iiinova — where your digital self keeps evolving

Mark A. Hanson @hansonmark.bsky.social · 07/08/2026

The Hanson lab is about to be positively BUZZING. Stay tuned...

A picture through the grate at a bumblebee colony

A box is sitting on a desk that says "LIVE BEES PLEASE KEEP LEVEL"

A green and white box with purple motifs containing bumblebees sits in an incubator on a white wire rack.

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Mark A. Hanson @hansonmark.bsky.social · 08/07/2026

I can confirm. But also, be prepared for the wonkiest measurement logic. And again, I can confirm!

A flow chart showing how to measure things like a Canadian. It starts with what you are measuring. And it progresses through things like "if temperature, are you cooking? Yes = fahrenheit. No -> is it a pool? Yes = Fahrenheit, No = Celsius."

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Mark A. Hanson @hansonmark.bsky.social · 02/07/2026

Day 3 of #ExE2026 we have a stellar plenary by @danielbolnick.bsky.social "Parasites Lost" Eco-Evo-Immuno species interactions and trait evolution through natural selection. Andnof course, amazing pictures of stickleback with tapeworms nearly the same size as they are!

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Mark A. Hanson @hansonmark.bsky.social · 01/07/2026

Day 2 of #ExE2026 ! Thank you to all our sponsor journals. I am proud to say ExE is sponsored strictly by society and non-profit journals! 👌📄 A huge thanks to our journal sponsors (see next post), who take their APC revenue and use it to support the sci communities like ExE ❤️ 1/2

A photo of the help desk from day 1 with organisers and volunteers standing around getting ready for the day.

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Mark A. Hanson @hansonmark.bsky.social · 30/06/2026

Kicking off #ExE2026, @erikpostma.bsky.social introduces the room to the "weaponisation of sea shanties" as a VERY STRICT timekeeping measure to ensure speakers keep to time. Will we all be cursing or singing "Wellerman" by the end of it? We shall see!

A conference speaker is addressing the room with a slide showing housekeeping

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Mark A. Hanson @hansonmark.bsky.social · 18/06/2026

You mean via the standard subscription model? I mean Development itself wants you to pay the APC (screenshot). I also don't have a problem with paying APCs to non-profits! Keep it in the community and I'm happy. Also for lurkers, just a screenshot of the Nature entrapment model (and alt text).

https://journals.biologists.com/dev/pages/open-access

From: https://www.science.org/content/article/9500-nature-journals-will-now-make-your-paper-free-read

The Nature group also announced a trial of a lower cost open-access option: when authors submit a manuscript to one of three journals—Nature Genetics, Nature Methods, and Nature Physics—they could pay €4790 or less per paper for open access, if they agree to participate in a process called "guided review." In that process, if editors of the three journals and colleagues decide a manuscript is worthy enough to send out for peer review, they will ask authors to pay an initial fee of €2190 to cover review costs and then pay an additional fee if the paper is accepted.

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Mark A. Hanson @hansonmark.bsky.social · 18/06/2026

Makes me sad more people don't know about @reviewcommons.org and the incredible system they've built! Get peer reviews independent of a journal, then submit with reviews in hand to a stable of excellent journals from across non-profit and society publishers. Review Commons: good for what ails ya.

Advertisement of the Review Commons process

Advertisement of the Review Commons stable of journals and reviewing editors

Advertisement of the Review Commons process in greater depth

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Mark A. Hanson @hansonmark.bsky.social · 18/06/2026

Case in point, Impact Inflation with 3-year cites/doc windows: Development = 2.875/1.600 = 1.797 IJMS = 6.170/1.316 = 4.688 Inflated Impact Factors are common across the MDPI stable because MDPI journals mostly self-cite or ring-cite. From: direct.mit.edu/qss/article/... And see the alt texts.

Figure 5: Changing behavior of citation metrics revealed by impact inflation (for journals with at least 1,000 annual citations). Statistical letter groups reflect significant differences (p < .05) in one-way ANOVA with Tukey HSD. A: MDPI and Hindawi have significantly higher impact inflation compared to all other publishers. Comparisons using samples of Clarivate IFs are shown in Figure S13. B: MDPI journals have the highest rate of within-journal self-citation among compared publishers, including in previous years (Figures S14 and S15). Here we specifically analyze journals receiving at least 1,000 citations per year to avoid comparing young or niche journals to larger ones expected to have diverse citation profiles.

