New post! A round up of the latest advances in biotech and medicine by @nikomccarty.bsky.social and me. Prime editing, curing whipworm, a new narcolepsy drug, designing protein nanoparticles, the 3D structure of E. coli's genome and more! Read it all here: www.worksinprogress.news/p/whats-new-...

Asimov Press party // September 30 // Boston // Asimov HQ There will be trivia. There will be winners (and losers). And there will be prizes. Come celebrate, answer questions, and show everyone how much esoteric biology stuff you know. Hope to see you there!

Out today: A useful review on AI-designed protein binders. It covers the history of this work + has lots of good case studies, including how these tools are being used to make snake anti-venoms. The tables are particularly valuable.

E. coli copies 600 bases of DNA/second. It makes one error every few billion bases, or one mutation per 1,000 generations. I made an animation to show just how crazy this is. Every green square is a copied nucleotide. The red squares (very rare) are mutations. 🔻

Behold the cursed noodles. Researchers mixed together chicken muscle cells and microalgal cells, and then extruded them with a 3D printer, to make a "plant and animal cell-based hybrid noodle." The reason for doing this, they say, is to tune textures, nutrition levels, etc.

Cable bacteria link together (thousands of cells, end-to-end) to conduct electrons across distances up to 7 centimeters. They are living batteries. They were discovered in Aarhus, Denmark in 2012. I visited Aarhus last year to see them in person, and wrote about it today.

What is a specific problem in biology that would be useful to solve, and could be solved for ~$10,000?

The flagellum motor is biological design of the highest order. The motor hits rotational speeds >1,000 rpm. The basal disk (that purple ring) alone is built from 51 tethered subunits. The tail whips at high torques thanks to interlocking cogs, an axial driveshaft, and propeller.

Using E. coli to convert post-consumer PET plastic into acetaminophen. The researchers discovered a biocompatible Lossen rearrangement; it uses phosphate as a catalyst. They start the Lossen rearrangement in phosphate buffer and add E. coli; PET to acetaminophen at 92% yield.

YouTube channel idea: Recreating famous biology experiments. Explain what was known at the time, go through the initial observations, and make the "discovery." e.g. Monod's biphasic E. coli growth curves, T.H. Morgan's fly breeding programs, and so on.

It's sad, in a way, that a magazine spending $4M a year to hire additional, talented writers is seen as "throwing a lot of money." It's good that The Atlantic is spending more money on writers. It is the anti-status quo. May their poaching drive up salaries elsewhere, too.

Biotech papers & news this week: 1. Chemical reactions can be affected by stir bars. 2. A tool to drag membrane transporters into peroxisomes. 3. Full computational design of Kemp eliminase enzymes. 4. UK government to approve crops made using precision breeding. & more...

"...we establish an all-cell-free viral cycle where T7 phages infect synthetic cells, equipped with lipopolysaccharides on the outer leaflet of the lipid membrane while encapsulating a cell-free gene expression system." Looks useful; an in vitro system to study viral infections.

Much like fingerprints, humans can be identified using their nasal airflow patterns. By measuring air as it flows in and out of the nose over a 24-hour period, researchers identified individuals with up to 96.8% accuracy (in a cohort of 97 people).

Today is my first day as Writer-in-Residence at @arcinstitute I'll be writing about the Virtual Cell, genome editing + much more. Grateful for the invitation to spend my summer here and learn more about AI+Bio!

I recently visited Rocinha, which is Rio de Janeiro's most populous favela. It is quite unsafe and sad, in many ways. I wouldn't recommend going there yourself. But here are some photos from that visit, which I plan to write about soon.

This study estimates that "a brain performing active tasks consumes just 5% more energy compared to a resting brain." Cognition is extremely energy efficient. Glucose provides most of this energy. The estimate was made by looking at fMRI, PET, and other data sources together.

We made a huge poster that illustrates all of the major genome editing tools in one place. You can download a copy for free from the @AsimovPress website. press.asimov.com/articles/cr...

I'll be living near Stanford this summer, from ~June 10 to August 10. I'm hoping to meet lots of people and learn a lot more about AI+Bio efforts. Let's hang out!

Journey of a pill. This article traces the making of a common drug, clonazepam, from the mining of raw materials in India to manufacturing in New Jersey and packaging in Tennessee. "The total distance travelled in this scenario is approximately 63,162 km..."

I'm doing weekly Links posts again. Maybe you'll hate it. But there's too much good stuff on the Internet not to share it!

I'm offering free copies of the @AsimovPress book to iGEM students, or college students enrolled in biotechnology courses, in the U.S. If you'd like copies for your team/class, DM me. I'll send out 1 book per student & 1 DNA capsule per shipment. While (limited) supplies last.

A new device "measures...milk volume during breastfeeding" and then sends the data "to a smartphone" for real-time tracking so that mothers can track how much milk is consumed by the infant. Seems really useful.

Another insane example of insect evolution. Female digger wasps: 1. Remember locations of <10 nests at once. 2. Feed their offspring in order, by age, to reduce chances of starvation. 3. Will delay feeding a child if that child was given a larger amount of food previously.

The first experimentally-solved, 3D structures of the human sweetness receptor. Resolved in complex with sucralose and aspartame; but the structures were identical. Upon binding, these molecules cause the protein to *slightly* bend & trigger a signaling cascade in the cell.

