Mark A. Hanson
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hansonmark.bsky.social
Mark A. Hanson
@hansonmark.bsky.social
6.7K followers 1.1K following 1.7K posts
New PI interested in #immune #evolution, host #pathogen interactions, and #ScientificPublishing @ University of Exeter, UK. He/him.

#immunity #infection #antimicrobialpeptides #microbiome #Drosophila #AcademicSky #AcademicChatter #OpenScience 🇨🇦
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hansonmark.bsky.social
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
November 15, 2025 at 3:35 PM
hansonmark.bsky.social
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).
November 15, 2025 at 3:02 PM
hansonmark.bsky.social
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.
November 11, 2025 at 11:52 AM
hansonmark.bsky.social
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.
November 11, 2025 at 11:52 AM
hansonmark.bsky.social
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.
November 11, 2025 at 11:52 AM
hansonmark.bsky.social
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 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. 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. 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.
November 11, 2025 at 11:52 AM
hansonmark.bsky.social
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.
November 1, 2025 at 12:15 PM
hansonmark.bsky.social
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.
October 29, 2025 at 4:08 PM
hansonmark.bsky.social
PhD studentship for interested chinese nationals funded by the China Scholarship Council!

Come work with us to investigate how innate immunity works in an important agricultural pest, and disentangle how the immune system evolves. 🇬🇧🇨🇳

For more info, see: bit.ly/4ntrsEe
#Drosophila #Aphid #Immunity
An advertisement for a PhD doing aphid immunity work
October 28, 2025 at 1:44 PM
hansonmark.bsky.social
Can download Hanson and Hedelin (2025) here if of interest: mahansonresearch.weebly.com/uploads/1/2/...

I apologise it's paywalled. It is something I won't be doing again so help me. But if you are interested in #InsectImmunity in general, this is our primer for #ImmuneEvolution beyond #Drosophila
A diagram detailing the conservation of Toll and Imd signalling genes across model insect species An overview of antimicrobial peptide types, including examples like various G-rich peptides that increasingly look like a pore if extended long enough. Also peptides like Apidaecin or Hymenoptaecin which are encoded as polypeptide precursors, and show multiple copies of the same peptide interspersed by furin cleavage sites and dipeptidylpeptidase motifs. A summary table of what is known of Toll and Imd signalling specificity to different microbial elicitors across diferent insects. Specific genes and their strengths of induction are annotated, alongside key references.
October 24, 2025 at 4:26 PM
hansonmark.bsky.social
Bizarre that our 2020 #Drosophila #AMP review already feels out of date.

Thanks to #AnnualReviews to cover the many updates in the field and present a much more complete picture of the diversity, mechanisms, topics, of fly immunity re: host defence peptides.

www.annualreviews.org/content/jour...
Diagrams of fruit fly larvae (left) and adult (right) annotated with genes expressed in different tissues, including male- or female-biased gene expressions. A diagram providing an overview of the regulation of antimicrobial peptide and other host effector peptides by Toll and Imd signalling, alongside diagrams showing the diversity of the peptides. A summary table illustrating sequence features common to antimicrobial peptides, and a summary table of gene families. A diagram giving a model for the mechanisms of antimicrobial peptide and host defence peptide actions in killing microbial cells, including precise mechanisms, broader host-pathogen relationships, and non-microbicidal roles of these peptides in protecting the host.
October 24, 2025 at 12:05 PM
hansonmark.bsky.social
A zoom in on this trident/Y-shaped branching of optic neurons(?)
October 21, 2025 at 2:34 PM
hansonmark.bsky.social
Hey #Drosophila: need to dissect and look a bit more closely, but do these puncta seem like an obvious pattern for a set of nerves, or resemble some sort of expression pattern in the brain (especially looking at the sort of Y-shape near the eye). Also thorax?
GenesOfInterest-GAL4>mCD8::RFP here 🔬
October 21, 2025 at 10:57 AM
hansonmark.bsky.social
A new one for the #NewPI feed. My lab member came in saying "Listen, I can deal with spiders. But this one is too big, and too personal."

All the tubes in the bag were pre-labelled. Henrique needed to go.

Thank you for your service guarding our precious tubes Henrique. 🫡
A wolf spider(?) in a bag of Starlab microtubes.
October 13, 2025 at 9:18 PM
hansonmark.bsky.social
It would be unfeasible to rear only the flies prescribed by power analyses (which can be flawed..).
The power of flies is we can do anything we want without thought for the ethics (see alt text). Not because we're amoral, but because we long had this convo & realised its irrelevant to our work..
2/2
Pictured: Shine-GAL4. An image of a fruit fly has been activated genetically on the eye of a fruit fly. Each dot is a cell expressing a cyan fluorescent protein(?). The precision of this cell pattern can be achieved because only cells exposed to certain wavelengths of light turn on/off gene expression. The utility of this tool is you can turn any gene on/off with the same light-based activation. You can even introduce genes (eg human cancer oncogenes) into the fly in tissue-specific ways. Or you can dissect the way neurons connect and mediate behaviour. Now imagine that boundless potential and multiply it by ~1000 similarly precise tools for gene expression, and you begin* to get a sense of why we use flies for genetic research. Their value as tools for biological study dwarfs the insignificant value one might ascribe to their individual 60-day simple lives by multiple, multiple orders of magnitude. ~1000 might be an underrepresentation by an order of magnitude itself, to be honest... it depends how nitpicky I might want to be.
October 6, 2025 at 11:31 PM
hansonmark.bsky.social
So nice to see everyone and meet many new faces at #EDRC2025! Possibly new collaborators, great sponsors, and it is so good to see the community holding strong. 🪰

