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Will Shoemaker

@shoestrapped.bsky.social
1.2K followers 612 following 346 posts

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

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Reposted by Will Shoemaker
Ilhan Omar @ilhanmn.bsky.social · 11h
I’m ok. Make no mistake: this is an attempt to target political enemies and weaponize federal law enforcement. For ten years, Trump has targeted me with baseless lies and smear campaigns. This is just the latest escalation in his campaign of political intimidation. I will not be silenced.
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 17h
Happy Indigenous People's Day! We are still here :)
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Anjali Dayal @anjalikdayal.bsky.social · 09/10/2026
The Trump administration is pushing forward with sanctions against the ICC. A coalition of domestic political opposition and concerned foreign firms governments supporting the ICC is vital for future accountability against human rights abusers, including the Trump administration
foreignpolicy.com
Here’s What to Do About Trump’s War Crimes
Despite the obstacles, foreign governments and U.S. lawmakers can begin the process of holding the president accountable.
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MP Broache @mbroache.bsky.social · 09/10/2026
This is an excellent piece. On the ICC, I would add that the next Democratic administration could lodge an Article 12(3) declaration accepting ICC jurisdiction for the period of the Trump administration; this would not require ratification of the Rome Statute (and so would avoid the Senate)
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Thibaut Brunet @thibautbrunet.bsky.social · 09/10/2026
How fast can speciation be? In less than 100 years, certain strains of lab mice have already (partly) lost the ability to hybridize with each others. The molecular mechanism has just been worked out - read below for a genetics detective story ⬇️
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Moby Dick @mobydickatsea.bsky.social · 08/10/2026
in this world, head winds are far more prevalent than winds from astern
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Will Shoemaker @shoestrapped.bsky.social · 08/10/2026
It cheats the author out of a chance to engage with a peer. A recent review I received was clearly written by AI but passed the AI tests. This was disappointing, as I had difficulty securing feedback on the manuscript before submission and was genuinely hoping for reviewer engagement
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Reposted by Will Shoemaker
Matt Olm @mattolm.bsky.social · 07/10/2026
My final postdoc project is out today in Nature! We show microbes co-migrated with humans out of Africa; three independent methods agree, and timing matches archaeological / genetic evidence (Fig. 4c). Seeing Fig. 4c for 1st time was one of my most memorable "eureka" moments! doi.org/10.1038/s415...
doi.org
Prehistoric global migration of vanishing gut microbes with humans - Nature
Microbial species disappearing from industrialized populations have evolved with humans over millennia and migrated worldwide with them—this may have consequences for human health.
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Journal of the History of Ideas @jhideas.bsky.social · 05/10/2026
For the Blog’s forum on the conceptual history of technology, Tianyi Ding traces zero’s emergence through a series of material practices, from bookkeeping in Renaissance Italy and weaving in eighteenth-century France to the 1890 US census and birth of IBM.
web.sas.upenn.edu
How Nothing Came to Matter: Zero as a Technique of Absence
"Zero" exists only in the apparatuses and techniques that produce it....
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Reposted by Will Shoemaker
Thomas Piketty @thomaspiketty.bsky.social · 06/10/2026
Le mouvement lycéen et étudiant signe le crépuscule du macronisme: les jeunes veulent se former et accéder aux études, et un pouvoir élitiste leur répond en réduisant de 20% le budget par étudiant entre 2017 et 2026 et en gérant la pénurie avec un algorithme opaque (Parcoursup)
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Michael Manhart @michaelmanhart.bsky.social · 06/10/2026
I am co-organizing the Ecological Dynamics session at the 2027 APS Global Physics Summit (Apr 11-16, Atlanta). The session will span all domains of life and theory/data/exps (more here tinyurl.com/382vkbrh). If you're interested, submit your abstract to this session by Oct 22! tinyurl.com/4jfpyux5
summit.aps.org
APS Global Physics Summit abstract submission
Present your physics research to over 14,000 physicists from around the world.
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Will Shoemaker @shoestrapped.bsky.social · 05/10/2026
They should reach out as early as possible to ensure they’re eligible for fellowships.
