natural-sciences.
136 of 1538 NOTE documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| NOTE-002 v2 | Eulalia impact shower | 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. | Read |
| NOTE-011 v2 | Quantum Thermodynamics | 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). | Read |
| NOTE-031 v2 | The Strongest El Niño Ever (Climate Brink) | 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. | Read |
| NOTE-032 v2 | Work capacity of channels with memory | 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. | Read |
| NOTE-043 v2 | Observational entropy meets maximum entropy | 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). | Read |
| NOTE-044 v2 | Grangier & Auffèves, What is quantum in quantum randomness? | 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. | Read |
| NOTE-061 v2 | Saeedian et al. 2021, delay in generalized Lotka–Volterra | 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. | Read |
| NOTE-067 v2 | The sound of an axon’s growth | 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. | Read |
| NOTE-075 v2 | Surface optimization in physical networks | 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). | Read |
| NOTE-076 v2 | REST2 MD simulations of disordered proteins | 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. | Read |
| NOTE-079 v2 | Ouazan-Reboul et al. 2023, non-reciprocal metabolic cycles | 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. | Read |
| NOTE-100 v2 | Bourrat — Reproducees, reproducers, Darwinian individuals | 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. | Read |
| NOTE-101 v2 | Luque — Philosophical analysis of the Price equation | 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. | Read |
| NOTE-103 v2 | SEP — Philosophy of statistical mechanics | 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. | Read |
| NOTE-109 v2 | Bender et al. — What Lives? (definitions of life) | 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. | Read |
| NOTE-111 v2 | Baedke et al. — Unknotting reciprocal causation | 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). | Read |
| NOTE-124 v3 | McKenzie — Emergence from physics to computer science | 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. | Read |
| NOTE-126 v2 | Worrall — Evidence in medicine and EBM | 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. | Read |
| NOTE-137 v2 | Hazelwood — Emerging dilemma for reciprocal causation | 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. | Read |
| NOTE-147 | Wigner — Symmetry and conservation laws | 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. | Skimmed |
| NOTE-155 v2 | Trappes — Defining the niche for niche construction | 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. | Read |
| NOTE-159 v2 | SEP — Philosophy of 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. | Read |
| NOTE-170 v2 | Takola & Schielzeth — Hutchinson’s niche for individuals | 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”. | Read |
| NOTE-173 v3 | Griesemer & Shavit — Scaffolding individuality (3Cs) | 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). | Read |
| NOTE-184 v2 | SEP — Units and levels of selection | 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. | Read |
| NOTE-295 | Thermodynamics of Prediction | 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. | Read |
| NOTE-296 | Stochastic Thermodynamics of Learning | 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. | Read |
| NOTE-304 | The intrinsic parity of elementary particles | 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. | Read |
| NOTE-310 | Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon | 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). | Read |
| NOTE-330 | Damasio & Carvalho — The nature of feelings | An Opinion with no new data. Feelings are the felt side of interoceptive body maps, and they report homeostatic value. Feeling does not need the insula: the authors’ own patient with both insulae destroyed still feels. It needs the upper brainstem, where whole-body maps first assemble. The evolutionary story (felt maps beat unfelt ones because they support learning and anticipation) and the cellular one (unmyelinated, ligand- and ion-permeable interoceptive axons, with ephaptic coupling, as the root of sentience) are hypotheses, and are presented as such. | Read |
| NOTE-341 | The Computational Boundary of a “Self” | A hypothesis essay. A Self is the set of parts that pursue goals together, and its boundary is the farthest region of space and time it can measure and act on, its “cognitive light cone”. Selves grow from homeostatic loops by adding memory, anticipation and networks, and cells form larger Selves by sharing bioelectric state through gap junctions. Every level that has its own goal is a Self, so living systems hold many nested Selves at once; the paper says this against IIT in one bracket. It has no model, no measurement of the light cone and no new data, and it confines claims about experience to a closing speculation. | Read |
| NOTE-401 | The Genetical Evolution of Social Behaviour. I | A one-locus, non-overlapping-generation model in which genotypes affect relatives’ fitness. Splitting each effect into a part on genes identical by descent (weight r) and a “diluting” part on other genes shows that the former alone fixes the direction of selection, and defines inclusive fitness. Mean inclusive fitness provably increases when no genotype harms others; with harm it only points uphill. A costly act spreads iff −k > 1/r: twice the cost to a sib, eight times to a cousin. | Read |
| NOTE-402 | The Evolution of Reciprocal Altruism | A verbal model: altruists who withhold help from non-reciprocators beat non-altruists when benefit exceeds cost, encounters are many, partners stable and exposure symmetric. Cleaner-fish hosts that do not eat their cleaners fit it; bird alarm calls are explained by a different, self-interested model. Human friendship, moralistic aggression, gratitude, sympathy, guilt, trust, suspicion and their sham forms are proposed as adaptations regulating exchange, supported by 1960s social psychology, not tested. | Read |
| NOTE-404 | The Logic of Animal Conflict | Five strategies for contests with dangerous weapons, simulated 2,000 times per pairing with payoffs +60 win, −100 serious injury, −2 per scratch, up to +20 for brevity. Hawk is not an ESS; Retaliator is called one though Mouse ties it, so by the paper’s own second condition it is only neutrally stable. In a war of attrition no pure strategy is stable; the exponential mixture p(x) = (1/v)e^(−x/v) is. Individual selection can explain limited war. No Hawk–Dove game, no ownership. | Read |
| NOTE-407 | Baumard, André & Sperber 2013, mutualistic morality | Partner choice with outside options constrains how the gains of cooperation are split: nobody accepts less than they could get elsewhere, so with equal options the stable split is proportional to each partner’s contribution of effort and talent. Being chosen then rewards a genuine sense of fairness over calculated fairness. Dictator, ultimatum, trust and public-goods results are read as allocations by perceived entitlement. Twenty-eight commentators accept partner choice and dispute that fairness is all of morality; the authors reply with a broad and a narrow position they have not settled between them. | Read |
| NOTE-408 | Curry 2016, morality as cooperation: a problem-centred approach | The founding statement of morality-as-cooperation. Nonzero-sum game theory gives seven cooperation problems (kin, coordination, exchange, hawk and dove contest displays, division, possession), and their solutions are said to be what morality is. Each domain gets an animal case, a human case and quotations from moral philosophers. No data are reported. The sharpest content is the predictions on pp. 39–40: non-cooperative behaviour is morally neutral, no culture moralizes “aesthetics or nutrition”, and religious morality and food taboos will turn out cooperative. | Read |
| NOTE-409 | Five Rules for the Evolution of Cooperation | A four-page review. Five mechanisms, each with a b/c threshold derived from a 2×2 game: kin selection r > c/b, direct reciprocity w > c/b, indirect reciprocity q > c/b, network reciprocity b/c > k, group selection b/c > 1 + n/m. For kin, network and group mechanisms the same condition makes cooperators ESS, risk-dominant and advantageous; for the reciprocities RD and AD need more. Derivations are in the unread supplement; the review itself proves nothing. | Read |
| NOTE-410 | The Genetical Evolution of Social Behaviour. II | Generalizes Part I into two principles (value neighbours by relatedness; discriminate so relatedness is determinate) and applies them qualitatively. Haplodiploid sisters (r = 3/4) favour worker altruism, weakened by multiple mating (eight drones give about 0.31); sibs fight to the death only for a gain above 50%; clonal colonies cooperate and sexual aggregates do not fuse. Evidence is anecdotal, partly contrary (Australian halictines), and anomalies are put down to error or misinterpretation. | Read |
| NOTE-411 | The Evolution of Cooperation | TIT FOR TAT won Axelrod’s two tournaments (14 entries plus random, 200 moves; 62 entries, expected 200 moves) and went to fixation in an ecological replay. Against it, only ALL D or alternation need be checked, so no strategy does better iff w ≥ (T−R)/(T−P) and w ≥ (T−R)/(R−S). ALL D is stable for all w; kinship or a cluster with enough in-cluster interactions lets reciprocity in, and a nice stable strategy resists clusters. ALL C ties with TIT FOR TAT, so stability is neutral, not strict. | Read |
