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Martin Johnsson

@mrtnj.bsky.social

600 followers 1.3K following 130 posts

PhD in genetics. Associate professor (docent) at the Swedish University of Agricultural Sciences (SLU), Uppsala. The Jar Jar Binks of animal genomics. Writes in English, svenska & gruntings. he/him

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Reposted by Martin Johnsson

bioRxiv Genetics @biorxiv-genetic.bsky.social · 23d

When large-effect damaging alleles enter small populations https://www.biorxiv.org/content/10.1101/2025.09.11.675554v1

Martin Johnsson @mrtnj.bsky.social · 9d

Researcher day with the Beijer laboratories. Here: Elin Hernlund, my fellow Beijer researcher in the laboratory for animal science, talking about her models of shape and posture of domestic animals.

Elin Hernlund presenting in front of a slide that shows 3D models of a human, a horse, a dog and a cow.

Martin Johnsson @mrtnj.bsky.social · 11d

(It doesn't help that Prisma's import publications function has been broken since what, 2019? Please, pretty please with sugar on top, let us enter the publication list as a pdf like VR does.)

Martin Johnsson @mrtnj.bsky.social · 11d

This year, the profile was cut down to a small text box, and we're back to list of 10 publications to be entered in Prisma. Gone are the ambitions to include more stuff than publications; it's now not even clear whether preprints count.

Martin Johnsson @mrtnj.bsky.social · 11d

Last year's call introduced the academic profile for describing the merits of applicants in a broader way than before, including a wider understanding of an academic contribution than just a publication list. It came with a prescribed template, which was unfortunately quite awkward and bad.

Martin Johnsson @mrtnj.bsky.social · 11d

The new format for the Formas Explore 2025 call--I say it's an improvement overall. Fewer boxes to fill in, and in the end a bit more space for implementation and references, so one doesn't have to hunt characters as much.

The new format of the academic profile is a step backwards, though.

Martin Johnsson @mrtnj.bsky.social · 12d

On that note, it's time to seriously learn Bibtex, so I can let go of the Zotero plugin and rid myself of Microsoft Word.

Martin Johnsson @mrtnj.bsky.social · 12d

Here's one powerful opening sentence:

"Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media."

Olivia Guest · Ολίβια Γκεστ @olivia.science · Sep 6

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n

Abstract: Under the banner of progress, products have been uncritically adopted or
even imposed on users — in past centuries with tobacco and combustion engines, and in
the 21st with social media. For these collective blunders, we now regret our involvement or
apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we
are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not
considered a valid position to reject AI technologies in our teaching and research. This
is why in June 2025, we co-authored an Open Letter calling on our employers to reverse
and rethink their stance on uncritically adopting AI technologies. In this position piece,
we expound on why universities must take their role seriously toa) counter the technology
industry’s marketing, hype, and harm; and to b) safeguard higher education, critical
thinking, expertise, academic freedom, and scientific integrity. We include pointers to
relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI
(black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are
in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are
both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and
Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf.
Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al.
2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms
are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

Martin Johnsson @mrtnj.bsky.social · 16d

Sad but probably justified! :(

My next lecture in the course is QTL, so it's still there, but it has morphed, and a lot of it is about molecular trait mapping, eQTL and that stuff now.

Martin Johnsson @mrtnj.bsky.social · 16d

Researchers should feel this often in contact with the literature. "There are tons of research about this ... but to different ends, and from other perspectives."

Martin Johnsson @mrtnj.bsky.social · 17d

She illustrated this with an anecdote about getting to know roaches (the fishes), wanting to know about their behaviour and learning, and going to the library to find only books about catching and cooking fish.

Martin Johnsson @mrtnj.bsky.social · 17d

Then philospher Jonna Bornemark talked about a model of knowledge (by her and Nicolaus Cusanus), going from sensations and drives through imagination, instrumental knowledge, intellectual critique, the absence of knowledge (the highest form of knowledge) and then back around again.