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Robin Hayward 🌳 🏳️‍⚧️ @canopyrobin.com · 05/10/2026
Did a little interview about the new trans-inclusive guidance 🙂 heart-magazine.com/2026/10/04/t...
heart-magazine.com
Reseachers publish guidelines for inclusive fieldwork for trans+ people
On Friday 25th of September 2026, three researchers at Leeds university released the Trans+ Guidelines for Inclusive Fieldwork.
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Gavin Jackson @gavinjackson.bsky.social · 05/10/2026
I visited the Amazon rainforest a year ago ahead of the cop conference in Belem. Historically the only thing that has stopped deforestation has been electing Lula da Silva has Brazilian president. www.economist.com/the-americas...
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Liam U. Taylor @liamtaylor.bsky.social · 03/10/2026
Thread for bangers from The Dialectical Biologist
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Ákos T Kovács @evolvedbiofilm.bsky.social · 30/09/2026
The phenotypic landscape of the model firmicute Bacillus subtilis PNAS from Carol A. Gross www.pnas.org/doi/10.1073/...
pnas.org
The phenotypic landscape of the model firmicute Bacillus subtilis | PNAS
Firmicutes are gram-positive bacteria with important roles in human health, disease, and industry. However, more than a quarter of genes in the mod...
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Will Shoemaker @shoestrapped.bsky.social · 29/09/2026
Cannot believe this graph. From Adam Tooze's Chartbook
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johnny connolly @jcons.bsky.social · 29/09/2026
As the use of metagenomics methods continues to expand, it is inevitable that researchers will attempt to use frontier AI for analysis. It is therefore critical that we have some kind of assessment of agent capabilities. I give you: MetagenomicsBench #MicroSky 🧪 🧬🖥️ blog.latch.bio/p/c55a6336-7...
blog.latch.bio
LatchBio
Intelligence Infrastructure for Biology. Click to read LatchBio, a Substack publication with tens of thousands of subscribers.
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Will Shoemaker @shoestrapped.bsky.social · 29/09/2026
Congrats Sophie!
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JL Weissman @jlw-ecoevo.bsky.social · 28/09/2026
Two weeks left to apply for these postoc positions! We seek two postdocs interested in 1) building trait prediction models capable of resolving complex microbial traits from genomes and metagenomes, and/or (2) building mathematical models of microbial community dynamics in the human microbiome.
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maria_from_ga @mariafromga.bsky.social · 26/09/2026
Given how the Hormuz and Bab el-Mandeb closure will likely continue until 2029 and green technology is going more available and cheaper (esp solar), wouldn’t be surprised if this further power a Green Industrial Revolution that US will be forced to partake in just bc of the economics
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EvoBio Crash Course @evobiocc.bsky.social · 23/09/2026
The Evobio Crash Course is coming back for its fifth edition! Join us from December 7 to December 18 for an incredible line up of classes and tutorials from amazing researchers in the field! The course is open to all, completely free and held online. Registration is OPEN, please share widely!
Poster for the Evobio Crash Course. Online from December 7-18, 2026.
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Giorgio Nicoletti @giorgionicoletti.bsky.social · 21/09/2026
Let's come back with a big update: our latest work landed us on the cover of PRL!
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Rowan Kuminski @rowankuminski.bsky.social · 17/09/2026
⚠️Please share!⚠️ We are recruiting participants to complete a written interview for a PhD chapter on linguistic experiences of ecologists from Catalonia. Participants do not need to currently reside in Catalonia and can participate in Catalan, Spanish, and/or English. Thank you! 🪶🕷️🌲🐡🍄 #ecology
A white background with the words "Are you a Catalan ecologist?" at the top in black and red, adn underneath the text "If you are a professional ecologist from Catalonia and would be willing to do a written interview about your linguistic experiences, please contact Rowan Kuminski at r01tk22@abdn.ac.uk", and underneath in yellow it says "Gràcies!". In the background are transparent digital images of a shearwater and an oak leaf.
