Will Shoemaker

As good an image as any to illustrate America’s contribution to Middle East peace, order, and stability over the last 30 years.

www.amazon.com/gp/aw/d/B0FW...

New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.

A personal honor to have the work of myself and my collaborators covered in Il Piccolo, the Trieste newspaper that published James Joyce when he lived here.

YouTube video by Foreign Policy Adam Tooze on the War on Iran | Ones and Tooze Ep. 232

www.youtube.com/watch?v=ndpk...

Some old(er) notes on magnitude abundance fluctuation scaling in ecological models (typo fixed)

wrshoemaker.github.io//posts/2026/...

This is a headshot of IU Biology Professor Jay Lennon.

Jay Lennon named IU Distinguished Professor!

IU President Pamela Whitten said of the six recipients,“Their teaching, scholarship and leadership have transformed students’ lives and earned the respect of peers around the world." go.iu.edu/Q8IIdW @jaytlennon.bsky.social

Pedro Sanchez continues his run as the only world leader convincingly acting like he cares to defend a rules based world order

The war on Iran likely brings a new oil price shock and windfall profits.

So, who stands to win?

Our research shows: Last time around (2022), the US reaped the largest fossil fuel profits of any country ($377bn). 50% went to the top 1%, only 1% to the bottom 50%. A🧵

Reminder: Only one in five Americans favor war with Iran
sadat.umd.edu/feature/do-a...

Parallel evolution of industrial melanism in the peppered moth: one locus, many alleles https://www.biorxiv.org/content/10.64898/2026.02.26.707722v1

🧪 This bacterial strain has been maintained in sterile water since 1994.

Possible carbon sources incl. “phthalic acid - a plastic degradation product likely leached from inoculation tubes“.

Genomic variations accumulated between 1994 and 2022 suggested adaptations to long-term nutrient deprivation

Vivid memory of being at the 2005 Jamboree where I snuck off into the woods during George W's Iraq War speech to get stung ~50X by ground nesting bees

War With Iran Would Be Illegal and Stupid. Democrats Should Care. Now is the time for Democratic leaders to stand firm against the risk of a catastrophic conflict.

An unpopular president is about to drag the country into an unpopular war. Democratic leader should be out front in opposition, not politely asking for a briefing.

My piece in @foreignpolicy.com foreignpolicy.com/2026/02/27/d...

Genomic Perplexity and the Evolution of Context-Dependent Function Abstract. The fundamental principle that selection acts on a gene’s function often assumes implicitly that this function is fixed and intrinsic. However, e

New paper out in MBE! 🧵
"Genomic Perplexity and the Evolution of Context-Dependent Function"
The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this. academic.oup.com/mbe/article/...

This post is about biologists' obligation to speak up for trans rights, in case I need to spell it out directly.

🙏🙏🙏

Feedback welcome!

Happy to share new work with @martinadalbello.bsky.social and @jacrickets.bsky.social! Microbial ecologists have historically used rRNA barcoding to investigate in situ community physiology. Here we examine if, and when, RNA provides information not captured by DNA.

www.biorxiv.org/content/10.6...

Thanks to ICTP for the nice write-up on our recent answer to the question “How many ATP does it take to make an endospore?”

www.ictp.it/news/2026/2/...

I’ve spent ten years trying to escape to a different field but here I am, still a dog trapped in macroecological theory’s hot car

Understanding how enzymes work: the journey to ensemble–function studies
febs.onlinelibrary.wiley.com/doi/10.1111/...

This is an exceptionally well written review on how enzymes work. Rather than the structure-function relationship, Herschlag & Du analyse the ensemble-function relationship

Pb concentration by decade in hair from Salt Lake City region residents. Value plotted for 1940 includes all samples from 1916 to 1959; value plotted at 2022 includes all samples from 2020 to 2024.

