, by partners or by transfer. The reading of length as time assumes proportional rates before and after LECA, and the alphaproteobacterial difference from other bacteria is P = 0.044. | Active — read in full 2026-10-27 (NOTE-1240) from the PubMed Central author manuscript (PMC4780264), not the version of record; worth reading as the first proteome-wide test of mitochondrion-early against mitochondrion-late, and for its finding that LECA families sort by origin and cell location (alphaproteobacterial with the mitochondrion, other bacterial with endomembranes, archaeal with the nucleus), with alphaproteobacterial families nearest their prokaryotic relatives (THEORY-1102). Read it knowing that stem length is read as time only under the assumption that rates before and after LECA are proportional; that the alphaproteobacterial difference from other bacteria, on which the chimaeric host turns, is P = 0.044; that stem length also shortens when a closer relative is sampled, as its own Lokiarchaeota control shows; and that it cannot say whether the chimaera came from partners or from gene transfer. |
| LIT-1596 v2 | Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS | Shigenobu et al. (2000). The first complete genome of an obligate insect endosymbiont: Buchnera sp. APS, maternally transmitted in aphid bacteriocytes, has a 640,681-bp chromosome with 583 ORFs and two small plasmids, a subset of E. coli’s gene set reached by loss. It keeps the genes for the amino acids essential to the host and lacks almost all of those for non-essential ones, and uses host-made glutamate and aspartate as precursors, so the two partners’ pathways interlock. It also lacks phospholipid and lipopolysaccharide synthesis, nearly all transcriptional regulators, and recA and uvrABC. The authors infer that it can live only in the bacteriocyte, with membrane lipids perhaps from the host, and compare it to an organelle. All of this is read from gene content. | Active — read in full 2026-10-27 (NOTE-1236) from the publisher’s free PDF of the version of record; worth reading as the first complete genome of an obligate insect endosymbiont, and for its gene-by-gene account of a symbiont that keeps the amino-acid pathways its host lacks, draws precursors from the host, and has lost phospholipid synthesis and nearly all its own regulators (THEORY-1103). Read it knowing that every functional statement is inferred from gene content in one strain, that the host’s dependence is cited from earlier work and maternal transmission stated, neither shown here, and that it names no mechanism of genome reduction: drift and Muller’s ratchet are not in it. |
| LIT-1597 v2 | The hydrogen hypothesis for the first eukaryote | Martin & Müller (1998). Eukaryotes arose from a symbiosis between a strictly hydrogen-dependent, autotrophic archaeal host and a eubacterial symbiont that could respire but produced hydrogen as waste. The host’s dependence on the symbiont’s hydrogen is the selective principle that forged the first eukaryote. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1602 v2 | Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas | Campbell, Łukasik, Simon & McCutcheon (2017). Every Magicicada species harbours Hodgkinia populations of at least twenty genomic circles, 256 in all, with little synteny except between the closest species. Most splitting happened within Magicicada and gives highly variable gene dosages, so Hodgkinia’s degradation has followed different paths in different hosts. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC8879801), the bioRxiv preprint is at biorxiv.org/content/10.1101/199760v1, and the publisher’s free PDF is at cell.com/article/S0960982217313118/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1611 v2 | The consequences of genetic drift for bacterial genome complexity | Kuo, Moran & Ochman (2009). Across sequenced bacteria, the genome-wide ratio of replacement to silent substitutions, a measure of how weak purifying selection is, falls strongly as genome size rises. Drift promotes genome reduction in bacteria. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC2720180) and the publisher’s free PDF is at genome.cshlp.org/content/19/8/1450.full.pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1612 v2 | Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia | Campbell et al. (2015). In the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has fragmented into many chromosomes or genomes, some in discrete cells, together about 1.1 Mb, nearly ten times the hypothetical single ancestor. The authors tested whether long host life cycles enable the splitting, and compare the result with organelle genome fragmentation. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: PubMed Central holds it (PMC4547289), and the publisher’s version is at pnas.org/doi/pdf/10.1073/pnas.1421386112. