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Paul Rainey

@paulbrainey.bsky.social
500 followers 268 following 83 posts

Evolutionary geneticist working with microbes. Absorbed by the curiosity of science and ideas. Department of Microbial Population Biology, MPI for Evolutionary Biology, Plön, Germany & ESPCI, Paris, France.

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Paul Rainey @paulbrainey.bsky.social · 10/09/2026
How does pressure from below begin? Often quietly, when early-career researchers discover that a calculation they have been making alone is widely shared. New on Academic Renewal: notes from conversations among ECRs. academicrenewal.substack.com/p/how-pressu...
academicrenewal.substack.com
How pressure from below begins
Notes from conversations among early career researchers
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FEBS Letters @febsletters.bsky.social · 08/09/2026
📨 You've got (𝘍𝘌𝘉𝘚) 𝘓𝘦𝘵𝘵𝘦𝘳𝘴! 📬 Our latest The Scientists' Forum piece proposes an accreditation system to stop predatory publishing — raising standards and restoring public trust in science. 📡#ResearchIntegrity, #ScholarlyPublishing, #Science 📝 @paulbrainey.bsky.social 🔍 tinyurl.com/4vkt923p
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Paul Rainey @paulbrainey.bsky.social · 07/09/2026
A beautiful piece of detective work by @honour.bsky.social + colleagues revealing the origins of Ralstonia disease of bananas on Martinique. As so often, ICEs (ICERs!) prove to be extraordinary capacitors for evolutionary change. Evolution for evolution's sake 🤔 doi.org/10.1093/gbe/...
doi.org
Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak
Abstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out
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Paul Rainey @paulbrainey.bsky.social · 27/08/2026
A further push to do something about the plague of journals that provide minimal editorial oversight, erode standards, distort incentives and threaten public trust in science; while at the same time reaping vast profit from tax-payer-funded research. febs.onlinelibrary.wiley.com/doi/10.1002/...
Shark-like behaviour of predatory publishers
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Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect
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The New York Times @nytimes.com · 22/08/2026
Crucial trade talks between the U.S. and Canada to stave off punishing new tariffs by the Trump administration on Canadian goods collapsed late Friday, with Canada saying it would retaliate “dollar for dollar.”
trib.al
Canada-U.S. Trade War Escalates as Talks Collapse
Intense negotiations to stave off new levies by the Trump administration ended in an impasse as Mark Carney suspended talks. U.S. tariffs on Canada, and retaliatory tariffs on the U.S., will come into effect.
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Seth Bordenstein @symbionticism.bsky.social · 22/08/2026
Science on! ⬇️ if you’re looking for some great stuff in the microbiome space.
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Paul Rainey @paulbrainey.bsky.social · 21/08/2026
A third-year student draws poster PS3.20.305 -- far corner, farthest wall -- and commits to standing there two hours. Barely anyone makes it that far. Two floors up, a senior colleague is having the week of his life. Same conference. A new essay. academicrenewal.substack.com/p/why-we-sti...
academicrenewal.substack.com
Why we still fly
The scientific conference was invented to solve a transport problem we no longer have. What is it for now?
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Paul Rainey @paulbrainey.bsky.social · 09/08/2026
Ever wondered how new evolutionary individuals arise? Wanted to engineer communities so the parts integrate to form a new whole? Or impose conditions that cause simple chemistries to become Darwinian? New MS shows how. Psst… don’t tell AI www.biorxiv.org/content/10.6...
biorxiv.org
Forging an evolutionary individual from separate replicators
A central puzzle in the evolution of individuality is the origin of heredity. Egalitarian transitions integrate formerly independent replicators into a higher-level individual, but this requires the c...
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Paul Rainey @paulbrainey.bsky.social · 04/08/2026
I'm not allowed to boil a kettle in my office; the electricity is public money. This rule can be justified in a sentence. Most of what lands on my desk has never had to be. New post on unnecessary bureaucracy. academicrenewal.substack.com/p/the-one-wa...
academicrenewal.substack.com
The one-way audit
Researchers are required to account for their time and money. Administrative procedures rarely include any account of the research time they consume.