| NOTE-413 | Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences | A finite-time fluctuation theorem for stochastic dynamics. If the dynamics are Markovian and microscopically reversible (path over reversed path = e^{−βQ}) and the entropy production ω = ln ρ(x_{−τ}) − ln ρ(x_{+τ}) − βQ is odd under time reversal, then P_F(+ω)/P_R(−ω) = e^{ω}. For processes that start and end in equilibrium ω = β(W − ΔF), so the Jarzynski equality is one line. For time-symmetric steady states, P(+ω)/P(−ω) = e^{ω} for any whole number of cycles. At long times it gives a heat fluctuation theorem and Gaussians with variance twice the mean. | Read |
| NOTE-414 | Belousov-Zhabotinsky reaction | An authoritative short review. BZ: bromate oxidizes an organic reductant, catalysed by Ce, Fe(phen)₃ or other metal ions. Oscillation is a relaxation cycle: autocatalytic HBrO₂ oxidizes the catalyst, Br⁻ (made when Ce⁴⁺ oxidizes bromomalonic acid) shuts the autocatalysis off. Phase resetting by Br⁻, Ag⁺ and Ce⁴⁺ confirms it. Closed: up to several thousand cycles. CSTR: indefinite oscillation, bursting, chaos. Unstirred: trigger waves, targets, spirals, scrolls; in microemulsion, Turing structures. The Oregonator is qualitative only. | Read |
| NOTE-415 | Life as a manifestation of the second law of thermodynamics | Proposes a “restated second law” (systems pushed from equilibrium resist the applied gradients by every available means) and reads Bénard cells, vortices, life and ecosystem succession as successive gradient destroyers, with the second law “necessary but not sufficient” for life. The law is asserted, not derived. The physics examples show organized structures raising dissipation, not that they must. The ecological evidence is one unreplicated marsh comparison and thermal-scanner and satellite correlations, one of whose tables is internally inconsistent. | Read |
| NOTE-416 | Statistical Physics of Adaptation | A macrostate fluctuation relation for driven systems, rearranged as an internal-entropy term, a reversal term and Ψ − Φ = −ln⟨e^{−βΔQ}⟩. It is read as a tendency of driven matter towards states formed by reliable work absorption and dissipation, “adaptation” without replication. The relation is exact. The tendency needs the other two terms held fixed, which the paper arranges only in contrived one-particle landscapes; the many-body claim and the “adaptive resonance” simulation are argued and reported, not shown. | Read |
| NOTE-417 | Nonequilibrium Equality for Free Energy Differences | The nonequilibrium work relation. Switch a classical system that starts in canonical equilibrium from H_0 to H_1 at any finite rate. Then ⟨e^{−βW}⟩ = e^{−βΔF} exactly, whatever the path or the switching time (Eq. 2). It is proved for an isolated Hamiltonian system by Liouville’s theorem, for a reservoir under weak coupling, and for a Nosé–Hoover thermostat with no extra assumption. Thermodynamic integration and the Zwanzig formula are its limits, ⟨W⟩ ≥ ΔF follows by Jensen, and Gaussian work gives W_diss = βσ²/2. Its practical reach is work fluctuations of order k_BT. | Read |
| NOTE-418 | Pattern formation outside of equilibrium | Read for the record’s question only. Patterns away from equilibrium are classified by the linear instability of a uniform state (type I_s, III_o, I_o) and described near onset by universal amplitude equations. There is in general no free energy or Lyapunov functional selecting them. Bénard’s own 1900 hexagons were surface-tension-driven, not Rayleigh’s buoyancy convection. Closed chemical systems must reach equilibrium, so their patterns are transients or need pumping. No global minimization principle exists beyond a perturbative one near threshold. | Skimmed |
| NOTE-419 | Statistical physics of self-replication | A coarse-grained second law, β⟨ΔQ⟩ + ln π(II→I) + ΔS_int ≥ 0, applied to self-replication: the heat a replicator releases per copy is bounded below by the log-odds against its copy falling apart within one generation, so durable, fast copies cost more heat. The general bound is sound. The E. coli and RNA numbers rest on an upper bound on the reverse probability that is argued from biology, not derived, and one printed logarithm has its argument inverted. | Read |
| NOTE-420 | Stochastic thermodynamics, fluctuation theorems and molecular machines | The 2012 reference review of stochastic thermodynamics. For Markovian dynamics coupled to baths of fixed temperature, work, heat and a stochastic entropy s = −ln p(x(τ),τ) are defined on single trajectories. Every known integral, detailed and Crooks-type fluctuation theorem follows from one master theorem, as the log-ratio of a path’s weight under the original and a conjugate dynamics. Dissipation measures how distinguishable forward and reverse paths are. Feedback adds the mutual information I to the second law (Sagawa–Ueda). Machine efficiency and efficiency at maximum power follow from a cycle decomposition. The integral theorems are not proofs of the second law, because the dynamics build irreversibility in. | Read |
| NOTE-421 | Life as we know it | The flow of internal and active states in an ergodic system with a Markov blanket, written in Helmholtz form, can be redescribed as gradient descent on a variational free energy once the variational density is set equal to the posterior over external states. On that redescription such systems “appear” to infer and to bound their own entropy, which the paper calls the marks of life. One simulated soup shows a blanket-enclosed cluster that predicts external motion and falls apart under lesions. The free energy is variational, not thermodynamic. The candle flame is excluded by a one-sentence assertion. The paper’s own reported p-value is not reproduced by the null it describes. | Read |
| NOTE-422 | Comments on a derivation and application of the ‘maximum entropy production’ principle | Two corrections to Dewar. First, Dewar 2005 derives MaxEP far from equilibrium from a fluctuation theorem plus a quadratic approximation to the flux distribution, used as if valid for all f. Both can hold together only for small F, where A(F) = ∂λ/∂F is constant: the linear regime. So the orthogonality condition ∂D/∂F = 4λ, which yields both maximum and minimum dissipation, fails for nonlinear constitutive relations, as an exactly solvable spin chain shows. Second, Dewar 2003’s SOC divergence disappears once the quartic term is kept. | Read |
| NOTE-423 | Nonequilibrium thermodynamics and maximum entropy production in the Earth system | A review by MEP’s leading Earth-system advocate. MEP: given enough degrees of freedom, a system adopts the steady state of maximum entropy production. It is distinguished from Prigogine’s minimum principle, which describes relaxation toward a steady state and does not select among several. Two-box models show MEP arising from a flux–force trade-off. The Earth’s entropy budget is estimated and dominated by absorption of sunlight. MEP fits are surveyed from Paltridge’s climate model to sediment ecology, and life is argued to push the planet toward MEP. The author concedes MEP is not established. | Read |
| NOTE-424 v2 | Time, Structure and Fluctuations | Prigogine’s Nobel statement. Near equilibrium δ²S < 0 with ½∂δ²S/∂t = P > 0 makes δ²S a Lyapounov function, and in the strictly linear regime (constant L_ρρ′) the steady state minimizes entropy production. Far from equilibrium ½∂δ²S/∂t = ΣδJ_ρδX_ρ has no fixed sign, and ΣδJδX ≥ 0 is offered only as a sufficient stability condition. The Brusselator goes unstable at B > 1 + A². Dissipative structures are instabilities of the thermodynamic branch, triggered by fluctuations and sustained by exchange with the outside. The microscopic §§6–7 is a programme, linked to macroscopic thermodynamics only “in the linear region”. | Read |
| NOTE-425 | Energy flow and the organization of life | An essay arguing that life, beginning with the reductive citric-acid cycle, was forced into existence as a channel relieving geochemical free-energy stresses, like lightning or a hurricane. The framework is Jaynesian entropy maximization over states that include currents, not entropy-production principles. The emergence of life is a phase-transition “collapse” of a metastable abiotic earth. The structure of core metabolism is the only evidence. The authors state that the thesis is not quantitatively demonstrated. | Read |
| NOTE-426 | Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states | Jaynes’s maximum-entropy inference, applied to microscopic paths of an open stationary system, gives p_Γ = exp(A_Γ)/Z. The action is a symmetric end-point term plus τσ_Γ/2k_B. A fluctuation theorem p(σ) = e^{τσ/k_B} p(−σ) and ⟨σ⟩ ≥ 0 follow exactly. Maximum entropy production follows only in a mean-field approximation, and only if the number of paths increases with their irreversible action, which is assumed. The self-organized-criticality corollary is a mean-field divergence. As Grinstein and Linsker showed, it does not survive keeping the quartic term. | Read |
| NOTE-427 | The Chemical Basis of Morphogenesis | Turing’s reaction–diffusion theory of pattern. Linearize about a homogeneous steady state of M morphogens on a ring of N cells: each Fourier mode grows or decays independently, and the fastest-growing one sets the pattern. Six forms of onset are possible. For two morphogens, stationary waves of finite wave-length need bc < 0 and 4√(μ′ν′)/(μ′+ν′) < (d−a)/√(−bc) < (μ′+ν′)/√(μ′ν′) (9.4a), with instability if d√(μ′/ν′)/√(−bc) − a√(ν′/μ′)/√(−bc) > 2 (9.4b). These cannot both hold when μ′ = ν′. A computed 20-cell ring gives three lobes. | Read |
