iiinova — where your digital self keeps evolving

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apaulalm.bsky.social @apaulalm.bsky.social · 16/03/2026

Really happy to see this preprint out on bioRxiv! An exciting project and results, a huge amount of work, and many people involved along the way. Thanks to everyone in Team PATHOCOM. Special thanks to Wei Yuan, Kevin Murray @kdm9.bsky.social, Ilja Bezrukov and Detlef @plantevolution.bsky.social!

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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/03/2026

1/11 🔥 New preprint alert 🔥 We wanted to know what plants in the wild really care about. So we asked them 🎤. Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations” www.biorxiv.org/content/10.6...

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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 28/02/2026

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

github.com

rambaut/figtree

Automatically exported from code.google.com/p/figtree - rambaut/figtree

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Kevin Bird @stairwaytokevin.bsky.social · 16/01/2026

Lmer Fudd be like “it’s wandom effects season”

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Berna Devezer @devezer.bsky.social · 15/01/2026

every big data paper with a bold story that is impossible to comprehend, evaluate, and independently verify reminds me of DOPRA. i've come to increasingly appreciate small, unassuming papers with humble conclusions that you can track word for word, data point by data point, assumption by assumption.

A tweet from Lior Pachter from July 26, 2024: "I think this paper is a Denial of Peer Review Attack (DOPRA). It's kind of like a DoS (denial of service) attack. There is so much data, so many methods, so much code, so many figures, so many panels, so much supplement, so much text, that it is overwhelming. 18/"

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Heng Li @lh3lh3.bsky.social · 06/01/2026

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

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Samuel Aroney @aroneys.bsky.social · 13/11/2025

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

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The Custom-Lab Institute @custom-lab.bsky.social · 18/10/2025

This is how our customizable powder and seed dispenser for 2 ml tubes works. Check it our here: custom-lab.de/products/48-...

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 18/10/2025

When the Hapsburgs find out corn does inbreeding better they’re really gonna take it on the chin.

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Meredith Whittaker @meredithmeredith.bsky.social · 06/10/2025

📣 Germany's close to reversing its opposition to mass surveillance & private message scanning, & backing the Chat Control bill. This could end private comms-& Signal-in the EU. Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.

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Stuart McDaniel @stuartmcdaniel.bsky.social · 09/10/2025

Lingua wanka is a hilarious moniker for scientific writing

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Malick Mbengue @malick-mbengue.bsky.social · 09/10/2025

I wished I could have written something like this. Rude, fun and meaningful. static1.squarespace.com/static/686d9...

static1.squarespace.com

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Philipp Bayer @philippbayer.bsky.social · 01/10/2025

'In Australia we are seeing the results of running universities like businesses without adequate governance: wage theft from staff, fee theft from students, and the academic equivalent of shrinkflation.'

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Dean Nicolle @deannicolle1.bsky.social · 30/09/2025

Less than 2 weeks until our arboretum open days! Here's a few of the eucalypts flowering at the moment. These free open days only occur biannually. Currency Creek Arboretum is about an hour's drive south of Adelaide in SA. Open details here: www.dn.com.au/Currency_Cre...

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Carl T. Bergstrom @carlbergstrom.com · 27/09/2025

Left unchecked, openAI and other infotech providers will destroy any remnants of the American education system that manage to escape the Trump administration. Read the full thread.

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Honour McCann @honour.bsky.social · 18/09/2025

There’s a leak - and a conceptual artist - at the Max Planck 👌

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samuel mehr @mehr.nz · 18/09/2025

new zealand government reaching new heights of stupidity next year our public dollars will go more to AI grants ($70 million) than all investigator-initiated basic science combined ($56 million in the Marsden fund)

Reti earmarks $70m of new agency's budget for AI commercialisation grants

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Heng Li @lh3lh3.bsky.social · 12/09/2025

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

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Randall Munroe @xkcd.com · 11/09/2025

Biology Department xkcd.com/3140/

Comic. [Building with large sign in front of it[ SIGN: Welcome to the *Biology Department* It has been [changeable sign: 3] days since we discovered something existentially horrifying about bugs that makes you question your whole reality

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K.D. Murray @kdm9.bsky.social · 11/09/2025

If you haven't seen @shenwei356.bsky.social's other near-magical tools (csvtk, taxonkit, seqkit; all in go IIRC), absolutely check them out. Top stuff!

