It’s like clockwork: Grant deadline? 💥 boom 💥 Kids are sick.

Dumpster Fire: What Is Even Happening?

ALT: Dumpster Fire: What Is Even Happening?

static.klipy.com

This may be the biggest mistake I’ve ever heard of anyone making in an undergraduate microbiology laboratory - and it wasn’t the students’ fault. arstechnica.com/health/2026/...

College lab class ends with 32 people on antibiotics for deadly germ exposure

Lab students were supposed to ID a mild germ. They all identified a deadly pathogen.

arstechnica.com

I was lucky to be invited by @bmj.com to be a Guest Editor for a series on COVID in the US For one paper, I commissioned my brilliant Duke colleague @keishabentley.bsky.social to lead an analysis on "Race, racism, & covid-19 in the US: lessons not learnt" Read it at www.bmj.com/content/384/...

Race, racism, and covid-19 in the US: lessons not learnt

Keisha Bentley-Edwards and colleagues argue that systemic racism and economic inequality are at the root of disparity in covid-19 outcomes and suggest how to distribute resources more equitably. The...

bmj.com

Trevon Logan@trevondlogan.bsky.social · 2d ago

By late Summer of 2020, COVID was the third leading cause of death for Black people in the USA. It’s like everyone has just forgotten that…

The Southern Three-Banded Armadillo (Tolypeutes matacus) is one of the only armadillo species capable of rolling into a completely sealed sphere: #AGoodPlace Source: www.reddit.com/r/NatureIsFu...

o my god. when he kisses the machine... magical

Becca@sciencelizard.bsky.social · 4d ago

I wonder if the people who made the Biorad PCR song know how often it just pops in my head. "When you want to find out who the Daddy is"🎶 www.youtube.com/watch?v=Fpxw...

I think I could probably post a Puffin photo every day for the next couple of years I took so many. They are just such an amazingly photogenic bird! #wildlife #birds

Pls share. Assistant Professor of Biological Sciences - Genetics/Genomics at Smith College. apply.interfolio.com/190342

Next summer's Epigenetics GRC (I'm co-chairing with Deborah Bouch'is) is shaping up nicely with an all-star lineup of speakers working on a broad range of organisms and systems and everything from molecular mechanisms to new phenomena. Apply and put it on your calendar! www.grc.org/epigenetics-...

Open position in our lab for a research engineer. The applicant must hold a PhD in life sciences and have demonstrable experience in molecular biology and biochemistry. For more info: emploi.cnrs.fr/Offres/CDD/U...

Institut Jacques Monod@ijmonod.bsky.social · 7d ago

#JobOffer 💼 Research Engineer (M/F) 📆 October 15th 📍Institut Jacques Monod, @sandraduharcourt.bsky.social 🔗 emploi.cnrs.fr/Offres/CDD/U...

Also see @nature.com ‘s editorial www.nature.com/articles/d41...

Mathematicians are developing rules for AI use — other fields should follow

The mathematics community is right to call for transparency, integrity and fairness to be protected when AI tools are used. Researchers in other disciplines could learn from this approach.

nature.com

Timnit Gebru@timnitgebru.blacksky.app · 2w ago

Weeks ago, @chanda.blacksky.app sent me this declaration, written and signed by a bunch of mathematicians. But I only had time to read it yesterday, which ended up being right on time given a new round of hype falling exactly under the patterns this document notes.🧵 leidendeclaration.ai

Pls share: U of Washington has an opening for a tenure-track faculty position at the rank of Assistant Professor. This position is expected to specialize in molecular virology or bacteriology. Here is a link: microbiology.washington.edu/index.php/ne...

In 2014, Jason Rosch and I met at a GRC in Tuscany and sketched an idea on a cocktail napkin: what if we evolved S.pneumo in mice, treated them with antibiotics, varied their immune systems and watched what won? 11 years and a huge team effort later, it's out in @cp-cellhostmicrobe.bsky.social 🧵

Andy Nishimoto from the Rosch lab at St. Jude led this massive project to evolve Spn in mice across 10 antibiotics and 3 immune states. Shockingly, classic resistance almost never evolved because it was too costly for fitness in the face of host immunity. www.sciencedirect.com/science/arti...

💯 I am more concerned about the niche barrier breakdown driving pathogen spillover than theoretical GOF experiments happening.

Jase Gehring@skyjase.bsky.social · last wk.

