iiinova — where your digital self keeps evolving

Michael Baym @baym.lol · 30/09/2026

I’m rebranding synbio

Michael Baym @baym.lol · 13/09/2026

And even the haters have been fun. Special shoutout to C.A.G. for the lovely turn of phrase "an appallingly incompetent, incoherent, and irrational farce masquerading as 'science'"

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Michael Baym @baym.lol · 13/09/2026

Ten years ago Tami, Roy, and I released a movie we made of antibiotic resistance evolving in real time. I thought maybe a couple thousand people tops would see it. I couldn't have imagined it would be seen millions of times, and be taught from middle school through the graduate level worldwide

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Michael Baym @baym.lol · 04/09/2026

You know what, I’ll keep my distance

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Michael Baym @baym.lol · 14/07/2026

Nothing like the sun changing color to make everything feel apocalyptic

A photo of what appears to be an overcast day, except the sky is grey and the sun is red

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Michael Baym @baym.lol · 14/07/2026

Boston is finally joining the big leagues

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Michael Baym @baym.lol · 11/07/2026

Super cool stuff, did you see the one that looks like a pirate ship? (Off in the background here, didn’t get a decent photo)

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Michael Baym @baym.lol · 11/07/2026

Square packing is all well and good, but real ones study circle packing

The optimal packing of ten circles inside a circle

Ten frozen dumplings in a steamer, optimally packed

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Michael Baym @baym.lol · 13/06/2026

The man just gives and gives

Martin Shkreli replying "You're the one wasting your time on a problem that doesn't exist" and me thanking him as I put that quote on another business card

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Michael Baym @baym.lol · 13/06/2026

Woohoo, Martin Shkreli (yes that Martin Shkreli!) has given me a new business card!

Martin Shkreli responding to my tweet with "ah, have you ever developed a drug? bullshit antibiotic resistance waste of time ass career"

A business card for me, Michael Baym, at Harvard Medical School, with, in place of a job title, the quote "Bullshit antibiotic resistance waste of time ass career"
-Martin Shkreli

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Michael Baym @baym.lol · 11/06/2026

I love being too dangerous for an AI to even talk to

A conversation with Claude Fable 5 in which I ask it only “Who am I?” and it replies “You’re Michael Baym, a microbiologist” and immediately downgrades to Opus 4.8

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Michael Baym @baym.lol · 10/06/2026

The technical term for this is “shitpost red teaming” 🦠🧬

Getting blocked by Claude Fable for just two emoji 🦠🧬

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Michael Baym @baym.lol · 05/06/2026

You: The world needs more bioproducts Me: Behold, the biblically accurate 96-well plate

A 96-well assay plate with a googly eye in each well, all looking at you

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Michael Baym @baym.lol · 28/05/2026

This is very cool: a simple statistical test of dysbiosis, or really any microbiome composition data relative to a reference. Outperforms Bray-Curtis and every other metric, while simultaneously being very simple to compute. Probably would work on RNAseq data too.

Three ROC curves showing RPD outperforming BCD for each dataset

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Michael Baym @baym.lol · 27/05/2026

Not a small amount of roads

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Michael Baym @baym.lol · 27/05/2026

Thrilled to announce I completed my two-year project to run or bike every street in Cambridge this morning

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Michael Baym @baym.lol · 19/05/2026

It is astounding the extent to which the people funded by billionaires to envision “new ways of doing science” do not understand the way it’s currently done

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Michael Baym @baym.lol · 21/04/2026

Wow, Nike's got a spicy take on bioinformatics

A poorly photoshopped version of the Nike "Runners welcome. Walkers tolerated." storefront reading "Nerds welcome. R tolerated."

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Michael Baym @baym.lol · 20/04/2026

It’s flatter here, and there’s more often water on the road than falling from the sky so single speed with a rack and fenders is ideal

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Michael Baym @baym.lol · 16/04/2026

Some day I’ll figure out how to work this into a talk

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Michael Baym @baym.lol · 08/04/2026

Huge congratulations to Dr. Arya Kaul on his successful thesis defense today! The fourth from my lab

The author and Dr. Kaul at his post-defense celebration

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Michael Baym @baym.lol · 24/03/2026

Most recent road trip: Barga to Genoa up the Ligurian Riviera with @audeber.bsky.social

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Michael Baym @baym.lol · 27/02/2026

Why yes, linkedin spammer, I _have_ been thinking that an MS in Biology might help my career in science

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Michael Baym @baym.lol · 13/02/2026

It's not the ultra-high res scan that APS will do, but it's a start

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Michael Baym @baym.lol · 13/02/2026

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

A quote from a letter from Darwin to Hooker in 1858 reading “Oh my God how I do hate species & varieties.”