| NOTE-444 | An Organizational Account of Biological Functions | Functions are contributions to a differentiated self-maintaining organization by traits that organization produces and maintains (C1–C3). Closure alone grounds teleology and normativity but is shared by flames and hurricanes; differentiation is what makes functions meaningful. The account unifies “why is T there?” and “what is T for?” in current organization, and distinguishes functional, useful, dysfunctional, primary and secondary contributions. Reproduction is left to future “second-order” self-maintaining systems. | Read |
| NOTE-458 | Defining Agency: Individuality, Normativity, Asymmetry, and Spatio-temporality in Action | Minimal agency needs a self-individuated system that is the source of modulations of its coupling with the environment and regulates them by norms it generates. An autonomous organization, a precarious network of mutually enabling processes, generates all three when it adaptively modulates its coupling for its own maintenance. Life is sufficient, not necessary. The definition is a proposal: the authors say asymmetry’s formalization is incomplete and modeller-relative. | Read |
| NOTE-467 | The Haken–Kelso–Bunz (HKB) model: from matter to movement to mind | Kelso’s retrospective on HKB. The relative-phase equation dφ/dt = −a sin φ − 2b sin 2φ has stable in-phase and anti-phase states for b/a > 1/4 and only in-phase below; with noise the switch is a nonequilibrium phase transition with critical fluctuations and slowing. Symmetry breaking gives metastability (relative coordination); merged with Kuramoto it models groups. The same dynamics is reported within and between people and in brain activity. A first-person account, not a review. | Read |
| NOTE-468 | Biological organisation as closure of constraints | A constraint acts on a process while being conserved at that process’s time scale; closure is a set of constraints, each directly dependent on and generative for another, that cannot be split. This separates closure from cycles of processes, grounds functions, and gives a boundary criterion, refined by a preliminary count-based tendency to closure for symbionts and by nested separated closures for levels. Applied only to schematic examples; closure is not claimed to define organisms. | Read |
| NOTE-507 | Damasio & Damasio — Homeostatic feelings and the biology of consciousness | An Essay with no data. Consciousness is the spontaneous identification of mind contents as one’s own, provided by continuous homeostatic feelings that are conscious in themselves and “lend” consciousness to exteroceptive images. Feelings are hybrid because interoceptive pathways (unmyelinated, partly non-synaptic, barrier-free) let the body act on its own map. Evidence is cited clinical contrast: posterior brainstem lesions cause coma, extensive cortical lesions may not; anaesthetics act at membrane-level sensing below feeling. | Skimmed |
| NOTE-509 | Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures | A radiative non-Hermitian Hamiltonian for N tryptophan 1La dipoles (single excitation) predicts superradiant states in microtubule architectures (max Γ/γ ≈ 4000 in a centriole, ≈ 7000 extrapolated for bundles) and a thermal quantum yield that grows with size and is insensitive to static disorder up to 200 cm⁻¹. Steady-state spectroscopy gives tryptophan QY 17.6 ± 2.1% in microtubules against 10.6 ± 0.6% in tubulin dimers. No lifetimes were measured, so the radiative rate is inferred, not observed. | Read |
| NOTE-555 | Conceptualization of the Holobiont Paradigm as It Pertains to Corals | A mini-review arguing that corals must be studied as holobionts. The holobiont is defined by location (coral plus microbiota in body, mucus and skeleton), and its membership can change. Traits belong to host–symbiont combinations: a novel anemone–alga pairing out-performed both natural ones in oxygen flux at 32–34 °C, and two octocorals lost symbionts by different routes, one per host cell and one with host cells. It asks, without answering, whether the holobiont is the unit of selection. | Read |
| NOTE-556 | Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont | A review that redefines bleaching as three holobiont dysbiosis stages: microbial buffering, Symbiodiniaceae reorganisation by shuffling or switching, and traumatic dysbiosis ending in death (Figure 3). The supporting material is cited and correlational. Vibrio rose from about 0 to 30% relative abundance in bleached corals and returned in resilient ones, but the authors say cause and consequence cannot be separated. “Dysbiosis” names both the disruption and the healthy adaptive response, and the stages have no operational boundaries. | Read |
| NOTE-557 | Signaling cascades and the importance of moonlight in coral broadcast mass spawning | Two experiments at Heron Island on Acropora millepora. In 2011, colonies under ambient night light (N = 6) spawned with the reef, while colonies lit after sunset (N = 5) or kept dark (N = 5) did not spawn that night. 184 transcripts selected by variance changed around gamete release only in ambient colonies. In 2006, 90 colonies under blue, green or white nocturnal light spawned 6–8 h or two nights late, and under red light on time. The GPCR and melanopsin cascade is a model built from correlated expression. | Read |
| NOTE-558 | Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change | Four roofless 25 m² cages on Orpheus Island’s reef crest kept large and medium fishes out for 30 months after the 1998 bleaching, against four partial cages and four open plots. Macroalgae averaged 56% cover in cages and 4.1% and 1.7% outside. Coral cover reached 7.7% inside against 19.2% and 20.2%. Recruitment fell to about a third (39 against 108 and 118 per 25 m²) and mortality of established colonies was 24.2% against 9.8% and 11.3%. Reopened, the cages lost their algae in 30 days. | Read |
| NOTE-562 | Cancer across the tree of life: cooperation and cheating in multicellularity | A review framing cancer as cheating on five foundations of multicellular cooperation and surveying cancer-like phenomena across the independent origins of complex multicellularity. Division-of-labour cheating appears in every form, resource and environment cheating only in animals and plants so far. Complex multicellularity is read as a cheater detection and suppression system, with proliferative units as a possible intermediate level of selection. | Read |
| NOTE-630 | Getting to the Bottom of Noether’s Theorem | Noether’s theorem in Hamiltonian form, “a generates symmetries of b iff b generates symmetries of a”, follows in Poisson algebras, complex *-algebras and Banach–Lie algebras from the antisymmetry of the bracket plus uniqueness of solutions; for a bilinear bracket antisymmetry is self-conservation, {a, a} = 0. What carries content is the map from observables (a Jordan algebra) to generators (a Lie algebra): i in complex quantum mechanics, none in the real or quaternionic case, and Alfsen–Shultz’s dynamical correspondence for JB-algebras. | Read |
| NOTE-655 | Irreversibility in bacterial regulatory networks | In an ensemble of sign-consistent Boolean rules on the 87-gene core of the E. coli regulatory network, 51 genes admit a transient knockout or overexpression that leaves the network in a different attractor; only genes that reach a positive circuit can, and the likelihood grows with the weighted number of paths to one. Transitions run from small basins to large. The comparison with evolved crp-knockout strains supports the network’s sign structure strongly and its irreversibility predictions only weakly; no transient perturbation was done in cells. | Read |
| NOTE-656 | A. baumannii PmrB oxidative-stress response memory | An unrefereed bioRxiv preprint arguing that the PmrA/PmrB two-component system in Acinetobacter baumannii senses sublethal oxidative stress through a periplasmic histidine box coordinating a nickel cofactor, activates iron-sulfur repair and peroxide-scavenging genes, holds a redox-gated conformational switch (from simulation), and retains a 30—90 min “response memory” that primes cross-protection against lethal peroxide and antimicrobial peptides and is required for virulence in mice and hypervirulence in a clinical isolate. | Read |
| NOTE-657 | Bhattacharyya et al. 2023, heritable iron memory in E. coli | In genetically identical E. coli, a single cell’s swarming potential is shared by its descendants for about four generations and lost by seven; it tracks the cell’s iron status as read by a Fur-repressed reporter (low iron, better swarmer), iron manipulation lengthens it, and a three-class switching model fits the lineages only if each founding cell holds its class for a fixed delay before switching. The iron link is a correlation through a promoter reporter, and the model is fitted to two time points. | Read |
| NOTE-672 | Hyperbolic geometry of the olfactory space | In four natural odour sources, rank-ordered concentration correlations match points near the surface of a 3D hyperbolic ball and not uniform Euclidean cubes; human odour-descriptor profiles match a full 3D hyperbolic ball. The evidence separates “hyperbolic shell” from “uniform Euclidean cube” only. On a thin shell, hyperbolic distance is nearly a monotone function of angle, so a sphere in flat space, which was not tested, would be a close rival, and the hierarchy that motivates the model is not recovered from the data. | Read |
| NOTE-674 | Mutual information, neural networks and the renormalization group | Makes “the relevant degrees of freedom” of real-space RG an optimizable quantity: the coarse variable of a block that carries the most mutual information about the system beyond a buffer. Learned from Monte Carlo samples, it recovers Kadanoff block spins for 2D Ising and the electric-field variables of the dimer model, discards decoupled noise, and, iterated, gives the Ising flow and ν ≈ 1.0 ± 0.15, while a distribution-fitting RBM keeps the noise. The equivalence with a short-ranged effective Hamiltonian is shown only for 1D and quasi-1D. | Read |