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1616 v2 | Deletional bias and the evolution of bacterial genomes | Mira, Ochman & Moran (2001). Bacterial genomes stay small and free of nonfunctional DNA because deletions outnumber insertions. In obligate parasites and symbionts, where selection is too weak to maintain genes, genome reduction comes from relaxed selection on gene function, not from selection to lose DNA. | Unavailable — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unavailable until it is read, not on merit. A lawful full text was looked for on 2026-10-27 and none was found: OpenAlex lists it as closed with no open location, Unpaywall reports it closed with no open locations, and Europe PMC has no free copy. |
| LIT-1621 v2 | Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes | Nowack, Melkonian & Glöckner (2008). The chromatophore genome of Paulinella chromatophora, from a primary endosymbiosis independent of and more recent than the plastids’, is 1.02 Mb with 867 protein-coding genes, 26% of a free-living relative’s. Pseudogenes show reduction still under way. It keeps photosynthesis genes and lacks essential amino-acid and cofactor pathways, so the chromatophore depends wholly on its host. | Unfetched — filed 2026-10-27, not read. Registered in the second pass on the exchange of 2026-10-27, “Repository coverage assessment”, at the owner’s request to find what it mentioned and did not cite (second curation entry of 2026-10-27). No NOTE is filed, and it stays Unfetched until it is read, not on merit. A lawful free copy was located on 2026-10-27: the publisher’s free PDF is at cell.com/article/S0960982208002376/pdf. This client could not fetch it: the publisher, repository and preprint hosts named answered with a challenge, a rate limit or a non-PDF page. |
| LIT-1632 v2 | The renormalization group: Critical phenomena and the Kondo problem | Wilson (1975). The renormalization group treats problems with many coupled scales by eliminating degrees of freedom scale by scale and following the flow of effective couplings; near fixed points most couplings are irrelevant, which explains universality in critical phenomena, and the method solves the Kondo problem. | Unavailable — filed 2026-10-27, not read. A close reading was attempted on 2026-10-27 and no lawful full text was reached: the article is closed on Unpaywall and OpenAlex (Reviews of Modern Physics), with no repository copy. It stays Unavailable until a copy is supplied. |
| LIT-1642 v2 | Spatial Localization in Dissipative Systems | Knobloch (2015). In systems where a homogeneous and a patterned state coexist, fronts between them can pin to the pattern’s phase, giving stable localized patches of pattern in a homogeneous background; as a parameter varies they grow by adding cells along a snaking bifurcation diagram (homoclinic snaking), shown in the Swift–Hohenberg equation and in fluid, optical and other experiments. | Unfetched — searched 2026-10-27 for a lawful full text; one exists but this client could not fetch it, so it is not read and no NOTE is filed (ADR-053). Unpaywall lists the publisher’s free copy at Annual Reviews, annualreviews.org/doi/pdf/10.1146/annurev-conmatphys-031214-014514; it answered curl with an HTTP 403 Cloudflare challenge, and a headless- browser fetch was not attempted, since it would be working around the challenge. The failure is on access, not availability. A browser fetch of the Annual Reviews copy is the cheapest way to read it. It stays Unfetched until a copy is supplied. |
| LIT-1664 v2 | Statistical theory of the decay of metastable states | Langer (1969). The decay rate of a metastable state is computed from the statistical mechanics of the saddle-point configuration (the critical nucleus) separating it from the stable phase, giving a field- theoretic basis for nucleation rates. | Unavailable — filed 2026-10-27, not read. A close reading was attempted on 2026-10-27 and no lawful full text was reached: the article is closed on Unpaywall (Annals of Physics, Elsevier), with no open copy listed. It stays Unavailable until a copy is supplied. |
| LIT-1670 v2 | Long-Range Order in a Two-Dimensional Dynamical XY Model: How Birds Fly Together | Toner & Tu (1995), PRL 75. A continuum theory of a flock: a coarse-grained velocity field with a convective term, a preferred speed and noise, coupled to a conserved density. Its linearized theory loses order in d ≤ 2, as the equilibrium XY model does under the Mermin–Wagner theorem, but the convective nonlinearity is relevant below d = 4, and in d = 2 symmetry gives z = 6/5, ζ = 3/5, χ = −1/5, so the velocity fluctuations stay bounded and the flock has true long-range orientational order. The exactness rests on a cubic vertex staying irrelevant, which the authors “strongly suspect”; the order also follows from z < 2, expected “on physical grounds”. | Active — read in full 2026-10-27 (NOTE-1228), from the arXiv preprint; worth reading as the founding hydrodynamic theory of flocking and as a clean case of order that an equilibrium system cannot have, stabilized by the coupling of order to transport. Its exponents are exact only on an argued-but-unproved step; its long-range order in two dimensions has a second, independent argument. |
