Paul Rainey

Equitable Open Access - EMBO Reports EMBO Reports - The predominant financial model for OA is based on Article Processing Charges (APCs), which often forces authors to assemble support from diverse sources, including research grants....

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...

An evaluation system for scientific journals - EMBO Reports EMBO Reports - Scientific journals disseminate research findings and serve as a currency for measuring the reputation of scientists. Given their importance for science and for scientists’...

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...

Thank you Ludo for taking the time to read and comment on the paper. Also for this tip. I changed it to preprint!

Editorial: Society journals matter—supporting science through renewed commitment Paul B Rainey, Puri López-García, Zeynep Ceren Karahan, Paul Williams, Stipan Jonjić, Kenneth N Timmis; Editorial: Society journals matter—supporting scien

Editorial: 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...

YouTube video by The DeepDive lab #48 Could humans and AI merge into an evolutionary individual?

😳😶‍🌫️🧐

youtu.be/Y7LM3ERa0SE

My 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

An Asgard archaeon with internal membrane compartments The emergence of eukaryotes from a merger between an archaeon and a bacterial cell ∼two billion years ago involved a profound change in cellular organisation. While the order in which different featur...

@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...

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 😥

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.

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.

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...

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!

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

@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/...

The 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/...

Aysha Chowdhury at her PhD defence

Paulien Hogeweg's inaugural EMBO lecture.

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 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.