Mark A. Hanson

@hansonmark.bsky.social

7129 Followers 1149 Following

#NewPI interested in #immune #evolution, host #pathogen interactions, and #ScientificPublishing @ University of Exeter, UK. He/him. 🇨🇦

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."
A speaker in a packed lecture theatre
A photo of the help desk from day 1 with organisers and volunteers standing around getting ready for the day.
A conference speaker is addressing the room with a slide showing housekeeping
https://journals.biologists.com/dev/pages/open-access
Advertisement of the Review Commons process
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.
A citation network profile for International Journal of Molecular Sciences (MDPI) showing that IJMS mainly gets is citations from other MDPI journals.
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.
An image of Ms Frizzle from The Magic School Bus cartoon with the caption "Take chances, make mistakes, get messy."
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.
A diagram showing Drosomycin loss in wood-feeding cockroaches and termites
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.
Drosomycin is found in mantises, cockroaches, two lineages of beetles, a single katydid, a pseudogene in booklice, and an independent long branch of Drosophila
A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insects
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.
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. 🦀
November 01 2024 The strain on scientific publishing Open Access Mark A. HansonCorresponding Author ORCID logo , Pablo Gómez Barreiro ORCID logo , Paolo Crosetto ORCID logo , Dan Brockington ORCID logo Crossmark: Check for Updates Author and Article Information Quantitative Science Studies (2024) 5 (4): 823–843. https://doi.org/10.1162/qss_a_00327 Article history Cite Icon Cite Open the PDFfor in another window Permissions Share Icon Share Views Icon Views Open Menu
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.
A headline from the BBC reads: Trump doubles down on Greenland, saying there is 'no going back'
Delgado jokes that, in the academic world, there is already talk of “MDPI professors,” which refers to those who have risen thanks to CVs based on this type of shoddy work. He notes that Spanish universities have become veritable “factory farms” for insubstantial studies. Delgado and his colleague Alberto Martín have analyzed this change in the behavior of Spanish scientists. Their data shows that, in 2015, barely 0.9% of Spanish production was published in MDPI journals, compared to a 0.6% rate worldwide. Six years later, the percentage in Spain shot up to nearly 15% — double the proportion in the rest of the world. Some universities focus on getting their studies published in MDPI journals, such as the Catholic University of Ávila (71%), Alfonso X el Sabio University (42%), the University of Extremadura (30%) and the Catholic University of Murcia (27%). At the most prestigious university in Spain — the Complutense University of Madrid — the percentage exceeds 12%.
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.
From Abalkina (2023; Learned Publishing). https://onlinelibrary.wiley.com/doi/10.1002/leap.1574
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.
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.
Phylogenetic signal of egg-to-adult development times and body mass of dozens of fly species reared on a common media.
Phylogenetic signal of egg-to-adult development times and body mass of dozens of fly species reared on a common media.
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
An infographic describing the drain of scientific publishing
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).
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).
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.
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.
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 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.
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.
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.
An advertisement for a PhD doing aphid immunity work
A diagram detailing the conservation of Toll and Imd signalling genes across model insect species
Diagrams of fruit fly larvae (left) and adult (right) annotated with genes expressed in different tissues, including male- or female-biased gene expressions.
A wolf spider(?) in a bag of Starlab microtubes.
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.
Myself standing next to my research poster presenting the Layers of Immunity work we recently published in eLife.
Two people dressed in giant fruit fly cloaks
A graphic outlining how the only real difference between a non-profit and for-profit entity is the ability to distribute profits to shareholders.