A further push to do something about the plague of journals that provide minimal editorial oversight, erode standards, distort incentives and threaten public trust in science; while at the same time reaping vast profit from tax-payer-funded research. febs.onlinelibrary.wiley.com/doi/10.1002/...

New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect

Crucial trade talks between the U.S. and Canada to stave off punishing new tariffs by the Trump administration on Canadian goods collapsed late Friday, with Canada saying it would retaliate “dollar for dollar.”

Canada-U.S. Trade War Escalates as Talks Collapse

Intense negotiations to stave off new levies by the Trump administration ended in an impasse as Mark Carney suspended talks. U.S. tariffs on Canada, and retaliatory tariffs on the U.S., will come into effect.

trib.al

Science on! ⬇️ if you’re looking for some great stuff in the microbiome space.

One Health Microbiome Center@psumbiome.bsky.social · 2w ago

Fall seminars are here! 🍂🦠 Our 2026 lineup features exciting microbiome research from Penn State + experts from far and wide. 🌎 External seminars are open to the public via Zoom — DM us for the registration link! #Microbiome #OneHealth

A third-year student draws poster PS3.20.305 -- far corner, farthest wall -- and commits to standing there two hours. Barely anyone makes it that far. Two floors up, a senior colleague is having the week of his life. Same conference. A new essay. academicrenewal.substack.com/p/why-we-sti...

Why we still fly

The scientific conference was invented to solve a transport problem we no longer have. What is it for now?

academicrenewal.substack.com

Ever wondered how new evolutionary individuals arise? Wanted to engineer communities so the parts integrate to form a new whole? Or impose conditions that cause simple chemistries to become Darwinian? New MS shows how. Psst… don’t tell AI www.biorxiv.org/content/10.6...

Forging an evolutionary individual from separate replicators

A central puzzle in the evolution of individuality is the origin of heredity. Egalitarian transitions integrate formerly independent replicators into a higher-level individual, but this requires the c...

biorxiv.org

I'm not allowed to boil a kettle in my office; the electricity is public money. This rule can be justified in a sentence. Most of what lands on my desk has never had to be. New post on unnecessary bureaucracy. academicrenewal.substack.com/p/the-one-wa...

The one-way audit

Researchers are required to account for their time and money. Administrative procedures rarely include any account of the research time they consume.

academicrenewal.substack.com

Today we celebrate the 160th anniversary of Beatrix Potter's birth. Before she became the world-beloved creator of Peter Rabbitt, she was a promising naturalist and scientific illustrator who was pushed out of the field by men whose ideas she challenged. tinyurl.com/4427xzsu #WomenInSTEM #BookSky

Mushrooms, Fossils, and a Pen to Draw Them With: Beatrix Potter, Naturalist.

"I don't know what to write to you, so I shall tell you a story about four little rabbits whose names were Flopsy, Mopsy, Cottontail and Peter." In 1893, when Beatrix Potter set these words, and the ...

tinyurl.com

Somewhere a university academic is being told to "do more with less" by someone whose job title didn't exist two reorgs ago.

Academic advice travels downhill: manage your supervisor, publish early, protect your time. Where is the genre in which early-career researchers advise the people who hire, fund and judge them? New post 👇 academicrenewal.substack.com/p/the-first-...

The first curriculum

Academic survival guides teach junior researchers how to live with the judgements of senior scholars. No corresponding genre gives young researchers authority to advise the people who judge them.

academicrenewal.substack.com

Absolutely! But not only reading: other activities involving language, including writing and especially thinking - see enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Scientists' Warning to Humanity: The Need to Begin Teaching Critical and Systems Thinking Early in Life

We live in a time of global crises: a deteriorating environment that is struggling to provide all the resources and services we demand of it, changing climate and its consequences for the biosphere, ...

enviromicro-journals.onlinelibrary.wiley.com

Ricard Solé@ricardsole.bsky.social · 2mo ago

Why is reading so fundamental to the human mind? In this fascinating paper, @standehaene.bsky.social & Co show how literacy reshapes and connects the brain’s visual and language systems. A timely reminder of what education could lose if LLMs replace reading & writing. www.unicog.org/publications...

After four years, several updates and a handful of CRAN releases, 𝗹𝘁𝗰 𝗰𝗼𝗹𝗼𝗿 𝗽𝗮𝗹𝗲𝘁𝘁𝗲 𝗥-𝗽𝗮𝗰𝗸𝗮𝗴𝗲, reached a version I feel genuinely good about sharing with the community. github.com/loukesio/ltc...

One faculty ad, 200 applicants, 600 papers before the first shortlist. Nobody can read that, so metrics do the reducing — and slowly a committee stops reading at all. An essay on what we lose when judgement is handed to citation counts and h-indices. 🧵 academicrenewal.substack.com/p/when-acade...

When academics stop reading

Metrics can help decide where to look, but they turn dangerous when they replace contact with the work itself.

academicrenewal.substack.com

George O'Toole is the real deal. He's an academic in the true sense: curious, inspirational, committed, candid & genuinely invested in making the system better. New interview: it's full of wisdom & humour. Thanks George! academicrenewal.substack.com/p/the-long-v...

