Seemay Chou

will give it a read, added to my list for the weekend!

😆

Big experiments are only big if they can fail Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist

We’ve been heads down @ArcadiaScience for a bit but the @arenabioworks news this week caused me to dump thoughts. hard things are hard; don’t be such a fucking hater. Reflections on parallels w our own institutional experiment here seemay.substack.com/p/big-experi...

this is most of all true for the actual trainees. protecting them can inadvertently block them from opportunities they want. don't be that guy

overall, way fewer people are arguing against our policy as change seems inevitable now

A few quick bullets: protecting trainees from career risk is a common argument

Why careerism can be bad for science training Some field notes from scholarly publishing discussions with scientists

I spend a lot of time talking to potential grantees about our open science policy. Some field notes here:
open.substack.com/pub/seemay/p...

Diffuse Project Interest Form Interested in the Diffuse Project? Please provide your information to help us shape community engagement and potentially direct you to the right project member.

Want to get involved, share your ideas, or just stay in the loop with email updates? Let us know here: forms.gle/37pK2smABwbg...

A note in here for other science philanthropists… we have a chance rn to help scientists rethink systems, technical & operational. They’re game to take useful risks, let’s help them. Coming soon: more open science research, experimenting outside journals… seemay.substack.com/p/from-syste...

It will certainly be important to include more modalities (and scientists) beyond X-ray, which we hope to do in the future! Lots of fun work to be done to ensure interoperability in that way

Haha I love that, thanks for actually clicking the link 😂

We are thrilled to be part of Project Diffuse, building infrastructure for the dynamic future of structural biology.

We are helping to lead the modeling and encoding efforts of this project, including designing infrastructure that allows AI to learn from the full complexity of experimental data.

From systems operators to systems architects Going up a level from data generation to think about the data systems we design and embed

Oops fixed! Also here seemay.substack.com/p/from-syste...

From systems operators to systems architects Going up a level from data generation to think about the data systems we design and embed

More on our reflections here seemay.substack.com/p/from-syste...

From systems operators to systems architects Going up a level from data generation to think about the data systems we design and embed

Announcing the Diffuse Project! We're unlocking protein dynamics through diffuse X-ray scattering - the overlooked signal that could revolutionize how we understand protein motion. seemay.substack.com/p/from-syste...

Doing this will require co-iterating across an entire data system, not just refining one part. And we're experimenting with how to share all of this (our real-time thinking, pivots, tools, data) openly and quickly all outside of traditional journals

Tldr, we're focusing on diffuse scattering, which is the messier background signal in X-ray diffraction images. These data are often tossed because they're complex, but this complexity is where so much of the interesting biology sits

Our take: more of the same data won't get us there. We're bringing together top experts across almost every node of the X-ray pipeline to generate the right kind of data to model ensembles of different protein conformations. Think: pictures to movies

We're dreaming about the next frontier in structural biology: protein motion. Understanding how proteins move will be the next big unlock for predicting function

The Diffuse Project The Diffuse Project

What’s the next PDB? Maybe it’s …the PDB.

We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇

www.diffuse.science

YouTube video by Arcadia Science Meet Ciona intestinalis

Most importantly, first in our new series of organismal spotlight shorts (open source illustrations coming soon!). Sea squirts! www.youtube.com/watch?v=-E9T...

Zoogle Suggested We Try a Sea Squirt, So We Did It’s true that no model is perfect, but how can we find ones that are less wrong? We’re excited to announce two research partnerships investigating predicted matches between diseases and research orga...

Wrote up a post summarizing some of our big picture lessons on bottlenecks, such as difficulties in finding tacit "folklore" knowledge in organismal systems arcadiascience.substack.com/p/zoogle-sug...

Hoped others would jump on it, but wasn't super straightforward so we ran with some predictions ourselves. Ultimately collaborating with sea squirt and choano experts to scope some pilots (biggest filter was finding people willing to publish openly/rapidly but we prevailed!)

We recently released the Zoogle dataset, which uses our workflows and publicly avail data to quantify how well different organisms model specific human genes/diseases. zoogle.arcadiascience.com/about

After many yrs building internally @arcadiascience.com we're now able to partner more with others on cool organisms. You won't hurt my feelings if you don't read my post, but don't miss out on our first organismal spotlight animation featuring sea squirts -- just skip to the bottom! 🧵

Props to those taking the first steps. Those first steps are scary, messy, and the only guarantees I can offer is that now we have a chance at something better. More announcements in coming months.

In the last 48h since announcing our policy, 4 academic PIs decided that they can indeed take this risk w us. They aren't the glam journal "elite" but they're damn good scientists. They're on the more junior side, and that's fucking awesome because they're our future.

#2 is actually a made-up concern in at least 50% of the cases that I help people work through. When you start talking to the real people involved, students are often hungry to try a different way but don't think their PIs will "let" them.

#1 makes sense because they actually think they have the most to lose since their success was built on the existing system. Why would they give up a winning hand even if it's in a broken game?

The "elite" scientists who publish in glam journals are actually waiting for the rest of you. When I talk to them, they either say: 1) Happy to do it once others do, and/or, 2) I can't do it because I have to protect so many trainees.