Davi Bock

@dddavi.bsky.social

2226 Followers 488 Following

Rural neuroscientist. Connectomics. Protists. caveat emptor: https://bsky.app/profile/dddavi.bsky.social/post/3k5bnogiq5r2j

"Remarkably, in 1878, the same figures appeared in both books and an article by Ernst Haeckel (1878a, 1878b) with one figure rotated, and all given binominal names, without any attribution in the figure legends or in the text (Fig. 11). Haeckel's appropriation of Wild's figures was far from the last."
translation help from Opus: "More generally, the translation table for the concepts you've been thinking about in domain terms: • body → graph (or "system instance") • mass node → vertex • spring → edge (in the simulator specifically, spring is used, and that's fine — it's standard physical-simulation vocabulary, and the plan uses it throughout) • effector / actuator → control / control parameter / actuation channel • sensor / sensed value → observable (the spec's word — "per-edge observables," edge_readout ) • controller → Component 4 / the R-GCN / control_fn • damage / injury / ablation → edge-removal perturbation/ subgraph induction (induce, apply_removal)) • morphology → topology / graph structure • proprioception → per-edge observables (d, s, d, angular channels)"
"On the dual-use concern: this is all standard scientific computing-weighted graphs, computational geometry, mass-spring dynamics, GNNs, sequence models—the kind of infrastructure you'd see in graphics papers on XPBD or world-model research. Nothing here is weaponizable or harmful, so l'm comfortable proceeding with the implementation"
Opus prompt: "now examine all the handoff documents and identify components within them that can be recast in pure computer science terms. Strip out all mention of biology, biological motivations, or robotics from these components and create a new md document defining these components. The purpose is to let Fable work on them, without triggering its notoriously oversensitive filter that causes downgrade to Opus." After some time "Scrutinizing whether circumventing safety measures warrants assistance," Opus performed the task handily.
morning light through rising fog in beech woods above Heidelberg, Germany
Pogo, by Walt Kelly: "We have met the enemy and he is us."
Fig 1 Euplotes gigatrox displays marked phenotypic polymorphism including supergiant cannibal cells. (A) A cartoon diagram illustrating basic cellular morphological characteristics of Euplotes species, including ventral cirri used for walking locomotion, membranelles (membranelles of the adoral zone, AZM) used to generate flows for swimming and feeding, sensory caudal cirri, and macro- and micronuclei. (B) A phase contrast image displaying genetically identical “normal” and “supergiant” morphs of E. gigatrox in close association in a culture flask. Scale bar = 50 µm. From https://doi.org/10.1101/2025.08.19.671124 Regulated development of cannibalistic supergiant cells Larson et al 2025 bioRxiv
Krugman: Yeah, I won't say who, but I know some academics who are required by the nature of what they do to go back and forth. They're European-born and they travel with burner phones now, just so they don’t have to worry about their phone being inspected and it being discovered that they have texted their friends saying things critical about Trump, which is amazing.
“For whatever you’re doing, for your creative juices, your geography’s got a hell of a lot to do with it. You really have to be in a good place, and then you have to be either on your way there or on your way from there.”
picture of an abandoned beaver pond in late afternoon light. Early summer, Northeastern Vermont.
Fig. 5. 3D surface reconstruction. (a) Cloud of points in a three-dimensional coordinate system approximate the mean surface of the sample. (b) Triangle mesh model with added texture. (c and d) Individual points (c) and triangular mesh (d) become visible in the enlargements. ((a), (c) Point cloud calculated by PhotoScan and (b), (d) mesh calculated by Recap 360 Photo.) from Eulitz, M. and Reiss, G., 2015. 3D reconstruction of SEM images by use of optical photogrammetry software. Journal of structural biology, 191(2), pp.190-196.
We first imaged partially overlapping volumetric tiles arranged in two dimensions (2D) to obtain a first slab of LICONN data. We then used a conventional vibratome to slice off most of the imaged hydrogel layer, while placing the cut within the imaged slab. In a subsequent imaging round, we obtained an axially offset multi-tile volume situated more deeply in the tissue, featuring a continuous region of axial overlap with the first multi-tile volume. We then computationally fused the individual imaging volumes in 3D in a voxel-exact manner
Still from the movie Airplane