The long view

A conversation with George O'Toole on publishing, peer review, and the unwritten rules of a scientific life

academicrenewal.substack.com

My postdoc director called my work "phenomenological" and forbade it. I walked to a museum, found Tinbergen had shared a Nobel for work of exactly that kind, and finished the study anyway. On temperament, luck, and what the system selects against 👇 academicrenewal.substack.com/p/a-certain-...

A certain cast of mind

The argument about research culture leaves out something personal, and no reform reaches it.

open.substack.com

The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...

Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome

Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of...

biorxiv.org

Check out this Symposium at Rice Univ this Sept 18 www.bakerinstitute.org/event/synthe.... Much of the conversation will go into environmental applications of Synthetic Biology 👇

Peer review is unpaid. Click "claim credit" for a review and that record enters a database owned by Clarivate, the company that also sells the impact factor. Your free labour becomes their inventory, and once anonymised, raw material for profit. academicrenewal.substack.com/p/who-owns-y...

Who owns your peer review?

The reward for reviewing has quietly become an asset on someone else's balance sheet.

academicrenewal.substack.com

In choosing where to submit our work for publication, we have more agency than we sometimes recognise. Every submission helps determine which journals prosper, which publishing models grow, and ultimately how science is communicated. academicrenewal.substack.com/p/choosing-w...

Choosing where to publish

Every submission helps shape the future of scholarly publishing

academicrenewal.substack.com

I remember Ananda from many Pseudomonas meetings!

International Microbiology Literacy Initiative - IMiLI@imili-micro.bsky.social · 2mo ago

Did you know? Ananda Mohan Chakrabarty transformed biotechnology by developing the first patented bacterium capable of breaking down oil. His pioneering work opened a new era in science and showed how innovation can help tackle major environmental challenges.

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

Please welcome @vscooper.micropopbio.org as the new ASM President and Federico Sisti, Ph.D., as President-Elect. They begin their terms on July 1. ASM congratulates its new & continuing leaders and looks forward to their leadership in advancing ASM’s mission. asm.social/2Zx

Our paper is out! 📣 we find that molecular measures of genetic variation do not predict heritable genetic variation across species - important implications for the application of genomic data for conservation! www.pnas.org/doi/10.1073/...

Nucleotide diversity is a poor predictor of short-term adaptive potential | PNAS

The capacity to adapt is essential for a population to avoid extinction in a changing world and is recognized as a global conservation priority. Ad...

pnas.org

The first Academic Renewal interview is now live! Denis Bourguet & Thomas Guillemaud, co-founders of Peer Community In, discuss peer review, diamond open access, and scholarly publishing organised around researchers rather than publishers. academicrenewal.substack.com/p/taking-pub...

Taking Publishing Back

Denis Bourguet and Thomas Guillemaud on Peer Community In, diamond open access, and why scholarly evaluation should be controlled by researchers

academicrenewal.substack.com

I really value: the dynamics of community assembly on 2 contrasting C sources. Daily sampling of communities derived from compost & maintained over 8 wks. No difference in diversity maintained on simple or complex C. AmaZinG. 🙏 all enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources

Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...

enviromicro-journals.onlinelibrary.wiley.com

Another study finds that base editing can deliver precise changes to human embryo DNA. @heidiledford.bsky.social reports on the insights it delivered, and the concerns the technique is fostering. www.nature.com/articles/d41...

Precise genome editing of human embryos triggers praise and alarm

The ‘base editing’ technique that researchers used is far from ready for the clinic, but critics worry that it will spur a rush to commercialize the approach.

nature.com

A short interview on research assessment and academic reform was published today by Forschung & Lehre. The article is in German, but with an English translation. This forms part of a broader initiative on Academic Renewal that can be found on Substack. www.forschung-und-lehre.de/management/w...

"Wettbewerb lässt sich in andere Bahnen lenken"

Warum wird Forschungsqualität zunehmend an Publikationszahlen gemessen? Ein Gespräch mit Paul Rainey über die Belohnung des Quantifizierbaren.

forschung-und-lehre.de

Ensuring that public money - via APCs - goes only to journals that meet recognised standards of editorial responsibility, transparency and cost. academicrenewal.substack.com/p/making-jou...

Making journal accreditation count

How money, visibility and reputation can be used to enforce public standards

academicrenewal.substack.com

Payment of APCs from public funds should only go to journals that can prove that they operate with genuine editorial responsibility. open.substack.com/pub/academic...

A journal code of conduct

What journals should demonstrate before receiving public APC funding

open.substack.com

New preprint up: the power of protein language models - using a single gene (adenylate kinase) to predict the temperature optima of bacteria and bacterial communities from genomes or metagenomes www.biorxiv.org/content/10.6...

Predicting optimal growth temperatures of bacteria using learned structural information from a single protein

Temperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species ...

biorxiv.org