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Michael Baym @baym.lol · 09/02/2026

It seems only fair this morning, since they renamed themselves Mayenard, that an appropriate Seattle suburb can come and sack the town

The Maynard, Mass sign renamed with an E

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Michael Baym @baym.lol · 23/01/2026

This is what the whole room looked like

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Michael Baym @baym.lol · 23/01/2026

Repairing the heaters was way sketchier

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Michael Baym @baym.lol · 23/01/2026

So you’re saying a DIY arduino-powered relay board might not be the safest way to turn them on and off?

The setup that kept the megaplate window clear for three years without a fault

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Michael Baym @baym.lol · 19/01/2026

Looks like it’s gonna be another banner aurora night if it’s clear where you are

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Michael Baym @baym.lol · 19/01/2026

No such thing as bad grilling weather, only bad grilling clothing Not shown: the large snowflakes that fell on the ribs

Two racks of ribs on a smoky grill surrounded by snow

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Michael Baym @baym.lol · 05/01/2026

We’re cool. It’s helping me write emails

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Michael Baym @baym.lol · 05/01/2026

Walked into my office and there’s a bear on my couch

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Michael Baym @baym.lol · 31/12/2025

Six years ago today, flights got delayed and we ended up spending New Year’s with barbecue in the Dallas airport. The next morning our flight got diverted, we had to rent a car and drive four hours through a snowstorm, and made it, thinking after all that went wrong, nothing else would in 2020

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Michael Baym @baym.lol · 04/12/2025

There’s a house in my neighborhood with this enticing red button at street level

A grey house with an enticing red button

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Michael Baym @baym.lol · 01/12/2025

Bioinformatics is in shambles at the Denver airport’s acronym game

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Michael Baym @baym.lol · 01/12/2025

How do they look even worse than you’d imagine

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Michael Baym @baym.lol · 30/11/2025

Your scientists were so preoccupied with whether or not they could

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Michael Baym @baym.lol · 20/11/2025

This turned out to be because once a high-benefit plasmid was established, the marginal benefit to more copies of it was minimal, but the cost to the plasmid was higher, so it took longer to fix. However, the high-benefit plasmid was much more able to establish immediately. 12/

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Michael Baym @baym.lol · 20/11/2025

The signal was overwhelming! Transcription interferes with replication. But that means that the thing we think most about with plasmids, the genes they carry, are something they don’t actually want to express. 9/

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Michael Baym @baym.lol · 20/11/2025

To make sure this wasn’t an artifact of the production of the gene having a cost to the cell, we turned to Carlos Sanchez and Daniel Eaton in Johan Paulsson’s lab to look at these dynamics in a microfluidic device that geometrically negates cellular growth advantages. 8/

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Michael Baym @baym.lol · 20/11/2025

Now that we understood neutral dynamics, we turned to competition. What could cause one plasmid to replicate better than another? Our first thought was transcription might interfere with replication, and it turns out there was a much larger tradeoff than we expected! 7/

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Michael Baym @baym.lol · 20/11/2025

But when we measured heterozygosity over time, there was a problem: it decayed too slowly for theory. We traced this down to a previously unappreciated dynamic, the Dam methylase system was pausing the plasmids after replication, which acted to suppress stochasticity. 6/

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Michael Baym @baym.lol · 20/11/2025

We then came up with a way to measure this precisely with DNA barcodes: here the idea is that the recombinase transiently re-dimerizes random plasmids on occasion. This is mathematically identical to measuring heterozygosity, for which there’s strong population genetic theory. 5/

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Michael Baym @baym.lol · 20/11/2025

With this working, as a first test we took two plasmids, identical save for 8 point mutations changing the color, and competed them against one another. Here’s a video of what it looked like when we activated the recombinase. You can see the two compete in real time: 4/

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Michael Baym @baym.lol · 20/11/2025

Fernando came up with a really clever way to do this: instead of introducing the two plasmids separately, fuse them together and then split them on command. This required finding a FLP recombinase in a Patagonian yeast that was temperature sensitive, but amazingly worked! 3/

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Michael Baym @baym.lol · 20/11/2025

How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/

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