Will Shoemaker

@shoestrapped.bsky.social

Microbial life scientist applying principles from physics CNRS Chaire de Professeur Junior @ Genoscope 🇫🇷 Grilli lab alumni @ ICTP 🇺🇳/🇮🇹 Lennon lab PhD @ IUB 🇺🇸 https://wrshoemaker.github.io

Beautiful work (Petrungaro, Bollenbach lab) on evo trajectories toward abx resistance (E. coli). Goes beyond many other studies in its attention to the experimental setup (identical selective pressure across all lines). I strongly recommend reading the entire paper! www.nature.com/articles/s41...

Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance - Nature Communications

Antibiotic resistance can evolve through the combination of factors but the predictability of this is unclear. Here, the authors used high-throughput evolution experiments to reveal that antibiotic re...

nature.com

“This complete mutagenesis of a biological system quantifies the limits of our current understanding of, and ability to predict, molecular biology.”

Ben Lehner@benlehner.bsky.social · 3d ago

1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...

as I understand the situation, the truly, truly perverse part of all this is that Anthropic siphoning a rare book’s information into its corpus is only legal *because* 1) they destroyed the original and 2) they are not sharing that information with archive.org or anyone else

Dr. Jeroen W.P. Wijnendaele@drdragases.bsky.social · last wk.

No longer content with pillaging intellectual work and dismembering our environment (already critically weakened), AI companies are now hellbent on destroying books galore including rare editions. Shut down these nefarious enterprises already.

Excited that this is finally out, led by @jhuisman.bsky.social with Jeff Gore, combining experiments, theory and natural microbiome data! As salinity rises, diversity and individual species growth rates fall, yet community's overall growth stays robust: faster growers take over and keep it going.

Nature Microbiology@natmicrobiol.nature.com · 3w ago

Out Now! Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress #MicroSky

BREAKING: Electrification Action Plan dropped. The EU just committed to doubling electrification: 46% of final energy consumption by 2040, up from 23% today, where it has sat for a decade. My rapid response analysis of the Electrification Action Plan: open.substack.com/pub/janrosen...

Nine times faster: the EU wants to double electrification by 2040

The Commission has launched its Electrification Action Plan. A 46% target and some serious policy measures.

open.substack.com

An important paper about protecting science from political interference. Europe needs to defend its science against the kind of attacks unfurling in the US. By Martin McKee, Christina Pagel & Tiago Correia in the European Journal of Public Health: academic.oup.com/eurpub/artic...

Europe must learn from America’s assault on science

In June 2026, several prominent diabetes researchers, including Steven Kahn, editor-in-chief of Diabetes Care, were removed by police from the annual meeti

academic.oup.com

Great to see this important study published. For some time I've pointed to the preprint version when students ask about co-evolution between humans and their microbiota. "Limited codiversification of the gut microbiota within humans"

BildBild

This is an important new paper. When we allocate responsibility for emissions, it's normally in terms of consumption. We tally up direct household emissions (eg, from household energy use) plus the emissions embodied in all the stuff that a household consumes.

Bild

What do single bacterial cells do when they run out of carbon source? If you missed the preprint, check out the official publication: doi.org/10.1038/s443... If the total bacterial population on earth stays roughly constant, then there must on average be as much death as replication. 1/n

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients - Molecular Systems Biology

Although in the wild bacteria likely spend most of their time deprived of nutrients and slowly starving to death, very little is known about how bacteria adapt their phenotype to starvation. Here we combine microfluidics with quantitative fluorescence microscopy of transcriptional reporters to comprehensively quantify growth and gene expression at the single-cell level in E. coli during carbon starvation. We find that all cells immediately stop growing upon loss of carbon source and that almost all remain alive for over 30 hours. Furthermore, entry into starvation triggers a dynamic expression program that is remarkably homogeneous across single cells, but highly variable across genes, causing dramatic remodeling of the proteome early in starvation. We further show that, as protein production and the rate of protein degradation both decay approximately exponentially, protein concentrations become essentially ‘frozen’ after the first 5 to 10 hours, setting phenotypes for several days of starvation. Finally, using experiments in which gene expression is inhibited for different periods, we show that protein production in the first 5 hours is crucial for protecting cells from stresses late in starvation.

doi.org

"Perhaps Hobsbawm’s canonization—his “myth,” to borrow Chabal’s term—was a Western tribute to a great historian who had erected a monument to Europe at the time of its decline." Enzo Traverso on Emile Chabal's intellectual biography of Eric Hobsbawm: www.theideasletter.org/essay/the-ce...

The Century of Eric Hobsbawm

Eric Hobsbawm’s enduring power lay in his ability to synthesize vast historical processes into compelling narratives that made the modern world legible. Yet, argues Traverso, the celebrated Marxist hi...

theideasletter.org