| NOTE-681 v2 | Statistical Physics through the Lens of Real-Space Mutual Information | Makes the real-space mutual-information principle a single-shot operator finder: a CNN coarse-graining co-trained against a neural InfoNCE bound, optimized once at a large buffer, returns on the interacting dimer model the order parameters below the BKT transition and the electric fields above it, and one fitted scaling dimension (1.00037 against 1). The maximal information is log 4 in the ordered phase and decays algebraically with the buffer in the critical one. The model’s operators were known; the optimality theorem is cited. | Read |
| NOTE-682 | Optimal Renormalization Group Transformation from Information Theory | Proves that a block coarse-graining keeping all of the block’s mutual information 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 with an extra assumption) and 1D disorder gains no correlations across it. Where the condition fails, as it does for its own examples, it shows on two-spin blocks of 1D Ising chains that longer-range, many-spin and disorder-correlation terms shrink as more information is kept. Explains decimation in 1D and majority rule in 2D by the cost of encoding into one binary spin. | Read |
| NOTE-683 v2 | An exact mapping between the Variational Renormalization Group and Deep Learning | Identifies Kadanoff’s variational RG kernel with an RBM energy by T = −E + H, so that 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. The identity is correct but definitional, and the paper concedes the approximate schemes differ; its evidence that trained networks do RG is qualitative. LIT-873 is right that fitting the distribution need not give RG, though it does not engage the identity. | Read |
| NOTE-688 v2 | Why does deep and cheap learning work so well? | Argues that cheap networks suffice because physical data have low-order, local, symmetric Hamiltonians, and that depth pays because inference must compose the sufficient statistics of a Markov generative hierarchy; proves that one hidden layer needs exactly 2^n neurons to multiply n inputs. On renormalization it is right that a coarse-graining needs a stated target, and its early appendix shows that neither a matched partition function nor the exact trace condition supplies one; it is wrong that the target must come from supervision. | Read |
| NOTE-690 | Relevance in the Renormalization Group and in Information Theory | Proves, for a short-range lattice model on a cylinder with block and environment as slabs separated by a buffer, that the information- bottleneck encoder at its first transition depends on the block only through the boundary weak value of the leading transfer-matrix eigenvector, which at large circumference is the lowest-dimension primary, with β_c = (λ0/λ1)^(2L_B); checked on a three-site Ising cylinder. It does not cover the planar block-in-a-shell geometry or the fixed-alphabet β → ∞ limit that RSMI uses, which LIT-878 relies on. | Read |
| NOTE-692 v2 | Symmetries and phase diagrams with real-space mutual information neural estimation | The long companion of LIT-878. Derives the RSMI-NE estimator and shows that the maximal real-space information counts ordered sectors (1 bit for the Ising ferromagnet, 2 for columnar dimers), decays exponentially with the buffer off criticality and algebraically at it, and that the ensemble of optimal filters from independent runs maps a degenerate subspace whose projections show broken lattice symmetries and the dimers’ emergent U(1). All the models’ answers were known; the non-equilibrium example is one figure. | Read |
| NOTE-694 | Comment on “Why does deep and cheap learning work so well?” | Schwab and Mehta concede that a preserved free energy does not give a preserved distribution and that the “iff” of LIT-882’s Eq. 8 should be one-directional, and show that Lin and Tegmark’s v1 counterexample violates the trace condition, so the mapping’s exact step stands. Right against v1; it places all of the mapping’s content at the trace condition, and says nothing to the later point that the trace condition does not select the coarse variables. | Read |
| NOTE-706 | Han et al. — From gut microbiota to host appetite | A narrative review, not systematic, by animal-nutrition scientists, of how gut-microbe metabolites and proteins may regulate host appetite. The mechanisms are plausible and mostly shown in rodents. The human evidence is associations in eating disorders and obesity, and prebiotic or metabolite trials that conflict across populations and durations. The authors say so. The framing is mutualist: no microbe “interest” in host eating is argued. | Read |
| NOTE-708 | Vekilov — Nucleation | For lysozyme, measured homogeneous nucleation rates of crystals from solution are about ten orders of magnitude below the classical prediction, level off as supersaturation rises, and pass through a maximum as temperature falls. The paper explains these by two things classical theory lacks. A solution–crystal spinodal, defined kinetically as where the nucleus shrinks to one molecule, so the barrier vanishes. And a two-step mechanism, in which crystals nucleate inside metastable clusters of dense liquid that form fast; ordering inside the clusters is the slow step. For metastable clusters the two-step mechanism is inferred from a kinetic model fitted to one protein’s data, not observed. The evidence for other systems is weaker and the author grades it so. The paper also argues that near the spinodal the barrier is negligible, so heterogeneous substrates must act on the prefactor, not the barrier. | Read |
| NOTE-709 | Ostwald — Studies on the formation and transformation of solids, I | Ostwald times how small a crystal fragment can be and still seed a supercooled melt or supersaturated solution (down to about 10⁻⁹–10⁻¹² g). He shows that only the solid substance itself, or a strictly isomorphous solid, seeds. He divides states beyond equilibrium into metastable ones, which change only on contact with the other phase, and labile ones, where the new phase forms spontaneously. In §§32–41 he states the rule later called the rule of stages: on leaving a state, the form reached is “not the most stable … but the nearest” (pp. 306–307), meaning the form with the next-highest free energy. He offers it “not as a law” but as “a frequently applicable rule” (p. 308), drawn from experience and backed by an analogy with the van der Waals isotherm. The rule covers spontaneous formation only. Whether a metastable intermediate goes on to the next form depends on whether it is labile with respect to it; if it is merely metastable it stays until seeded (p. 308). The word “Stufenregel” does not appear in the paper. | Read |
| NOTE-788 v2 | Das, Manikandan and Banerjee — Information flow with hydrodynamic interactions | Two colloids are symmetrically coupled by the fluid, and the trap of one is moved by recorded Ornstein–Uhlenbeck noise. Mutual information, its time-delayed form and transfer entropy recover the order drive → driven particle → other particle. Under moderate drive they also show some backflow, which disappears under strong drive (numerics only). Stronger coupling lowers the information the driven particle shares with the drive and raises what the particles share. Without the drive, the coupled particles are statistically independent. | Read |
| NOTE-821 | Kupiainen — Rigorous renormalization group | A three-page orientation by a principal of rigorous RG. It covers Wilson’s block-spin map as an iteration on Hamiltonians, made rigorous by cluster (polymer) expansions that control large fields, and what this proved. The massless 4D lattice φ⁴ model is Gaussian at long distances. The continuum 4D φ⁴ limit is always Gaussian (Aizenman and Duminil-Copin). The Gross–Neveu model and Hall-conductivity universality have been constructed or proved. The method stays near Gaussian, and a non-perturbative formalism is missing. The piece makes no new claim of its own. | Read |
| NOTE-831 | Farrell & Ioannou — Generalized Stability Theory I | For a linear system du/dt = Au with A non-normal, the eigenvalues fix only the t → ∞ behaviour. Growth over a finite time t is the largest singular value of e^{At}, bounded below by the fastest mode and at t → 0 set by the numerical abscissa, the top eigenvalue of (A + A†)/2. A system with every mode damped can amplify a perturbation a hundredfold, and its forced and stochastic responses exceed those of the normal system with the same spectrum. | Read |
| NOTE-839 | Trefethen et al. — Hydrodynamic Stability Without Eigenvalues | The linearized operators of plane Couette and Poiseuille flow are far from normal. With every eigenmode decaying, perturbations can grow transiently by O(R) and resonate by O(R²), and an operator perturbation of norm O(R⁻²) makes the flow eigenvalue-unstable, all read off the pseudospectra. That transition to turbulence then follows from linear growth plus energy-neutral nonlinear mixing is a conjecture, from a 2 × 2 model. | Read |
| NOTE-842 | Farrell & Ioannou — Generalized Stability Theory II | For du/dt = A(t)u there are no modes, but the propagator’s singular vectors and the Lyapunov exponents and vectors carry generalized stability theory over. A time-dependent operator that is stable, or neutral, at every instant can be asymptotically unstable, and only if it is non-normal. Random variation of the operator destabilizes generically, with less variation needed the more non-normal and the less damped the mean operator. | Read |
