Paul Rainey
@paulbrainey.bsky.social
Evolutionary geneticist working with microbes. Absorbed by Major Evolutionary Transitions. Fighting the decline to grumpiness. MPI for Evolutionary Biology, Plön, Germany & ESPCI, Paris, France.
#48 Could humans and AI merge into an evolutionary individual?
YouTube video by The DeepDive lab
youtu.be
November 15, 2025 at 8:42 AM
Reposted by Paul Rainey
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
apply.interfolio.com/177547
Apply - Interfolio
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November 13, 2025 at 3:23 PM
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
apply.interfolio.com/177547
@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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 12, 2025 at 9:20 AM
@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...
www.biorxiv.org/content/10.1...
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...
doi.org/10.5281/zeno...
Pursuit of Knowledge: A Charter for Academic Renewal
This paper identifies systemic problems in how academic research is structured, evaluated, and supported. It argues for a realignment of incentives and institutional cultures to restore trust, enable ...
doi.org
October 30, 2025 at 10:18 PM
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...
doi.org/10.5281/zeno...
@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/...
www.pnas.org/doi/10.1073/...
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...
www.pnas.org
October 28, 2025 at 6:36 PM
@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/...
www.pnas.org/doi/10.1073/...
Reposted by Paul Rainey
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....
—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....
October 28, 2025 at 7:57 AM
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....
—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/...
journals.asm.org/doi/10.1128/...
journals.asm.org
October 28, 2025 at 8:08 AM
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/...
journals.asm.org/doi/10.1128/...
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 🎉
October 23, 2025 at 5:15 AM
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/
Autogenic transitions in individuality - PhilSci-Archive
philsci-archive.pitt.edu
October 8, 2025 at 12:18 PM
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 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_...
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
October 6, 2025 at 11:17 AM
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_...
Pls repost 🙏
www.evolbio.mpg.de/3838377/job_...
Reposted by Paul Rainey
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...
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
September 25, 2025 at 2:31 PM
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...
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.
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
#AI #evolution #singularity #ChatGPT #LLM #MajorEvolutionaryTransition
September 23, 2025 at 8:12 PM
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
September 21, 2025 at 1:18 PM
Next season’s harvest - already on a roll
Summer’s delight
September 21, 2025 at 12:37 PM
Summer’s delight
Reposted by Paul Rainey
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/...
September 11, 2025 at 3:52 PM
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/...
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/...
www.pnas.org/doi/10.1073/...
September 10, 2025 at 4:31 PM
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/...
www.pnas.org/doi/10.1073/...
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
August 18, 2025 at 8:12 PM
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...
Reposted by Paul Rainey
🦠 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 ⬇️
General across bacteria + potential in synbio.
📄 academic.oup.com/mbe/advance-ar…
🔗 James’s thread ⬇️
https://academic.oup.com/mbe/advance-ar…
August 13, 2025 at 4:37 PM
🦠 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 ⬇️
General across bacteria + potential in synbio.
📄 academic.oup.com/mbe/advance-ar…
🔗 James’s thread ⬇️
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...
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
August 11, 2025 at 7:50 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Paul Rainey
“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
August 4, 2025 at 7:12 PM
“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
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
July 29, 2025 at 3:44 PM
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.
this powerfully direct open-letter published in the BMJ, written by a team @ LSH&TM, shames us into recognition
www.bmj.com/content/390/...
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
July 4, 2025 at 10:42 AM
this powerfully direct open-letter published in the BMJ, written by a team @ LSH&TM, shames us into recognition
www.bmj.com/content/390/...
www.bmj.com/content/390/...
Reposted by Paul Rainey
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
June 20, 2025 at 7:31 AM
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.
May 27, 2025 at 10:26 AM
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.
Reposted by Paul Rainey