Ewen Callaway

@jdiggans.bsky.social Hi James, I'm interested in speaking to you for a Nature news story. I've also contacted media team at Twist, but not yet heard back. Thanks!

The results are finally in! 🏆💻🧬

I'm thrilled to announce that the manuscript for the Bits to Binders protein design competition is out on bioRxiv! Here's a summary of our findings, including some simple criteria that nearly *double* success rates when applied as a filter 🧵

AI can write genomes — how long until it creates synthetic life? The Evo2 genomic language model can generate short genome sequences, but scientists say further advances are needed to write genomes that will work inside living cells.

Ewen's writeup of the new Evo 2 paper in Nature is reliably good. I can imagine this foundation model will be useful for doing synthetic biology in microbes.
But it's important to recognize that making this work for eg humans is not just a scaling-up issue...
www.nature.com/articles/d41...

Thanks, Phil. Did you see this preprint raising questions about Evo2 genome designs, and raises the question of whether synthetic genomes need to be resemble natural genomes to be functional. I'm not sure we have an answer. www.biorxiv.org/content/10.6...

Yeah a missed reference. I do cite some papers benchmarking single cell models (which some are now calling ‘virtual cells’). They don’t do well at all! I heard lotsa scepticism over whether ssRNA-seq is going to get us even close to useful virtual cells.

With huge thanks to my sources for their generosity with their time: @jbloomlab.bsky.social @eddieholmes.bsky.social @systemsvirology.bsky.social @peacockflu.bsky.social @firefoxx66.bsky.social @angierasmussen.bsky.social l Alex Sigal and Ravi Gupta @ahri-news.bsky.social & Susan Weiss.

Four ways COVID changed virology: lessons from the most sequenced virus of all time After 150,000 articles and 17 million genome sequences, what has science taught us about SARS-CoV-2?

After 5 years, 150k papers and 17 million genomes, here's what we learned about SARS-CoV-2 and viruses in general.

It holds lessons for future pandemics - only if we listen. "We’re in a worse place in terms of pandemic prevention" @eddieholmes.bsky.social told me.

www.nature.com/articles/d41...

Anyone been to Park Street lately? Me neither.

I wrote about Colossal's new woolly mouse (left), engineered with a mix of mammoth-inspired edits and mouse phenotypes. My story: www.nature.com/articles/d41....

20+ years ago Jackson Lab bred a 'wooly' mouse (right) missing a gene called Fam83g. bmcresnotes.biomedcentral.com/articles/10....

This. Again, RFK Jr is lying and needs to be called out as a liar by the press. This is the first U.S. death *in 10 years*! So yeah, pretty damn unusual.

I feel so strongly about the need for evidence-based policy and a dogged defence of science

I said it in 2020, and will reiterate it til the end of time.

The world may change - our principles should not

This is indeed a great story from Ewen (Science magazine has reported on this too). Ewen makes it properly clear that there are many questions about the functionality (or not) of all these "mini-proteins". Many may turn out to be "junk peptides". BUT...

‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do.

I wrote for @natureportfolio.bsky.social about 'dark proteins' encoded by our genomes. Once overlooked, they may be central to cancers, cellular biology and evolutionary innovation. As @sebastiaanvheesch.bsky.social told me: "There's new biology here."

www.nature.com/articles/d41...

Screen shot of the fake Robyn Pickering account. It’s a direct clone of the real account but the account name has an extra bsky after Robyn and before the full stop for .bsky.social

Hi palaeopeople - this new Robyn Pickering account is a fake. The real Prof Pickering is @pickeringrobyn.bsky.social

This new account has an extra ‘bsky’ after the handle and started DM-ing me immediately after I followed it.

Medicine Nobel awarded for gene-regulating ‘microRNAs’ Victor Ambros and Gary Ruvkun identified a class of tiny molecules that have a crucial role in controlling gene expression.

The 2024 Nobel prize in physiology or medicine has been awarded to Victor Ambros and Gary Ruvkun, who discovered microRNAs, a class of tiny RNA molecules that help to control how genes are expressed in multicellular organisms. Read the Nature article. 🧪

Thanks! (I meant lost in news coverage if AF gets a gong next week. It's tempting and easy to give AI magic all the credit.)

Is there a free-to-read version? I pre-wrote an AlphaFold Nobel story last year that I'll probably update this week. One point that I hope doesn't get lost is that AlphaFold's success was enabled by decades of experimental work and freely available structures and sequences.