One of last week’s most-viewed PNAS articles is “Lead in archived hair documents a decline in lead exposure to humans since the establishment of the US Environmental Protection Agency.”
Explore the research: https://ow.ly/SMKg50YetGP

More trending articles: https://ow.ly/bQ8f50YetzE

Eukaryogenesis in light of an expanded catalogue of Asgard genomes. a, Simplified, scaled timeline spanning from before the Last Asgard archaea Common Ancestor (LAsCA) to today. Thin bands mark predicted time ranges of relevant events (for example, GOE), thicker bands represent processes (for example, eukaryogenesis), and brackets indicate the period shown in b. The timeline further highlights milestones, including potential early eukaryotic fossils60 and the modern-day co-occurrence of Heimdallarchaeia and Alphaproteobacteria observed in this study (interaction likely originated earlier).

Fig. 1 | Expanded genomic diversity of Asgard archaea. a, Maximum-likelihood phylogeny based on 47 non-ribosomal markers (NM47)using the WAG + C10 + R4 model with 100 nonparametric bootstrap pseudoreplicates, including 869 Asgardarchaeota MAGs and 309 outgroup genomes. The blue branches (lower right) indicate the new Asgardarchaeota classes, Ranarchaeia, and the recently proposed Asgardarchaeia4. The concentric rings denote (in to out): the predicted genome size, metabolic guilds based on Pfam clustering, sampling locations, and black stars on the outside mark MAGs added by this study. Asgard, Asgardarchaeia; Atabey, Atabeyarchaeia; Baldr, Baldrarchaeia; Frey/Jord, Frey/Jordarchaeia; Gerd, Gerdarchaeales; Heimdall, Heimdallarchaeaceae; Hel, Helarchaeales; Hermod, Hermodarchaeia; Hod, Hodarchaeales; Kari, Kariarchaeaceae; Loki, Lokiarchaeales; Njord, Njordarchaeales; Odin, Odinarchaeia; Ran, Ranarchaeia; Sif, Sifarchaeia; Thor, Thorarchaeia; Wukong, Wukongarchaeia. b, SR4-recoded phylogeny of the same genome set inferred with the model GTR + C60 + G and 100 nonparametric bootstrap pseudoreplicates (Methods). This updated catalogue constitutes a large increase in the medium- to high-quality publicly available genomes (completeness >50% and contamination and redundancy <10%) with 65.3% from the Guaymas Basin and 34.7% from the Bohai Sea. The encircled numbers represent MAGS added by this study. The scale bars in bothsubpanels represent the average number of substitutions per site.Map created in BioRender; Appler, K. https://biorender.com/147ieoc(2025).

Our work is published today: ‘Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor’. This was a huge effort lead by @katyappler.bsky.social. Extremely grateful to have been a part of this amazing project! 😊🦠🧬

Links: www.nature.com/articles/s41...
www.nature.com/articles/s41...

‘The trend is irreversible’: has Romania shattered the link between economic growth and high emissions? Emissions have plunged 75% since communist times in the birthplace of big oil – but for some the transition has been brutal

Romania has decoupled economic growth from pollution faster than anywhere else in EU. Its net greenhouse gas emissions intensity fell 88% between 1990 & 2023, so each euro’s worth of economic activity heats planet 10 times less. Emissions have plunged by 75%. www.theguardian.com/environment/...

USA : Hungary :: San Juan : Rijeka

Posted notes I never published from ~2021 providing a quick demonstration why LD should never be inferred on binned allele frequency data, even in the ideal case. Problem seems mostly solved through weighted estimators, but would be interested in follow up.

wrshoemaker.github.io//posts/2026/...

Rubio's speech was obviously imperialist and repulsive (and all global South states should take note, and plan deterrence accordingly).

How it feels when someone appreciates your paper.

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n

Making the Vortex Mixer The forgotten story of an invention found in every biology lab.

The science writing over at @asimovpress.bsky.social is fantastic!

From the origin of the lab vortex, to the history of Xenopus, their content is creative, beautiful, and thoughtfully researched.

Consider assigning some of their pieces in science courses.

www.asimov.press/p/vortex?utm...