| LIT-1692 | Holocaust Exposure Induced Intergenerational Effects on FKBP5 Methylation | Yehuda et al. (2016). Holocaust survivors and their adult offspring, compared with Jewish families living outside Europe during the war, showed methylation differences at a site in the stress-related gene FKBP5, in opposite directions in parents and offspring. The samples are small, and the paper is widely cited and widely criticized. | Unfetched — filed 2026-10-29, not read; set Unfetched the same day under ADR-053: the publisher’s copy is free to read at biologicalpsychiatryjournal.com (doi:10.1016/j.biopsych.2015.08.005), listed by Unpaywall as bronze; it is not in PMC and has no author manuscript. On 2026-10-29 the publisher answered with a Cloudflare challenge (HTTP 403). A human reader can likely open it. No NOTE is filed. It stays Unfetched until it is read, not on merit. Read in its place, and not a substitute for reading it: Youssef et al. 2018 (LIT-1725). |
| LIT-1694 | ”Surviving Early Childhood Trauma: Effects of the Holocaust on Survivors’ Psychological and Physiological Well-Being” | A Leiden thesis of four empirical papers on one Israeli sample drawn from the population registry: female child survivors who lost both parents in the Holocaust, matched women who emigrated from Europe to Palestine with their parents before it, and the daughters of both. More than 60 years on, survivors reported more dissociation, less life satisfaction, more cognitive impairment and more stress from recent life events. They had higher diurnal cortisol and an anomalous response to a laboratory stressor, and in an exploratory analysis this held only for ADRA2B wildtype carriers. Their daughters did not differ from comparison daughters on any psychological, cognitive, health or cortisol measure. The one intergenerational signal: daughters of more dissociative survivors had lower diurnal cortisol (n = 17 against 10). The introduction and discussions restate the authors’ two meta-analyses, which found no second- or third-generation traumatization in non-clinical, well-designed samples. | Active — read in full 2026-10-29 (NOTE-1291), in place of LIT-1718 and LIT-1770, which could not be reached; worth reading as the record’s only account, at second hand and by their own authors’ student, of the 2003 and 2008 meta-analyses (LIT-1718, LIT-1770, both Unavailable), and as a primary two-generation study whose matched design holds national identity constant and finds no family transmission. |
| LIT-1696 | Intergenerational transmission of paternal trauma among US Civil War ex-POWs | Costa, Yetter & DeSomer (2018). Among 19,903 children of Union Army veterans born after the Civil War and surviving to 45, sons of men held in Confederate camps in the no-exchange period (July 1863 to July 1864), when conditions were worst, had an older-age mortality hazard 1.11 times that of sons of non-POWs (P = 0.009) and about 1.09 times that of sons of exchange-period POWs. Daughters were unaffected. Within families, sons born after the war to no-exchange POWs died at 2.23 times the rate of their brothers born before it (P = 0.056). The effect was 1.20 among sons born in the second quarter and absent among those born in the fourth, which the authors read as adequate maternal nutrition reversing it. Paternal and maternal socioeconomic controls and maternal lifespan did not change the result. By elimination, the authors judge an epigenetic route most consistent, while granting they cannot reject psychological or cultural transmission. | Active — read in full 2026-10-29 (NOTE-1255) from the published text (PMC6217388, CC BY-NC-ND), served by NCBI’s PMC OAI-PMH service; the supplementary information was not read; worth reading as the largest human study of a father’s trauma and his sons’ longevity, with an unusually clean natural experiment in the timing of captivity. Read it knowing that the effect is about 10% on the older-age hazard, that its mechanism is argued by elimination without biological data, and that its within-family and nutrition results rest on the SI and on modest P values. |