From the Strain explorer: https://pagoba.shinyapps.io/strain_explorer/

The Impact Inflation of most MDPI journals is super inflated. Society journals like CoB's DMM and Development are far less inflated than the average journal.

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Mark A. Hanson @hansonmark.bsky.social · 18/06/2026

And look at who is citing who: IJMS sends cites to all sorts of journals, including Development. Only MDPI et al. cites IJMS. Development, meanwhile, gets cited by all sorts of journals. This includes IJMS (because IJMS is huge, yet somehow no one cites it...). See alt text for summaries.

$A citation network profile for Development (CoB) showing that Development gets is citations from many journals, including IJMS, but also a substantial fraction from Nat Comms, Dev Cell, Curr Biol, Dev Biol, Cell Stem Cell, Science Advances, etc...$

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Mark A. Hanson @hansonmark.bsky.social · 28/05/2026

+15k signatures now in just over one day. Britons now favour rejoining the EU with a strong majority (+21). At 100k, it became "considered for debate in parliament." This is worth sharing. Tell parliament in clear terms what they're debating, and for who.

From Yougov tracker: public support for Britain rejoining the EU IS AT 56 support, 35 oppose. A net support of +21.

Among those who voted "Leave" in 2016, 22% would now vote "Remain."

They're vewy sowwy.

Screenshot of the UK gov petition update that this petition passed 100k signatures in on May 27, 2026.

While the petition started 6 months ago, it has only recently garnered attention. On May 26th, it was near ~90k signatures.

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Mark A. Hanson @hansonmark.bsky.social · 15/03/2026

This lesson is so obvious we literally wrote it as the call-and-response of kids cartoons.

An image of Ms Frizzle from The Magic School Bus cartoon with the caption "Take chances, make mistakes, get messy."

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Mark A. Hanson @hansonmark.bsky.social · 06/03/2026

AMPs can be duplicated, and they evolve rapidly. AMP genes can also be lost over time, perhaps due to selection imposed by host ecology-relevant 🦠. Here we suggest gain of tried-and-tested AMPs can occur just as suddenly; a mechanism to generate lineage-specific defence competence. 8/8

First page of the PDF. We even formatted it nicely so you could pick it up and read it like it was a mature piece of reasearch - because it is.

This is something I'm experimenting with in my group to boost the utility of preprints.

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Mark A. Hanson @hansonmark.bsky.social · 06/03/2026

Lastly, we also observed that Drosomycin is secondarily lost in some lineages. The clearest case is of wood-feeding cockroaches and termites relative to cockroach/mantis outgroup – a loss associated with dietary shift akin to our previous finding in flies (Hanson et al., 2023; Science). 7/n

A diagram showing Drosomycin loss in wood-feeding cockroaches and termites

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Mark A. Hanson @hansonmark.bsky.social · 06/03/2026

TLDR: we characterise multiple Drs loci & sequences. In at least one seeming HGT event, Drs genes are even immune-induced. We also found 4 conserved serine codons that let us check if any gene lineages could be convergent evolution[3]. 0/4 on convergence! 3. www.pnas.org/doi/10.1073/... 6/n

Drosomycin is found in the distance lineage of Drosophila busckii on different chromosomes from where it is found in D. melanogaster. The loci do not share ancestry, as neighbour genes do not overlap. Two copies of D. busckii Drs are immune induced.

The diversity of Drosomycin mature peptide sequences. The signal peptide is poorly conserved (and more similar between mantises and beetles than beetles and flies). 85-90% similarity across insect Drs residues in the mature peptide domain. But there are some key sites with widespread polymorphisms, and also some fixed Serine residues that let us do codon analyses investigating whether these sequences arose via convergent evolution or orthologous sequence.

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Mark A. Hanson @hansonmark.bsky.social · 06/03/2026

Here we present a case of similar AMPs scattered across multiple insect orders being explained by horizontal gene transfer. The #Drosophila antifungal peptide Drosomycin was thought to be restricted to D. melanogaster and friends. It's not. It's really not. Immune novelty emerging via HGT❕ 5/n

Drosomycin is found in mantises, cockroaches, two lineages of beetles, a single katydid, a pseudogene in booklice, and an independent long branch of Drosophila

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Mark A. Hanson @hansonmark.bsky.social · 06/03/2026

Pleased to finally share this fun collab that began at #Ento23 @cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun). Horizontal transfer of an #AntimicrobialPeptide across insects bit.ly/DrsHGT 1/🧵

A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insects

Various phylogenetic secondary loss events are mapped to a tree of insects to explain the parsimony calculations necessary to explain the diversity of insect Drosomycin antimicrobial peptide genes

Antimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of
horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the
distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired
pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT
events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.

