Lightnews — Scholar-powered news

Julian Catchen @jcatchen.bsky.social · Aug 26

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!

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Julian Catchen @jcatchen.bsky.social · Jun 19

“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.

www.forkingpaths.co

Julian Catchen @jcatchen.bsky.social · May 8

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

Electronic sign in a UIUC campus building advertising free ChatGPT use during finals

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Reposted by Julian Catchen

Mark Follman @markfollman.bsky.social · Mar 13

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."

www.motherjones.com

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Josh Marshall @joshtpm.bsky.social · Mar 11

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

Remembering Kevin Drum

Kevin Drum died on Friday. Many of you knew Kevin’s blog. For...

talkingpointsmemo.com

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Steven L. Johnson @stevenljohnson.org · Mar 10

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

Kevin Drum - Wikipedia

en.wikipedia.org

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Josh Marshall @joshtpm.bsky.social · Mar 6

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

Act Now

I may do a longer, maybe several longer versions of this post....

talkingpointsmemo.com

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Jeremy BOO! Yoder 🎃💀🕷️ @jbyoder.org · Mar 2

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...

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Julian Catchen @jcatchen.bsky.social · Jan 16

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/)

Molecular Ecology Resources journal cover image of the Klumpy algorithm.

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Julian Catchen @jcatchen.bsky.social · Jan 10

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 · Jan 10

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

Validate User

academic.oup.com

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Reposted by Julian Catchen

Daniel Bolnick @danielbolnick.bsky.social · Dec 10

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...

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Bluesky @bsky.app · Dec 3

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

Altmetric @altmetric.com · Dec 3

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.

‘A place of joy’: why scientists are joining the rush to Bluesky
Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.: https://www.nature.com/articles/d41586-024-03784-6

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Julian Catchen @jcatchen.bsky.social · Nov 24

Wow, Iverson's interview with McNeely gives an in-depth feel for the jazz scene in Champaign-Urbana in the early 1970s -- super interesting. As a jazz enthusiast and fan of the early to mid 1970s period, and someone who moved to C-U in 2015, that was fascinating!

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Jay 🦋 @jay.bsky.team · Nov 19

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:

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Reposted by Julian Catchen

Milton Tan @mtanichthys.bsky.social · Nov 15

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 · Aug 8

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. 🐟

A map of the Northern Hemisphere highlighting ecoregions by their species richness in minnows.

A phylogeny with branches highlighted red and blue to indicate differences in rates of diversification.

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Julian Catchen @jcatchen.bsky.social · Nov 5

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

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Will Ratcliff @wcratcliff.bsky.social · Oct 26

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

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Julian Catchen @jcatchen.bsky.social · Jul 18

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/

Stacks

catchenlab.life.illinois.edu

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Rachel Moran @rachelmoran.bsky.social · Apr 5

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

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Julian Catchen @jcatchen.bsky.social · Mar 27

The populations VCF import function is designed only for variant sites. You could re-export the VCF from populations with the alt population map. If you want to keep your filtering, you can use the loci that were not filtered by vcftools to make a whitelist to feed into populations at the same time

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Julian Catchen @jcatchen.bsky.social · Mar 27

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

Julian Catchen @jcatchen.bsky.social · Feb 18

Yes, there is a flag to output all sites in the VCF file. The populations program will also calculate Pi and Dxy, accounting for variant/invariant sites, by default.

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Julian Catchen @jcatchen.bsky.social · Feb 16

This project was led and implemented by Gio Madrigal (first, first author!) with assistance from Bushra Minhas.

Julian Catchen @jcatchen.bsky.social · Feb 16

The tool has two modes of operation – you can give it one or more queries, and it will k-merize and search for them in an assembly and the raw reads, or you can turn it loose to scan a long-read genome (and its raw reads) for inconsistent areas of assembly.

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Julian Catchen @jcatchen.bsky.social · Feb 16

We built Klumpy – a combined k-mer search and visualization tool, written in Python – to help us find and verify antifreeze genes in fishes and we have since used it for a lot more.

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