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M Hobart @mhobart.bsky.social · 11/09/2025

Must read, and not just for higher ed folks: anyone concerned about education and people’s ability to think rigorously and critically should read this manifesto.

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Ben Abraham @afterclimate.com.au · 11/09/2025

Absolutely fantastic piece on the interfaces between climate risk and insurance in the Polycrisis newsletter today, by @70sbachchan.bsky.social and @katemac.bsky.social Not a doom loop, but “communities of fate” and the moral economy of the welfare state. www.phenomenalworld.org/analysis/ins...

phenomenalworld.org

Insurance in the Polycrisis | Kate Mackenzie & Tim Sahay

The future is triage on an uninsurable earth.

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Zamin Iqbal @zaminiqbal.bsky.social · 05/09/2025

Ok this is mad "...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste" www.nature.com/articles/s41...

nature.com

One mother for two species via obligate cross-species cloning in ants - Nature

In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

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Philipp Bayer @philippbayer.bsky.social · 04/09/2025

I LOVE that you can see pur Cocos Keeling voyage eDNA data on this figure. It's that straight line going north-west from Western Australia/Perth!

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/09/2025

Save the date! #PEQG26 June 9-12 2026 in Asilomar, CA. Happens only every 2yrs, but is my favorite conference. Full website coming soon, and registration and abstract submission opens November 14, but I'm allowed to tease that keynotes will be @jnovembre.bsky.social @jennytung.bsky.social and me!

genetics-gsa.org

Homepage - Population, Evolutionary, and Quantitative Genetics Conference

Visit our website to learn more.

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Julie Blommaert @drjulieb.bsky.social · 02/09/2025

Omg nerd day made

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naturepoker @binomicalabs.org · 26/08/2025

I feel like there should be a "median rent in the area" based guidelines for conference registration fees. If your 3 day academic conference costs more than a median whole month's rent to live there, maybe something can be improved 🫠

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Elisabeth Bik @elisabethbik.bsky.social · 04/08/2025

Fantastic new paper by @reeserichardson.bsky.social et al. An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors. The number of fraudulent publications grows at a rate far outpacing that of legitimate science. www.pnas.org/doi/10.1073/...

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 11/08/2025

SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes www.biorxiv.org/content/10.1101/202…

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K.D. Murray @kdm9.bsky.social · 14/08/2025

Feel free to ask any q's here

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K.D. Murray @kdm9.bsky.social · 14/08/2025

This is obviously a colossal group effort, led by Luisa Teasdale (not on bsky) and supervised by @coevolution.bsky.social and @plantevolution.bsky.social, with very valuable contributions from @aconga.bsky.social, @hajkdrost.bsky.social and many more not on bsky

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K.D. Murray @kdm9.bsky.social · 14/08/2025

We also highlight the importance of using multiple independent measures of NLR diversity, including expression, structural, sequence, and domain diversity, as each tells a different story of NLR diversification.

(A) Variation of OG70 diversity across different axes. If not stated otherwise, always for all OG70 members across all accessions (A). π, mean nucleotide pairwise distance; entropy, mean Shannon entropy of column states within an amino acid multiple sequence alignment, excluding positions with fewer than 10 non-gap characters; local complexity, mean pangenome local complexity; severe mutations, sum of allele frequencies of mutations with severe predicted consequences among the 1,001 Genomes collection for OG70s present in at9852; copies, mean number of copies per accession; domains, mean Simpson’s index of diversity of NLR-associated domains detected by NLRtracker; isoforms, mean of Simpson’s index of diversity of isoform variation affecting the open reading frame of each transcript; gene-body methylation, mean percentage of methylated CpG sites. Enlarged in Figure S4, and Figures S5–S8 explore each individual axis in more detail.

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K.D. Murray @kdm9.bsky.social · 14/08/2025

We show that pangenome graphs provide a flexible way to define the context within which NLR evolution occurs, and that graph metrics capture diversity in both sequence and structure, and show that such diversity is centered on NLRs themselves

The neighborhood containing RPP4/RPP5 is among the most complex, and the highly elevated local complexity is focused on NLR genes and pseudogenes. Each per-accession track consists of both a trace of local pangenomic complexity (above the abscissae), and a representation of the gene annotation (below the abscissae). Individuals show extreme haplotypic diversity of NLRs, which is reflected in highly elevated local complexity focused on NLR genes and their immediate surrounds, while TE genes or other protein-coding genes show little elevation in complexity above the genome background. For an enlarged version contrasting two nearby neighborhoods, please see Figure S3.

