Jamie 🇨🇦

Save the Whales. But Save the Microbes, Too.

Microbes sustain all ecosystems yet they’re nearly absent from conservation frameworks.
The @IUCN Microbial Conservation Specialist Group aims to change that.
Honored to co-chair this global effort.
Great @nytimes piece by Carl Zimmer:
www.nytimes.com/2025/10/17/s...

Rule number one for gremlins is keep them out of bright light, especially sunlight. This photo proves it - not a gremlin!

Phenomenal. In my 10 year update of A Brief History, I make the point that in the first edition, not one disease had been successfully treated using gene therapy. Today that number is at least 7.

Genome evolution of Acinetobacter baylyi ADP1 during laboratory domestication: acquired mutations impact competence and metabolism | Applied and Environmental Microbiology Acinetobacter baylyi ADP1 is a bacterial chassis of interest to microbiologists in academia and industry due to its extreme natural competence and wide metabolic range. Its ability to take up DNA from...

Genome evolution of Acinetobacter baylyi ADP1 during laboratory domestication: acquired mutations impact competence and metabolism

#ApplEnvironMicrobiol from Jeff Barrick

journals.asm.org/doi/10.1128/...

A deep dive into the destruction of US cancer research by @jonathanmahler.bsky.social “It’s an absolutely unmitigated disaster,” a former top official at NIH told him. “It will take decades to recover from this, if we ever do.” Gift link: nyti.ms/48iH3Cr

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

Biology Department

xkcd.com/3140/

Phosphorus constrains global photosynthesis more than nitrogen does - Nature Ecology & Evolution Nitrogen and phosphorus limitations are both key to spatial patterns and temporal trends in primary production. This global analysis indicates that phosphorus limitation on terrestrial primary product...

Phosphorus constrains global photosynthesis more than nitrogen does www.nature.com/articles/s41... #jcampubs

Frequency-dependent fitness effects are ubiquitous In simple microbial populations, the fitness effects of most selected mutations are generally taken to be constant, independent of genotype frequency. This assumption underpins predictions about evolutionary dynamics, epistatic interactions, and the maintenance of genetic diversity in populations. Here, we systematically test this assumption using beneficial mutations from early generations of the Escherichia coli Long-Term Evolution Experiment (LTEE). Using flow cytometry-based competition assays, we find that frequency-dependent fitness effects are the norm rather than the exception, occurring in approximately 80\% of strain pairs tested. Most competitions exhibit negative frequency-dependence, where fitness advantages decline as mutant frequency increases. Furthermore, we demonstrate that the strength of frequency-dependence is predictable from invasion fitness measurements, with invasion fitness explaining approximately half of the biological variation in frequency-dependent slopes. Additionally, we observe violations of fitness transitivity in several strain combinations, indicating that competitive relationships cannot always be predicted from fitness relative to a single reference strain alone. Through high-resolution measurements of within-growth cycle dynamics, we show that simple resource competition explains a substantial portion of the frequency-dependence: when faster-growing genotypes dominate populations, they deplete shared resources more rapidly, reducing the time available for fitness differences to accumulate. Our results demonstrate that even in a simple model system designed to minimize ecological complexity, subtle ecological interactions between closely related genotypes create frequency-dependent selection that can fundamentally alter evolutionary dynamics. ### Competing Interest Statement The authors have declared no competing interest.

How common are frequency dependent fitness effects?

New preprint out today 👇
doi.org/10.1101/2025...

#OnThisDay in 1858, a seminal journal article comprised of papers by Alfred Russel Wallace FRS and Charles Darwin FRS on the theory of evolution by natural selection was published by the Linnean Society, the first public announcement of the theory of evolution. bit.ly/3k8fq4u

So sorry to hear this news. Elio was exceptionally kind and supportive over my few years attending the SD microbiology group. Such an inspiration and role model.

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

Scatterplot showing fitness effect of ~7000 synonymous mutations in yeast: read count at start vs log2 fold change. Most data points are not significant but 204 points are significant outliers, either advantageous or deleterious.

At the same time, we made thousands of synonymous mutations in endogenous yeast genes and measured their growth. We used careful statistics and controls. Only 3%, 204 of 6874, had a fitness effect! This goes against a controversial recent result that most synonymous mutations had fitness effects.