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Will Shoemaker @shoestrapped.bsky.social · 20/09/2026
Two weeks of troubleshooting wonky statistics later…
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Will Shoemaker @shoestrapped.bsky.social · 20/09/2026
FYI don’t upload *subsampled* raw reads to NCBI
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Jason Leopold @jasonleopold.bsky.social · 18/09/2026
HUGE EXCLUSIVE from @bloomberg.com Inside the US ‘Kill Chain’ That Destroyed an Iranian School Pentagon investigators discovered that flawed intel, outdated imagery & overreliance on AI contributed to a missile strike that killed 123 children in Minab 🎁 www.bloomberg.com/graphics/202...
bloomberg.com
Inside the US ‘Kill Chain’ That Destroyed an Iranian School
Pentagon investigators have discovered that flawed intelligence, outdated imagery and an overreliance on AI contributed to a missile strike that killed 123 children in Minab.
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Snorre Sulheim @sulheim.bsky.social · 18/09/2026
Finally online! Cross-feeding enables robust coexistence between four bacterial species | PNAS www.pnas.org/doi/10.1073/... #microsky
pnas.org
Cross-feeding enables robust coexistence between four bacterial species | PNAS
Resource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether...
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New York Times Opinion @nytopinion.nytimes.com · 17/09/2026
“We’re living through a dispiriting moment of global climate fatigue, when companies worldwide are backtracking on their climate commitments, but someday the pendulum will swing back toward climate action,” Michael Grunwald writes.
nyti.ms
Opinion | The Latest Corporate Climate Ruse
Making deforestation look climate-friendly will encourage a lot more deforestation.
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Will Shoemaker @shoestrapped.bsky.social · 17/09/2026
Hitting me just now that community coalescence experiments are analogous to yeast crossing wrt function vs. fitness
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Purushottam Dixit @pdixit.bsky.social · 15/09/2026
1/ Our new paper is out in PRX Life. Physicists' often treat microbiomes as disordered systems with coexistence in very high-dimensional niche spaces. We asked whether empirical data supports this picture, and found the data point somewhere else: journals.aps.org/prxlife/abst...
journals.aps.org
Low-Dimensional Coexistence in Complex Microbial Ecosystems
Analysis of nearly 200 human gut microbiome datasets shows that microbial coexistence is governed by a few effective ecological dimensions, rather than the high-dimensional niches assumed by prevailing theory.
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Pierre Charbonnier @picharbonnier.bsky.social · 10/06/2026
Soon! Fall 26 in the UK Winter 26-27 in the US A book I wrote after the beginning of the Ukraine war, and that's unfortunately been vindicated by further events. Global security lies in decarbonization: in times of war, green energy means peace.
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Will Shoemaker @shoestrapped.bsky.social · 16/09/2026
Incredible to see Fetterman doing his job for once.
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Will Shoemaker @shoestrapped.bsky.social · 15/09/2026
The monkey virus in bebop
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Reposted by Will Shoemaker
Sridhar Ramesh @radishharmers.bsky.social · 14/09/2026
terrytao.wordpress.com/2026/09/12/w...
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Jennifer Goff, PhD @jlgoff.bsky.social · 31/08/2026
New preprint! This one is actually from my class! We did metagenomic sequencing on a Winogradsky column. In my Microbial Biochemistry class, the students learned to assemble and analyze the MAGs, directly applying what they learned in lecture to make predictions about their organism’s metabolism. 🧵
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Moby Dick @mobydickatsea.bsky.social · 13/09/2026
all that cracks the sinews and cakes the brain
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Sarah T Roberts, PhD @ubiquity75.xyz · 12/09/2026
In a rare move, Chancellor Frenk just publicly and boldly affirmed academic freedom. Oh, wait, no. He did the opposite. The idea that anyone was advancing support for the attacks is absurd and obscene and that’s what they should be ashamed of. Use archive.ps for non-paywall.
latimes.com
UCLA chancellor rebukes law school event featuring attorney of alleged 9/11 'mastermind'
After a UCLA law school symposium on 9/11 that featured an attorney who represented alleged 9/11 'mastermind' Khalid Sheikh Mohammed, UCLA Chancellor Julio Frenk issued a rare message distancing the u...