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The Women In Science Archive @wisarchive.bsky.social · 28/07/2026
Today we celebrate the 160th anniversary of Beatrix Potter's birth. Before she became the world-beloved creator of Peter Rabbitt, she was a promising naturalist and scientific illustrator who was pushed out of the field by men whose ideas she challenged. tinyurl.com/4427xzsu #WomenInSTEM #BookSky
tinyurl.com
Mushrooms, Fossils, and a Pen to Draw Them With: Beatrix Potter, Naturalist.
"I don't know what to write to you, so I shall tell you a story about four little rabbits whose names were Flopsy, Mopsy, Cottontail and Peter." In 1893, when Beatrix Potter set these words, and the ...
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Simon J. Greenhill @simongreenhill.bsky.social · 28/07/2026
Somewhere a university academic is being told to "do more with less" by someone whose job title didn't exist two reorgs ago.
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Paul Rainey @paulbrainey.bsky.social · 24/07/2026
Academic advice travels downhill: manage your supervisor, publish early, protect your time. Where is the genre in which early-career researchers advise the people who hire, fund and judge them? New post 👇 academicrenewal.substack.com/p/the-first-...
academicrenewal.substack.com
The first curriculum
Academic survival guides teach junior researchers how to live with the judgements of senior scholars. No corresponding genre gives young researchers authority to advise the people who judge them.
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Ken Timmis @kentimmis.bsky.social · 20/07/2026
Absolutely! But not only reading: other activities involving language, including writing and especially thinking - see enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Scientists' Warning to Humanity: The Need to Begin Teaching Critical and Systems Thinking Early in Life
We live in a time of global crises: a deteriorating environment that is struggling to provide all the resources and services we demand of it, changing climate and its consequences for the biosphere, ...
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Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026
After four years, several updates and a handful of CRAN releases, 𝗹𝘁𝗰 𝗰𝗼𝗹𝗼𝗿 𝗽𝗮𝗹𝗲𝘁𝘁𝗲 𝗥-𝗽𝗮𝗰𝗸𝗮𝗴𝗲, reached a version I feel genuinely good about sharing with the community. github.com/loukesio/ltc...
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Paul Rainey @paulbrainey.bsky.social · 20/07/2026
One faculty ad, 200 applicants, 600 papers before the first shortlist. Nobody can read that, so metrics do the reducing — and slowly a committee stops reading at all. An essay on what we lose when judgement is handed to citation counts and h-indices. 🧵 academicrenewal.substack.com/p/when-acade...
academicrenewal.substack.com
When academics stop reading
Metrics can help decide where to look, but they turn dangerous when they replace contact with the work itself.
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Paul Rainey @paulbrainey.bsky.social · 15/07/2026
George O'Toole is the real deal. He's an academic in the true sense: curious, inspirational, committed, candid & genuinely invested in making the system better. New interview: it's full of wisdom & humour. Thanks George! academicrenewal.substack.com/p/the-long-v...
academicrenewal.substack.com
The long view
A conversation with George O'Toole on publishing, peer review, and the unwritten rules of a scientific life
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Paul Rainey @paulbrainey.bsky.social · 13/07/2026
My postdoc director called my work "phenomenological" and forbade it. I walked to a museum, found Tinbergen had shared a Nobel for work of exactly that kind, and finished the study anyway. On temperament, luck, and what the system selects against 👇 academicrenewal.substack.com/p/a-certain-...
open.substack.com
A certain cast of mind
The argument about research culture leaves out something personal, and no reform reaches it.
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Manuel Kleiner @manuelkleiner.bsky.social · 10/07/2026
The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...
biorxiv.org
Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome
Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of...
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Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 10/07/2026
Check out this Symposium at Rice Univ this Sept 18 www.bakerinstitute.org/event/synthe.... Much of the conversation will go into environmental applications of Synthetic Biology 👇
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Paul Rainey @paulbrainey.bsky.social · 08/07/2026
Peer review is unpaid. Click "claim credit" for a review and that record enters a database owned by Clarivate, the company that also sells the impact factor. Your free labour becomes their inventory, and once anonymised, raw material for profit. academicrenewal.substack.com/p/who-owns-y...
academicrenewal.substack.com
Who owns your peer review?
The reward for reviewing has quietly become an asset on someone else's balance sheet.
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Paul Rainey @paulbrainey.bsky.social · 07/07/2026
In choosing where to submit our work for publication, we have more agency than we sometimes recognise. Every submission helps determine which journals prosper, which publishing models grow, and ultimately how science is communicated. academicrenewal.substack.com/p/choosing-w...
academicrenewal.substack.com
Choosing where to publish
Every submission helps shape the future of scholarly publishing
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Paul Rainey @paulbrainey.bsky.social · 05/07/2026
I remember Ananda from many Pseudomonas meetings!
