Paul Rainey
Evolutionary geneticist working with microbes. Absorbed by Major Evolutionary Transitions. Fighting the decline to grumpiness. MPI for Evolutionary Biology, Plön, Germany & ESPCI, Paris, France.
- Parasites of jumbo phages… 🤔 Muchas gracias, @jrpenades.bsky.social por tu excelente comentario. Much to discover. DNA moves through populations (and communities) at a pace that if we could measure, would stun. Bacteria: inert bags of froth? Hapless? There for the bidding? doi.org/10.1073/pnas...
- Our piece on evaluating journals is accompanied this week by a related EMBO Reports editorial on equitable open access and journal funding. The two pieces speak closely to one another. doi.org/10.1038/s443...
- Scientific journals function like a stock market: impact factor as price, citations as trades—yet without analysts, regulation, or real oversight. Our OpEd argues it is time to evaluate journals themselves, not just the scientists who publish in them. doi.org/10.1038/s443...
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- Thank you Ludo for taking the time to read and comment on the paper. Also for this tip. I changed it to preprint!
- 😳😶🌫️🧐 youtu.be/Y7LM3ERa0SE
- @buzzbaum.bsky.social (and team) blazes trails with this new work. As always, I'm a bit behind... much excitement already expressed about this paper. If you haven't caught it, then catch it. The study is painstaking, beautiful, persuasive and ever so elegant. www.biorxiv.org/content/10.1...
- Many are painfully aware that the environment within which we function -- as scientists -- needs fixing. We've come up with a proposal for academic renewal. It's not perfect, but its a start. Input, comments, suggestions are welcome. Making a difference matters 👇 doi.org/10.5281/zeno...
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- I agree, but then there is reality. It would be super if there were more academic positions, but the current system seems fully expanded. I'm behind your wish to fight, but without major societal shifts, I can't see progres. It comes down to money and priorities. Politics 😥
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- Agree. But at a golbal level, training too many PhD students -- many of whom desire an academic position -- is problematic if academic positions are in short supply.
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- Totally agreement: we do state that people acheiving doctorate-level training have a multiplicity of career paths that extend well beyond those offered by the standard academic route. And these options are in no way lesser paths. 🙏 for engagement.
- @prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...
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- thank you. all credit to yansong who just kept on keeping on. we knew that something in the compost juice was transfering the GIs, but the jumbo phage, being much less numerous cf other lytic phages also present in the juice, was a real challenge to find. But we played a few tricks and we go it!
- Who would have thought: nitrogen-fixing vibrios 😱 that interact with Pokkali rice roots and promote plant growth in brackish water. Amazing! Wonderful to see this detailed and careful investigation out for all to oogle. Many congratulations Ramesh 🎉 journals.asm.org/doi/10.1128/...
- A week of special delights: Aysha Chowdhury admirably presents and defends her thesis at ESPCI in Paris followed by Paulien Hogeweg and her inaugural address as newly elected member of EMBO in Heidelberg. Very happy to have shared both occasions. Congratulations on fine achievements 🎉
- Could major evolutionary transitions arise "from within" -- through internal innovation rather than merger? The case for autogenic transitions in individuality is developed here: philsci-archive.pitt.edu/26847/
- Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science. Pls repost 🙏 www.evolbio.mpg.de/3838377/job_...
- A ghost in the machine? It appears when parts merge, a new logic takes hold, and a higher-level individual emerges. Life showed it in eukaryogenesis. Humans and AI could unwittingly stumble into something similar.
- Opinion: As human–AI interdependence deepens, could they form an integrated evolutionary individual, subject to collective selection? Explore this perspective in PNAS Front Matter: www.pnas.org/doi/10.1073/... #AI #evolution #singularity #ChatGPT #LLM #MajorEvolutionaryTransition
- Next season’s harvest - already on a roll
- Summer’s delight
- Curious to hear thoughts from #popgen, #humangenetics, #genomics folks on recent paper: www.pnas.org/doi/10.1073/... "Directed mutation" in specific human pop'ns seems unlikely to me. DM didn't stand up as proposed in bacteria, but there are hot spots shaped by past selection. Plausible here?
- Unlikely to me too. Assuming the diffs are real (need side-by-side batch-matched samples and larger n), then the most parsimonious explanation would be an ancestry-associated mutational hotspot at APOL1. Evidence of "fitness aligned mutagenesis"? Didn't see it. Mechanistic basis? Absent.
- In a just published OpEd, with @mkhochb.bsky.social, we draw upon Major Evolutionary Transitions thinking to outline future scenarios in which humans and AI might come to form new kinds of evolutionary units: humans as subsystems within an AI-coordinated whole. www.pnas.org/doi/10.1073/...
- I am in awe at what @jeroenmeijer.bsky.social extracted from the @stevenquistad.bsky.social experiment. The molecular evolutionary dynamics of Theomophage, given evolutionary opportunity, are amazing: that this can be deduced from metagenomic data is... oh my 😮 www.biorxiv.org/content/10.1...
