Milo Johnson

What is the best strategy to win any contest? Eliminate your opponents of course. Recently, my colleague @fernpizza showed how plasmids compete intracellularly (check out his paper just published in Science today!). Together with @baym, we now know how they can fight.

Excited to share pt 2 of my blog on genotype-phenotype maps! We are good at predicting protein sequence->structure. How did it happen? Why was it possible? Can we make similar predictions for protein function, whole-cell phenotypes, or community function open.substack.com/pub/topossibil…

Curious about how evolution takes place? Are you looking for a "first-course" in the subject? My book, Fundamentals of Evolutionary Biology (CRC Press), takes a microbe-first approach and explains how molecular and cellular processes drive evolution.

Also I'm miloj over on blue sky, there more often these days!

I'm very excited to share something I've been working on off-and-on for a long time now: a new blog about genotype-phenotype landscapes! The first post is a Gödel-Escher-Bach-style dialogue to introduce the topic. If you like it please share/repost! open.substack.com/pub/topossibil…

And also also shout out to @bkoskella for making RaMP happen and advising on this project!

Also I'm @ miloj on bsky!

Know any recent or upcoming college graduates who are looking for a (full-time&paid!) microbio research experience? Point them towards RaMP! @darian_doakes and I are co-mentors for an MGE project that I think is going to be really cool. Apps+recs by 5/25 sites.google.com/berkeley.edu/r…

@parambulat0r yesssssss I'm so glad you're making them widgets this is excellent

...okay it may be slightly more complicated. nitro.bio/blog/widgets-d… covers the missing links

Making custom Jupyter widgets with React is surprisingly straightforward 🐍❤️🌐 1) Build React component 2) `npm run dev` and `jupyter lab` 3) Use anywidget to bridge Python/JS

@PetrovADmitri @skryazhi It also could be important that the backgrounds are from a cross (so maybe gene regulation is very non-optimal) - again really speculating wildly here, but I think that is one possible form of specificity of these results.

@PetrovADmitri @skryazhi To tack onto what Sergey said with some wild speculation: maybe in the really really slow growing strain/env combos, just not expressing any nonessential gene is likely to be beneficial. I don't know enough about cell biology to know how reasonable that sounds, but it's an idea.

It looks like I never posted anything (*but see below) on what are probably the most surprising results my lab obtained so far. Anyway, this work—led by an outstanding former PhD student Sarah Ardell in collaboration with @_miloj—is now published: science.org/doi/10.1126/sc…

@BrittAbrahamson Thanks Britt!

A little late to the party, but I'm really excited to see this work out from Sarah Ardell, Alena Martsul, and Sergey Kryazhimskiy over at UCSD, with some help from me from afar. Sergey's thread goes over the main results. Here's why I think they are fun to think about:

@MRebolleda @skryazhi Thanks so much María! I hope we can talk science again soon!

This is an incredible paper; if you care about fitness effects and epistasis, you cannot miss this one! If you know anything about @skryazhi you'll know this paper is careful, creative, and insightful! Sarah and @_miloj are also brilliant and incredibly nice! Congratulations!!!

(I don't think Sarah and Alena are on here, but I'll tag @skryazhi because I forgot to above)

Major thanks to Alena for leading the experimental work on this, to Sarah for leading the analysis, and to Sarah and Sergey for carefully pulling it all together, writing, etc.!