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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 01/07/2026
We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...
In this example, we're showing the improvement in the percentage of annotated genes from prophage "Maintenon" from Clostridium innocuum (doi: 10.1186/s40168-023-01541-x) using the phageFACTor pipeline
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ASM @asm.org · 01/07/2026
Please welcome @vscooper.micropopbio.org as the new ASM President and Federico Sisti, Ph.D., as President-Elect. They begin their terms on July 1. ASM congratulates its new & continuing leaders and looks forward to their leadership in advancing ASM’s mission. asm.social/2Zx
Headshots of ASM's new leaders
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Katie Abson @katieabson.bsky.social · 30/06/2026
Our paper is out! 📣 we find that molecular measures of genetic variation do not predict heritable genetic variation across species - important implications for the application of genomic data for conservation! www.pnas.org/doi/10.1073/...
pnas.org
Nucleotide diversity is a poor predictor of short-term adaptive potential | PNAS
The capacity to adapt is essential for a population to avoid extinction in a changing world and is recognized as a global conservation priority. Ad...
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Paul Rainey @paulbrainey.bsky.social · 30/06/2026
The first Academic Renewal interview is now live! Denis Bourguet & Thomas Guillemaud, co-founders of Peer Community In, discuss peer review, diamond open access, and scholarly publishing organised around researchers rather than publishers. academicrenewal.substack.com/p/taking-pub...
academicrenewal.substack.com
Taking Publishing Back
Denis Bourguet and Thomas Guillemaud on Peer Community In, diamond open access, and why scholarly evaluation should be controlled by researchers
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Paul Rainey @paulbrainey.bsky.social · 26/06/2026
I really value: the dynamics of community assembly on 2 contrasting C sources. Daily sampling of communities derived from compost & maintained over 8 wks. No difference in diversity maintained on simple or complex C. AmaZinG. 🙏 all enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources
Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...
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Carl Zimmer @carlzimmer.com · 25/06/2026
Another study finds that base editing can deliver precise changes to human embryo DNA. @heidiledford.bsky.social reports on the insights it delivered, and the concerns the technique is fostering. www.nature.com/articles/d41...
nature.com
Precise genome editing of human embryos triggers praise and alarm
The ‘base editing’ technique that researchers used is far from ready for the clinic, but critics worry that it will spur a rush to commercialize the approach.
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Paul Rainey @paulbrainey.bsky.social · 25/06/2026
A short interview on research assessment and academic reform was published today by Forschung & Lehre. The article is in German, but with an English translation. This forms part of a broader initiative on Academic Renewal that can be found on Substack. www.forschung-und-lehre.de/management/w...
forschung-und-lehre.de
"Wettbewerb lässt sich in andere Bahnen lenken"
Warum wird Forschungsqualität zunehmend an Publikationszahlen gemessen? Ein Gespräch mit Paul Rainey über die Belohnung des Quantifizierbaren.
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Paul Rainey @paulbrainey.bsky.social · 24/06/2026
Ensuring that public money - via APCs - goes only to journals that meet recognised standards of editorial responsibility, transparency and cost. academicrenewal.substack.com/p/making-jou...
academicrenewal.substack.com
Making journal accreditation count
How money, visibility and reputation can be used to enforce public standards
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Paul Rainey @paulbrainey.bsky.social · 22/06/2026
Payment of APCs from public funds should only go to journals that can prove that they operate with genuine editorial responsibility. open.substack.com/pub/academic...
open.substack.com
A journal code of conduct
What journals should demonstrate before receiving public APC funding
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Noah Fierer @noahfierer.bsky.social · 19/06/2026
New preprint up: the power of protein language models - using a single gene (adenylate kinase) to predict the temperature optima of bacteria and bacterial communities from genomes or metagenomes www.biorxiv.org/content/10.6...
biorxiv.org
Predicting optimal growth temperatures of bacteria using learned structural information from a single protein
Temperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species ...
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Harmit Singh Malik @harmitmalik.bsky.social · 19/06/2026
It would be hard to find a better metaphor than the ongoing tragi-comedy of the algal bioreactor project (previously the reflecting pools) in Washington DC, emblematic of knee-jerk big decisions made about the US scientific enterprise without any thought to long term (even short-term) consequences.
