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Paul Rainey @paulbrainey.bsky.social · 1h

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/

Autogenic transitions in individuality - PhilSci-Archive

philsci-archive.pitt.edu

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Paul Rainey @paulbrainey.bsky.social · 2d

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_...

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.

www.evolbio.mpg.de

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Reposted by Paul Rainey

Craig MacLean @craigmaclean.bsky.social · 12d

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...

Job Details

my.corehr.com

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Paul Rainey @paulbrainey.bsky.social · 14d

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.

Proceedings of the National Academy of Sciences @pnas.org · 14d

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

An illustration of a human and a robot watering a tree together.
Image credit: Dave Cutler (artist).

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Paul Rainey @paulbrainey.bsky.social · 17d

Next season’s harvest - already on a roll

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Paul Rainey @paulbrainey.bsky.social · 17d

Summer’s delight

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Paul Rainey @paulbrainey.bsky.social · 25d

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.

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Reposted by Paul Rainey

Michael Hochberg @mkhochb.bsky.social · 26d

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/...

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Paul Rainey @paulbrainey.bsky.social · 27d

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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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).

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Paul Rainey @paulbrainey.bsky.social · Aug 18

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...

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,...

www.biorxiv.org

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Reposted by Paul Rainey

Tiffany Taylor @taylorlabgroup.bsky.social · Aug 13

🦠 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 ⬇️

https://academic.oup.com/mbe/advance-ar…

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Paul Rainey @paulbrainey.bsky.social · Aug 11

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...

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...

www.biorxiv.org

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Reposted by Paul Rainey

Carl Zimmer @carlzimmer.com · Aug 4

“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

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.

nyti.ms

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Paul Rainey @paulbrainey.bsky.social · Jul 29

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.

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

www.journals.uchicago.edu

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Paul Rainey @paulbrainey.bsky.social · Jul 4

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

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

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 ...

www.bmj.com

Reposted by Paul Rainey

Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · Jun 20

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/...

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....

enviromicro-journals.onlinelibrary.wiley.com

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Paul Rainey @paulbrainey.bsky.social · May 27

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.

STCmicrobeblog @stcmicrobeblog.bsky.social · May 26

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

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

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Reposted by Paul Rainey

STCmicrobeblog @stcmicrobeblog.bsky.social · May 26

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

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

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Paul Rainey @paulbrainey.bsky.social · May 18

@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...

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...

www.biorxiv.org

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Paul Rainey @paulbrainey.bsky.social · May 16

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.

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Reposted by Paul Rainey

Microbiology Society @microbiologysociety.org · May 7

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

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Paul Rainey @paulbrainey.bsky.social · May 6

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.

Yuya Karita @yuyakarita.bsky.social · May 6

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]

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Reposted by Paul Rainey

MGE Workshop @mgeworkshop.bsky.social · May 1

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

MGE Workshop

www.ukmgeworkshop.org

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Paul Rainey @paulbrainey.bsky.social · May 2

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/...

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...

royalsocietypublishing.org

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Reposted by Paul Rainey

Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · Apr 30

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 👇

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