How can we hope to understand organismal development when it is controlled by huge, complex networks of interacting genes?
One option is to move away from molecular details and focus on learning representations and rules.
Check out the new perspective from me and @jamesbriscoe.bsky.social
So when do authors preprint? Many do long before they submit to a journal (to get feedback to improve the work?); many submit around the same time (just want the work out?). Only a minority are submitting once the paper is under review [evidence against claims by some detractors]. 3/n
Apply to become a Preprint Editor Development
We are inviting experienced researchers to apply to become Preprint Editors, a new type of editorial role responsible for handling our 'In preprints' articles and forging links with preprint literature. #prepints
Learn more and apply before 30 March 2026:
journals.biologists.com/dev/pages/pr...
Applications are open for @dev-journal.bsky.social 2026 Pathway to Independence (PI) programme, supporting postdocs applying for group leader positions:
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
What are fairer ways to judge research without relying on flawed proxies like journal brand or impact factor?Leonardo points to NIH-style grant application panel discussions as a model. Could scientific societies adopt a similar approach to review articles or evaluate preprints? 6/6
Peers evaluation remains a cornerstone of scientific research. But the current format of peer-review is ungrateful and opaque. Leonardo's approach to peer-review is straightforward: does the author's data match their claims? If not, it is up to them to change their claims or generate more data. 5/6
One disadvantage is in case of patent applications, where public disclosure needs to be carefully times. For career progression in academia, preprints seem to be taken into account, although university policies regarding their consideration for hiring and promoting faculty are often unclear. 4/6
The advantages of preprints are overwhelming: opportunity for rapid & free sharing, getting feedback from the community, proof of productivity in grant applications and for trainees to apply to grants and jobs, and generally a great way to network and generate enthusiasm around our science. 3/6
For fields where it's become common, such as SynBio, preprinting has become a "no brainer". Preprints are becoming the currency in the field, and the line between pre- and post-peer-review is blurring. Some researchers still resist, for unclear reasons. So what are the advantages of preprints? 2/6
How are preprints perceived and evaluated in the life sciences from a PI's perspective? Check our my podcast episode through the @asapbio.bsky.social Fellow's program, where I interviewed @leonardomorsut.bsky.social about his perspective on the topic! My key takeaways: 1/6
The Drain of Scientific Publishing details very clearly how for-profit publishers making >30% profit margins have corrupted any solution the research community has attempted.
Let's cut ourselves free.
Drain: arxiv.org/abs/2511.04820
Strain: bit.ly/StrainQSS
Oligopoly: bit.ly/OligSciPub
12/12
This will be challenging and will require advocacy and persistence, but I believe it is necessary to maintain public trust in science – because we steward taxpayer’s money, and we have a responsibility to use it wisely. 5/5
My slides, feel free to check out or reuse: docs.google.com/presentation...
Change is on the horizon thanks to initiatives such as preprints and open peer-review. But scientists need to embrace this change and move beyond the status quo of an outdated system. 4/5
Is it working? Not really - the current system struggles to root out scientific fraud in the form of paper mills or questionable research practices. It also lacks transparency in peer-review and editorial decisions. Most people agree that publishers generous profit margins (>35%) are unfair. 3/5
How do we do science? When and how are we evaluated as scientists? The enthusiasm in the room was palpable - this is a subjects scientists of all career stages deeply care about. I first introduced the endless cycle of "getting money-doing stuff" that characterises an researcher's career. 2/5
Why do we do science?
This was my opener for a department roundtable “Reimagining Scientific Evaluation: Are we judging a book by its cover?”, inspired by @asapbio.bsky.social’s Fellows program. Now more than ever, we should strive for an academic culture that’s transparent, efficient, and fair. 1/5
🎉🎉 We finally have a website! 🎉🎉
Did you miss a thread?
Want to know who our delegates are?
Do you want to join our big club?
Check it out:
epithelialmechanics.github.io
Huge thanks to all thread-contributors and to you for following us!
📣Announcing the 4th edition of the EMBL‑IBEC Conference on “Engineering Multicellular Systems”, taking place 11–13 March 2026 in Barcelona. Exploring organoids, mechanobiology, embryo models, organ-on-chip systems, multiomics and more. Abstracts open now!
events.ibecbarcelona.eu/embl-ibec-co...
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
🚨JOB ALERT
Dr. Buceta at @i2sysbio.es welcome applications for 36-month postdocs on:
👉 Mechanical markers of tissue dysfunction due to ageing – digital twins & machine learning
Details here: fgcsic.es/convocatoria...
📩 Contact javier.buceta@csic.es to shape your proposal!
@epimechfc.bsky.social
A Nobel-winning scientist of great modesty and humour, John Gurdon died on 7 Oct. Not only did he make a discovery that laid the foundations for stem cell research, he also created one of the best environments for research at the Wellcome/CRUK Gurdon Institute wellcome.org/news/sir-joh...
A bold call to challenge the status quo in scientific publishing: «Science advances through disagreement, through competing hypotheses tested against reality. Why should scientific communication be any different? »
The Jane Goodall Institute of Canada has learned this morning, Wednesday, October 1st, 2025, that Dr. Jane Goodall DBE, UN Messenger of Peace and Founder of the Jane Goodall Institute, has passed away due to natural causes.
She was in California as part of her speaking tour in the United States.
So how do we judge the quality & impact of a preprint?
What platforms exist for journal-agnostic peer review?
👀 Let’s talk about that next week.
5/5
Do preprints have to end up in journals? Stefano Vianello boldly says no.
He preprinted his PhD work, then had it peer-reviewed via a journal-agnostic platform — refusing to choose between paywalls or APCs.
A great read: stefanovianello.github.io/posts/2021/0...
4/5
Why is preprint uptake so low?
❌ Cons often cited:
* ❓ Lower perceived quality (though studies show minor changes pre vs post vs. peer-review): tinyurl.com/plosbiologyP...
* 📉 Variable recognition for promotions/graduation
* 🏁 Scooping concerns
* ⚠️ Risk of misinformation
3/5
✅ Pros of preprints:
* 🚀 Rapid sharing
* 👀 More visibility&citations (tinyurl.com/bioRXiv-cita...)
* ⏱ Priority (who did it first)
* 📑 Proof of productivity for job&grant applications
* 🌍 Open access
* ⚖️ No journal branding bias
Yet only ~13% of life science papers are preprinted first.
2/5
When I asked my PI @leonardomorsut.bsky.social why he publishes all our lab’s work first as preprints, he said:
“It seemed like the obvious thing to do.”
In mammalian synBio, we’re lucky: most of the community uses preprints. Why it matters 👇 1/5
Different cell types are like oil and water - check out my @epimechfc.bsky.social thread on differential adhesion and its potential applications in tissue engineering!