| NOTE-858 | McAllister & McCrea — Long-term consequences of repetitive concussion | A narrative review: almost all athletes recover clinically within 1–2 weeks of a sport concussion, but when it was written (published March 2017) no prospective longitudinal study had measured the long-term cognitive, psychiatric or neurodegenerative risk of repeated concussion or of non-concussive head impacts. The evidence for such risk, CTE included, is retrospective, case-based or survey-based and mixed, and the authors call for large prospective cohorts with controls. | Read |
| NOTE-969 | Eyink and Aluie — Localness of energy cascade I | Builds an exact band-pass decomposition of kinetic energy from smooth filters, a multiscale Germano identity, in which each band’s energy changes by the flux into it minus the flux out. It then restates, with heuristic sketches, Eyink’s (2005) bounds: under a scaling hypothesis on velocity increments with exponents strictly between 0 and 1, the mean energy flux across ℓ takes at most O((ℓ/Δ)^(2/3)) from scales above Δ and O((δ/ℓ)^(2/3)) from scales below δ. It argues, without proof, and checks on one 512³ simulation, that sign cancellations give Kraichnan’s faster 4/3 decay. Locality here is in scale, for one field. Nothing in it bears on units. | Read |
| NOTE-970 | Granero-Belinchón, Roux and Garnier — Scaling of information in turbulence | Estimates, with k-nearest-neighbour estimators, the conditional entropy of a velocity sample given samples a lag τ before it (the “entropy rate”) on one Modane wind-tunnel record, as a function of τ. It finds slopes of −1/3 (inertial) and −1 (dissipative) against log of inverse lag, and shows these are S₂’s scaling through a Gaussian formula the data obey. A sign-of-increment conditioning gives unequal entropy rates, which the paper reads as proof of the energy cascade. That inference fails: one-point skewness alone produces the inequality. No information quantity is tied to the energy balance, and none is transferred. | Read |
| NOTE-972 v2 | Raju, Machta and Sethna — Information loss under coarse graining | For a Boltzmann distribution linear in its couplings, the Fisher information that coarse-grained data lose is the expected conditional covariance of the energy operators. Under an exact RG step with linear beta functions it is the Hessian of the analytic constant, so the singular part of the metric is kept. In the diffusion model it is exact: the metric scales as n^(1−μ) by Hermite order. The claims that every relevant direction is kept and that irrelevant ones contract at b^−(d−2λ) rest on a scaling argument. On the paper’s own scalings the dividing line is λ = d/2, not 0. | Read |
| NOTE-973 | Parish and Duraisamy — Non-Markovian closure for LES via Mori–Zwanzig | Derives large-eddy-simulation closures from the Mori–Zwanzig identity by Stinis’s finite-memory approximation, which turns the memory integral into auxiliary relaxation equations, a finite Markovian augmentation of the resolved modes. Its error is not bounded and its memory length is fitted (Burgers: τ₀ ≈ 0.2 over the spectral radius of the resolved Jacobian) or preset. Against filtered DNS it matches dynamic Smagorinsky on isotropic turbulence and channel flow, beats Smagorinsky and the t-model on the Taylor–Green vortex, and puts the subgrid drain at the cutoff, as DNS does. | Read |
| NOTE-974 v2 | Isett — A proof of Onsager’s conjecture | 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, in C^α in space and time, that vanishes outside a finite time interval and so does not conserve energy. It is built by iterating a Main Lemma that first glues exact local Euler solutions so that the error lives on separated short time intervals, then cancels each piece with a single transported Mikado-flow wave. For the record, it shows that a coarse-grained energy flux can survive the limit of vanishing scale for rough fields; it does not show a one-way dissipative cascade, since these solutions gain energy and then lose it. | Skimmed |
| NOTE-975 | Chorin, Hald and Kupferman — Optimal prediction with memory | Writes the resolved components of an ODE with random unresolved initial data as an exact generalized Langevin equation (Markovian term, memory, noise) under three projections, and approximates the memory two ways: by solving a Volterra equation for its expansion coefficients from Monte Carlo correlation functions, and by the t-damping (t-model) equation dΦ/dt = R(Φ) + tS(Φ), which needs no prior data. On one 4-variable Hamiltonian example both restore the decay of the conditional mean that the Markovian truncation misses, the Volterra scheme to about t ≈ 8. No error bound for any approximation, and no Markovian augmentation. | Read |
| NOTE-982 | Constantin, E and Titi — Onsager’s conjecture on energy conservation | A one-page proof that a weak solution of the 3D incompressible Euler equations on the periodic box conserves energy if it lies in L³(0,T; B^α_{3,∞}) ∩ C([0,T]; L²) with α > 1/3. The flux of energy into scales below a mollification scale ε is written exactly as a commutator, (u⊗u)^ε − u^ε⊗u^ε = r_ε − (u−u^ε)⊗(u−u^ε), of size ε^(2α), against a gradient of size ε^(α−1), so the flux is O(ε^(3α−1)) and vanishes. This is the positive half of Onsager’s conjecture only. It does not show that rougher solutions dissipate. Two printed formulas in the manuscript are wrong as typeset, without effect on the result. | Read |
| NOTE-989 | Chorin, Hald and Kupferman — Optimal prediction and the Mori–Zwanzig representation | Writes Zwanzig’s nonlinear Mori–Zwanzig identity with the projection taken as conditional expectation on the resolved variables under an invariant measure: ∂ₜSᵗA = R(SᵗA) + ∫₀ᵗ K(s, S^{t−s}A) ds + S⊥ᵗF, with R(A) = E[LA|A], F = LA − E[LA|A] and K(s, A) = E[LS⊥ˢF|A]. First-order optimal prediction, dv/dt = R(v), is that identity with the memory and noise dropped, and for a canonical Hamiltonian system it is Hamiltonian in a renormalized 𝓗 = −log∫e^{−H}. In a perturbative nonlinear Schrödinger example with one resolved mode, a memory kernel cut off at a hand-chosen time recovers the decay of the conditional mean that the Markovian scheme misses. The paper states no fluctuation–dissipation relation and no criterion for when the Markovian term suffices. | Read |
| NOTE-1013 v2 | Buckmaster, De Lellis, Székelyhidi and Vicol — Onsager’s conjecture for admissible weak solutions | The admissible version of the negative half of Onsager’s conjecture. For every β < 1/3 and every smooth strictly positive e(t) on [0, T] there is a C^β weak solution of 3D Euler on the torus with ∫|v|² = e(t) exactly, so with e decreasing the energy only falls and the coarse-grained flux runs into vanishing scales on every time interval (THEORY-776). That is the one-way transfer Isett’s solutions lacked, but one-way only for the box as a whole (no local energy inequality), and chosen by the prescribed profile, since an increasing e works just as well. | Read |
| NOTE-1018 | Machta, Chachra, Transtrum and Sethna — Parameter space compression | Two physics models are not sloppy at their microscopic scale and become so when observed coarsely. For the hopping model the Fisher eigenvalues of the density at time t scale as t^(3/2−k), proved here (THEORY-774). For a decimated critical Ising model, Monte Carlo shows the field and temperature eigenvalues staying put while the rest fall in bands drawn at b^(2y−d) per step (THEORY-777, Proposed). That rate, the source of LIT-1254’s Eq. 21, is argued by the same scaling argument, read off a figure without error bars, so THEORY-742’s scaling claim stays scaling-only. The supplement already states the d/2 line. The causal claim about emergent theories is not shown. | Read |
| NOTE-1020 | Del Vecchio and Slotine — Contraction and singular perturbation | Contraction gives global, explicit, uniform-in-time bounds for singular perturbation: the fast state reaches an εχ_z(d + K)/λ_z neighbourhood of the slow manifold at rate λ_z/ε, and the reduced (quasi-steady-state) trajectory is O(ε)-accurate for all time. Theorem 3 as printed is false: it needs the reduced system, not f alone, to be contracting. The robustness lemma is proved for constant metrics only; the reading re-derives it for state- and time-dependent ones, and with it the two steps THEORY-771 lacked. | Read |
| NOTE-1022 | Giri, Kwon and Novack — The L³-based strong Onsager theorem | The L³-based strong Onsager theorem: for every β < 1/3 there are weak Euler solutions in C⁰_t(B^β_{3,∞} ∩ L^{1/(1−3β)}) satisfying the local energy inequality and strictly dissipating total energy. In the proof the Duchon–Robert measure is exactly the smooth density −e e′ρ₀², positive in a periodic array of pipes and zero outside, fixed at the first step; so the coarse-grained flux into vanishing scales is one-signed locally in space and time, in the limit (THEORY-772), with its place and rate chosen by the construction. | Skimmed |
| NOTE-1027 | Isett — Continuous, globally dissipative Euler flows | The first continuous weak Euler solutions satisfying the local energy inequality with nonzero dissipation: C^α_{t,x}, α < 1/15, on T^d, d ≥ 3, with a Cantor family sharing one initial datum and one dissipation measure. In the construction that measure is a function of time alone, so the coarse-grained flux into vanishing scales is one-way at every place in the limit and uniform in space, switched on only while the solution is drained to zero (THEORY-821). | Skimmed |
