Foundations

Ferrari and colleagues profile 5,778 small domains with multiplexed HDX-MS and compare 13 domains with site-resolved HDX NMR.

Turing proposed that reacting and diffusing morphogens can destabilize an initially homogeneous equilibrium and generate patterned states.

Traction microscopy infers forces from cell-induced substrate displacements using a substrate mechanics model.

Predicting conformational free energies, kinetics and function from sequence/static structures remains an open research challenge.

IGoR infers generative V(D)J models by considering alternative gene choices, deletions and insertions for each receptor sequence.

A receptor’s abundance or generation probability is not itself its antigen affinity.

Calcium fluorescence is an indirect activity proxy, and spike inference depends on indicator dynamics, noise and the trained/calibrated model.

Rupprecht and colleagues benchmark GCaMP8 inference against simultaneous mouse-neocortical electrophysiology.

FlyWire reconstructs chemical-synapse wiring in a sampled adult female Drosophila brain using electron microscopy and proofreading.

MICrONS combines visual-response calcium imaging and dense electron-microscopy reconstruction in one mouse visual-cortical volume.

Forward simulators encode reproduction, mutation, recombination, selection and population regulation through a specified life cycle.

Niche differences and near-neutral fitness similarities can act concurrently in a competition–colonization model.

The 2014 point/counterpoint compares emphasis on developmental bias, plasticity, niche construction and broader inheritance with the view that evolutionary theory already integrates such evidence.

Ecological change and heritable trait change can influence one another, but parallel time-series changes do not identify their causal directions.

Water's molecular interactions help explain solvation, cohesion and thermal buffering.

For geometrically similar cells, volume grows faster than surface area.

Total particle concentration and lasting cell-volume effect are different properties.

DNA replication doubles DNA content without doubling chromosome-set ploidy.

Ecological levels describe different interacting sets and environments.

Total individuals and individuals per area or volume must be distinguished.

Mutations do not generally appear because an organism needs their future advantage.

Shared ancestry is represented by topology, not by the left-to-right order of tips.

Osmotic and mechanical contributions together determine passive water movement.

Genomic sequence variants and observable traits describe different levels of biological information.

Substrate recognition and catalysis depend on a dynamic molecular environment.

Covalent subunit linkage and water-assisted cleavage explain biological polymer structure.

Sugar connectivity distinguishes energy-storage and structural polysaccharides.

Lipids include several architectures rather than one repeating-monomer polymer class.

The peptide backbone and variable side chains are different parts of protein structure.

Bases carry sequence information on a chemically directional sugar–phosphate backbone.