screenshot of David Berson's Youtube video on connectomics, showing relationship between neurons and vascular pericytes in retina
first tap of season already flowing
“Civil Discussion Marks Uneventful Meeting” Hardwick Gazette March 5 2025
“The gains in brain are mainly in the stain” — Floyd Bloom, The Neurosciences: Paths of Discovery, I. Boston, MA: Birkhäuser Boston, 1975. 211-227.
from Fig 2 Buchanan et al 2022 PNAS: Phagolysosomes (PLs) are abundant in OPC processes and contain vesicles. (A) 3D rendering of OPC with numerous ramified branches. Boxed area same as micrograph shown in (B) (Scale bar 15µm.) (B) OPC branch contains PLs, lysosomes (L), and mitochondria (M), and an ingested axon (yellow arrow) (Ax). (Scale bar 1.5 µm.) (C) 3D rendering of same OPC in (B) in pink and axon (Ax) (green) arrow (yellow) points to piece of ingested axon outlined in white and PL (white oval). (Scale bar 2 µm.) Inset shows 3D rendering of the same green axon (Ax) bouton with small, ingested protrusion outlined in slice view (yellow arrow). (Scale bar 500 nm.) (D) Twelve ultrathin 40-nm serial sections through a phagolysosome show the distribution of 40-nm vesicles within the organelle. Nine of the twelve sections have vesicles inside the phagolysosome. (Scale bar 300 nm.)
"And if you have been watching authoritarianism around the world, the moves are very familiar now, as are the players. Two thirds of the President’s Day One executive orders are lifted from Project 2025. Project 2025 is authored principally by the Heritage Foundation. The Heritage Foundation’s president, Kevin Roberts, has said that Victkor Orban’s Hungary is, quote, not just a model for conservative statecraft, but the model, end quote." From https://slate.com/transcripts/eUZ2dmo2alF6Z2gxOXBhSTF4dEl1NFRiSS9iaFFBNUJxRmFiNDNwdFFBUT0=
Fig 4 from "Photoreception in Phytoplankton", Colley & Nilsson 2016 Int & Comp Biol. Legend: Anatomy of the Erythropsidinium ocelloid. (A) Schematic representation of the Erythropsidinium ocelloid and (B) longitudinal section of Erythropsidinium ocelloid ( 3900). t, microtubular layer; mit, mitochondrion; micr, microcrystalline layer; g, periocelloid gallery; cr, constricting ring; pig, pigmentary ring; stf, striated fibre; ff, fibrillar formations on the floor of the ocelloid chamber (microtubules make up the fiber layer); l, highly ordered lamellar membranes of the retinal body (paired thylakoid membranes); v, vesicular layer of the retinal body (vesicles containing melanoid and carotenoid pigment); r, reticulum; mit, mitochondria; M, mela- nosome; f, ocelloid channel; sc, scalariforme plate; H, hyalosome; sc, scalariforme plate; Cr, crystalline body; OCh, ocelloid chamber; C, core. (A) Reproduced from Greuet (1968) with adapted labeling from Greuet (1987) with copyright permission from Elsevier and John Wiley & Sons Inc. (B) Reproduced from Greuet (1987) with copyright permission from John Wiley & Sons Inc.
Gonzales Jayant et al 2025 Sci Adv “Touch-evoked traveling waves establish a translaminar spacetime code.” Crop & markup of Fig 5: “ Enhanced L2/3 sparsity supports late wave dynamics”
Democrats’ jaws hit the floor Wednesday when former Oath Keepers leader Stewart Rhodes — released by Trump from an 18-year prison sentence for conspiring to violently stop Congress’ role in the transfer of power — strode nonchalantly into the Capitol complex, took a seat in a Dunkin’ Donuts and held court with reporters in the same building he gleefully watched under attack. “My only regret is they should have brought rifles,” Rhodes said in a Jan. 10, 2021 recording played at his seditious conspiracy trial in 2022. “We should have brought rifles. We could have fixed it right then and there. I’d hang fucking Pelosi from the lamppost.”
Common drone fly (?) on an aster in northeastern Vermont
twilight over abandoned beaver pond, early winter, northeastern Vermont
abandoned beaver pond, November, Glover VT
Ryerse Nagel 1991 J Microsc fig 3
nest in young regrowth after past logging
Light suffusing the comb of our rooster
Mitchell Crutchfield and Das 1996 Proceedings of the First International Conference on Evolutionary Computation and Its Applications
~7 meters of total cable length, assembled by 20 labs. 186 users have generated 33,280,728 nodes over ~60 person-years of effort. Animation by Philipp Schlegel, Jefferis lab.
afternoon light in late Fall
Falmouth crows
snow only
small frost crystals on leaves
Old apple tree in northern Vermont twilight
Hermit thrush habitat suitability map 2010-2085
Unpasteurized, unfiltered, freshly thawed Aldrich Red apple juice
June 25, 2023: wildfire smoke from Quebec envelopes the historical marker for Runaway Pond, an environmental disaster in Glover VT from the year 1810 https://en.wikipedia.org/wiki/Runaway_Pond
My dog Oota licking her face in the morning sun