Paul Rainey

Fraudulent Scientific Papers Are Rapidly Increasing, Study Finds A statistical analysis found that the number of fake journal articles being churned out by “paper mills” is doubling every year and a half.

“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

Best Publishing Practices and Open Access Options at The American Naturalist | The American Naturalist: Vol 206, No 2

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.

The UK must not fail Gaza—a call for government action For nearly 20 months, since October 2023, Palestinians in Gaza have endured a relentless campaign of annihilation. The statistics alone defy comprehension: over 56 000 people killed—one third of them ...

this powerfully direct open-letter published in the BMJ, written by a team @ LSH&TM, shames us into recognition

www.bmj.com/content/390/...

Journals Operating Predatory Practices Are Systematically Eroding the Science Ethos: A Gate and Code Strategy to Minimise Their Operating Space and Restore Research Best Practice Scientific research seeks to extend knowledge and understanding, an activity that perhaps more than any other advances society and humanity. In essence, it is the search for truth. But, because it se....

Predatory 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.

The Remarkable Julian Davies by Roberto — If I were asked to name scientists who have deeply influenced the evolution of my own thinking along the decades, there's little doubt that Julian Davies would be at the top of the list. ...

schaechter.asmblog.org/schaechter/2...

Jumbo phage-mediated transduction of genomic islands Bacteria acquire new genes by horizontal gene transfer (HGT), typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages and certain integrative and conjugative elements (ICE...

@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.

Abstract 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.

MGE Workshop

We 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 nascent multicellular lineages | Proceedings of the Royal Society B: Biological Sciences The evolution of multicellular organisms involves the emergence of cellular collectives that eventually become units of selection in their own right. The process can be facilitated by ecological condi...

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/...

Dear 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 👇

Horizontal Transfer of Bacterial Operons into Eukaryote Genomes Abstract. In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coreg

Bacterial 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!

Why constrain this magnificent diversity to the whims of plant breeders. Equal rights for helliborus (and bryophytes).

Coliologists taking Monod's statement "what's true for E. coli is true for elephants" too literally?

Substitution load revisited: a high proportion of deaths can be selective Abstract. Haldane's Dilemma refers to the concern that the need for many “selective deaths” to complete a substitution (i.e. selective sweep) creates a spe

Our 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

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!

Postdoctor, 2 years, in predicting the evolution of antibiotic resistance The Department of Molecular Biology seeks a postdoctoral researcher who will work with forecasting and steering experimental evolution of antibiotic resistance. The employment is full-time for two yea

We 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?

This is powerful and deeply moving. You don’t need to be a NZer to understand (but it helps)

this is wonderful on so many levels. i want one!

An extreme mutational hotspot in nlpD depends on transcriptional induction of rpoS Genetic mutations drive evolution, with effects ranging from harmful to beneficial. While typically considered random, some genomic positions – called “mutational hotspots” – mutate more frequently. H...

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...

This 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

For this French senator, Trump is a traitor—and Europe is now alone In one month, Trump has done more harm to the Atlantic alliance than in four years of his last presidency. Europeans now see him as a traitor.

Very clear-eyed assessment of how the US is failing our allies:

thebulletin.org/2025/03/for-...

Three AI-powered steps to faster, smarter peer review Tired of spending countless hours on peer reviews? An AI-assisted workflow could help.

Let'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...

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 🥹.

Enabling evolvability to evolve A multilevel population architecture enables bacteria to evolve increased adaptability

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/...

Experimental evolution of evolvability Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...

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?