Andres Legarra

The strain on scientific publishing Abstract. Scientists are increasingly overwhelmed by the volume of articles being published. The total number of articles indexed in Scopus and Web of Science has grown exponentially in recent years; ...

In the strain on scientific publishing, we showed that total publications have grown out of control. A huge part of that was guest edited special issues by groups like #MDPI and #Frontiers.

This ongoing practice is the largest delegation of editorial power academia has ever seen.

2/n

A more hands-on approach could start with patchy, messy data and what we can do (or not) with it. This is what most practitioners face, they are confronted with the problem before having any clue on the solution. Or the solution was never programmed, and go modify someone else's code...

The 5 stages of the ‘enshittification’ of academic publishing Academic publishing now shows the same decline that has hit social media and online marketplaces.

Reading “The 5 stages of the ‘enshittification’ of academic publishing”
theconversation.com/the-5-stages...

nice, this is similar thinking to @daniel-innerarity.bsky.social

there's snow inside the room. A cup has a flame. Tissue would burn.

This certainly aligns with my perceptions after talking with people who use these tools.

Which Kind of Science Reform What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

Can you hit repost? Marjorie Taylor Greene doesn't want you to know the name of her opponent but will try every desperate attempt to save her seat.

My name is Shawn Harris. I am a Democrat, husband, father, Retired Brigadier General, farmer, and I'm running against MTG. Can you share and follow me?

A photo of Watterson at his drawing table.

A panel of Calvin and Hobbes riding their radio flyer red wagon.

Happy birthday to Bill Watterson, the creator of Calvin and Hobbes! Born on July 5, 1958.

Springer Nature Discovers MDPI – The Strain on Scientific Publishing Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro

Springer-Nature launched a series of "Discover" journals that closely mimic MDPI titles -- sharing *identical* journal names, and likely similar business model.

What is going on, and why researcher will - as always - fall for it?

A 🧵

the-strain-on-scientific-publishing.github.io/website/post...

the talks from Ignacy Misztal's symposium at UGA on the future of Animal Breeding & Genetics are there: nce.ads.uga.edu/wiki/doku.ph...

A Sting Inside a Papermill “It’s clear that any academically corrupt individual — particularly one with editorial connections — could easily “place” dozens of these Anzen products into indexed journals and collect a ha…

This is a must-read. Csaba Szabó, the author of Unreliable, was approached by a paper mill, and he decided to conduct a sting operation. He documented how paper mills operate.

forbetterscience.com/2025/05/19/a...

I enjoyed this article a lot. I'm hoping the Moneyball analogy will finally get dairy cow genetics mentioned on an episode of the @shutdownfullcast.bsky.social.

"sic transit gloria mundi"

Assistant Professor in Quantitative Genetics - IRBV is located in the Montreal Botanical Garden, one of the largest in North America. job with Université de Montréal / IRBV | 12835129 Tenure-track Assistant Professor position to develop a research program related to quantitative genetics of plants or plant-associated systems.

Sharing for a friend.
Job opening, Université de Montréal, Institut de recherche en biologie végétale (IRBV).
Assistant Prof in Quantitative Genetics. #PlantSci
www.nature.com/naturecareer...
Apply by March 9.
Should speak French or be willing to learn!

Leveraging ancestral recombination graphs for quantitative genetic analysis of rice yield in indica and japonica subspecies Rice (Oryza sativa L.) has two main subspecies, indica and japonica , which coexist in many regions but are often treated separately during breeding. Combining both subspecies in quantitative genetic ...

New pre-print: “Leveraging ancestral recombination graphs for quantitative genetic analysis of rice yield in indica and japonica subspecies” by Ines Rebollo, Jana Obsteter, Daniel Tolhurst, Juan Rosas, and me www.biorxiv.org/content/10.1...

Also worth reading the reviews of the original article. Obviously these reflect past versions of the article. It would be interesting to read the first submission to see how extreme a position the first submission took.

static-content.springer.com/esm/art%3A10...

Genome Editing and Eugenics The one hundred and third Take:

Thoughtful piece by Greg Gibson pushing strongly back on the "Heritable polygenic editing" article
genomestake.substack.com/p/genome-edi...

As part of a conference on the topic I wrote a commentary on why I was quite pessimistic about this approach, echoing some of the concerns lifted here. The proceedings are online: www.nibjournal.ed.ac.uk/article/view...

More false expectations created. More public money wasted.

One reason is that reviewers and editor for journals do a good job. I've seen quite a few preprints (including mine) improve *a lot* and remove mistakes after revision. The same process can catch fraud.

Tools to refine unknown parent groups definition Unknown Parent Groups model missing parentships according to breed, year, and pathway of selection. Genetic evaluations need a sensible definition of rules to form Unknown Parent Groups to ensure its accurate estimation. With more complex evaluations, there is a need for systematic rules to form Unknown Parent Groups. We propose several methods to ascertain the informativity and to join consecutive Unknown Parent Groups within breed and pathway. First, a pseudo-count of records based on descendants with record can be easily computed from a pedigree and a list of animals in records, by propagating fractions of one from the flagged animals to ancestors through the pedigree, from youngest to oldest.

We tried to solve a 40-year old question: how to define Unknown Parent Groups?
www.journalofdairyscience.org/article/S002...
and the missing Appendix (with actual code !):
doi.org/10.6084/m9.f...

Cassava Sciences Topline Phase 3 Data Did Not Meet Co-Primary Endpoints Simufilam did not show a significant reduction in cognitive or functional decline versus placebo in patients with mild-to-moderate Alzheimer’s disease in...

Breaking:
Cassava Sciences Topline Phase 3 Data Did Not Meet Co-Primary Endpoints

$SAVA CEO: "(T)he loss of cognition in the placebo group was less pronounced than ... in other placebo-controlled studies in AD. We are working to understand this better".

www.globenewswire.com/news-release...

Unearthed university investigation found research ethics failings at French medical institute Studies conducted by Didier Raoult and colleagues flouted French and international ethical standards, report concludes

Quand Didier Raoult est dans le journal *Science* ce n'est pas en tant qu'auteur, c'est en tant que sujet de honte de la recherche française.

#JeSuisUnGrandChercheur

www.science.org/content/arti...

quand en France on arretera de penser que la science est fait *que* par des "Pasteur"

28th retraction for the IHU.
24th for Didier Raoult.
doi.org/10.1186/s128...

in one paper we compared "per farm" weights with average weights and genetic gains were nearly identical: doi: 10.1017/S1751731107657814

agreed. What one can try is to show that very crude weights are much better than just improving milk or milk+repro or desired gains or whatever

you may think in Pythagoras theorem, if you select only for milk you gain 1, if you select only for repro you gain 1, if you select both you gain 0.71 in each of them (or something like that) but 1.41 overall

"too many traits" is true in the sense that if you improve 2 traits simultaneously you may have smaller gains in both than improving them alone. But that will make you loose money.