Michael Baym
@baym.lol
Associate Prof @HarvardMed. Microbial evolution, antibiotic resistance, mobile genetic elements, algorithms, phages, molecular biotech, etc. Basic research is the engine of progress.
baymlab.hms.harvard.edu
baymlab.hms.harvard.edu
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
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/
November 20, 2025 at 9:42 PM
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/
Holy crap go look at the sky right now
November 12, 2025 at 1:59 AM
Holy crap go look at the sky right now
With a green-herb forward mayo rub it works so so well
November 11, 2025 at 7:49 PM
With a green-herb forward mayo rub it works so so well
Reading the microbial warfare literature
October 30, 2025 at 2:23 AM
Reading the microbial warfare literature
When you buy a cutting board from bioinformaticians
October 26, 2025 at 10:56 PM
When you buy a cutting board from bioinformaticians
Some good news: the NIH has now reinstated my R35 since the termination was found unconstitutional (still waiting on NSF), though the government continues to withhold the contractually obligated funds
September 13, 2025 at 1:02 AM
Some good news: the NIH has now reinstated my R35 since the termination was found unconstitutional (still waiting on NSF), though the government continues to withhold the contractually obligated funds
I’m thrilled to share that after several months of using the lessons from this paper, my cacio e pepe has meaningfully improved
September 5, 2025 at 11:09 PM
I’m thrilled to share that after several months of using the lessons from this paper, my cacio e pepe has meaningfully improved
Nope. The termination note cited Harvard’s “antisemitism”
August 21, 2025 at 8:46 PM
Nope. The termination note cited Harvard’s “antisemitism”
Presenting my new faculty profile photo
July 30, 2025 at 1:38 AM
Presenting my new faculty profile photo
Still a kind of pool, just significantly more deadly
July 28, 2025 at 1:49 AM
Still a kind of pool, just significantly more deadly
What a two weeks with the Micro Pop Bio and Eco-Evo Genomics GRCs!
>70 talks, 200 posters, 24 miles run, 3 road trips, and so many new ideas
Thank you to @reeskassen.bsky.social, Christina Burch, @chicascientifica.bsky.social, and @samyeaman.bsky.social for the amazing meetings
>70 talks, 200 posters, 24 miles run, 3 road trips, and so many new ideas
Thank you to @reeskassen.bsky.social, Christina Burch, @chicascientifica.bsky.social, and @samyeaman.bsky.social for the amazing meetings
July 19, 2025 at 5:45 AM
What a two weeks with the Micro Pop Bio and Eco-Evo Genomics GRCs!
>70 talks, 200 posters, 24 miles run, 3 road trips, and so many new ideas
Thank you to @reeskassen.bsky.social, Christina Burch, @chicascientifica.bsky.social, and @samyeaman.bsky.social for the amazing meetings
>70 talks, 200 posters, 24 miles run, 3 road trips, and so many new ideas
Thank you to @reeskassen.bsky.social, Christina Burch, @chicascientifica.bsky.social, and @samyeaman.bsky.social for the amazing meetings
Check out what I found at the Milan Triennale
July 18, 2025 at 5:21 PM
Check out what I found at the Milan Triennale
Welcome to 2011!
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
July 14, 2025 at 4:41 PM
Welcome to 2011!
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...