woof ≈80% of assignments this summer term have essentially been just raw chatgpt/claude output, including assignments that required designing stuff in illustrator/affinity/canva. The battle is lost for asynchronous online courses.

New post, on why people shouldn't 'never-skill' themselves with AI: kucharski.substack.com/p/dont-never...

New strategy: ask prospective applicants to write their best idea for how to make a bioweapon in the application

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

Important post on the ongoing Bundibugyo outbreak in DRC/Uganda. The clock appears to be fairly well-calibrated by now, even if a little slower than what we might have expected. Timing ~early-mid March and a bit of uncertainty re. 1 or possibly 2 intros. virological.org/t/genomic-ep...

Surprised LinkedIn so low….

In some recent blog posts, I had a Klebsiella genome with a mysteriously higher ONT error rate. But Michael Biggel (University of Zurich) emailed me with the likely explanation: 7-deazaguanine mods. Thanks, Michael! Here's his preprint about this: www.biorxiv.org/content/10.6...

139 genomes now sequenced from the ongoing 2026 Bundibugyo virus disease outbreak in DRC, spanning 16 Health Zones. Led by INRB with support from the ARTIC network (Wellcome Trust and Gates Foundation). Full analysis: virological.org/t/genomic-ep...

Great reporting on this perspective in Science: www.science.org/doi/10.1126/... 1. Risks of ultra-processed foods are likely caused by their differences in specific nutritional properties, not in being 'processed' 2. 'Ultra-processed' miscategorizes many healthy + sustainable plant-based products

"a universal approach to quality assurance of research is no longer appropriate...we propose a layered approach...mov[ing] away from the norm all research must be peer-reviewed [to] a combination of trust markers, peer engagement, and evidence synthesis" researchonresearch.org/the-future-o...

Solar and wind are currently meeting 90% of Britain's electricity demand. grid.iamkate.com

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

Important results of collab led by ⭐surgeon-microbiologist Ken Urish w/ @dariavantyne.bsky.social @ironark.bsky.social and us: Chronic suppression of a multidrug-resistant Pseudomonas aeruginosa in prosthetic joint infection using personalized bacteriophage treatment www.nature.com/articles/s41...

Write a critical AI book, and you become everyone's confessor for their AI sins. People in my life keep telling me about their guilty AI pleasures, in search of an explanation, absolution or condemnation: us.macmillan.com/books/978037... 1/

'‘Infection control becomes almost impossible’: four doctors on the NHS heatwave crisis' Intersection of climate change, infectious diseases and AMR www.theguardian.com/society/2026...

I'd put Colassal Biosciences somewhere in between Greenwater Services and Four Seasons Total Landscaping on a scale of trustworthiness and competence. Trump always finds the worst goddamn people.

Tried looking up how much I spent on 16 GB of RAM for my router build just over a year ago to see if I could transplant it into the Steam Machine and it was like looking at menu prices at a diner from the 1940s.

Good read on @doctorow.pluralistic.net’s latest AI analysis www.theguardian.com/technology/2...

RFK Jr. says that HPV vaccine is “dangerous and defective”. A new study from England shows that HPV vaccines have reduced deaths from cervical cancer to ZERO for women aged 20-24. Significant reductions in older age groups were observed as well, though the latter have lower vaccination coverage.

I’m building a home server rack for absolutely no reason other than it looks cool.

Here's a fun fact about Elon Musk: in 2020, his (nominal) net worth was $20b, and today it's $1t (nominally). But *that's* not the fun fact; *this* is: everything he's done since 2020 was a flop. 1/

Does Bundibugyo virus, now causing the devastating outbreak in DRC and Uganda, differ in important ways from Ebola virus? Scientists aren’t sure. “You can read the entire Bundibugyo literature in an afternoon,” says virologist Jens Kuhn. My story in @science.org:

At the end of the term I asked my college creative wriing students to submit anonymous thoughts on AI. No real surprises: Mood ranges from resignation to despair, capitulation from embittered erosion of standards to total, feelings of betrayal from deep to furious. 1/

"The water is more or less the color of a sour apple Jolly Rancher now. It looks like they're brewing Yodas in there. It is so uncannily green and visibly slimy that it feels inevitable that video will soon surface of Robert F. Kennedy Jr. splashing around in it with jeans on"

“If we don't stop the outbreak very soon, it will be worse than what we had in West Africa and eastern ‌DRC” – Africa CDC Director-General Jean Kaseya www.cidrap.umn.edu/ebola/africa...