| NOTE-1028 | Chorin and Lu — Discrete stochastic parametrization by NARMAX | Model reduction done wholly in discrete time: advance the resolved variables by a fixed integrator and fit the exact one-step discrepancy as a NARMAX series, so memory lives in a few lags of the discrepancy, the resolved variable and the innovations. On Lorenz 96 with ε = 0.5 one or two lags reproduce x₁’s statistics and double forecast lead time at δ = 0.05. The link to Mori–Zwanzig is analogy, not derivation; nothing is proved and no error is bounded. The record’s check: a partially observed linear Gaussian VAR(1) is exactly ARMA, with order 1 + the rank of its MZ memory kernels, so a memory non-zero at every lag is carried exactly by finitely many history-measurable coordinates. | Read |
| NOTE-1029 | Lin and Lu — Wiener projections and the Koopman–Mori–Zwanzig formalism | An exact link between Mori–Zwanzig and NARMAX, with the approximation named. For an invertible map with an invariant measure, projecting onto the whole past of chosen functions of the resolved variables removes the memory term: the reduced equation is the causal Wiener filter on the coarse variable’s own history, with a residual orthogonal to all of it. NARMAX follows only by an “uncontrolled” rational approximation of the filter; no error is bounded. The record’s checks: Mori’s kernels and the Wiener filter are both fixed by the coarse variable’s autocovariance; for a scalar coarse variable of a linear Gaussian VAR(1) both are rational with the same numerator, the rational form is exact, and the memory Hankel rank is d − 1 for any rational autocovariance of rank d. | Read |
| NOTE-1212 | Morris, Lenski & Zinser — The Black Queen Hypothesis | Proposes that in free-living microbes, losing a costly function whose product leaks to neighbours is favoured by ordinary individual selection, and the loss runs until the remaining producers (“helpers”) just supply the community, leaving most cells (“beneficiaries”) dependent on a rare few. No relatedness, cooperation or collective is needed, only leakiness and frequency dependence. The one worked case is the loss of catalase-peroxidase (katG) in Prochlorococcus, which cannot survive the hydrogen peroxide that its community removes. The other cases are suggestions. | Read |
| NOTE-1213 | McCutcheon, Garber, Spencer & Warren — How do bacterial endosymbionts work with so few genes? | An essay on the endosymbionts with genomes under about 200 kb, which the authors call “tipping-point endosymbionts”. Below about 400 kb, symbionts almost always lose the genes to build their own envelope and to move proteins across it. Below about 200 kb, even translation erodes: ribosomal proteins, tRNAs and aminoacyl-tRNA synthetases go. Their proteomes are among the most compositionally biased in bacteria. The paper asks four questions it cannot answer: where their membranes, transporters, missing translation parts and protein stability come from. Its best guess is from the host, as in organelles. The thresholds come from a hand-picked set of genomes, and the composition analysis is called preliminary. | Read |
| NOTE-1228 | Toner & Tu — How birds fly together | 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, but the convective nonlinearity is relevant below d = 4, and in d = 2 symmetry fixes the exponents at z = 6/5, ζ = 3/5, χ = −1/5. Since χ < 0 the transverse velocity fluctuations stay bounded as the flock grows, so a flock has true long-range orientational order in two dimensions. The exactness rests on a cubic vertex staying irrelevant, which the authors “strongly suspect”; a fallback argument gives χ < 0 from z < 2, which they “expect on physical grounds”. | Read |
| NOTE-1234 | Kay et al. — Dated gene duplications and the assembly of eukaryotes | A relaxed molecular clock dates 135 gene duplications that happened on the two stem lineages of eukaryotes, inside a species tree dated with 18 fossil calibrations. The authors take the onset of duplications in genes of alphaproteobacterial origin, about 2.2 billion years ago, as the mark of mitochondrial endosymbiosis. Most duplications of archaeal origin are older than that, including ones in actin, tubulin, vesicle trafficking and nuclear-targeted families, so the host was already elaborating its cytoskeleton, endomembranes and nuclear machinery. Most duplications of non-alphaproteobacterial bacterial genes come later, which the authors take as evidence against serial endosymbiosis. Each duplication date is a maximum age for its paralogues’ functions, many intervals reach below 2.2 billion years, and the order of phagocytosis and the mitochondrion is left open by the authors. | Read |
| NOTE-1235 | Campbell et al. — Changes in endosymbiont complexity drive host-level compensatory adaptations in cicadas | In cicadas whose endosymbiont Hodgkinia has split into many lineages, each essential, the mother must put every lineage into every egg. A simulation shows that random transmission would need far more cells as lineages multiply and grow uneven. Counts in eggs of four species find Sulcia numbers roughly constant, and Hodgkinia numbers up to about six times higher in Magicicada septendecim than in a single-lineage species. Amplicon sequencing found every tracked Hodgkinia genotype in every egg sampled. The transmission route looks the same under the light microscope. Only M. septendecim differs significantly; the six-lineage species does not. So the compensation rests on one species. The authors call the raised titre a cost of fragmentation, and speculate that it could feed further splitting. | Read |
| NOTE-1236 | Shigenobu, Watanabe, Hattori, Sakaki & Ishikawa — Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS | The first complete genome of an obligate insect endosymbiont. Buchnera APS, from the pea aphid, has a 640,681-bp chromosome with 583 ORFs and two small plasmids. It is a subset of the E. coli gene set, produced by loss from a larger common ancestor. It keeps the pathways for the amino acids its host cannot make, lacks almost all of those the host can, and draws some precursors from the host, so the two partners’ pathways interlock. It also lacks phospholipid and lipopolysaccharide synthesis, almost all transcriptional regulators, and recA and uvrABC. The authors infer that it can live only in the bacteriocyte and compare it to an organelle. Everything here is read from gene content; no experiment on the symbiont is reported, and the host’s dependence is asserted from the literature, not shown. | Read |
| NOTE-1237 | Bernabeu, Manzano-Morales, Marcet-Houben & Gabaldón — Gene ancestries reveal diverse microbial associations during eukaryogenesis | A fresh reconstruction of the last eukaryotic common ancestor’s proteome from three 100-genome eukaryotic datasets, with each family’s origin read from its sister group in a maximum-likelihood tree. Under thresholds tuned to maximize assignments to Alphaproteobacteria and Asgard archaea, two further bacterial donors pass in every dataset, Myxococcota (3.92% of the proteome) and Planctomycetota (2.24%), comparable to Alphaproteobacteria (3.99%) and Asgard (3.28%). A control that removes Alphaproteobacteria from the database does not reproduce their pattern. About 4.5% of families have a viral sister, mostly giant viruses. Stem-length distributions place Asgard earliest and Planctomycetota before the mitochondrion and Myxococcota. The authors read this as waves of transfer from several partners and challenge two-partner models. They concede their data say nothing about whether any donor was a symbiont. | Read |
| NOTE-1238 | Imachi et al. — Isolation of an Asgard archaeon at the prokaryote–eukaryote interface | After 12 years from sampling to culture, an archaeon of the Asgard group, Ca. Prometheoarchaeum syntrophicum MK-D1, was obtained in stable co-culture with a methanogen (not alone, hence the Candidatus name). It is a small coccus, about 550 nm across, doubling in 14–25 days. It degrades amino acids only in syntrophy, handing off hydrogen and formate to partners that can be swapped. It has long, often branching membrane protrusions and no visible internal compartments. It is the closest cultured relative of eukaryotes, among cultured organisms only. From its genome and other Asgard genomes the authors propose that the Asgard ancestor was a partner-dependent amino-acid degrader. The entangle–engulf–endogenize model they build on it is a hypothesis that the authors call not definitive. | Read |
| NOTE-1239 | Santana-Molina, Williams, Snel & Spang — Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes | Sixty-four gene-family phylogenies for eukaryotic central carbon metabolism (glycolysis, the pentose phosphate pathway, pyruvate and acetate conversion, and the TCA cycle), set against a 317-marker eukaryotic species tree. LECA had essentially the whole pathway set. Its enzymes came from several sources: six putative Asgard contributions, mostly cytosolic glycolytic and pentose-phosphate enzymes (support between 39% and 97%, two cases ambiguous); seventeen alphaproteobacterial ones, mostly mitochondrial and ten of them in the TCA cycle; and others from various bacteria, with no third dominant donor. Since then, loss, horizontal replacement and retargeting have reshaped the pathways, and targeting no longer follows origin. The authors read the split, archaeal glycolysis in the cytosol and bacterial TCA in the mitochondrion, as support for syntrophy models. The split is what any archaeal-host, bacterial-endosymbiont model predicts, so it does not single syntrophy out. | Read |
