Ira Zibbu
@coolscootre.bsky.social
Evolution enthusiast/ Computer Nerd/ Molecular wizard-in-training.
PhD student watching 80,000 generations of bacterial evolution @ Barrick Lab, Michigan State University.
Enjoyer of all things post-modern and in the zeitgeist.
PhD student watching 80,000 generations of bacterial evolution @ Barrick Lab, Michigan State University.
Enjoyer of all things post-modern and in the zeitgeist.
destroyed in seconds
February 17, 2026 at 11:40 PM
destroyed in seconds
Reposted by Ira Zibbu
Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!
Davis Summer Population Genomics Program
Want to learn population genetics? Please fill out this form to indicate your potential interest in a 2-week intensive online summer population genetics course taught by Jeffrey Ross-Ibarra and Graham...
docs.google.com
February 9, 2026 at 6:24 PM
Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!
If you're in the Lansing area this week, you have to stop by!
I'm giving a public talk at Biology on Tap on how watching microbes as they evolve in the lab can help us figure out some fundamental questions about the nature of evolution.
Venue: Michigan Wildlife Conservancy
When: 05 Feb 2026, 7pm
I'm giving a public talk at Biology on Tap on how watching microbes as they evolve in the lab can help us figure out some fundamental questions about the nature of evolution.
Venue: Michigan Wildlife Conservancy
When: 05 Feb 2026, 7pm
February 3, 2026 at 9:17 PM
If you're in the Lansing area this week, you have to stop by!
I'm giving a public talk at Biology on Tap on how watching microbes as they evolve in the lab can help us figure out some fundamental questions about the nature of evolution.
Venue: Michigan Wildlife Conservancy
When: 05 Feb 2026, 7pm
I'm giving a public talk at Biology on Tap on how watching microbes as they evolve in the lab can help us figure out some fundamental questions about the nature of evolution.
Venue: Michigan Wildlife Conservancy
When: 05 Feb 2026, 7pm
Reposted by Ira Zibbu
Today is the last day to apply for the International Travel Stipends to attend #Evol2026 in Cleveland, Ohio in June! Funds can cover registration, transportation, food, and lodging. A budget template is available on the website. @evolmtg.bsky.social www.evolutionsociety.org/content/soci...
Society for the Study of Evolution
Site description
www.evolutionsociety.org
January 30, 2026 at 8:01 AM
Today is the last day to apply for the International Travel Stipends to attend #Evol2026 in Cleveland, Ohio in June! Funds can cover registration, transportation, food, and lodging. A budget template is available on the website. @evolmtg.bsky.social www.evolutionsociety.org/content/soci...
Reposted by Ira Zibbu
The Smithsonian’s National Museum of Asian Art will repatriate three bronze sculptures to the Indian government, half a century after they were stolen from a Hindu temple in Tamil Nadu.
Smithsonian to Return Three Looted Bronzes to Indian Government
The sculptures of Hindu gods and their followers were stolen from Tamil temples and smuggled out of India in the mid-20th century.
hyperallergic.com
January 29, 2026 at 4:42 PM
The Smithsonian’s National Museum of Asian Art will repatriate three bronze sculptures to the Indian government, half a century after they were stolen from a Hindu temple in Tamil Nadu.
Reposted by Ira Zibbu
I really want to know the back story about how this person ended up with so many Amtrak cafe car sandwiches to give away on our local buy nothing group
January 29, 2026 at 2:23 PM
I really want to know the back story about how this person ended up with so many Amtrak cafe car sandwiches to give away on our local buy nothing group
Reposted by Ira Zibbu
New paper out in @pnas.org, and it made the cover! 👁️
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
January 27, 2026 at 8:23 PM
New paper out in @pnas.org, and it made the cover! 👁️
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.
‼️Check Paula’s 🧵 and the paper👇
𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
Most biologists self-proclaimed lack of mathematical or quantitative skills is simply learned helplessness.
January 27, 2026 at 3:31 AM
Most biologists self-proclaimed lack of mathematical or quantitative skills is simply learned helplessness.
Reposted by Ira Zibbu
Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework?
Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
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.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
STEPS To It
Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.
telliamedrevisited.wordpress.com
January 20, 2026 at 4:12 PM
Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework?
Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
Reposted by Ira Zibbu
Second, most scientists aren’t academics (& the vast majority are not tenured academics). I actually think the most important product of academic research is not knowledge, but scientists. That’s why it needs to keep going, even under duress totalinternalreflectionblog.com/2023/05/30/w...