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Mark A. Hanson @hansonmark.bsky.social · 23/02/2026

Very excited to be advertising this project with the excellent cosupervision of Peter Mergaert through @i2bcparissaclay.bsky.social and @uniexecec.bsky.social. This position is open to international applicants and will involve stints in both Penryn UK and Paris France. Please share! Apply: adum.fr

An advertisement for a PhD position studying "Revealing the mechanistic basis of defence peptide antibacterial specificity." It shows fruit flies infected by green-fluorescent protein expressing bacteria, and describes the project and way to apply.

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Mark A. Hanson @hansonmark.bsky.social · 19/02/2026

Plus you'll have to suffer through me and my terrible puns. 🦀

A post showing horseshoe crab illustrations that says "We're horeposting post your horses." is quote-posted with the text:

In undergrad, I had a classmate present on the diversity of crabs (carcinization talk I think?). They put a picture up that was a horseshoe crab. I turned to my now-wife and said:

"Of all the crabs that aren't crabs they could have chosen, the possibilities are Limulus."

Been together 17 years. 🦀

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Mark A. Hanson @hansonmark.bsky.social · 02/02/2026

All set for New Horizons 💎 #OpenAccess in Nijmegen! Thank you to the organisers for the opportunity to speak on the Strain, Stain, & Drain of scientific publishing. Looking forward to great conversations on moving #ScientificPublishing forward! bit.ly/StrainQSS www.horizondiamond.nl#schedule

The Drain of Scientific Publishing
Fernanda Beigel, Dan Brockington, Paolo Crosetto, Gemma Derrick, Aileen Fyfe, Pablo Gomez Barreiro, Mark A. Hanson, Stefanie Haustein, Vincent Larivière, Christine Noe, Stephen Pinfield, James Wilsdon
The domination of scientific publishing in the Global North by major commercial publishers is harmful to science. We need the most powerful members of the research community, funders, governments and Universities, to lead the drive to re-communalise publishing to serve science not the market.
Comments: 1 Figure, 1 Table, 1 Supplementary Table
Subjects: Digital Libraries (cs.DL)
Cite as: arXiv:2511.04820 [cs.DL]
(or arXiv:2511.04820v2 [cs.DL] for this version)

https://doi.org/10.48550/arXiv.2511.04820
Focus to learn more
Submission history
From: Dan Brockington [view email]
[v1] Thu, 6 Nov 2025 21:20:22 UTC (2,101 KB)
[v2] Mon, 17 Nov 2025 20:05:17 UTC (2,113 KB)

The Issue with Special Issues: when Guest Editors
Publish in Support of Self
Paolo Crosetto1*, Pablo Gómez Barreiro2
, Mark Austin Hanson3*
1. Univ. Grenoble Alpes, INRAE, CNRS, Grenoble INP, GAEL; Grenoble, France
2. Department of Science Operations, Royal Botanic Gardens, Kew; Wakehurst, UK
3. Centre for Ecology and Conservation, University of Exeter; Penryn, Cornwall, UK
* corresponding authors – PC: paolo.crosetto@inrae.fr, MAH: m.hanson@exeter.ac.uk
Open Researcher and Contributor ID (ORCID)
PC: 0000-0002-9153-0159
PGB: 0000-0002-3140-3326
MAH: 0000-0002-6125-3672

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Mark A. Hanson @hansonmark.bsky.social · 25/01/2026

But if you want the story in brief... Screenshot from: mahansonresearch.weebly.com/blog/what-ar...

Going off PISSte
While the acronym is whimsical, and pejorative, it's apt. We settled on "PISS" because the term "endogeny" has a gross mouth-feel, and the existing lexicon lacked a term for "excess endogeny" that communicated the scientific misconduct aspect of it all. PISS began as a joke, but its versatility as a noun, verb, adjective, etc... (a bit like the word "ass") somehow convinced us to keep it right to the very end.