5. any threat from manmade bioweapons must be taken in consideration with the natural rate of pathogen emergence. we are already participating in a planetary scale natural gain of function experiment (zoonosis) 6. efforts to prevent and mitigate natural outbreaks work equally well on manmade ones

5. any threat from manmade bioweapons must be taken in consideration with the natural rate of pathogen emergence. we are already participating in a planetary scale natural gain of function experiment (zoonosis) 6. efforts to prevent and mitigate natural outbreaks work equally well on manmade ones

3. current AI models provide very little 'uplift' in biological science. we are not seeing acceleration at this time 4. bioweapons are ineffective weapons. they are disfavored by bad actors (and state actors) who choose conventional weapons and cyberattacks almost every time.

These events are a driving force for why we wrote this 👇 link.springer.com/article/10.1...

Addressing the dark matter of gene therapy: technical and ethical barriers to clinical application - Human Genetics

Gene therapies for genetic diseases have been sought for decades, and the relatively recent development of the CRISPR/Cas9 gene-editing system has encouraged a new wave of interest in the field. There...

link.springer.com

www.science.org/content/arti...

Exclusive: Death of girl in Chinese gene-editing trial was never made public

Parents want accountability after study went disastrously wrong, Science and Retraction Watch investigation reveals

science.org

Facing federal science budget cuts, biologist Daniel Blumstein resorted to uploading marmot videos to OnlyFans to raise funds for his marmot research. However, when he uploaded his driver’s license for verification, OnlyFans informed him that his appearance didn’t match the marmots in the videos.

‘OnlyMarms’: Marmots Are on OnlyFans to Raise Money for Research (Gift Article)

A team of scientists uploaded videos of the squirrel-like rodents in the wild on the adult-content site OnlyFans to raise money amid government budget cuts.

nytimes.com

My lab at #Yale has two #riboswitch research openings: 1. Postdoc with mammalian gene manipulation experience (tinyurl.com/zzb269em); 2. Postdoc (or BS, MS) with bioinformatics skills (tinyurl.com/3j73jfcn). Send your cv to me or to Kavita at kumari.thakur@yale.edu.

What kind of person is proud to put kids in the hospital?!

ProPublica@propublica.org · 2w ago

Regulators have linked Mark McAfee’s raw dairy farm to more than a dozen recalls and outbreaks that left hundreds of people ill. “I’ve put a couple kids in the hospital,” McAfee said. “But here’s the thing: I’m a pioneer.”

Regulators have linked Mark McAfee’s raw dairy farm to more than a dozen recalls and outbreaks that left hundreds of people ill. “I’ve put a couple kids in the hospital,” McAfee said. “But here’s the thing: I’m a pioneer.”

He Profits Off Raw Milk That’s Making People Sick. The Government Isn’t Stopping Him.

With Raw Farm, the largest raw-milk dairy in the country, Mark McAfee has capitalized on a once-fringe product that’s been thrust into the mainstream in recent years and backed by Health Secretary Rob...

propublica.org

How do you know if the fruits and vegetables you buy at the grocery store come from farms where workers were harmed? Read this thread by our reporter @maxblau.bsky.social 🧵

Max Blau@maxblau.bsky.social · 2w ago

I’ve reported at length about abuses of foreign farmworkers who come to the U.S. on H-2A visas: stolen wages, guns pointed in their faces. One woman I met was kidnapped, raped and nearly killed. I wanted to know: How do I tell if the produce I buy is part of the problem? 👇

This is just a mini dachshund puppy account now. Sorry.

OSSOFF: You stated on the 14th day of this conflict that Iran's military was 'destroyed.' Was that an accurate statement -- yes or no? HEGSETH: Iran's ability to challenge the US-- OSSOFF: That's not what I asked. Yes or no? HEGSETH: What the milit--- OSSOFF: Will you answer the question?

Takeaway: structural ensembles—not single predicted structures—contain the biophysical signal needed for robust generalization in TCR:pMHC prediction. The same framework should extend beyond AF3 to Boltz, RoseTTAFold, OpenFold, and related models.

SHAP identifies the key features: iPAEs dominate, iPTMs contribute, top global feature is pLDDT. Interestingly the peptide:MHC interface also matters, suggesting successful presentation contributes alongside TCR recognition. Both ensemble means and SDs contribute independently.

And the neoantigen task: cognate vs non-cognate when the peptide differs by ONE residue. Across 8 mutational-scan datasets enFoldX leads the field (median AUC 0.71) — ahead of sequence models, TCRen, and a single-structure version of our own features.

Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX

Ensembles of in silico structures enable T cell peptide-MHC binding prediction

Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data rem...

biorxiv.org

you wake up the next morning bound to a chair, and this is the last thing you ever see

Elle@elleisanisland.bsky.social · 2w ago

When you've defeated the cone they put you in the Hannibal Lector