What’s the (by-)product?
Is knowledge really the primary product of academic research?
totalinternalreflectionblog.com
January 17, 2026 at 7:16 PM
Second, most scientists aren’t academics (& the vast majority are not tenured academics). I actually think the most important product of academic research is not knowledge, but scientists. That’s why it needs to keep going, even under duress totalinternalreflectionblog.com/2023/05/30/w...
I am confused why people are mad. This paper uses a language model to identify "AI papers" across fields (biology, physics, chemistry etc). This picks up on (IMO) completely benign methods like CNNs, kNN, PCA, random forests. 1/n
One of my concerns with AI-assisted research in biology is that we're already looking only in the lamplight and AI incentivizes us to narrow the beam. Seems like it's happening...
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Artificial intelligence tools expand scientists’ impact but contract science’s focus - Nature
Artificial intelligence boosts individual scientists’ output, citations and career progression, but collectively narrows research diversity and reduces collaboration, concentrating work in data-rich a...
www.nature.com
January 15, 2026 at 7:03 PM
I am confused why people are mad. This paper uses a language model to identify "AI papers" across fields (biology, physics, chemistry etc). This picks up on (IMO) completely benign methods like CNNs, kNN, PCA, random forests. 1/n
Dustbin Baby
The Bluest Eye
Perks of Being a Wallflower
The Bluest Eye
Perks of Being a Wallflower
Something that I think would be really helpful in building a broader coalition here: a substantive conversation about what the "newer era" of the canon can/should be?
Like, which 10-12 books should be part of the canon from the past 50 years?
That should be a conversation!
Like, which 10-12 books should be part of the canon from the past 50 years?
That should be a conversation!
January 5, 2026 at 3:58 PM
Dustbin Baby
The Bluest Eye
Perks of Being a Wallflower
The Bluest Eye
Perks of Being a Wallflower
Reposted by Ira Zibbu
Reposted by Ira Zibbu
@laasya2.bsky.social @deepaagashe.bsky.social et al. quantified the growth cost of mistranslation rates and exposure to antibiotics in E. coli, finding that altered translation accuracy can shape adaptive outcomes.
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
December 19, 2025 at 6:53 PM
@laasya2.bsky.social @deepaagashe.bsky.social et al. quantified the growth cost of mistranslation rates and exposure to antibiotics in E. coli, finding that altered translation accuracy can shape adaptive outcomes.
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf312
🖌️ Nishant Asawadekar
#evobio #molbio
Reposted by Ira Zibbu
This paper contains some good arguments about an issue that concerns me a lot when I hear my colleagues talking about LLM use in developing their research:
Whose ideas are you presenting as your own?
(Though the fatalist argument the authors make at the end of paper is disappointing/bizarre.)
Whose ideas are you presenting as your own?
(Though the fatalist argument the authors make at the end of paper is disappointing/bizarre.)
December 14, 2025 at 12:38 PM
This paper contains some good arguments about an issue that concerns me a lot when I hear my colleagues talking about LLM use in developing their research:
Whose ideas are you presenting as your own?
(Though the fatalist argument the authors make at the end of paper is disappointing/bizarre.)
Whose ideas are you presenting as your own?
(Though the fatalist argument the authors make at the end of paper is disappointing/bizarre.)
Reposted by Ira Zibbu
It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027!
See you there!!
@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social
#microsky #mevosky
See you there!!
@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social
#microsky #mevosky
December 10, 2025 at 2:35 PM
It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027!
See you there!!
@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social
#microsky #mevosky
See you there!!
@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social
#microsky #mevosky
Reposted by Ira Zibbu
On scientific "style" for @undark.org:
"[Style] is a positive feature of science that facilitates different routes to solving problems.....We can embrace differences in our approaches while still promoting rigor and clarity."
undark.org/2025/12/04/o...
"[Style] is a positive feature of science that facilitates different routes to solving problems.....We can embrace differences in our approaches while still promoting rigor and clarity."
undark.org/2025/12/04/o...
Science Needs to Embrace the Idea of Style
How do individual scientists approach their work? These stylistic differences can influence the process of discovery.
undark.org
December 4, 2025 at 5:54 PM
On scientific "style" for @undark.org:
"[Style] is a positive feature of science that facilitates different routes to solving problems.....We can embrace differences in our approaches while still promoting rigor and clarity."
undark.org/2025/12/04/o...