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Mark A. Hanson @hansonmark.bsky.social · 21/01/2026

I try to stay out of politics here, but... wtf are american elected officials doing? Your president is threatening war with NATO. Impeach him. "But we have a 4 point lead in the midterms." "He'll support a challenge to my seat." Impeach him. Now. Wtf. I can't even. www.bbc.com/news/article...

A headline from the BBC reads: Trump doubles down on Greenland, saying there is 'no going back'

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Mark A. Hanson @hansonmark.bsky.social · 19/01/2026

Aurora borealis visible even down here in #Cornwall right now! 1st image closer to what's actually visible with naked eye. Second is overexposed and adjusted.

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

So there ya have it. We hope our data are useful to indexers, and to the public to help corral this widespread academic misconduct. The cost of inaction is immense. Without it, we will continue to piss hundreds of millions of research funds down the drain. arxiv.org/abs/2601.07563 17/17

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

To help with this effort, the brilliant @paolocrosetto.bsky.social has made an app to explore our data. Sort by publisher or journal. You can even click the bubbles in the plots & it links to the special issue in question 👏 bit.ly/PISSpaper We also have reams of appendix tables. Have at 'em! 15/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

Most journals practice special issues fairly responsibly. But it's the worst offenders that contribute most of the PISS. ~90% of PISS in our data come from just 150/904 journals. And it's exactly who you think it is. #MDPI #Frontiers 13/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

Far from enforcing their policies, publishers *hide* PISS. We learned most publisher policies ACTIVELY hide PISS by altering article metadata post-hoc. At a *minimum* #Frontiers, #Elsevier, #MDPI all do it publicly! Yikes. 🤯 Thanks to @deevybee.bsky.social et al. for noting this (see pics). 11/n

Elsevier formal special issue policy. Elsevier arbitrarily hides the fact that an article was published under the context of an open call for special issue articles if that special issue ultimately has less than three articles. As if the COI of the handling and guest editors, and financial motives to retain the guest editor, don't matter.

Frontiers Media formal special issue policy. Frontiers arbitrarily hides the fact that an article was published under the context of an open call for special issue articles if that special issue ultimately has less than four articles. As if the COI of the handling and guest editors, and financial motives to retain the guest editor, don't matter.

From Dorothy Bishop's blog at https://deevybee.blogspot.com/2024/09/now-you-see-it-now-you-dont-strange.html

https://onlinelibrary.wiley.com/doi/10.1002/leap.1660?utm_source=researchgate.net&utm_medium=article

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

And let's be clear: that's a fair comparison. Indexers treat excess endogeny as misconduct. That's why they're putting hard limits on it. The processing fees we spend on PISS could be funding hundreds to thousands of multi-year research grants. This problem sounds niche. It's really not. 9/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

Most PISS comes from journals where only 20-30% of issues are PISS. But when you publish 100s-1000s of special issues per year... oof. Analysing just 904 journals, we find ~16-43k excess endogenous articles in PISS issues. PISS in just these 904 journals rivals #ResearchIntegrity and fraud. 8/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

It's not just the extremes. Sure, we found >1300 special issues with >75% of the articles authored by guest editors themselves. But the bulk of PISS, endogeny beyond any existing threshold, comes from systematic mild abuse. The real danger is how we've normalised mild abuse, not the extremes. 7/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

In fact we actually saw pretty similar rates of PISS across all publishers tested: #MDPI, #Frontiers, #BMC, #Discover, but also the non-profit RSoc. Give authors a chance to guest edit and they'll PISS. Relative rate: 1 in 7 editors PISS 😬 Still, the real problem is about ABSOLUTE quantity... 6/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

First, let's talk journals. Of 904 journals, ~60% hosted at least some PISS. Mean endogeny across all issues has hovered between 12-16% since 2017, peaking in 2021 alongside the explosive growth of special issues we showed in the Strain paper. But that's just the mean. 🙃 5/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

With data from >100k special issues, we set out to tackle this problem. Guest editors publishing in their own issues is a form of "endogeny". In this study, we define special issues with extreme endogeny as Published In Support of Self (PISS). So, how much of this literature is PISS? 4/n

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

Systematic self- and ring-citation is established scientific misconduct. Why don't we treat editors publishing in their own special issues the same? Groups like COPE and DOAJ have now issued guidelines to limit this, but a lack of data has prevented enforcement. You know what that means... 3/n

From Abalkina (2023; Learned Publishing).
https://onlinelibrary.wiley.com/doi/10.1002/leap.1574

From Hanson et al. (2024; QSS).
https://direct.mit.edu/qss/article/5/4/823/124269/The-strain-on-scientific-publishing

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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026

We've got ISSUES. Literally. We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do? arxiv.org/abs/2601.07563 A 🧵 1/n

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Mark A. Hanson @hansonmark.bsky.social · 15/12/2025

Houndukiah, 1st night. Turns out baking clay is slightly flammable.