| LIT-1704 | Human transgenerational responses to early-life experience: potential impact on development, health and biomedical research | Pembrey, Saffery and Bygren (2014). A position paper by an 18-member network, two of whose authors led the Överkalix studies. It uses “transgenerational” for any outcome in offspring of an exposure in a parent before conception or in an earlier ancestor. In Överkalix cohorts of about 100 people each, a paternal grandfather’s good food supply in mid-childhood went with higher mortality in his grandsons (rate ratio 1.67) and poor supply with lower (0.65); for paternal grandmothers and granddaughters, 2.13 and 0.72. In ALSPAC, sons of fathers who began smoking before 11 carried more fat from age 13. The authors answer the charge of multiple testing with prior hypotheses and coherence across studies, grant that replication is needed, and hold that a sensitive period in the grandparent’s mid-childhood, not adolescence, makes cultural or genetic inheritance alone unlikely. They stay agnostic on mechanism and ask cohorts to collect ancestral exposure data. | Active — read in full 2026-10-29 (NOTE-1320), in place of LIT-1764, which could not be fetched here; worth reading as the Överkalix authors’ own later account of their findings and of how they answer the charges of multiple testing and cultural confounding. |
| LIT-1708 | Transgenerational epigenetic inheritance: a critical perspective | Bird (2024). A Perspective by a DNA-methylation biologist. Transgenerational epigenetic inheritance rests on two assumptions: that the environment instructs the epigenome, and that acquired marks reach the germline and affect offspring. Both are weak in mammals. Marks usually follow transcription factors rather than lead; DNA methylation is largely stripped from gametes and early embryos; no validated mechanism links environment to epigenome. Organisms work to erase marks (mice inherit them when Dppa2 is mutated). The Agouti diet effect did not replicate. The rodent effects are short-lived or unreplicated, and the one robust paternal effect (microbiome ablation) seems not to go through the sperm epigenome. The human claims are weak: the Swedish (Överkalix) study ignored cultural transmission, failed to replicate in a larger cohort, and risks multiple testing; the Holocaust FKBP5 study had 32 people. Human genetics keeps explaining conditions once put down to environment. The article does not separate inter- from transgenerational effects. | Active — read in full 2026-10-29 (NOTE-1264) from the publisher’s PDF (CC BY); worth reading as the most recent sceptical statement, and the only one of the three to name and dispute the human trauma claims. |
| LIT-1715 | Intergenerational transmission of trauma effects: putative role of epigenetic mechanisms | Yehuda & Lehrner (2018). Reviews evidence that parental trauma raises offspring’s risk of PTSD and alters their stress physiology, and the putative routes: preconception germline effects, in utero exposure and postnatal care. Argues that such effects may be adaptive, and that their mechanisms in humans are not yet established. | Unfetched — filed 2026-10-29, not read; set Unfetched the same day under ADR-053: a lawful free copy is in PMC (PMC6127768), and the publisher’s PDF is open at Wiley. On 2026-10-29 the PMC page answered with a reCAPTCHA, Europe PMC with HTTP 500, NCBI’s E-utilities refused because the publisher does not allow full-text XML, and Wiley with a Cloudflare challenge. A human reader can likely open it. No NOTE is filed. It stays Unfetched until it is read, not on merit. |
| LIT-1725 | The Effects of Trauma, with or without PTSD, on the Transgenerational DNA Methylation Alterations in Human Offsprings | Youssef et al. (2018). A short narrative review of human studies of parental trauma and offspring DNA methylation, PubMed to March 2018. It finds two studies of parents and children: Rwandan mothers pregnant during the genocide (25 exposed, 25 abroad), with higher NR3C1 methylation and lower cortisol in mothers and children; and Holocaust survivors (32) and offspring (22) against 8 controls and their 9 offspring, with higher FKBP5 intron 7 methylation in survivors and lower in their offspring. Three more concern stress in pregnancy (Congo, intimate partner violence) and NR3C1 methylation in newborns and adolescents. The authors call the evidence accumulating but preliminary: small samples, cross-sectional designs, unmeasured confounds, possible publication bias. They use “transgenerational” for any parent-to-child effect, in utero exposure included. | Active — read in full 2026-10-29 (NOTE-1310), in place of LIT-1692, which could not be fetched here; worth reading as a brief, sympathetic account of the Holocaust FKBP5 study and the few human studies beside it, by authors not on that study (though Rutten has published with its second author, Daskalakis; ref. 13). |