> be plant > leaves attacked by insect > warn neighbors by releasing molecules into air > neighbors get the signal > neighbors trigger molecular cascade and "talk to" soil bacteria > soil microbes "increase plant growth and enhance plant defences." Plants are highly underrated.

The first step toward solving big problems is often just figuring out what to work on. To that end, this "Gap Map" is an extraordinarily useful starting point for learning about bottlenecks in biology & other scientific domains. Highly recommend!

> bacteria were engineered to make molecules that absorb light in unique ways. > the microbes were buried in soil. > using a drone with a hyperspectral camera, one can "see" where the microbes are buried from ~300 feet away. one of the most sci-fi papers I've seen in awhile.

TIL that intelligence likely evolved twice; once in birds and then again in mammals. Key evidence seems to be that distinct cell types and brain regions are used to perform similar computations in both birds and mammals. From Quanta magazine.

A single E. coli is 70 percent water. The other 30 percent is mostly proteins. A single type, called Lpp, accounts for ~1/3 of all proteins in a cell. It takes less energy to build a cell than it takes to lift an apple from the ground to a height of one meter. New post by me🔻

New op-ed argues that prions, infectious proteins that causes devastating conditions like Creutzfeldt-Jakob disease and kuru, may also be our best model for understanding protein dynamics.... ...and, thus, improve our ability to design better proteins in the laboratory.

It blows my mind that human engineers have figured out how to build towering machines, which fill small rooms and cost ~$6 million dollars, capable of imaging INDIVIDUAL AMINO ACIDS in proteins by blasting them with electrons. Who can explain how these machines really work?

The plight of Gaston Ramon: - Made effective vaccines against diphtheria and tetanus. - Discovered adjuvants, which make many modern vaccines far more effective. He was nominated for the Nobel Prize >150 times, but never won it. Chart from an @AsimovPress article; out tomorrow.

A 3D map of mRNA transcripts in a zebrafish embryo. This video was not made using a microscope. Researchers tag nucleotides with barcodes, which then "link" together in the tissue. Sequencing those links can then be used to computationally infer the 3D positions of genes.

Computational design of filaments made from 2- or 3 different proteins. Earlier work made fibers from one designed protein. But this paper more closely reflects the switch-like behavior of natural cytoskeletal filaments, which are made from multiple self-assembling components.

More photos of the Asimov Press book. Our book printer (based in Minneapolis) had to custom-make several parts for each order, including a display stand to hold each DNA capsule. The DNA was made by CATALOG DNA, sealed by Imagene in France, and sequenced by Plasmidsaurus.

We're now shipping out the second book from Asimov Press (the first commercial book sold in DNA + print). We're packing and shipping thousands of books today! Here are some photos. We think the final product turned out really well.

The "Protein Design Archive" catalogs and tracks "designed" proteins, dating back to 1991. It currently includes 1,553 structures. You can download the whole dataset for free; it gives a description of each protein, its PDB ID, and much more. Link below.

"Our nano-PeLEDs with characteristic pixel lengths down to about 90 nm represent the smallest LEDs reported, enabling a record-high pixel density of 127,000 pixels per inch (PPI)...." For context, ~2.5 trillion E. coli could fit on a 1 square inch surface.

When we got the pitch for this story, I hadn't even *heard* of Serratia marcescens. But then I learned that it's: 1. First bacterium named after a person. 2. First microbe grown as a pure culture. 3. Used for >100 years to study how microbes spread through built environments...

Our latest book was mentioned in The New Yorker magazine. Specifically, in a March 20th article on DNA data storage. Bucket list item ✅

We're finally making some Asimov Press stickers. We'll give them out to people we meet, stick them in the books we ship out, and so on. They were designed by Ella Watkins-Dulaney, an artist from Pasadena. My favorite is the jellyfish (its tentacles are made from GFP).

I'm excited to share that Stripe is supporting our work at Asimov Press through this year. I've been a huge fan of the publishers they support, Stripe Press and Works in Progress, for years. Asimov Press was initially modeled on the latter, actually. We got lots of great pieces coming up!

The E. coli genome is >4 million base pairs. When a cell copies its genome, it pieces together each nucleotide, burning energy along the way. Surely this costs the cell lots of energy, right? Well, not really. Estimates suggest it's 1.1% of the cell's total energy consumption.

What limits a cell's size? One factor is its surface area-to-volume ratio. A spherical cell's internal volume grows proportionally to the cube of its radius, and its surface area grows proportionally to the square of that radius. A cell’s volume thus grows much more swiftly than its surface area.

Companies that make medical devices are required to report "adverse events" to the FDA within 30 days of hearing about them. 71% of reports are submitted on-time. And a tiny handful of companies are responsible for the vast majority of all late submissions.

This is a great review on using nanopores to sequence proteins. Out today. It covers how nanopores work, why they haven't historically been able to sequence individual proteins, and how researchers are adapting them to solve those problems. Clear writing throughout.

These long, icicle-looking things on the Titanic are made from communities of bacteria. These bacteria, Halomonas titanicae, can corrode and feed on iron in extremely cold, high-pressure conditions. The wreck is 12,400 feet deep, corresponding to ~375 atmospheres of pressure.

We're really grateful that @AsteraInstitute will support our work (for the next two years!) at @AsimovPress. It means more long-form articles, more reporting, and ... a new metascience column. If you want to write about "new institutions of science," please pitch us! DMs open.

Come work with us at @asimovpress.bsky.social! We're hiring a researcher to contribute original reporting and curate datasets for our "Data" series. Link to apply in the post below.