Jennifer Doudna is named 2026 Priestley Medalist The award recognizes the biochemist for discoveries on ribozyme function and CRISPR gene editing, and international science leadership

@acs.org is recognizing Jennifer A. Doudna with the Priestley Medal for her discoveries on ribozyme function, the Dicer RNase enzyme, double-stranded RNA processing, and CRISPR gene editing, along with her impactful international science leadership. cen.acs.org/people/award... #chemsky 🧪

So, a large fraction of the people following me are academics, and already know this stuff.

But for those of you who aren't, very short thread on a bit of the sausage of research.

Hardware/wetware codesigned data loop VISTA makes use of generative model sampling and synthesis "on chip" on-board by leveraging oligosynthesis setup shown here.

The biggest challenge for AI in biology isn't just models, it's the data used to train them. Standard biological data isn't built for AI. To unlock generative AI for drug discovery, we must rethink how we generate and capture data. 1/

CRISPR researchers and startup entrepreneurs will share new building in UC Berkeley's Innovation Zone - Berkeley News A planned addition to the campus's Innovation Zone will expand lab space for the Innovative Genomics Institute and build out the largest innovation hub — Bakar Labs — at any U.S. university.

We’re thrilled to announce IGI–Bakar Labs. This new building will allow the IGI to continue expanding our impact in health and agricultural applications of #CRISPR, and will be shared with the Bakar Labs incubator for growing biotech companies. Learn more: news.berkeley.edu/2025/07/17/c...

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment. Gift article:
www.nytimes.com/2025/07/07/s...

In an unconscionable decision, the Smithsonian Institute has decided to no longer support the Biodiversity Heritage Library from 1 Jan 2026. Please someone step up and take it over.

I spoke to @ninalakhani.bsky.social for this article and reading it was still a gut punch. The US’s gold-standard scientific funding system has been completely demolished. I genuinely don’t know what to do with what remains.

And it’s going to get even worse under the new budget.

BREAKING: A federal judge in Massachusetts (the Reagan-appointed William Young) has declared the Trump administration's cuts to NIH grants — ostensibly over Trump's EOs on gender ideology and DEI — are "illegal" and "void." He's ordering many grants restored.

I loved the chapter about biology in "The Magic of Code," as I discussed in my @wsj.com review now out -> www.wsj.com/arts-culture... @daphnezohar.bsky.social @matthewherper.bsky.social @bijans.bsky.social @carolynbertozzi.bskyverified.social @euanashley.bsky.social @peterkolchinsky.bsky.social

How a discovery in Yellowstone National Park led to the development of PCR - Richmond Scientific A discovery in Yellowstone National Park led to the development of PCR, the gold-standard COVID-19 tests used to fight the global pandemic.

Reminder: Nobel-prize winning PCR (1983), used in basically all genetic tech today, was only possible because of extremophile bacterium discovered in 1964 in Yellowstone funded by a small ~$80k NSF grant with no obvious application at the time. #science 🧪
www.richmondscientific.com/how-a-discov...

Phage people: Rich Losick and I are combing the world looking for T4 rIIB mutant FC0 (also known as P13). FC0 was the starting point for Francis Crick's beautiful 1961 paper on the triplet nature of the genetic code. We want to sequence it. Anyone have it in an ancient stock collection?

This, by Michael Lynch.

I'd include AI techbros as well.

www.pnas.org/doi/10.1073/...

Estimates for # of people involved in NSF activities

From over 300k to less than 100k. A picture of smaller, reduced science.

#MicroSky

Death Star has partially successful trip to Yavin.

a man in a dark room says fewer ALT: a man in a dark room says fewer

- also a Ser

Tracing the Path from Basic Research to Transformative Therapies

28 of the most important drugs approved by the Food and Drug Administration (FDA) between 1985 and 2009. They found that 80 percent stemmed directly from basic discoveries made in the lab, often by scientists trying to understand a biological process or disease

bit.ly/4jLCfbC

YouTube video by Amanpour and Company Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company

David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏

youtu.be/8YhJM6zxYDw?...