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Time for me to repeat one of my ‘sayings’. If you try to solve a problem by passing a law, but people don’t obey the law, you now have two problems where you used to have one.

Social media bans for teens? Meh. Facebook ban for boomers? LinkedIn ban for business influencers? Let’s go.

AI + publish-or-perish -> huge increase in publications Publication volume becomes meaningless as a metric. Might academia adapt to produce fewer, better papers? substack.com/@journalolog... Or will output continue to increase and we just accept that the only readers are AI agents...? 1/2

Douglas Adams: > Anything in the world when you're born is normal, ordinary and a natural part of the world. Anything invented between when you’re 15-35 is new, exciting and revolutionary and you can get a career in it. Anything invented after you're 35 is against the natural order of things. 1/

guy has a trillion dollars, 0 friends, and has never landed a joke. I know a pact with the devil when I see one.

When #hantavirus broke out on the MV Hondius cruise ship I wasn't concerned about global transmission. I did think it was a very interesting outbreak & likely to generate new knowledge about the Andes species of hantavirus. That's already underway: @kakape.bsky.social www.science.org/content/arti...

Academic writing should be addressed neither to the public nor to other academics. It should be addressed to a single interlocutor with whom you have a petty rivalry and whose work you are trying to discredit

New blog post! I analyse the new [email protected] basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

Elon egging on migrant’s houses being burned down while his dad has a drink with Tommy Robinson in Moscow hotel bar talking about how Russia is the UK’s ally, at this point I don’t think you can deny that social media has been a net boon both to authoritarian regimes & authoritarians in democracies.

there were already many reasons to do this but Elon Musk actively encouraging racist violence in Belfast should be the final straw for every UK government institution to stop doing business - including being on X - with him in any way, and for him to be barred from entry to the country.

Terrific Q&A with #WHO 's Chikwe Ihekweazu about DRC's #Ebola response: how long the outbreak has likely been underway, whether Bundibugyo virus is more transmissible than other Ebola species & what it's like not having US experts on the ground. By @kakape.bsky.social www.science.org/content/arti...

ASV is alarmed by the US HHS to suspend and debar Dr. Ralph Baric from federal funding. Read our open letter below:

09 Jun 2026 – Bundibugyo virus disease outbreak: Confirmed cases in DRC increase to 550, contact tracing remains below target https://beaconbio.org/en/report/?reportid=c1a66e5b-a839-4c4c-9cc7-a812b500cfc1&eventid=1a9a0ef4-262f-45a1-9018-aa8f99d93a7c&utm_source=bluesky&utm_medium=social

No, no, of course your child can still talk to the machine that tells you to kill yourself

This is exactly it. The work is the point.

Registration is closing for our Early Career Summer Conference 🤝👩‍🔬 Join us on 6–7 July 2026 at the University of Birmingham for a career development and networking opportunity for early career members, secure your place: https://microb.io/ECConf26 #ECConf26

I met a microbiologist yesterday. He was much bigger than I expected.

I spoke with doctors on the frontline of Ebola in Congo, and it made my heart race. “We live with fear in our stomachs,” Dr. Furaha told me. “Every day, there are healthcare providers and patients dying.” My latest @kffhealthnews.org kffhealthnews.org/public-healt...

#r4today @drtedros.who.int: "While investing in defence… Please don't forget the common enemy that we have: a virus that doesn't care about our borders, our politics, or about whatever excuses we have. We have to be also prepared for that." www.bbc.co.uk/sounds/play/...

Very interesting @jburnmurdoch.ft.com piece this morning - how much value AI is creating is exactly the right question. The evidence from coders here suggests it’s so far creating a lot of extra output - 290% more files, 30% more software releases - but no extra valuable outputs (app downloads)

This is extremely chilling - virologists being targeted for what appears to be minor (if any) "offenses". We all know _why_ this is happening, so I'm not going to belabor that point - but I want to provide some context on the technical details. 🧵 www.science.org/content/arti...