Paul Rainey

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 full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

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_...

New 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.

Next season’s harvest - already on a roll

Summer’s delight

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.

What 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/...

As interdependencies between humans and AI grow, the two could come to function not merely as interacting agents, but as an integrated evolutionary individual subject to selection at the collective level. Image credit: Dave Cutler (artist).

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/...
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Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities Bacteriophages are important drivers of microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. To address this gap,...

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...

🦠 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 ⬇️

Diverse microbial communities assemble on both recalcitrant and labile carbon sources Microbial community assembly is shaped by the nature of available resources, with labile carbon sources such as glucose often expected to support low diversity due to rapid growth and competitive excl...

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...

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