Congrats!!!
07.03.2026 01:48
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Congrats!!!
Great read, one small correction - pretty sure it's Dan's wife Marian who was nicknamed "Bunny" not Dan Koshland...
12th episode (full year!) of the Tortured Protein Department Podcast with@fraserlab.com!
podcasts.apple.com/us/podcast/s...
Do we need a go-fund-me for a Claude Code Max subscription for @jeremymberg.bsky.social to unlock even more valuable reports?
I've been working on Surface Morphometrics for a new version (coming soon), and made some significant (AI-assisted) performance improvements, especially in pycurv (20-50x!). If you've had technical issues or just felt like it was too slow, give it another try! #teamtomo github.com/GrotjahnLab/...
'to treat peer review as a throughput problem is to misunderstand what is at stake. Review is not simply a production stage in the research pipeline; it is one of the few remaining spaces where the scientific community talks to itself.' 1/3
On the plus side - hallucination is dramatically lower now than a year ago. In the downside- peer review should be fun an a mental exercise (two things you should never outsource to AI)
Post your reviews! And only review preprints - helps with this: fraserlab.com/reviews/
New TTPD with @fraserlab.com! We chat about travels, new preprints, and vibe coding.
podcasts.apple.com/us/podcast/b...
open.spotify.com/episode/6QCR...
🤯
New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...
A recent podcast by Stephanie Wankowicz and James @fraserlab.com picked up our work (with Alex Bronstein & coworkers) on Guiding AlphaFold3 with experimental data (cryoEM, X-ray, NMR) to generate protein ensembles. (Thanks for the kind words 🙂)
👉 creators.spotify.com/pod/profile/... (from 35:50)
As soon as NIH decided that preprints were A-OK we started preprinting everything.
The biggest negative is that now once we've preprinted I lose interest in the actual peer-reviewed article. Which for me isn't a big deal (I'm tenured) but my folk aren't. So I need to force myself to keep up on it
Do you have a repo I can look at invite github.com/fraserlab if private if you are comfortable?
This is cool - is it: app.benchmate.ai/pricing or something you are writing?
Happy new year #teamtomo! We've resumed our OHSU tomo journal club, and this year I am going to be sharing it on bluesky. This week we did a roundtable, where attendees each brought a paper and did a 3-5 minute discussion of what they thought was cool about it. Here are the papers they discussed!
Me too. Just trying to brainstorm ideas that might incentivize more retirement without a forcing function of a hard cutoff
Sorry. I misread! Many reacting strongly the other way - they should just be forced to retire at age X.
I think the trouble is that people are still competitive- and don’t have an off-ramp for their identity as a scientist. I’m with you, I’ll exit stage right when the time comes. But I see many who don’t….
from: hhmicdn.blob.core.windows.net/policies/Inv... "expanded phase out" of 5 years, rather than going through competitive renewal (7 years if successful and 2 years if not)
Based partially on observations of this working: bsky.app/profile/fras...
A point in favour of this: an off ramp exists for HHMI investigators and many actually take it
I agree it’s hard. Much like convincing them to retire. But the alternative isn’t retiring. It’s renewing their R01.
People just don’t do it though. I think an off-ramp program would allow people to hold their heads high, maintain identity as a scientist ,etc.
Trying to brainstorm policy ways to get people to do actually do it.
Great. I don’t think advocating for either or both of these are mutually exclusive. Need many policy ideas for this problem…
Tenure is tenure.
www.nytimes.com/1990/10/21/s...
And I knew and really loved Howard (TAed his ethics class for many years)…
Yes. We have such programs but - How do you get them to transition out to free up resources? Hence the reverse K99 as a potential off ramp policy…
The problem is people don’t retire. What’s a policy solution to help?
I also do- but I’ll tell you there aren’t really any levers of incentives to get people to do that
The alternative isn’t no money. It’s 4-5 years of them renewing.