Martin Johnsson @mrtnj.bsky.social · 17d

This course (Genome Analysis for MSc students) is always fun. When I came in to talk GWAS, my colleague had this on the board and a linkage map of the chicken Z chromosome on the projector. :)

Martin Johnsson @mrtnj.bsky.social · 17d

Vice Chancellor Maria Knutson Wedel, SLU, opening the first "studium generale", a series of meetings on knowledge--I suppose--and reflection.

Maria Knutson Wedel talking in front of a audience of SLU colleagues and students.

Martin Johnsson @mrtnj.bsky.social · 17d

Circuits and microsats on the whiteboard.

A whiteboard with DNA sequence of microsatellites and a circuit diagram, half erased, on top of each other.

Reposted by Martin Johnsson

Suvi Mäkeläinen @suvimake.bsky.social · 28d

Genetic variation is the key to species resilience, enabling populations to adapt to changing environmental conditions. Our research group will take a deep dive into the variation present in the genes encoding for central roles of the immune system. www.slu.se/en/news/2025...

The price of perfection: Opting out of variety - a danger to animal immunity and survival | slu.se

For thousands of years, humans have been controlling the breeding of dogs, horses and farm animals. Despite the benefits, this has led to unexpectedly high risks for the animals. With knowledge from r...

Reposted by Martin Johnsson

Jarrett Byrnes @jebyrnes.bsky.social · 28d

Me right now reading “It is also the 18th anniversary of ggplot2…”

Martin Johnsson @mrtnj.bsky.social · Aug 30

My favourite paper from the dissertation was this one, on the NK Treadmill model: direct.mit.edu/artl/article...

Continuous Evolution in the NK Treadmill Model

Abstract. The NK fitness landscape is a well-known model with which to study evolutionary dynamics in landscapes of different ruggedness. However, the model is static, and genomes are typically small,...

Martin Johnsson @mrtnj.bsky.social · Aug 30

And there are examples of using NK-style models for plant breeding, for instance: onlinelibrary.wiley.com/doi/10.1002/...

The E(NK) model: Extending the NK model to incorporate gene‐by‐environment interactions and epistasis for diploid genomes

The haploid NK model developed by Kauffman can be extended to diploid genomes and to incorporate gene-by-environment interaction effects in combination with epistasis. To provide the flexibility to i...

onlinelibrary.wiley.com

Martin Johnsson @mrtnj.bsky.social · Aug 30

It's funny how you're sometimes the most computer-minded among biologists and sometimes the most biology-brained among computer people. I feel I might have been on the latter pole yesterday, trying to drag the discussion down into the mud of application.

Martin Johnsson @mrtnj.bsky.social · Aug 30

Going home from Borlänge and Högskolan Dalarna after Priyanka Mehra's PhD defence--an exciting full day of theoretical genetics and computational modelling.

du.diva-portal.org/smash/record...

Blue skies over Borlänge, and a hydroelectric dam.

Reposted by Martin Johnsson

Carl T. Bergstrom @carlbergstrom.com · Aug 23

In 25 years, every business school in the country will be doing case studies about how a long defunct company known as “Google” once had an unbeatable lock on online information retrieval and then started doing shit like this.

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Martin Johnsson @mrtnj.bsky.social · Aug 23

I saw great uses of genetic simulation in combination with data, but I'd love to see even more of it.

Martin Johnsson @mrtnj.bsky.social · Aug 23

I had pretty much given up on measuring load from sequence variants, because predictions of variant function are so dodgy. Apparently in evolution and conservation genetics, people use GERP and SIFT without worrying about their accuracy. I'm concerned.

Martin Johnsson @mrtnj.bsky.social · Aug 23

Some subjective impressions of trends from #eseb2025.

Genomic inbreeding through F_ROH has made it big. As it should.

Genomic prediction hasn't. Perhaps single step would help bridge the gap between pedigree and genotype datasets.

Selection mapping has calmed down, but I still saw some Fst scans.