A channukkiah lit with the shamash and the first candle nearly fully burned down. The channukkiah is a crude dachsund shape made of baking clay.

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Mark A. Hanson @hansonmark.bsky.social · 01/12/2025

TLDR: we found elevated clean injury mortality if we flipped infected flies on this food. But we could rescue it by just flipping them on "fly McDonalds" instead - high sugar, low microbiota Corn. This confounded our phylogenetic infection experiment, but at least we learned something from it! 3/4

Our "Prop recipe" food supports a far greater microbiota load than the Cornmeal food we were using previously. Perhaps as a result, some species were susceptible to infection when flipped on the Prop recipe as adults, but not if we flipped them on the Cornmeal recipe - they were reared on the Prop recipe as larvae in both cases.

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Mark A. Hanson @hansonmark.bsky.social · 01/12/2025

The recipe rears specialists and generalists alike. Notes: 1. It works for almost every species we've tried. 2. It performs about as well or better for rearing success as other diets across species. 3. It supports a rich microbiota. 4. That rich microbiota might affect infection experiments. 2/4

Phylogenetic signal of egg-to-adult development times and body mass of dozens of fly species reared on a common media.

Example vials and bottle showing the recipe. We also add dry yeast, and dental wicks or cotton balls as climbing structures to improve rearing success.

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Mark A. Hanson @hansonmark.bsky.social · 01/12/2025

Paper for the #Drosophila community on a food recipe that rears dozens of species. This was a full team effort, with key contributions from UG, MSc, and PhD students! 👩‍🎓🎉 Plus an #infection observation re: Diet x #Microbiota 🦠 www.biorxiv.org/content/10.1... #EvolBiol #AcademicSky #SymbioSky 1/4

Egg-to-adult development times, lipid floating assay of larvae, and body mass of select fly species reared on various media.

The Prop recipe we're using supports a rich microbiota, and when we flip adults on it, some species die to a coinfection(?) that occurs when flipped on the prop recipe, rather than the pathogen we introduced.

One microbiota member we recovered from the Prop recipe was a virulent strain of Providencia rettgeri, a known pathogen of Drosophila. Fly species infected by P. rettgeri previously showed a high phylogenetic signal in infection susceptibility, and P. rettgeri has an interaction of critical importance with a single host gene (Diptericin/Dpt, shown in FigC). This microbe, alongside other potential pathobionts (e.g., Serratia, Pseudomonas) likely explains a key part of the susceptibility of different species to infection when flipped on the Prop recipe.

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Mark A. Hanson @hansonmark.bsky.social · 28/11/2025

Now published as version of record at @elife.bsky.social ! Layers of Immunity: Deconstructing the Drosophila effector response. The tools are now deposited in the VDRC (link ⬇️) elifesciences.org/articles/107... shop.vbc.ac.at/vdrc_store/d... #Drosophila #IDsky #SymbioSky #Infection #Immunology

eLife Assessment
This work provides one of the first important attempts to look at Drosophila immune responses against bacterial, viral, and fungal pathogens in a way that combines the roles of four major arms in immunity (Imd signaling, Toll signaling, phagocytosis, and melanization) rather than studying them separately. The findings are compelling and the tools provided can be used as they are, or built upon, in various contexts.

https://doi.org/10.7554/eLife.107030.3.sa0

Figure 3 summarising the survival results from a 14-genotype 25-pathogen panel.

Tracking of mortality and pathogen growth over time, complemented by Figure 5 (not shown) looking at pathogen load upon death.