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Cameron Thrash @jcamthrash.bsky.social · 19/06/2026
Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models bg.copernicus.org/articles/23/... #jcampubs
bg.copernicus.org
Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models
Abstract. Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass ...
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Mark O. Martin @markowenmartin.bsky.social · 19/06/2026
Wonderful #MattersMicrobial podcast recording today with Dr. Morgan Sobol about nitrogenase, early Earth, and astrobiology. SUCH MICROBIAL FUN! @msobol.bsky.social
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Paul Rainey @paulbrainey.bsky.social · 19/06/2026
New on Academic Renewal: early-career voices. I’d like to include written interviews with ECRs on publication pressure, career strategy, mentoring, metrics, and the pursuit of knowledge. Named or anonymous contributions welcome. DM is interested academicrenewal.substack.com/p/early-care...
academicrenewal.substack.com
Early-career voices
Academic renewal cannot be a conversation among senior academics alone.
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Paul Rainey @paulbrainey.bsky.social · 18/06/2026
Public money should not flow automatically to journals that fail to meet acceptable standards of editorial quality, transparency and accountability. In this post I ask what a journal accreditation system might look like & how it could work. academicrenewal.substack.com/p/building-a...
academicrenewal.substack.com
Building a journal accreditation system
How journals could be assessed without favouring size, wealth or brand
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Paul Rainey @paulbrainey.bsky.social · 16/06/2026
seems i'm still in spain. damn, too bad
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Paul Rainey @paulbrainey.bsky.social · 16/06/2026
Cool. Shortsighted evolution of a bug that is maladapted in the human context, but gains ability to persist via loss of function mutations leading it to become (worryingly) more tuberculous-like. Lovely to see. BIG unanswered Q: what is Pa's natural habitat? Money on some small eukaryote 🎰
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Paul Rainey @paulbrainey.bsky.social · 16/06/2026
I no longer live in NZ, but my heart lies there in wild places. Learning that wilderness is at risk for the sake of profit is soul-destroying. It has to stop. Short-sighted stupidity and greed know no bounds. But I am sure that the spirit of NZ - the tangata whenua - will rise and win the fight 💪
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Paul Rainey @paulbrainey.bsky.social · 15/06/2026
Did someone mention Spain? Was that you Ken? Victor? Juan? Un almuerzo. Todos eligimos lo mismo
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Paul Rainey @paulbrainey.bsky.social · 15/06/2026
To the latest attempt to scam APCs I sent an admittedly infantile response. But it made me smile 😈
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c0nc0rdance @c0nc0rdance.bsky.social · 14/06/2026
MBARI captured these views of glass squids in family Cranchiidae. I want to talk about some of the unique adaptations these Ghosts of the Midwater have & how they're adaptive to life in the twilight waters of the mesopelagic zone (200 m to 1000 m). (📷: Monterey Bay Aquarium Research Institute)
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Rajini Rao @madamescientist.bsky.social · 15/06/2026
Falafel for dinner on a gorgeous summer evening. Served on a bed of baba ganoush and mohamarra. #foodsky
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Ran Blekhman @blekhman.bsky.social · 15/06/2026
Just start writing. My new post: substack.com/home/post/p-...
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Microbiology Society @microbiologysociety.org · 15/06/2026
Registration closes soon for Early Career Conference 2026 🤝👩‍🔬 Join us on 6–7 July 2026 at the University of Birmingham for a career development and networking opportunity for early career members, secure your place: microb.io/ECConf26 #ECConf26
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Paul Rainey @paulbrainey.bsky.social · 15/06/2026
Monday's thought's on APCs and why we should stop paying fees to publishers who do not earn the money (and plunder the system) academicrenewal.substack.com/p/stop-payin...
academicrenewal.substack.com
Stop paying publishers who do not earn the money
Public money should support scholarly service, not unscrupulous publishers who rob the system
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Paul Rainey @paulbrainey.bsky.social · 14/06/2026
Why not enjoy burning days?
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Paul Rainey @paulbrainey.bsky.social · 13/06/2026
Amongst it all: science is the most humanising of activities. It crosses boundaries, breaks boundaries & reminds that no matter our individual backgrounds or professions, we all delight in figuring out how things work. And fundamentally, we are all scientists: marvel at the curiosity of kids.
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