| LIT-1738 | Molecular insights into transgenerational non-genetic inheritance of acquired behaviours | Bohacek & Mansuy (2015). Reviews rodent evidence that acquired behaviours and stress responses are transmitted through the germline, by sperm RNAs, DNA methylation and chromatin, and what remains open in humans. | Unavailable — filed 2026-10-29; reading attempted the same day, no lawful copy reached. Unpaywall lists no open copy and a web search found none posted by an author, their institution or the publisher. The ETH Research Collection and the Zurich repository (ZORA) list it without a file, as they do Mansuy’s other reviews of 2013–2017. No NOTE is filed. It stays Unavailable until a copy is supplied (ADR-041). Read in its place, and not a substitute for reading it: Jawaid and Mansuy 2019 (LIT-1774). |
| LIT-1745 | Transgenerational Epigenetic Inheritance: Myths and Mechanisms | Heard & Martienssen (2014). A review of the mechanisms of epigenetic inheritance (small RNA, RNA-directed DNA methylation, paramutation, histone modification) and of germline reprogramming. Transgenerational inheritance is well documented in plants and nematodes, mostly at transposons and transgenes, and is rarely induced by the environment and more rarely adaptive. In mammals two rounds of reprogramming, in the germline and in the early embryo, erase most marks; the few bona fide epialleles (Agouti viable yellow, Axin fused) sit at retrotransposons. Effects of an exposed pregnant female count as transgenerational only from F3, of an exposed male only from F2. Human evidence, mostly nutritional (the Dutch famine, the thrifty phenotype), is intergenerational and confounded, so “so far there is little support”; human culture is the inheritance that is Lamarckian. | Active — read in full 2026-10-29 (NOTE-1254) from the authors’ accepted manuscript (PMC4020004), served by NCBI’s PMC OAI-PMH service; worth reading as the standard map of epigenetic inheritance across plants, worms and mammals, and as the source of the F2/F3 rule the human trauma claims are measured against. |
| LIT-1746 | Parental olfactory experience influences behavior and neural structure in subsequent generations | Dias & Ressler (2014). Male mice fear-conditioned to acetophenone or propanol before mating sired offspring (F1) and grand-offspring (F2) with heightened startle to, and lower detection thresholds for, the odour their F0 father was conditioned to, and not the other one. The offspring of acetophenone-trained males also had more M71 (Olfr151-expressing) olfactory neurons and larger M71 glomeruli; the anatomy, but not behaviour, was also tested and replicated in offspring conceived by IVF and carried by surrogates. Conditioning mothers before mating gave the same behavioural and anatomical effects, which survived cross-fostering. Olfr151 was less methylated in the sperm of conditioned F0 males (n = 12 vs 10) and of their naive F1 sons (n = 4 vs 4), but not in F1 or F2 olfactory epithelium. The authors read the effect as inherited sensitivity to a salient cue, not inherited fear, and leave open how an odour reaches sperm. | Active — read in full 2026-10-29 (NOTE-1281) from the authors’ accepted manuscript (PMC3923835), served by NCBI’s PMC OAI-PMH service; worth reading as the standard animal case for germline transmission of a parent’s experience: a specific, double-dissociated effect with IVF and cross-fostering controls, small groups, and a methylation result that is modest, confined to sperm and of unclear unit of analysis. This NOTE does not assess the later critique of the paper. |
| LIT-1751 | Persistent epigenetic differences associated with prenatal exposure to famine in humans | Heijmans et al. (2008). Sixty people conceived during the Dutch Hunger Winter of 1944–45 had, about six decades later, less methylation in blood at the imprinted IGF2 gene’s differentially methylated region than their unexposed same-sex siblings (0.488 vs 0.515, −5.2%, P = 5.9 × 10⁻⁵). Sixty-two people exposed only late in gestation, who were born lighter, showed no difference, and the timing interaction was significant. The authors read this as the first human evidence that a transient early-gestation exposure can be recorded as a lasting epigenetic change. The exposure is the person’s own, in or around conception, so this is an intergenerational effect, not inheritance across untouched generations. | Active — read in full 2026-10-29 (NOTE-1248) from the paper as reprinted in chapter 3 of Tobi’s 2013 Leiden thesis (hdl.handle.net/1887/22065, Open Access); worth reading as the first human report of a prenatal exposure associated with a methylation difference decades later, and as the record’s clearest case of the womb route: a mark from the person’s own exposure, at the very start of gestation, with no claim about the next generation. |