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Mark A. Hanson @hansonmark.bsky.social · 28/11/2025

In general, let's just stop paying companies that host this BS. Fight the drain of scientific publishing. arxiv.org/abs/2511.04820

An infographic describing the drain of scientific publishing

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Mark A. Hanson @hansonmark.bsky.social · 28/11/2025

Scientific Reports has a ⬆️ Impact Inflation: a very high IF given their citation network (self-citing, citation cartels, etc). They'll even typeset & publish AI slop for a fee! Strain: bit.ly/StrainQSS Strain explorer β: pagoba.shinyapps.io/strain_explo... #SciPub #ResearchIntegrity #AcademicSky

A chart showing the Impact Inflation of Scientific Reports is much higher than the average journal. Biology Open, the "anything technically sound" megajournal of the non-profit Company of Biologists is shown for comparison given these two journals started in 2012 and 2013 respectively. The two have different management strategies: one focuses on profit via immense publication output (SciRep), the other focuses on publishing sound science (BiolOpen).

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Mark A. Hanson @hansonmark.bsky.social · 15/11/2025

WE ARE RECRUITING PHD STUDENTS!!! We have three(!) funded PhD studentships advertising presently. If any of these are of interest, please reach out! Thread below with links to more information on each project. #Drosophila #Evolution #Immunity #SelfishGene #Aphids Thread with links below 🧵 1/4

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Mark A. Hanson @hansonmark.bsky.social · 15/11/2025

We have a funded NERC PhD studentship! Selfish X chromosomes are these bizarre things where males carrying the selfish X suffer from imploding testes. Lots to do in this space, especially in evolutionary, stress, and infection biology. Please share! #PhDchat #AcademicSky @uniexecec.bsky.social

An advertisement for the project Cryptc consequences of a selfish X chromosome. It shows chromosome mapping indicating many inversions, flies with eye colour phenotypes (wild-type brighter than selfish X), and sections of testes that show ordered (wild-type) or deformed structure (selfish X).

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Mark A. Hanson @hansonmark.bsky.social · 11/11/2025

Fundamentally, what we need is leadership. But we break with the chorus of most #OpenScience initiatives here and emphasize very strongly that this leadership must come from funders and institutions. We researchers can support the battle, but we cannot lead the charge. Funders hold the cards. 6/n

The costs of inaction are plain: wasted public funds, lost researcher time, compromised
scientific integrity and eroded public trust. Today, the system rewards commercial publishers
first, and science second. Without bold action from the funders we risk continuing to pour
resources into a system that prioritizes profit over the advancement of scientific knowledge.

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Mark A. Hanson @hansonmark.bsky.social · 11/11/2025

More fundamentally, every active scientist has been brought up in a system where The Drain was already normalized. This system hasn't always existed. For-profit publishers are a recent invention. Their value proposition has always been awful, and now they are actively eroding trust in science. 5/n

2. Stopping the drain
Back in the 1950s, when for-profit journal publishing was just getting going, British scientific
leaders predicted that ‘the moment commercial gain began to dominate this field, the welfare
of the scientific community would suffer’ (1). They were right – and it is past time that we
acted. The first step we must take is to recognize the seriousness of the problems that
scientific publishing’s engagement with for-profit publishing have become.

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Mark A. Hanson @hansonmark.bsky.social · 11/11/2025

The solutions of the past 3 decades have failed to change the incentives of #PublishOrPerish. As a result, researcher funding, time, control, and trust has been lost. The ONE CONSTANT in the wake of the serial crisis, #PlanS and #OpenAccess reform has been publish profit margins. 2/n

A table showing profit margins of major publishers. A snippet of text related to this table is below.

1. The four-fold drain
1.1 Money
Currently, academic publishing is dominated by profit-oriented, multinational companies for
whom scientific knowledge is a commodity to be sold back to the academic community who
created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis,
which collectively generated over US$7.1 billion in revenue from journal publishing in 2024
alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit
margins have always been over 30% in the last five years, and for the largest publisher
(Elsevier) always over 37%.
Against many comparators, across many sectors, scientific publishing is one of the most
consistently profitable industries (Table S1). These financial arrangements make a substantial
difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor &
Francis revenues were generated in North America, meaning that North American
researchers were charged over US$2.27 billion by just two for-profit publishers. The
Canadian research councils and the US National Science Foundation were allocated US$9.3
billion in that year.

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Mark A. Hanson @hansonmark.bsky.social · 11/11/2025

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

A figure detailing the drain on researcher time.

