Genomic epidemiologist at the Centre for Genomic Pathogen Surveillance in Oxford. How can microbial genomics improve health in high infectious disease settings?

Blantyre, Malawi
Joined May 2010
Phil Ashton retweeted
Introducing Microbiome Repo, a catalog of every public human gut metagenome (>500k samples) with metadata pulled straight from sequence archives, papers, and supplements olmlab.github.io/microbiome_… Published gut metagenomes? Search your name and see if it got your study!
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Phil Ashton retweeted
Tyler Cowen showing up to defend EA here gives me mild nightmares because I remember him calling the top in 2022: xitter.cf/MargRev/status/1503404… But his bottom line that EA is “directionally correct, even if you should not follow its recommendations all the way” seems directionally correct to me, and in line with what I was getting at last week about EA’s pragmatism: xitter.cf/albrgr/status/21058269… He says more attention to AI safety would be good, and gives EA some credit there. I’d add that EAs were saying this years before most others, which is a pretty good example of Tyler’s closing line that “interesting and valuable ideas” can spring from weird places. (And I say this as someone who was pretty skeptical on the AI safety work for a long time.) And I agree that EAs can be offputtingly arrogant. That’s one reason I’m really glad we practice “worldview diversification” at CG (coefficientgiving.org/resear…) - though I still wish we had a more robust intellectual grounding for it and a better/more principled way to translate it into ultimate allocations. I’m also sympathetic to Tyler’s view that some EAs “perceive a high risk of doom without sufficient evidence,” though I also think that the best available estimates from people who are trying as hard as possible to be neutral (e.g., xitter.cf/Research_FRI/status/20…) suggest plenty of reason for concern. I think a lot of the problem here is just the fundamental difficulty of our epistemic position here, as I think @Research_FRI and @michael_nielsen have done a good job pointing out. With concrete harms like the Hugging Face attack starting to show up in practice, I do sometimes feel like Tyler is unfairly shifting the epistemic goalposts (though not particularly in this case). And as a small correction - CG doesn't have a “$40 billion fund,” or really an endowment of its own at all. I think that number might have come from a back-of-the-envelope guess I gave here (semafor.com/article/09/03/20…), building on @nanransohoff’s estimate of what all AI-linked donors might eventually give each year. Anyway, I agree w/ the upshot that more EA at the margin would be a good thing!
"Effective altruism is directionally correct, even if you should not follow its recommendations all the way." @tylercowen self-recommending as usual thefp.com/p/in-defense-of-ef…
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The greatest UX failure of my lifetime is the fact that people are listening to their whatsapp voice notes like this WhatsApp has an audio switch which moves the audio from the main loudspeaker to the earpiece if you hold the phone next to your ear and... they just don't tell people @kunalb11 this is your time. Be the hero we need
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Phil Ashton retweeted
Saturday
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Phil Ashton retweeted
Opus 4.8 is insane, nothing will be the same after this model 💀
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Phil Ashton retweeted
The world map, but it’s all Africa
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Phil Ashton retweeted
Imperdible mensaje de Chistina Koch tras su vuelta del espacio. Oratoria 10/10. Contenido 10/10. Emoción 10/10. Gente que sí ♥️
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Oh hi FungiDB
Everyone has one email that they receive daily, can't unsubscribe to, and are gradually driven insane by
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It's also a reservoir for AMR determinants that could transfer to dominant invasive Salmonella lineages like Typhimurium. ⚠️
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South Africa's surveillance infrastructure caught this. Malawi's didn't exist to. This gap is not just a technical problem, it's a global equity problem. We cannot fight AMR without investing in surveillance capacity in low-resource settings.
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It was a wonderful honour to be awarded an honorary doctorate by my alma mater today - all the more so because my fellow honorands were such lovely and brilliant people. Thank you @UniofOxford and @WilliamJHague. It was an unforgettable day. ox.ac.uk/news/2026-02-24-cha…
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📣New pre-print alert! 🦠We sequenced S. Typhi from a vaccine trial in Malawi🇲🇼 📊No genomic differences between vaccine and control arms, but short follow-up. 💡That’s why ongoing genomic surveillance after vaccination is essential to detect escape. medrxiv.org/content/10.64898…
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Alison Gopnik's insight: babies learn like scientists. Tyler's question: are scientists actually good learners? New episode on childhood cognition, the ‘intuitive apprenticeship’ model of teaching older kids, AI as a cultural technology, and why she thinks nature vs. nurture is a misleading framework. Timestamps: 0:00:00 - How children—and scientists—learn 0:14:35 - Consciousness, episodic memories, and aphantasia 0:23:06 - Freud’s and Piaget’s theories about childhood 0:27:49 - Twin studies and nature vs. nurture 0:39:33 - Teaching strategies for younger vs. older children 0:44:07 - AI's ability to generate novel insights 0:53:57 - What Autism and ADHD diagnoses do and don’t reveal 0:58:02 - The success of the Gopnik siblings
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Was there any need to underline the word Nature in the text body?
In 1992 Peter Ratcliffe received this rejection letter from Nature. His findings were not "a sufficient advance in our understanding". 27 years later he won the Nobel Prize for the same discovery. Don't lose faith in the things you believe in.
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I thought my son said his bum was hurting so I got him to bend over and I put some cream on it, turns out he said his thumb hurt 😭
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