| LIT-1762 | A critical view on transgenerational epigenetic inheritance in humans | Horsthemke (2018). A Comment. Transgenerational epigenetic inheritance is documented in plants, nematodes and fruit flies; in mammals it must pass the Weismann barrier and two waves of reprogramming. Rodent reports mostly await independent confirmation, and the human ones (grandparental food supply, a Prader–Willi imprint) rest on unique cohorts. The Dutch Hunger Winter shows fetal programming, not germline transmission. Familial epimutations usually turn out to be secondary to a genetic variant. A proof needs: genetic, ecological and cultural inheritance excluded (F3 after an exposed pregnant female, F2 after an exposed male, with IVF and fostering); the factor found in pure germ cells; and the factor shown to cause the effect. In humans only genetic effects can be excluded. Cultural transmission very likely outweighs any epigenetic inheritance; the author remains sceptical. | Active — read in full 2026-10-29 (NOTE-1265) from the published text (PMC6065375, CC BY), served by NCBI’s PMC OAI-PMH service; worth reading as the shortest statement of what would prove germline epigenetic inheritance in humans, and of why the proof may be out of reach. |
| LIT-1764 | Sex-specific, male-line transgenerational responses in humans | Pembrey et al. (2006). In historical records from Överkalix, Sweden, the food supply of paternal grandfathers in mid-childhood was associated with their grandsons’ mortality, and that of paternal grandmothers with their granddaughters’. In the ALSPAC cohort, fathers who smoked early had sons with higher body mass. The authors propose sex-specific male-line transmission. | Unfetched — filed 2026-10-29, not read; set Unfetched the same day under ADR-053: Nature marks the article free to read (nature.com/articles/5201538), but on 2026-10-29 the page served no body text and the PDF link redirected through Nature’s sign-in back to the article page; it is not in PMC, and Unpaywall’s submitted version is the abstract page. A human reader can likely open it. No NOTE is filed. It stays Unfetched until it is read, not on merit. Read in its place, and not a substitute for reading it: Pembrey, Saffery and Bygren 2014 (LIT-1704). |
| LIT-1774 | Inter- and transgenerational inheritance of behavioral phenotypes | Jawaid & Mansuy (2019). A short review from Mansuy’s laboratory, the proponents’ side. Rodent studies show that parental trauma, stress, drugs and in-utero insults pass behavioural phenotypes to offspring, in some models to the third or fourth generation, and that parental environmental enrichment passes benefits, and can prevent the transmission of trauma’s effects. Germline dependence is shown by IVF and by injecting sperm RNA, which reproduces the phenotypes; non-coding RNAs are the best candidate carriers. Human studies of genocide survivors’ descendants are offered as similar, and the review itself tables them as intergenerational. How a stimulus reaches the germline, and how effects pass beyond the first generation, are unknown. Germline reprogramming and the sceptics’ objections are not discussed. | Active — read in full 2026-10-29 (NOTE-1296), in place of LIT-1738, which could not be reached; worth reading as the proponents’ short statement of the rodent case for germline transmission of behaviour, read in place of Bohacek and Mansuy 2015 (LIT-1738), and for what it does not answer. |
| LIT-1851 | Nonequilibrium phase transitions in coordinated biological motion: critical fluctuations | Kelso, Scholz & Schöner (1986), Physics Letters A 118(6):279–284. In bimanual wrist and finger movement paced to rising frequency, the standard deviation of relative phase grows as the anti-phase pattern nears its switch to in-phase and peaks in the transition, while the in-phase pattern shows neither growth nor a switch: the critical fluctuations HKB’s stochastic extension predicts. Critical slowing is predicted, backed only by “very preliminary” spectral evidence, and left to later experiments. | Active — read 2026-10-30 (NOTE-1433) in full, from an offprint scan posted on Kelso’s lab page at Florida Atlantic University (https://ccs.fau.edu/hbblab/pdfs/Kelso_1986_PhysLettersA.pdf), read from the page images; worth reading as the first quantified report of critical fluctuations in human coordination: the standard deviation of relative phase rises before the anti-phase to in-phase switch and peaks in it, in wrist and finger experiments, with no such rise when the same movement starts in-phase. Read it knowing that its figures average a few subjects or show one representative subject, that it gives no statistical test, and that critical slowing and hysteresis are not measured in it. |
