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.
- Reposted by Paul RaineyContext-dependent adaptation in structured environments Proc Biol Sci by @yuyakarita.bsky.social et al from @paulbrainey.bsky.social royalsocietypublishing.org/rspb/article...
- 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...
- Reposted by Paul RaineyEditorial: Society journals matter—supporting science through renewed commitment Editorial in @femsjournals.bsky.social microLife by @paulbrainey.bsky.social and colleagues academic.oup.com/microlife/ad...
- 😳😶🌫️🧐 youtu.be/Y7LM3ERa0SE
- Reposted by Paul RaineyMy department at UT Austin is looking to hire an Assistant Professor in Evolutionary Biology, broadly defined. Feel free to reach out to me with any questions you may have. apply.interfolio.com/177547
- @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...
- @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/...
- Reposted by Paul RaineyThe scientific & ethical legacy of the late Ioannis Economidis—a champion of Env Biotech & SynBio at the @ec.europa.eu —is captured in this article, based on his last lecture. A testament to an exceptional mind & a remarkable human being enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....
- 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_...
- Reposted by Paul RaineyNew ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration! my.corehr.com/pls/uoxrecru...
- 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
- Reposted by Paul RaineyWhat future does AI hold? With @paulbrainey.bsky.social, we hypothesize that human-AI coevolution is leading to the emergence of a new evolutionary unit of selection. Science fiction or looming fact? Read our paper and judge for yourself. www.pnas.org/doi/10.1073/...
- 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...
- Reposted by Paul Rainey🦠 New paper led by James Horton (feat. J Cherry & @gretelwaugh.bsky.social) reveals GnT DNA motif can boost T→A mutation rates up to 1000×, & how tweaking nearby bases can fine-tune its potency. General across bacteria + potential in synbio. 📄 academic.oup.com/mbe/advance-ar… 🔗 James’s thread ⬇️
- 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...
- Reposted by Paul Rainey“If these trends are not stopped, science is going to be destroyed." Here's my story on the accelerating growth of systemic research fraud--aka paper mills. Gift link: nyti.ms/45rDirw
- 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/...
- Reposted by Paul RaineyPredatory practices—journals, meetings etc—are spoiling the research landscape and erasing trust in science. But what can be done? Here Timmis et al inspect the phenomenon & propose a few measures to contain and even revert the damage enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
- 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.
- Reposted by Paul Rainey
- @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.
- Reposted by Paul RaineyAbstract submission for Understanding and Predicting Microbial Evolutionary Dynamics 2025 is now open until 7 July 2025 at 23:59 BST. microb.io/MicroEvo25 #MicroEvo25
- 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]
- Reposted by Paul RaineyWe are pleased to announce that registration for 3rd MGE Workshop is now live! If you are interested in giving a talk please register online through our website by Friday 16th May. We look forward to seeing you all in Southampton in June! www.ukmgeworkshop.org
- 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/...
- Reposted by Paul RaineyDear Pseudomonas aficionados: Please check this hands-on Cold Spring Harbor Asia Course on the sexiest science and technology of our favourite bug. All info in the QR code 👇
- Reposted by Paul RaineyBacterial operons may persist in eukaryotes (e.g. fungi) after horizontal gene transfer, according to Kogay et al. Operon-derived gene pairs suggest initial neutral retention and later functional integration or degeneration. 🔗 doi.org/10.1093/gbe/... #NewPaperAlert #genome #evolution #fungi
- 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).
- Reposted by Paul RaineyOur latest paper revisits Haldane 1957 on speed limits to adaptation, the paper that triggered neutral theory. We clarify and then significantly extend the theory, and apply the resulting model to @mexpositoalonso.bsky.social's data doi.org/10.1093/gene... 1/14
- Reposted by Paul RaineyWe have a 2-year postdoc position available in the Lind Lab at Umeå University, Sweden! Predicting and steering experimental evolution of antibiotic resistance in Pseudomonas aeruginosa. Reposts appreciated. umu.varbi.com/en/?jobtoken...
- 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...
- Reposted by Paul RaineyThis International Women’s Day, we want to highlight the ‘Women Microbiologists in Academia: Challenges and Opportunities’ being organised by Champion, @enasnewire.bsky.social at #Microbio25 on 2 April. Find out more: microb.io/3Fi5ByU #IWD2025
- Reposted by Paul RaineyVery clear-eyed assessment of how the US is failing our allies: thebulletin.org/2025/03/for-...
- Reposted by Paul RaineyLet's talk about this Nature piece in more detail. I've rarely read something so anti-scientific anywhere short of the National Review. www.nature.com/articles/d41...
