Matt Durrant

Me to son: You have way too many toys! Go pick one and we’ll donate it to charity.

*10 minutes later*

Me: woah woah woah slow down, too many memories with that one.

I’d guess that a lot of ancestral exploration was driven toward some material gain. For example, “I wonder if there’s some food over there…”

My wife woke up angry because Ariana Grande stole me from her in a dream.

As kids, my mom used to regularly take me and my sister to public recycling dumpsters, have us climb in, and we’d dig around to find coupons in magazines and newspapers. We were not poor.

My grandfather compiled a history of all of my ancestors on his side going back 5 generations, 62 people in total, some born in the mid 1700s. I can confirm that life is much better now than it was then.

Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements Abstract. The co-evolution of prokaryotes, phages and mobile genetic elements (MGEs) has driven the diversification of defense and anti-defense systems ali

Out in NAR, AntiDefenseFinder & our "systematic" analysis of inhibitors of antiphage systems wt Bondy-Denomy lab led by @ftesson.bsky.social and E. Huiting.

Not so "systematic" as very few known, fun stuff on MGE, antidefense islands and cool phages exaptations!

academic.oup.com/nar/advance-...

This whole story is amazing, intuitive in retrospect, and likely exceptionally important medically. Do read the paper and the whole thread!

Isn’t the solution to ChatGPT doing everyone’s homework to just have more exams and to weight them more heavily?

Come join us at @arcinstitute.org !

If the government is going to start banning food dyes and vaccines I only ask that they ban such things in a time-staggered way throughout the country so we can get some nice natural experiment data.

I hereby announce my candidacy for the presidency in 2028. If you vote for me, I will give you complete immunity for all crimes you commit between now and the end of my time in office.

Where can I get my hands on a woolly mammoth genome? Was expecting more than mitochondria on NCBI.

Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵

Microbiology will always be one of the most satisfying fields of natural science. Nigh-infinite levels of biodiversity, perpetual room for novel findings, and an evergreen requirement for the advancement of human civilization. 10/10. Big fan. Would recommend.

🦠💪

That’s the last of my faculty applications! Now we wait🤞

Could really use the bookmark button….

Really is impressive to see the growth here!

Wow

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...

We've long been able to find new phages and figure out what they interact with. But what about the other direction: if you have a gene, like an antibiotic resistance efflux pump, or a phage defense system, and you want to find phages that do or do not interact with it?

Now you can!

Thanks for adding me! This is great.

New at Science
Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale
science.org/doi/10.1126/...

Evo, a 7-billion-parameter genomic foundation model, learns biological complexity from individual nucleotides to whole genomes.

Pretraining a genomic foundation model across prokaryotic life.

Fine-tuning on CRISPR-Cas sequences enables generative design of protein-RNA complexes.

Fig. 4. Fine-tuning on IS200/IS605 sequences enables generative design of transposable biological systems.

Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons.

@brianhiestand.bsky.social

www.science.org/doi/10.1126/...

Really cool model from Brian Hie and Patrick Hsu! www.science.org/doi/10.1126/...

The Great Kettlebell Swing Forward

Thrilled to see this published! Lots of progress since our preprint, including experimental validation of Evo-generated Cas9 and IS200/IS605 transposases. I am definitely a true believer when it comes to DNA language models, they have quickly become central to my discovery efforts. bit.ly/3OsmUPr

Where is this tree from?

The 8 Fallacies of Assembly Theory In response to the alleged misunderstandings evident in our exposure of the many serious issues undermining the foundations and methods of…

This post is long but informative (even if mostly written before the newest paper):

The 8 Fallacies of Assembly Theory
hectorzenil.medium.com/test-8f0be54...

What are some unwritten rules in academia that would be helpful for new folks to know?

One rule I learned the hard way was that you don't reach out to other PIs about collaborating without discussing it with your PI first.

Does anyone know where I could find some measure of brain drain per year for each country?