| LIT-1861 | Can populations be healthy? Perspectives from Georges Canguilhem and Geoffrey Rose | Giroux (2021), HPLS 43:111. Canguilhem held that health and disease apply only to individuals taken as organic totalities, because normativity, the capacity to institute new norms, is anchored in the organism; at the population level he preferred “hygiene” or “salubrity”. Giroux argues that debates over units of selection and biological individuality loosen his link between individuality and organism, and that social epidemiology (Rose’s causes of incidence, integral variables such as herd immunity and social capital, multilevel models) gives reasons for a concept of population health not reducible to individual health, while denying populations the ontological unity of an organism. | Active — read in full 2026-10-30 (NOTE-1452), from the published article in PubMed Central (PMC8527978; made available in the PMC Open Access Subset under Springer Nature’s COVID-19 terms), fetched as XML through the Europe PMC REST API. Worth reading for two things. It argues, from social epidemiology (Rose’s population causes, herd immunity, integral variables), that some health properties belong to populations and not to their members, against Canguilhem’s restriction of health to the individual organism. And it quotes Canguilhem’s definition of health as normativity in his own (translated) words: “the possibility of tolerating infractions of the habitual norm and instituting new norms in new situations” (The Normal and the Pathological, 1991, pp. 196–197). The Canguilhem it reports is at second hand. |
| LIT-1873 | Dynamics governs switching among patterns of coordination in biological movement | Kelso, Scholz & Schöner (1988), Physics Letters A 134(1):8–12. When people switch on cue between in-phase and anti-phase finger movement, the switch from in-phase to anti-phase takes about twice as long as the reverse (four subjects, each p < 0.0001), with a longer-tailed distribution. Adding to the stochastic HKB equation a term that pulls relative phase toward the intended pattern reproduces the asymmetry and the distributions’ shapes: intention acts within the pattern dynamics, not over them. | Active — read 2026-10-30 (NOTE-1449) in full, from the publisher’s PDF posted on Kelso’s lab page at Florida Atlantic University (https://ccs.fau.edu/hbblab/pdfs/1988_Kelso_Scholz_Schoner_Dynamics_governs_switching_among_pattern.pdf); worth reading as the experiment showing that an intended switch between bimanual patterns is shaped by their stability: switching from in-phase to anti-phase takes about twice as long as the reverse, with a longer tail, as the HKB dynamics with an added intentional term predicts. Read it knowing that it has four subjects, that the model’s one new parameter was set to match the order of magnitude of the switching times, and that the critical slowing it mentions is cited from an earlier paper, not shown. |
| LIT-1885 v2 | Thermodynamic Uncertainty Relation for Biomolecular Processes | Barato & Seifert (2015). In a nonequilibrium steady state of a Markov jump network obeying local detailed balance, the entropy produced while a current is counted times the current’s squared relative uncertainty is at least 2k_BT, independent of time. Proved within linear response for any network and for unicyclic networks at any affinity, where the sharper bound is (A/N) coth(A/2N), which also tightens the Fano-factor bound on the number of states in an enzyme cycle. For multicyclic networks far from equilibrium it is a conjecture supported by numerics on seven networks. | Active — read in full 2026-10-31 (NOTE-1480); worth reading as the letter that named the thermodynamic uncertainty relation: a current counted in a steady state with relative uncertainty ε costs at least 2k_BT/ε² of dissipation, proved within linear response and for single-cycle networks, conjectured with numerical support for many-cycle ones (THEORY-1268). It bounds the precision of currents, not of occupations. |
| LIT-1890 v2 | Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisited | Vellela & Qian (2009). The Schlögl model A + 2X ⇌ 3X, B ⇌ X by rate equation, chemical master equation and open-system thermodynamics. Bistability requires the two chemostats out of equilibrium. The master equation has one two-peaked stationary distribution, so the long-run occupancy of the two states is set by parameters and volume, not by the initial condition, and which state dominates can change with volume alone. The slow eigenvalue, exponentially small in volume, is the sum of the two escape rates. The more stable state can carry the higher or the lower entropy production, and the Fokker–Planck approximation can pick the wrong dominant state. | Active — read in full 2026-10-31 (NOTE-1474) from the PMC copy; worth reading as the clearest worked case of a maintained chemical state that is metastable at finite size: bistability needs the chemostats out of equilibrium, long-run occupancy does not depend on the starting state, the slow eigenvalue is the sum of the escape rates (THEORY-1273), and entropy production does not pick the stable state (THEORY-1270). Its large-volume rate formula carries a spurious 1/V, so its reported breakdown of asymptotics is mostly that factor. |