| NOTE-1240 | Pittis & Gabaldón — Late acquisition of mitochondria by a chimaeric host | For 1,078 eukaryotic protein families inferred to be present in LECA, the length of the branch joining each family to its closest prokaryotic relatives, divided by the family’s median branch length within eukaryotes, is shortest for families of alphaproteobacterial origin and mitochondrial location, longer for other bacterial families (endomembrane-associated), and longest for archaeal families (nucleus and information processing). Read as time, that puts the mitochondrion last, into a host whose proteome was already chimaeric. The reading of length as time needs rates before and after LECA to be proportional, the alphaproteobacterial difference from other bacteria is marginal (P = 0.044), and stem length also falls when a closer relative is sampled, as the paper’s own Lokiarchaeota control shows. | Read |
| NOTE-1241 | Sørensen, Stiller, Kröninger & Nowack — Protein import into bacterial endosymbionts and evolving organelles | A review of the evidence that hosts import their own proteins into bacterial endosymbionts, which has long been taken to mark an organelle off from an endosymbiont. Import of hundreds of nucleus-encoded proteins is established, by proteomics of isolated endosymbionts, in two systems only: the chromatophore of Paulinella and the nitroplast of Braarudosphaera. In both, the imported proteins come mostly from the host’s own genes and from bacteria other than the endosymbiont, and the authors say that gene transfer from the endosymbiont “is not a precondition” for genetic integration. Elsewhere, in a trypanosomatid, a diatom and four insects, there are one to seven imported or targeted proteins per system, each found by antibodies or proteomics. The authors propose an order, effector proteins first and dependence on an imported redundant protein second, which they call plausible on limited data. The import mechanisms are almost entirely unknown. | Read |
| NOTE-1242 | Tobiasson, Luo, Wolf & Koonin — Dominant contribution of Asgard archaea to eukaryogenesis | A large phylogenomic survey that assigns each widespread eukaryotic protein family to its most likely prokaryotic sister by likelihood weights on constrained trees. In the 4,290 best-resolved families, Asgard archaea take about half of all likelihood weight and lead in nearly every functional system, information processing above all. Alphaproteobacteria contribute a small, coherent set centred on the mitochondrion (oxidative phosphorylation, Fe–S cluster assembly, mitochondrial translation). About a third of families point to other bacteria, scattered across functions with no pathway from one donor except a narrow Myxococcota signal, which the authors read as piecemeal gene transfer and not further symbioses. A stem-length analysis leads them to doubt that stem lengths time gene acquisition. They favour a complex Asgard ancestor that took up the mitochondrion late. The limiting caveat, theirs, is sparse and biased genome sampling. | Read |
| NOTE-1243 | Karnkowska et al. — The oxymonad genome displays canonical eukaryotic complexity without a mitochondrion | An inventory of the draft genome of Monocercomonoides exilis, an oxymonad gut commensal and the only well-studied eukaryote with no mitochondrion. Apart from the mitochondrion, peroxisomes and the machinery for degrading them, nothing in the cell looks reduced: about 75 Mb, 16,768 genes, 31,693 introns, and canonical systems for DNA replication and repair, transcription, the cytoskeleton, membrane trafficking and autophagy. It has kept more ancestral eukaryotic protein families than the parasitic metamonads. The only changes the authors tie to the loss are two preadaptations, the SUF system for Fe–S clusters, which all examined relatives share, and the loss of the glycine cleavage system and SHMT, plus the loss of mitophagy. No gene was found that compensates for the absence. The work is homology searches on a draft genome, with two cells imaged by FIB-SEM. | Read |
| NOTE-1248 | Persistent epigenetic differences associated with prenatal exposure to famine in humans | Sixty people conceived during the Dutch Hunger Winter of 1944–45 (daily rations averaging 667 kcal) had, about 58 years later, less methylation of the imprinted IGF2 gene’s DMR in blood than their unexposed same-sex siblings: 0.488 vs 0.515, −5.2%, 0.48 SD, P = 5.9 × 10⁻⁵, lower in the exposed sibling in 43 of 60 pairs. Sixty-two people exposed only late in gestation were born 296 g lighter but showed no difference, and the timing interaction was significant. Birth weight did not track methylation. The authors read it as the first evidence that a transient early-gestation exposure is recorded as a lasting epigenetic change in humans. The exposure is the person’s own; no later generation is studied. | Read |
| NOTE-1254 | Transgenerational Epigenetic Inheritance: Myths and Mechanisms | A review. In plants and C. elegans, epigenetic states pass through many generations, carried by small RNA, DNA methylation and histone H3K9 methylation, mostly at transposons and transgenes. In mammals, two rounds of reprogramming, in the germline and the early embryo, erase most marks; the few bona fide epialleles are at retrotransposons. An exposed pregnant female’s effects count as transgenerational only in F3, an exposed male’s only in F2. Environmentally induced changes are rarely inherited and more rarely adaptive. Human nutritional evidence is intergenerational and confounded: “so far there is little support”. Human culture, the authors say with Gould, is the inheritance that is Lamarckian. | Read |
| NOTE-1255 | Intergenerational transmission of paternal trauma among US Civil War ex-POWs | Children of Union Army veterans born after the Civil War and surviving to 45 (19,903 children of 6,367 fathers). Sons of men held in Confederate camps when prisoner exchanges had stopped and conditions were worst had a mortality hazard 1.11 times that of non-POWs’ sons (P = 0.009); exchange-period POWs’ sons and all daughters were unaffected. Within families, sons born after the war died at 2.23 times the rate of brothers born before it (P = 0.056). The effect was 1.20 among sons born in the second quarter and nil in the fourth, read as maternal nutrition reversing it. Socioeconomic and maternal controls left it unchanged. By elimination the authors favour an epigenetic route but cannot reject psychological or cultural ones. | Read |
| NOTE-1264 | Transgenerational epigenetic inheritance: a critical perspective | A Perspective. Transgenerational epigenetic inheritance needs the environment to instruct the epigenome and the marks to reach the next generation; in mammals both are weak. Marks follow transcription factors; DNA methylation is stripped from gametes and early embryos; no validated mechanism links environment to epigenome, and organisms actively erase marks. The Agouti diet effect did not replicate, rodent effects fade or fail to replicate, and the one robust paternal effect seems not to go through sperm epigenetics. The Swedish famine study ignored cultural transmission and failed to replicate in a larger cohort; the Holocaust study had 32 people. The article does not separate inter- from transgenerational effects. | Read |
| NOTE-1265 | A critical view on transgenerational epigenetic inheritance in humans | A Comment. In mammals, germline epigenetic inheritance must cross the Weismann barrier and two waves of reprogramming, and human studies are confounded by genetic, ecological and cultural inheritance. The Dutch Hunger Winter shows fetal programming, not germline transmission; grandparental food-supply and Prader–Willi findings await replication; familial epimutations are usually secondary to a nearby mutation. A roadmap: exclude the other inheritances (F3 after an exposed pregnant female, F2 after an exposed male), find the factor in pure germ cells, show it causes the effect. In humans only genetic effects can be excluded. Cultural transmission “very likely” outweighs any epigenetic inheritance; the author remains sceptical. | Read |
| NOTE-1281 | Parental olfactory experience influences behavior and neural structure in subsequent generations | Male mice fear-conditioned to acetophenone or propanol before mating had sons and grandsons, never exposed to either odour, who startled more to, and detected at lower concentrations, the odour their grandfather or father had learned, and not the other. Sons and grandsons of acetophenone-trained males had more olfactory neurons carrying its receptor (M71, gene Olfr151) and larger M71 glomeruli; the anatomy, not tested behaviourally, held in IVF offspring carried by surrogates. Mothers conditioned before mating gave the same results, which survived cross-fostering. Olfr151 was less methylated in F0 and F1 sperm (n = 12 vs 10; 4 vs 4), not in the olfactory epithelium. The authors call it inherited sensitivity to a salient cue, not inherited fear. | Read |
| NOTE-1291 | Surviving Early Childhood Trauma: Effects of the Holocaust on Survivors’ Psychological and Physiological Well-Being | Four studies of one registry-drawn Israeli sample: 32 female child survivors who lost both parents, 33 matched women who left Europe with their parents before the war, and 79 daughters. Survivors, now about 77, reported more dissociation and less life satisfaction, scored lower on cognition, and had higher diurnal cortisol and an anomalous response to a laboratory stressor, the last two only in ADRA2B wildtype carriers in an exploratory analysis. Daughters did not differ on any psychological, cognitive, health or cortisol measure. Only an exploratory split found lower cortisol in daughters of more dissociative survivors. The thesis restates its promotors’ meta-analyses: no secondary or tertiary traumatization in non-clinical samples with adequate designs. | Read |