"[Style] is a positive feature of science that facilitates different routes to solving problems.....We can embrace differences in our approaches while still promoting rigor and clarity."
undark.org/2025/12/04/o...
My first paper came out earlier this year, and I have been thinking about scientific taste, and the gap between one's early work and that taste.
irazibbu.substack.com/p/the-scient...
I hope this is something many people can relate to. Let me know what you think!
irazibbu.substack.com/p/the-scient...
I hope this is something many people can relate to. Let me know what you think!
The Scientific Taste Gap
"All of us who do creative work, we get into it because we have good taste. But there is this gap. For the first couple years you make stuff, it’s just not that good."
irazibbu.substack.com
November 30, 2025 at 5:54 PM
My first paper came out earlier this year, and I have been thinking about scientific taste, and the gap between one's early work and that taste.
irazibbu.substack.com/p/the-scient...
I hope this is something many people can relate to. Let me know what you think!
irazibbu.substack.com/p/the-scient...
I hope this is something many people can relate to. Let me know what you think!
Reposted by Ira Zibbu
The Long-Term Evolution Experiment has returned home. Led by Professors Richard Lenski (@relenski.bsky.social) and Jeffrey Barrick, this groundbreaking work continues to reveal how bacteria evolve in real time. 12 flasks. 1 legacy.
🔗https://tinyurl.com/f6vjyjvr
🔗https://tinyurl.com/f6vjyjvr
November 10, 2025 at 3:25 PM
The Long-Term Evolution Experiment has returned home. Led by Professors Richard Lenski (@relenski.bsky.social) and Jeffrey Barrick, this groundbreaking work continues to reveal how bacteria evolve in real time. 12 flasks. 1 legacy.
🔗https://tinyurl.com/f6vjyjvr
🔗https://tinyurl.com/f6vjyjvr
Reposted by Ira Zibbu
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy
Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...
rdcu.be
November 18, 2025 at 9:01 PM
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Omg so excited to see this come out! Loved the preprint when it came out earlier, and it is definitely a front runner for my paper-of-the-year for 2025
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 25, 2025 at 8:59 PM
Omg so excited to see this come out! Loved the preprint when it came out earlier, and it is definitely a front runner for my paper-of-the-year for 2025
❌ Clearly communicate the issue with the people in my lab
✅ Write a passive aggressive limerick
✅ Write a passive aggressive limerick
June 27, 2025 at 3:12 PM
❌ Clearly communicate the issue with the people in my lab
✅ Write a passive aggressive limerick
✅ Write a passive aggressive limerick
Reposted by Ira Zibbu
In the words of Nelson Mandela: it always seems impossible until it’s done.
My friends, it is done. And you are the ones who did it.
I am honored to be your Democratic nominee for the Mayor of New York City.
My friends, it is done. And you are the ones who did it.
I am honored to be your Democratic nominee for the Mayor of New York City.
June 25, 2025 at 5:54 AM
In the words of Nelson Mandela: it always seems impossible until it’s done.
My friends, it is done. And you are the ones who did it.
I am honored to be your Democratic nominee for the Mayor of New York City.
My friends, it is done. And you are the ones who did it.
I am honored to be your Democratic nominee for the Mayor of New York City.
Okay can someone explain to me why the Datsenko and Wanner method is "one step"?? Even when I get stuff to work right away, it's always a week of work! Especially if you follow it up with a FLP recombinase step!
June 25, 2025 at 10:52 PM
Okay can someone explain to me why the Datsenko and Wanner method is "one step"?? Even when I get stuff to work right away, it's always a week of work! Especially if you follow it up with a FLP recombinase step!
2024 update: The genes have been moved around far, far more than I originally expected.
Nice post from Ira Zibbu, a visitor in @barricklab.bsky.social working on the #LTEE.
the-ltee.org/who-moved-my...
#biology #genomics #evolution #microbiology #MicroSky
the-ltee.org/who-moved-my...
#biology #genomics #evolution #microbiology #MicroSky
Who Moved My Genes? Analyzing Chromosomal Rearrangements in the LTEE
There is a quote by Theodosius Dobzhansky that goes: “Nothing in biology makes sense except in the light of evolution.” In response, I wish to offer up a corollary: “Nothing in evolution makes s...
the-ltee.org
January 18, 2024 at 5:24 AM
2024 update: The genes have been moved around far, far more than I originally expected.