I am sure next time will be a Bonn voyage! 😉
#Drosophila
Myself standing next to my research poster presenting the Layers of Immunity work we recently published in eLife. Two people dressed as giant fruit flies.
September 30, 2025 at 10:14 AM
hansonmark.bsky.social
When at the #EDRC2025
Two people dressed in giant fruit fly cloaks Two people dressed in giant fruit fly cloaks
September 25, 2025 at 2:28 PM
hansonmark.bsky.social
Excited for the #EDRC #EDRC2025 in Alicante. But first, some cats from the Castillo de San Fernando
September 24, 2025 at 12:04 PM
hansonmark.bsky.social
The other reason why is obvious: boy would that piss off for-profit publishers. They'd deride the decision as peurile and unhelpful.

Good news guys: if you're in it for the ❤️ of science, just open non-profit journals. If we have to publish in non-profits, that's not our problem, it's yours.

5/n
A graphic outlining how the only real difference between a non-profit and for-profit entity is the ability to distribute profits to shareholders.
August 4, 2025 at 8:10 AM
hansonmark.bsky.social
So why haven't we done this yet?

Scientists are stuck in the #PublishOrPerish rat race 🐀. It's tempting to go to the journal with the most prestige that will publish your paper.

Fixing that is a collective action problem. i.e. impossible. But FYI, non-profit journals have high IFs too guys!

4/n
The Publish or Perish Game. A real board game.
August 4, 2025 at 8:10 AM
hansonmark.bsky.social
The Gates foundation already requires all researchers to preprint all work. Unis require all research to be uploaded to their Green OA repositories. Just take the extra step guys...

It will take courage. It will demand leadership. But it's actually a really easy and self-explanatory policy.

3/n
Gates Foundation 2025 Open Access Policy Preprint Guide HOW TO POST A PREPRINT EFFECTIVE JANUARY 1ST, 2025, ALL GRANTEES ARE REQUIRED TO POST THEIR FUNDED MANUSCRIPT AS A PREPRINT IN A RECOGNIZED PREPRINT SERVER.
August 4, 2025 at 8:10 AM
hansonmark.bsky.social
Ah right. Forgot this was also somewhat directly in the article, which I broadly agree with. Though I think people do care about the scientific record!

www.experimental-history.com/p/science-is...
CHEATERS SOMETIMES WIN AND THAT'S OKAY I think there are two reasons why scientists act like science is a weak-link problem. The first reason is fear. Competition for academic jobs, grants, and space in prestigious journals is more cutthroat than ever. When a single member of a grant panel, hiring committee, or editorial board can tank your career, you better stick to low-risk ideas. That's fine when we're trying to keep beetles out of asparagus, but it's not fine when we're trying to discover fundamental truths about the world. (See also: Grant funding is broken. Here's how to fix it.) The second reason is status. I've talked to a lot of folks since I published The rise and fall of peer review and got a lot of comments, and I've realized that when scientists tell me, "We need to prevent bad research from being published!" they often mean, "We need to prevent people from gaining academic status that they don't deserve!" That is, to them, the problem with bad research isn't really that it distorts the scientific record. The problem with bad research is that it's cheating. I get that. It's maddening to watch someone get ahead using shady tactics, and it might seem like the solution is to tighten the rules so we catch more of the cheaters. But that's weak-link thinking. The real solution is to care less about the hierarchy. If you spend your life yelling at bad scientists, you'll make yourself hoarse. If you spend your life trying to do great science, you might forever change the world for the better, which seems like a better use of time.
August 3, 2025 at 7:30 AM
hansonmark.bsky.social
Entrenching systems that allow people to be initially rewarded for corrupting the literature, and later reward people for catching them, spends time and effort on an economy I'd rather never existed. So it's rather hard for me to celebrate it.

A bit reminiscent of views on repro in screenshot. 2/2
A snippet from "Science is a Strong Link Problem": (Peer review also does a pretty bad job at stamping out bad research too, oops.) Giant replication projects—like this one, this one, this one, this one, and this one-also only make sense for weak-link problems. There's no point in picking some studies that are convenient to replicate, doing 'em over, and reporting "only 36% of them replicate!" In a strong-link situation, most studies don't matter. To borrow the words of a wise colleague: "What do I care if it happened a second time? I didn't care when it happened the first time!"
August 3, 2025 at 7:18 AM
hansonmark.bsky.social
when I repost myself
The white ninja meme, "C'mon do something."
July 22, 2025 at 9:48 AM
hansonmark.bsky.social
CONCLUSIONS:

To promote the best science being done, we need to look at the incentives of science publishing and funding. Long-term funding produces better science. Short-term and topical agendas encourages irreproducibility.

Funding model organisms generates science we can build on! 🪰🪱🦠🐠🐁🐸

6/6 🧵
A lovely graphic from The Allied Genetics Conference 2020 depicting the many model organisms that contribute to our understanding of science. https://genetics-gsa.org/drosophila-2025/professional-development/careers-at-tagc/
July 10, 2025 at 8:23 AM