“A beloved, useful, free website, run carefully by a competent, honest person for nearly thirty years, was crushed between two features of the new AI economy.” (AI bots and prediction market dipshits.) [stephenfollows.com]

What just happened to TheNumbers.com should worry us all

If you work in or around the film industry, there is a decent chance you have used the work of The Numbers this month, whether you realise it or not.

stephenfollows.com

"The dream of every cell is to become two cells." - François Jacob, paraphrasing Jacques Monod.

1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...

I am recruiting graduate students to my genomics-focused lab in EEB at Illinois Urbana-Champaign. Please spread the word if you know any students with an interest in a computational focus to genomics research! evol.mcmaster.ca/brian/evoldi...

Our EEB department at the University of Illinois at Urbana-Champaign is hiring an assistant professor in evo-devo. See go.illinois.edu/EEBAsstProf for details. Please share!

“Aware of my inability to detect AI use with certainty, I implored the students: please don’t use AI. It’s terrible for you. It’s terrible for me, a dystopian experience of spending weeks giving detailed constructive feedback to a machine.” www.forkingpaths.co/p/the-death-...

The Death of the Student Essay—and the Future of Cognition

One professor's reflections on the end of an era, as AI tools such as ChatGPT have murdered the student essay (RIP). Here's why that threatens the future of human cognition—and how to save ourselves.

forkingpaths.co

Finals start tomorrow here at UIUC. You may have seen the NYMag article outlining how pervasive AI has become in student course work, how it's degrading the learning experience. I wrestled with it all semester in my own course. But OpenAI knows the effects, and they known exactly what they are doing

We will greatly miss our friend and longtime colleague Kevin Drum, as will all who knew him and his tremendous body of work. I had the privilege of editing Kevin for a spell, and I learned a lot from that, too. A top-notch thinker and writer, and a true mensch. www.motherjones.com/media/2025/0...

Goodbye, Kevin Drum

"Take care of Donald Trump for me."

motherjones.com

Remembering Kevin Drum talkingpointsmemo.com/edblog/remem...

Just learned political blogger Kevin Drum, who I've read daily since his CalPundit days 20+ yrs ago, has died. Along with Friday cat photos, his most enduring legacy may be bringing attention to the links between childhood lead exposure and early adult crime. I will miss his old-school blogging

Everybody (me included) is getting bogged down on the details of events at NIH et al. Fatal mistake. The big picture is Musk/Trump are trying to shut down all gov-funded Medical/Disease research in the US. Have to understand that to have any hope of stopping it. talkingpointsmemo.com/edblog/act-now

And, my @sciencehomecoming.bsky.social-inspired op-ed is online at LNP/Lancaster Online — in print, it's alongside a piece from two geoscientists with local roots on the front page of the Sunday Perspectives section lancasteronline.com/opinion/colu...

Plant biologist who went from Manheim to the Mojave makes case for federal funding for science [column]

If there’s a single origin to my scientific career, it’s the moment Charlie Longenecker introduced me to chicory.

lancasteronline.com

Jeremy Yoder says no war@jbyoder.org · last yr.

So I did this today: banged out a couple hundred words of a pitch while managing lab, sent it to the opinion page editor at the newspaper my parents still somehow get in print, and got back a "yes" in, I absolutely kid you not, under 15 minutes

If you want to search and/or visualize how a set of long reads lay down on a reference genome -- whether to check a gene annotation, for assembly error, or another reason, Gio Madrigal's Klumpy can help you do it. Excited to see it on the cover! (and online: catchenlab.life.illinois.edu/klumpy/)

Happy to see our latest work out in G3 @genetics-gsa.bsky.social. This is the fourth notothenioid genome our group has assembled so far -- a highly cold-specialized fish with a large complement of antifreeze proteins and an interesting set of chromosomal fusions/rearrangements.

