Elizabeth McDaniel

Fig. 3 from the paper, showing that model performance levels off around 300M parameters and ESM C variants tend to outperform the other available protein language models.

Figure 5 from the paper, showing a wide range of model performance across datasets, with R^2 values ranging from 0.1 to 0.8. Only a small fraction of this variation is explained by either dataset size or protein length.

Now published: Systematic comparison of protein language models for transfer learning.

Key points:
- You don't need gigantic models. The two smaller ESM C variants work great.
- There is huge variability in performance across datasets. We have no idea why.

www.nature.com/articles/s41...

What the microbiome teaches us about aging gracefully... ...and why we shouldn't necessarily 'turn back the clock'

I started a personal #Substack to cultivate my creative writing skills. Let's see how it goes. Opinions are my own.

The first essay: why I think it's probably a bad idea to give 80-year-olds fecal transplants from 20-year-olds. gibbological.substack.com/p/what-the-m...

Subscribe if, you're into it

The way people are talking about the current demolition of research funding and HE legitimacy reminds me of the early days of COVID when I (and others) said it would be at least six years before any normalcy. Rage, despondency, rejection…eventually voting for a dictator just to feel alive.

An acrylic painting by Jim Musil depicting a farm in Wisconsin. A red barn sits at the end of a dirt road in the middle of a verdant green field. A colorful sky dominates the composition.

My painting WISCONSIN FARM

I hate to be that guy, but this is the five-alarm fire, and every elected Democrat and frankly, every Washington reporter should be ringing the bell. If it can happen to him, it can happen to anyone. Nobody with a voice should give this administration a moment’s peace about it.

Cory Booker Just Gave The Longest Speech In The History of The US Senate Only two men have spoken on the floor of the U.S. Senate...

In his 1957 filibuster, Strom Thurmond said "Negroes ... are not so well qualified to vote as are the white people.”

A Black senator just broke the record Thurmond set with that speech.
talkingpointsmemo.com/news/cory-bo...

I laughed so hard at this, and then cried, because it's so painfully true

Find Your Voting Locations | WISDEMS Voter Protection Team This searchable map shows you early voting and dropbox info for hundreds of villages, towns, and cities across Wisconsin. Enter the address you're registered at and your options will pop up!

Right now, there’s an important race happening that will shape the Wisconsin Supreme Court for the next 10 years. Judge Susan Crawford is ready to protect the fundamental rights and freedoms of all Wisconsinites.

Make a plan to vote early today — don’t wait until April 1st: wisdems.org/vote

Attorney General Bonta Urgently Issues Consumer Alert for 23andMe Customers Californians have the right to direct the company to delete their genetic data OAKLAND — California Attorney General Rob Bonta today issued a consumer alert to customers of 23andMe, a genetic testing ...

23andMe is going under. Californians have the right to delete their genetic data before it's turned over to next party buying the assets. If you have a 23andMe account, go log in to download whatever reports you want to save, then follow these instructions to delete your data.

Yes! But also it's just really great to come back to a clean house. I went on a week long yoga retreat in Costa Rica last year, and it was life changing. Hope you have a great time!

Brown Medicine doctor deported despite federal court order. What we know. A court order that would have delayed the deportation of Dr. Rasha Alawieh was issued while her plane was on the tarmac, but it took off anyway.

This is so evil that it defies understanding. A transplant surgeon on an H1B visa was deported, despite a court injunction. She had committed no crimes.

This must stop. We must stand together to protect immigrants and visitors against state terrorism.

www.providencejournal.com/story/news/l...

Immune history shapes human antibody responses to H5N1 influenza viruses - Nature Medicine H5N1 strain-specific antibodies are higher in older individuals and correlate more with birth year than with age, suggesting that younger individuals are potentially more likely to benefit from H5N1 v...

Today @natmedicine.bsky.social published our study showing the older individuals born prior to 1968 have more antibodies that cross-react to #H5N1 relative to younger individuals. If H5N1 causes a pandemic, children will likely be the most susceptible. 1/2

www.nature.com/articles/s41...

Department of Music Mourns Passing of Robert Mueller; Memorial Scheduled for March 12 Professor Robert Kent Mueller, a beloved member of the U of A community for 37 years, died March 6. A visitation will be held today at Good Shepherd Lutheran Church with a memorial on Wednesday.

My college symphony orchestra director Dr. Robert Mueller passed away last week, and he was an incredibly passionate musician and teacher. Some of my most cherished memories were very small acts of kindness on his behalf. He will be incredibly missed.
news.uark.edu/articles/769...

geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. github.com/nvelden/gene... #Rstats

Carl Zimmer on the Hidden Life in the Air We Breathe (Ep. 235) From the mysteries of airborne disease to the search for extraterrestrial life, what are we missing about the unseen world around us?

I'm on the new episode of Tyler Cowen's podcast talking about AIR-BORNE, plus some of my other books. Listen here: conversationswithtyler.com/episodes/car...

Breaking: FDA's March meeting to select flu shot strains for 2025-2026 season has been canceled per email sent to committee members, a VRBPAC member told me. drug companies need about 6 months leeway to make shots in time for fall vax campaigns. #healthpolicy

Haha yes! There are people I've never met or had a full conversation with online other than Github issue discussions.

Happy to be added as well!

What Lichen Tell Us About Ecology, Air Quality, And More Ira is joined on stage by experts in Portland, Oregon, to talk about the amazing world of lichen and their role in a changing climate.

Last October, we took a trip to the World Forestry Center in Portland, Oregon, for a daylong exploration of lichen—the fuzzy growths often found on trees, roofs, and gravestones. Two experts joined us to discuss the fascinating world of lichen and their role in a changing climate.

I stayed there for a short vacation last June (was super surprised that you can just stay there outside of a conference!) and I loved walking along the boardwalk and reading by the fire at night. Enjoy!

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

Congrats Vince!!

I had the pleasure of being interviewed by @markowenmartin.bsky.social on his Fantastic "Microbial Matters" podcast about my group's work on the #drinkingwatermicrobiome. You can watch it here. www.youtube.com/watch?v=JDAU...

A photo of groundcherries (Alkekengi) in a garden in winter. The round, orange, cherry tomato-like fruits are suspended in the center of pendulous, vaguely heart-shaped husks made of networks of dried beige veins. The husks have a delicate, skeletal, lattice-like structure, reminiscent of laser-cut papercraft.

In winter through early spring, you can sometimes find unspoiled, still-bright groundcherries sitting in the latticed remnants of their husks, like hearts suspended in paper ribcages

Ten species comprise half of the bacteriology literature, leaving most species unstudied

@biorxiv-microbiol.bsky.social by Paul A Jensen

www.biorxiv.org/content/10.1...

B. subtilis is #6 😍, anyhow, the literature is biased to models

Would publications on plants or animals be similarly biased?

There are really only two "mystery box" shows that I felt were worth my time last year and this coming year (for "mystery box shows," think LOST): FROM and SILO. As always, your mileage may differ.

We're doing an *emergency* Bookstore and Chocolate Crawl on Saturday Jan. 11.

We'll visit Medicine For Nightmares and Adobe, which suffered massive flood damage recently.

Then we'll hit East Bay Booksellers, recovering from a fire. Plus Pegasus!

Details/RSVP: www.eventbrite.com/e/emergency-...