| LIT-1892 v2 | Macroscopic stochastic thermodynamics | Falasco & Esposito (2025). Takes stochastic thermodynamics of jump processes with local detailed balance to a large-size limit. Extensive rates and potentials give a deterministic dynamics whose Lyapunov function is the quasi-potential, and a large-deviation theory of fluctuations that keeps the fluctuation theorem. Equilibrium, linear irreversible and Onsager–Machlup theories are recovered as limits. Transition rates between attractors go as e^{−VΔI} and are bracketed by the entropy produced along relaxation and escape paths, tightly only near detailed balance. Each attractor has a housekeeping dissipation, and Langevin approximations miss it and misjudge barriers. Minimum and maximum entropy production principles hold only in special regimes. | Active — read in part 2026-10-31 (NOTE-1472, Skimmed: §§I–III, IV.A–D, IV.G–H, VI, VII.A.1, VIII and appendix A read in full; field theory and two of three applications not read); worth reading as the systematic statement of how maintained nonequilibrium states behave at large size: a quasi-potential, not a free energy, sets their lifetimes, which dissipation along relaxation and escape paths brackets (THEORY-1264); each carries its own housekeeping dissipation; and Gaussian-noise Langevin models get both barriers and entropy production wrong (THEORY-1265). |
| LIT-1940 | Ecological scaffolding and the evolution of individuality | Black, Bourrat & Rainey (2020), DOI-10.1038/s41559-019-1086-9. A model in which an ecological scaffold, patchy resources with a regime of dispersal, imposes Darwinian properties on collectives of cells before any collective-level mechanism exists, so that selection can act on collectives from the start. Unread here; described from LIT-188 §2 and the record’s Bourrat readings. | Deferred — filed 2026-11-01, not read. Registered as the model Bourrat’s endogenization account and Griesemer and Shavit’s §2 (LIT-188) rest on. No reading was attempted. |
| LIT-1956 v2 | Early-warning signals for critical transitions | Scheffer et al. (2009), Nature 461. A review of generic early-warning signals for critical transitions. Near a fold bifurcation the dominant eigenvalue goes to zero, so recovery from perturbations slows; under ongoing perturbation this shows as rising lag-1 autocorrelation and variance. Skewness and flickering are further signals. Spatial systems add rising cross-correlation and pattern sequences. Climate, ecosystem, epilepsy, asthma and finance cases are reviewed. The same signals, weaker, precede non-catastrophic thresholds; the timing of a shift stays hard to predict; cyclic and chaotic systems are “less well studied”. | Active — read 2026-11-03 (NOTE-1536, Skimmed), from the version reprinted as chapter 2 of Dakos’s 2011 Wageningen thesis (edepot.wur.nl/168815), its two technical boxes not extractable; worth reading as the standard review of generic early warnings of tipping points, critical slowing down above all, and for its own caution that the same signals precede non-catastrophic thresholds. |
| LIT-1958 | Integrals of motion as slow modes in dissipative many-body operator dynamics | Yang & Abanin (2025), PRB 112, 094304. Under weak local noise an operator’s norm decays at a rate proportional to its size, the number of sites it acts on. Under chaotic Hamiltonian dynamics generic operators grow, so they decay ever faster, while small-sized integrals of motion do not grow and decay slowly. Exact diagonalization of the Lindbladian for Ising and Heisenberg chains of up to nine sites finds the slowest eigenoperators to be linear combinations of the known exact and approximate integrals of motion, and turns up approximate ones not put in by hand. A perturbation theory argues that this survives at large size because the relevant gap is not the level spacing but one of order min(γL, √(v_Bγ)); the authors add that hydrodynamic modes may close that gap. | Active — read in full 2026-11-02 (NOTE-1534), from arXiv:2506.02970v3 with its supplementary material; worth reading as a clean physical case of slowness picking out structure: under weak local noise, a Hamiltonian’s small conserved quantities are the slowest modes because they do not spread, while generic operators spread and decay. The correspondence is shown by exact diagonalization at nine sites or fewer; its large-system footing is a perturbative argument the authors qualify themselves. |