Angel G. Rivera-Colón@arcolon14.bsky.social · 2y ago

Our paper on the genome assembly and annotation of the Antarctic bald notothen (Trematomus borchgrevinki) is now available in G3! This paper was lead by @niraj-rayamajhi.bsky.social, in collaboration with Bushra Fazal Minhas, Chris Cheng, and @jcatchen.bsky.social. doi.org/10.1093/g3jo... 1/n

We know that immune genes often show stronger signatures of selection than the genomic average. But what about immune cell types? In a new preprint www.biorxiv.org/content/10.1... we merge single-cell RNAseq (defining stickleback cell types) and population genomic measures of selection...

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

Altmetric@altmetric.com · 2y ago

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research. A Place of Joy.

Bluesky now has over 20M people!! 🎉 We've been adding over a million users per day for the last few days. To celebrate, here are 20 fun facts about Bluesky:

Just a quick reminder that PhD applications to work on this funded project are due Dec 1. If you're interested please feel free to reach out to me by e-mail.

Milton Tan@mtanichthys.bsky.social · 2y ago

I am excited to announce our NSF grant has been funded to study the evolution and diversification of N American minnows, including genomics/phylogenomics and comparative phylogenetic methods. This includes funds for a postdoc and PhD student! I can be reached at miltont (at) illinois (dot) edu. 🐟

This post by Tim Lee on his AI Substack is really good. It describes how 3 trends converged to create the AI boom: the (re)discovery of neural networks, the creation of the 1st massive training dataset, and CUDA, which allowed GPUs to be generalized to train models open.substack.com/pub/understa...

Why the deep learning boom caught almost everyone by surprise

"You’ve taken this idea way too far," a mentor told Prof. Fei-Fei Li.

open.substack.com

New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30

Happy to release Stacks v2.67 today. This release updates process_radtags to make it easier to use SRA data and to filter poly-G (error) runs coming from Nextseq/Novaseq machines + bugfixes. We also added a genotype depth filter to populations #RADseq catchenlab.life.illinois.edu/stacks/

Please share! My lab will be hiring 2-3 postdocs over the coming months to study the genetic basis of behavioral traits in darters using brain transcriptomics & population genomics. First ad is posted here: tamus.wd1.myworkdayjobs.com/TAMU_Externa... #behavior #popgen #evolution #neuroethology

If you are interested in the recent attempts to regulate Apple in Europe with the DMA, this is a really interesting (and long) piece by Steven Sinofsky, a major software engineer at Microsoft during its antitrust days (and after). hardcoresoftware.learningbyshipping.com/p/215-buildi...

Building Under Regulation [215.]

An essay on the EU Digital Markets Act and Apple’s Update on apps distributed in the European Union (and some personal history)

hardcoresoftware.learningbyshipping.com

If you have a sequence that you love – a gene family, transposable element, regulatory feature – you probably spend a lot of time looking for it in different sets of sequence. If so, you might find our latest preprint and software tool, Klumpy, useful. www.biorxiv.org/content/10.1...

Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org

Interesting paper from J Pritchard's lab: "GWAS variants differ from eQTL variants along many axes…GWAS hits are biased toward more constrained genes…with complex regulatory landscapes…eQTLs show strong promoter bias largely absent from GWAS hits"

Systematic differences in discovery of genetic effects on gene expression and complex traits - Natur...

This study seeks to explain the poor overlap of genome-wide association study and cis-expression quantitative trait locus variants using a model of differential selective constraint, suggesting that t...

nature.com

Ever wondered whether adapting to icy, oxygen-rich #Antarctic waters influenced #hemoglobin gene #evolution in #notothenioid fishes? And how white-blooded #icefish lost their hemoglobin genes? Our new MS is for you! A quick 🧵on our finding in @MolBioEvol! #Marinelife tinyurl.com/5n7ym3jp

I have been having a lot of fun revising private allele analysis in #Stacks from #RADseq data. What are private alleles? Given SNPs in a set of populations, a private allele is found only in a specific population. 1/n

Next week! Please join us: The Practice of RADseq: Population Genomics Analysis with Stacks, October 2-6, 2023 The course will focus on de novo (with parameter optimization) and reference analyses of RAD data, with new modules on PCR duplicates/allele dropout and private allele analysis

ONLINE COURSE – The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) This cou...

prstatistics.com