- Makes sense that diverse microbial communities can be maintained on a recalcitrant substrate like cellulose, but on glucose, surely not? Surprisingly there is no difference 🤔 The first part is live 👇 but more to come (including answers). www.biorxiv.org/content/10.1...
- Publish in non-profit society journals. Am Nat makes the case www.journals.uchicago.edu/doi/full/10..... Fight erosion of scientific standards, distortion of researcher incentives, redirection of research funds to publishers. Predatory publishing threatens public trust in science.
- this powerfully direct open-letter published in the BMJ, written by a team @ LSH&TM, shames us into recognition www.bmj.com/content/390/...
- Poignant memory: Bellagio, Rockefeller centre. Sitting beside fire. Rest earned. Julian decides we need drama. A real life whodunnit unfolds. Exceptionally reluctant actor was appointed protagonist. Turns out I could act. Successfully incriminated Jeff H Miller for sloppy repair.
- @prczhaoyansong.bsky.social posted an update of elegant work on genomic islands. Captured via real-time expts, the GIs define a widespread class of MGE (eg VPI-1 de V. cholerae), encode a diverse cargo of genes & exploit jumbo phages for horizontal transfer 😎👇 www.biorxiv.org/content/10.1...
- AlphaEvolve edits its own genome @matejbalog.bsky.social. When Lamarckian AI becomes Darwinian, the pace of change 🚀. Humans and AI becoming a new kind of entity is foreseeable -> humans the equivalent of mitochondria in the eukaryotic cell. Fascinating & horrifying. Not science fiction.
- It so often happens: new work blasts away prior concepts. Turns out that building a wrinkly spreader mat is more challenging that we thought (and vastly more interesting) with dependency on ancestral types for a leg-up.
- Excited to share my postdoc work with @paulbrainey.bsky.social ! Common adaptive types in air-liquid-interface colonization turn out to grow slowly and colonize the niche inefficiently. They even fail when monocultured from low inocula. How can they reliably succeed in laboratory evolution? [1/5]
- Evolutionary dynamics of lineages and predicting adaptive mutations using colgen with @gdoulcier.bsky.social, Philippe Remigi and Daniel Rexin. Never thought we'd finish: data acquired years back was wandering the void. So glad we pulled it back 🙏 royalsocietypublishing.org/doi/10.1098/...
- Amazingly cool!
- This 👉🏻 www.nature.com/articles/s41...
- Why constrain this magnificent diversity to the whims of plant breeders. Equal rights for helliborus (and bryophytes).
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- Coliologists taking Monod's statement "what's true for E. coli is true for elephants" too literally?
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- Those of us not in the US should not be cowed. We need to increase visits to the US, support friends and colleagues - give reality to the fact that science is the most humanising of pursuits: it cuts boundaries, prejudices, furthers knowledge. It keeps us curious and hungry. See y'all next month!
- A repost of a recent post, but this work by @andydfarr.bsky.social, @peteralind.bsky.social and Christina Vasileiou, warrants it! Assaying mutation rates at promoters requires a special set of circumstances. Maybe promoters are generally more mutation-prone, but undetected through lack of assay?
- 🚨 Bacterial gene promoters mutate faster than expected! 🚨 Scientists found a 5,000-fold mutation rate increase in a bacterial gene promoter, linking it to gene activity—potentially reshaping evolution and antibiotic resistance understanding! www.evolbio.mpg.de/3810964/news... #Genetics #Mutation
- This is powerful and deeply moving. You don’t need to be a NZer to understand (but it helps)
- Dominik Abelen, a soldier of the HUR Legion died in battle in #Ukraine On March 11, 2025 a farewell ceremony was held in Kyiv for Dominik, a soldier of the Int Legion of the AF 🇺🇦 The 28y old soldier was a citizen of New Zealand, a representative of the indigenous Maori people 🎥 Def 🇺🇦
- this is wonderful on so many levels. i want one!
- Mutation rates vary within genomes.., sure, but: @andydfarr.bsky.social describes a single transcription-dependent C->T mutation in the promoter of rpoS that is ~5,000 times > background. Are promoters places where shit happens, or facilitators of adaptive change? journals.plos.org/plosgenetics...
- Returning from 22nd Winter School in Mol Bio & Genetics in Istanbul. Organised each year by an exceptional team of knowledge-hungry undergrads. Everything 💯. Will def return to stunning Istanbul. Extra special thanks to Irmak & Iman (in pic) who ensured everything was perfect 🥹.
- A recent paper www.science.org/doi/10.1126/... described the evolution of evolvability in 46 mutational steps. The refining hand of selection - working lineages - was key, but @michael-barnett.bsky.social used just 8 lineages 🫠. Can selection above the level of the individual really be so potent?
- Without lineage-level selection the number of replicate populations required to have some chance of achieving the same end (roughly the same 46 mutations in more or less the same order), would be so vast as to be effectively infinite. Edo Kussell nicely elaborates www.science.org/doi/10.1126/...