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K.D. Murray @kdm9.bsky.social · 14/08/2025

Long story short: we assemble 17 representative Arabidopsis thaliana genomes, exhaustively annotate NLRs with long read evidence & manual curation, and assay many measures of NLR diversity.

(A and B) Our 17 accessions (squares) are broadly representative of both the geographic and population genetic distributions of the broader 1,001 Genomes collection (circles23); inset shows the UMAP embedding of 17 accessions in the co-ancestry space of all 1,135 accessions (adapted from Shirsekar et al.21). Colors in (A) and (B) represent the haplotype sharing groups from Shirsekar et al.21; samples in gray represent the three haplotype sharing groups not represented by our 17 accessions and their corresponding selected accession (see E).
(C) Phenotypic diversity of 17 accessions (rows) with respect to the oomycete pathogen Hyaloperonospora arabidopsidis (Har; columns), with resistant phenotypes denoted as black. 104 Har accessions were collected across Europe, as described in STAR Methods.
(D) Universal, pangenome-wide syntenic anchors define NLR neighborhoods.
(E) Representative example of an NLR neighborhood, highlighting accurate delineation of the borders of NLR-containing variable regions, regardless of structural or presence/absence variation. Black bars indicate pangenomic neighborhoods, syntenic anchors in pink. A fixed-sized window approach centered on a focal NLR (in yellow) would produce a very different outcome. Note accession codes used in this paper of the form atNNNN represent Arabidopsis ecotype IDs, see Alonso-Blanco et al.23 and Table S1.

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Philipp Bayer @philippbayer.bsky.social · 14/08/2025

'And the need for grants long ago ceased to prioritize scientific questions, per se, supplanting them with a basic and insatiable institutional hunger for money as an end in itself (got to feed the beast!). This is both demoralizing and demotivating. ' 💔I feel this very much (and that's why I left)

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Carl T. Bergstrom @carlbergstrom.com · 05/08/2025

"With [some AI bullshit] you can go from a rough idea to a structured draft — in just 3 minutes" We're so cooked.

No more endless academic paper searches!

Writing a research paper used to take weeks. With tlooto AI, you can go from a rough idea to a structure draft -- in just 3 minutes.

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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 02/08/2025

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab. Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes. #plantscience www.biorxiv.org/content/10.1...

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David Ho @davidho.bsky.social · 29/07/2025

WTF? I was quoted in this story but I have never spoken to the reporter nor would I have said those things. Is everything just generated by LLMs these days? cosmosmagazine.com/earth/oceans...

To whom it may concern, and it should concern the editor:

I was quoted in your publication:

https://cosmosmagazine.com/earth/oceans/can-we-engineer-our-way-out-of-ocean-acidification/

Still, others aren't convinced that good intentions are enough. Dr. David Ho, Professor of Oceanography at University of Hawaii at Manoa, a cofounder and the Chief Science Officer of |C|Worthy, a non-profit that works on verifying ocean-based carbon dioxide removal, believes carbon removal efforts like ocean alkalinity enhancement shouldn't be left solely in the hands of private companies.

"They have no way to prove that what they're doing is effective - that's a big problem," Dr Ho said.

The crux of the dilemma, he explains, is that we are fighting a planetary-scale problem, but are doing it with tools that are still being built and tested. Geoengineering is not inherently good or bad, but it is inherently powerful. And power, especially when exercised in ecosystems as complex and fragile as the ocean, must be handled with caution.
However, I have never spoken to your reporter, nor would I have said those things. I would like you to remove my quote from your story, and issue a public correction and apology. Furthermore, you should look into whether the other parts of the article are also factually correct. Thanks.

d.

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Nina Jankowicz @ninajankowicz.com · 23/07/2025

A lot of you had questions so I wrote about what I think happened here! Behold: wiczipedia.substack.com/p/i-got-trap...

wiczipedia.substack.com

I Got Trapped in the AI Ouroboros

A foreign news outlet fabricated a quote from me. LLMs have already picked it up.

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