| NOTE-1296 | Inter- and transgenerational inheritance of behavioral phenotypes | A review from Mansuy’s laboratory. In rodents, parental trauma, stress, drugs of abuse and in-utero insults pass behavioural phenotypes to offspring, in the MSUS model “up to the third or even the fourth generation”; paternal environmental enrichment passes benefits and can prevent trauma’s transmission. IVF and sperm-RNA injection show germline dependence, and non-coding RNAs are the best candidate carriers. Human descendants of genocide survivors show more psychopathology; the review’s own table calls these intergenerational. How a stimulus reaches the germline, and how effects pass beyond the first generation, “remains unknown”. Germline reprogramming is not mentioned. | Read |
| NOTE-1310 | The Effects of Trauma, with or without PTSD, on the Transgenerational DNA Methylation Alterations in Human Offsprings | A short narrative review of human studies of parental trauma and offspring DNA methylation. Two parent–child studies: Rwandan mothers pregnant during the genocide and their children, with higher NR3C1 methylation and lower cortisol than a group abroad (25 and 25); and Holocaust survivors (32) and offspring (22) against 8 controls and their 9 offspring, with FKBP5 intron 7 methylation higher in survivors and lower in their offspring. Three studies of stress in pregnancy link it to NR3C1 methylation in newborns and adolescents. The authors call the evidence accumulating but preliminary, and use “transgenerational” for any parent-to-child effect. | Read |
| NOTE-1320 | Human transgenerational responses to early-life experience: potential impact on development, health and biomedical research | A position paper of the Network in Epigenetic Epidemiology. It defines “transgenerational” broadly: any outcome in offspring of a parent’s exposure before conception or an ancestor’s. In the Överkalix cohorts (about 100 probands each), a paternal grandfather’s good mid-childhood food supply went with higher grandson mortality (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 had more body fat from 13. Against multiple testing, the authors cite prior hypotheses and coherence and grant that replication is needed. Against cultural inheritance, they cite the sensitive period in the grandparent’s mid-childhood. On mechanism they stay agnostic. | Read |
| NOTE-1402 | Hazen, Griffin, Carothers and Szostak — Functional information and the emergence of biocomplexity | Defines functional information I(E_x) = −log2 F(E_x), F the fraction of all configurations that reach at least degree E_x of a stated function, and illustrates it on letter strings, random Avida genomes and GTP aptamers. Its one empirical observation is that I against E_x is stepped in Avida, which it attributes to distinct classes (“islands”) of solutions. The measure is relative to a function and to a uniform measure on configurations, and says nothing about history or identity. | Read |
| NOTE-1424 | Haken, Kelso & Bunz — A theoretical model of phase transitions in human hand movements | A theory paper. It takes relative phase as the order parameter of bimanual rhythmic movement and models the switch from anti-phase to in-phase at a critical frequency with φ̇ = −∂V/∂φ, V = −a cos φ − b cos 2φ, anti-phase being lost when |b| < |a|/4. It derives that equation from two self-sustained oscillators whose coupling must be nonlinear, and shows the switch and hysteresis in one simulation. The data it models are Kelso’s earlier experiments, summarized, and critical fluctuations and slowing are left to future work. | Read |
| NOTE-1433 | Kelso, Scholz & Schöner — Critical fluctuations | As bimanual wrist or finger movement is paced faster, the standard deviation of relative phase grows as the anti-phase pattern nears its switch to in-phase, peaks in the transition (about 85° mean phase, near the 90° of a uniform spread), and falls once in-phase is reached; started in-phase, the same movement shows neither a switch nor that growth. The authors take this as critical fluctuations, a mark of a nonequilibrium phase transition. Critical slowing is predicted, not measured, and the evidence is shown for a few subjects without a test. | Read |
| NOTE-1437 | Moreno & Mossio — Biological Autonomy, the Introduction | The Introduction alone. Moreno and Mossio state their programme: the organism, not natural selection, is biology’s central idea; its core is a closure of constraints, which they say fundamentally differs from the process loops and self-organisation of dissipative structures, and which grounds teleology, normativity and function. With regulation and agency, closure makes an autonomous system, an organism; ecosystems meet only closure. The arguments are announced for chapters 1–7, which this reading does not cover. | Skimmed |
| NOTE-1449 | Kelso, Scholz & Schöner — Dynamics governs switching | Four people switched on cue between in-phase and anti-phase finger movement. Going from in-phase to anti-phase took about twice as long as the reverse at every frequency tested, with a longer-tailed distribution, significant for each subject. A stochastic HKB equation with the earlier experiments’ parameters plus a term pulling relative phase toward the intended pattern reproduces the asymmetry and the shapes, with one parameter set to the right order of magnitude: the less stable a pattern, the faster it is left. Loss of stability before spontaneous switches is cited, not shown. | Read |
| NOTE-1452 | Giroux — Can populations be healthy? | Giroux argues against Canguilhem that health can be a property of populations. His restriction of health to the individual organism rests on normativity, which he locates in organic totalities, and on a Darwinism centred on individuals; both are weakened by later debates on units of selection and individuality. Social epidemiology supplies population-level comparisons, integral variables such as herd immunity, and Rose’s distinction between causes of cases and causes of incidence, which justify a population health that is relatively autonomous but less unified than an organism. The paper also quotes Canguilhem’s definition of health as the capacity to institute new norms. | Read |
| NOTE-1472 | Falasco & Esposito — macroscopic stochastic thermodynamics | Builds macroscopic stochastic thermodynamics from Markov jump processes with local detailed balance. Under extensive rates and potentials, a deterministic dynamics emerges whose Lyapunov function is the quasi-potential I_ss, and a large-deviation theory of fluctuations around it. Transition rates between attractors go as e^{−VΔI_ss} and are bracketed by the entropy produced along relaxation and escape paths; the bracket closes only near detailed balance. Gaussian-noise Langevin equations mis-estimate both the barriers and the entropy production. Read for those parts and the Schlögl example; field theory and two of three applications not read. | Skimmed |
| NOTE-1474 | Vellela & Qian — Schlögl model, stochastic and thermodynamic | The Schlögl model A + 2X ⇌ 3X, B ⇌ X, treated by rate equation, chemical master equation and nonequilibrium thermodynamics. Bistability needs the chemostats out of equilibrium; the master equation has one stationary distribution with two peaks, so in the long run which state the system occupies does not depend on where it started; the slow eigenvalue, exponentially small in volume, is the sum of the two escape rates; the more stable state can have the higher or the lower entropy production. The paper’s asymptotic rate formula carries a spurious factor 1/V, so the “breakdown” of asymptotics it reports at small volume is mostly that factor. | Read |
| NOTE-1480 | Barato & Seifert — thermodynamic uncertainty relation | For counting currents in nonequilibrium steady states of finite Markov jump networks, the total entropy produced over time t times the squared relative uncertainty of the current is at least 2k_BT, whatever t. The letter proves this within linear response and, for unicyclic networks, at any affinity, with the sharper unicyclic bound (A/N) coth(A/2N); for multicyclic networks far from equilibrium it gives numerical evidence on seven networks and states the general case as a conjecture. | Read |
| NOTE-1534 | Yang & Abanin — Integrals of motion as slow modes | Under weak local noise an operator decays at a rate set by its size; chaotic dynamics makes generic operators grow, while small-sized integrals of motion do not, so they are the Lindbladian’s slow modes. Exact diagonalization at L ≤ 9 bears this out for Ising and Heisenberg chains and finds approximate conservation laws, including some not put in by hand. The large-L footing is a perturbative argument through a gap of order min(γL, √(v_Bγ)), which the authors say hydrodynamic modes may close. Stronger noise reorders the slow modes in favour of approximate conservation laws. | Read |
| NOTE-1536 | Scheffer et al. — Early-warning signals for critical transitions | A review of generic early-warning signals for critical transitions. At a fold bifurcation the dominant eigenvalue goes to zero, so recovery from small perturbations slows (critical slowing down). Under ongoing perturbation that shows as rising lag-1 autocorrelation and rising variance. Skewness and flickering are further signals, not caused by slowing down. Spatial systems add rising cross-correlation and specific pattern sequences. Evidence from climate, ecosystems, epilepsy, asthma and finance is reviewed. The signals mark proximity to a broad class of thresholds, not only catastrophic ones, so they do not say which kind; false positives and negatives are named. Cyclic and chaotic systems are “less well studied”. | Skimmed |