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Young Biophysicists Meeting @youngbiophymeet.bsky.social · 11/09/2026
Submission open for the 12th YBM Meeting (deadline - 28th September)! Abstract submission link: forms.gle/UK1fBmzGtLwn...
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Car Talk Names @cartalknamebot.bsky.social · 14/06/2026
Statistician: Marge Innovera
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Victor Jack @victorjack.bsky.social · 10/09/2026
NEW: The U.S. asked NATO allies to help “systematically dismantle” the ICC, according to three NATO diplomats. In July, Washington requested allies quit the international body as part of its campaign to take down the court. www.politico.eu/article/us-p...
politico.eu
US pressures NATO allies to destroy International Criminal Court
Washington said it “would be watching closely” to see which allies help in its campaign against the court during a closed-door meeting this summer.
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Prof Ian Hall @ianhall.bsky.social · 10/09/2026
Understatement of the year… “Humanity has now spent more than 38 years trying collectively to stop climate change, with sub-optimal results.” www.ft.com/content/2bec...
ft.com
An IPCC stand-off risks a historic climate rupture
Pointless obstruction by governments over publishing scientific climate evaluation is threatening crucial work
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Quantian @quantian.bsky.social · 08/09/2026
Dancing very very VERY close to saying “OpenAI stole our almost-complete proof of Navier-Stokes from internal access to our ChatGPT sessions because they were desperate to scoop Anthropic” which is absolutely 100% a believable thing OpenAI would do right now cims.nyu.edu/~tristanb/st...
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Will Shoemaker @shoestrapped.bsky.social · 08/09/2026
Make a short list of the groups that make you excited about science and reach out. Mention that you are open to obtaining funding to join, time permitting. If you end up interviewing with someone you did not reach out to or previously consider, be as clear as possible about what you do/do not want.
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Molecular Microbiology @molmicrounihoh.bsky.social · 07/09/2026
super interesting paper: 👇 Evolutionary Maintenance of Amino Acid Prototrophy in Escherichia coli! academic.oup.com/gbe/article/...
academic.oup.com
The Evolutionary Maintenance of Amino Acid Prototrophy in Escherichia coli
Abstract. Escherichia coli is a prototroph and can synthesize all twenty proteinogenic amino acids when required to grow in minimal medium. There are appro
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Javier Aguilar @javiersanguilar.bsky.social · 07/09/2026
New paper with my good friend Pablo Moreno-Spiegelberg! We propose a simple noise-driven mechanism to explain excitability in ecological populations: rapid growth followed by sudden disappearance 👀 ⬇️ pubs.aip.org/aip/cha/arti...
pubs.aip.org
Noise-induced excitability: Bloom, bust, and extirpation in autotoxic population dynamics
Species populations often modify their environment as they grow. When environmental feedback operates more slowly than population growth, the system can undergo
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
The effect is fairly dramatic in both nematodes and mice. For example: a young adult nematode (equivalent to a teen-ager) contains ~700 million mRNA molecules total. This drops eight-fold by old-age. 3/22
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Will Shoemaker @shoestrapped.bsky.social · 05/09/2026
But certain forms of heterogeneity may be required to get something interesting. E.g., how types of fitness perturbations do/do not break WF universality in Ben's lecture notes.
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Will Shoemaker @shoestrapped.bsky.social · 05/09/2026
Thanks! Yes, w/ increased focus on heterog. in the microbe lit, it seemed hard to square its existence w/ the relevant pop gen regime. My naive guess would be interesting behavior arises as a fxn of "fitness" variance per-genotype (heterogeneity) vs. inheritable fitness variance over the population
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Will Shoemaker @shoestrapped.bsky.social · 05/09/2026
Congrats John! I was wondering how Cvijović, Good et al. would relate to the MM regime. Have you all looked at plasticity/heterogeneity in your model? As in, how selection operates on trade-offs under MM when genotypes encode params controlling the dist of s_i rather than constant s_i across cells?
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