1. The four-fold drain

1.2 Time
The number of papers published each year is growing faster than the scientific workforce,
with the number of papers per researcher almost doubling between 1996 and 2022 (Figure
1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material
has aligned well with the competitive prestige culture in which publications help secure jobs,
grants, promotions, and awards. To the extent that this growth is driven by a pressure for
profit, rather than scholarly imperatives, it distorts the way researchers spend their time.
The publishing system depends on unpaid reviewer labour, estimated to be over 130 million
unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of
peer-review for decades, but the scale of the problem is now worse, with editors reporting
widespread difficulties recruiting reviewers. The growth in publications involves not only the
authors’ time, but that of academic editors and reviewers who are dealing with so many
review demands.
Even more seriously, the imperative to produce ever more articles reshapes the nature of
scientific inquiry. Evidence across multiple fields shows that more papers result in
‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow
progress until one considers how it affects researchers’ time. While rewards remain tied to
volume, prestige, and impact of publications, researchers will be nudged away from riskier,
local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with
limited progress whereas core scholarly practices – such as reading, reflecting and engaging
with others’ contributions – is de-prioritized. What looks like productivity often masks
intellectual exhaustion built on a demoralizing, narrowing scientific vision.

A table of profit margins across industries. The section of text related to this table is below:

1. The four-fold drain
1.1 Money
Currently, academic publishing is dominated by profit-oriented, multinational companies for
whom scientific knowledge is a commodity to be sold back to the academic community who
created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis,
which collectively generated over US$7.1 billion in revenue from journal publishing in 2024
alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit
margins have always been over 30% in the last five years, and for the largest publisher
(Elsevier) always over 37%.
Against many comparators, across many sectors, scientific publishing is one of the most
consistently profitable industries (Table S1). These financial arrangements make a substantial
difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor &
Francis revenues were generated in North America, meaning that North American
researchers were charged over US$2.27 billion by just two for-profit publishers. The
Canadian research councils and the US National Science Foundation were allocated US$9.3
billion in that year.

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Mark A. Hanson @hansonmark.bsky.social · 01/11/2025

Finally, qed hallucinated on me. It helps that this was my own paper, so my response was "I'm... pretty sure I never said that." I'll leave the explanation to the image Alt Text for those who are curious. The main thing is: we never said this. qed massively overextrapolated from what we did. 6/n

The "related claim 1.1" qed made was: "Acetobacter pathogenicity requires systemic infection rather than oral colonization. - No gaps found."

First: nowhere in the main text did we say this. What we said was: "Gnotobiotic association with A. sicerae did not cause mortality, even in AMP14 flies (fig. S6A). However, pricking flies with a needle contaminated with A. sicerae killed AMP14 flies (12, 36), also causing an abdominal bloating phenotype that preceded mortality (shown later)."

What we did in Figure S6 was we mono-associated flies with Acetobacter sicerae and monitored their lifespan. We describe clearly in the figure caption that we made flies germ-free by bleaching, then reared them on antibiotic food, and then fed emerging adults Acetobacter-spiked food to mono-associate them with Acetobacter. We saw no major effects on fly lifespan even out to 40 days.

But to argue that Acetobacter pathgenicity requires systemic infection rather than oral colonization is a massive overreach. First, we never did any sort of force-feeding of repeated inoculations of Acetobacter. Had we done so, I bet the mutant flies would have died faster, if nothing more, because oral infection is just a stochastic route to systemic infection. Second, this phrasing imagines that pathogenicity is the same thing as mortality. We did not measure fitness parameters in mono-associated flies, and we may have found DptB mutants were less fecund, or displayed behavioural defects. The word "virulence" might have been a better choice here... but in general, we did not do a proper test to speak to Acetobacter's virulence during oral infections. What we tested was whether a benign monoassociation (that likely broke down as time went on, as happens in such experiments) led to downstream lifespan effects.

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Mark A. Hanson @hansonmark.bsky.social · 29/10/2025

PhD studentshipship available through @swbiodtp.bsky.social! This project will take advantage of an incredible RNAseq dataset we are generating using 40 species and multiple infection types to learn how immune systems evolve. For more info, see: bit.ly/43zNa20 #Drosophila #Immunity

Advertisement for PhD studentship involving a host-pathogen panel, RNA sequencing, and functional genetics. The aim is to use fly species to learn how immune responses evolve.

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