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chris macdonald

@ccmm.bsky.social
289 followers 474 following 226 posts

Postdoc @fraserlab @willowcoyote at UCSF, messing around with proteins. Sentimental empiricist.

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Reposted by chris macdonald
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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chris macdonald @ccmm.bsky.social · 10/08/2026
the twin specters of l'islamo-gauchisme and le wokisme haunting twitter
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chris macdonald @ccmm.bsky.social · 05/06/2026
saw that as lee hazlewood and was very confused for a second
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chris macdonald @ccmm.bsky.social · 29/05/2026
electrons smh
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chris macdonald @ccmm.bsky.social · 29/05/2026
“elections” like there’s more than one
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chris macdonald @ccmm.bsky.social · 23/05/2026
is this loss?
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chris macdonald @ccmm.bsky.social · 10/05/2026
the “reserve?” i went there this morning and it was unsettling
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jamelle @jamellebouie.net · 09/05/2026
the most anti free speech administration in this country’s history
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Simon Willison @simonwillison.net · 28/04/2026
Available as a TTF font here bsky.app/profile/dftb...
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 21/04/2026
May's Variant Effect Seminar features Thea Klarsø Schulze of the MRC Laboratory of Molecular Biology, Cambridge, UK and Jerome Freudenberg from the Pimentel lab at UCLA, USA. Bookmark the event in your calendar: www.varianteffect.org/seminar-seri... #AtlasOfVariantEffects
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chris macdonald @ccmm.bsky.social · 12/04/2026
i haven’t watched the world tour in a few years…is pogacar winning roubaix now too?
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chris macdonald @ccmm.bsky.social · 11/04/2026
do you know if maven/automation used as a justification for rif or just a side effect?
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chris macdonald @ccmm.bsky.social · 11/04/2026
yes
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chris macdonald @ccmm.bsky.social · 11/04/2026
i appreciate the insight from someone who’s used them.
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chris macdonald @ccmm.bsky.social · 11/04/2026
i remember as an insomniac teen it was nice to turn on the radio at 3 am or so and feel like the world wasn’t as empty as it felt…not sure streamers are an improvement.
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chris macdonald @ccmm.bsky.social · 11/04/2026
is there an element of these tools shifting the (percieved) moral responsibility for targeting onto an automated system? have you seen kevin baker’s piece on maven? www.theguardian.com/news/2026/ma...
theguardian.com
AI got the blame for the Iran school bombing. The truth is far more worrying
LLMs-gone-rogue dominated coverage, but had nothing to do with the targeting. Instead, it was choices made by human beings, over many years, that gave us this atrocity
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chris macdonald @ccmm.bsky.social · 11/04/2026
economists independently discovering decades-old fields, a tale as old as time
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Magnus Kjærgaard @proteinmagnus.bsky.social · 10/04/2026
Why are de novo designed proteins so extremely thermostable? We try to answer this question by dissecting the thermodynamics of unfolding of mini-binders emerging from our protein design pipeline – and establish a convenient GUI for data analysis in the process. doi.org/10.64898/202...
Graphical abstract for pre-print showing a) theoretical model for thermostability, b) a GUI based analysis platform, c) protein denaturation data of mini-binders assessed by nanoDSF and d) a correlation plot that shows the de novo designed mini-binders have a much lower deltaCp than expected for a protein of their size.
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chris macdonald @ccmm.bsky.social · 10/04/2026
it’s really not good.
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chris macdonald @ccmm.bsky.social · 03/04/2026
it’s no efv
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Nils Homer @nilshomer.com · 31/03/2026
If you use fgbio or UMIs at all, you should start using fgumi. Up to 100x faster, and soon 2x faster sort than samtools, it’s been a labor of love and something we’ve wanted to do for a long time.
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chris macdonald @ccmm.bsky.social · 30/03/2026
That seems worth unpacking a little bit more. Not a great sign
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chris macdonald @ccmm.bsky.social · 30/03/2026
condolences
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Ben Good @benjaminhgood.bsky.social · 27/03/2026
Happy to share the final version of @oliviamghosh.bsky.social's paper on inferring low dimensional phenotype-fitness maps from high-throughput fitness measurements across environments. Fun collaboration with @oliviamghosh.bsky.social, @grantkinsler.bsky.social, & @petrovadmitri.bsky.social
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chris macdonald @ccmm.bsky.social · 26/03/2026
en.wikipedia.org/wiki/Assassi...
en.wikipedia.org
Assassination market - Wikipedia
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NPR @npr.org · 15/03/2026
Associated with the Frankfurt School, Habermas was a world-renowned thinker on modernity and democracy who helped shape German post-war and post-reunification political discourse. n.pr/3Nptb1g
n.pr
Acclaimed 20th century philosopher Jürgen Habermas dies at 96
Associated with the Frankfurt School, Habermas was a world-renowned thinker on modernity and democracy who helped shape German post-war and post-reunification political discourse.
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jproney @jproney.bsky.social · 13/03/2026
I'm excited to announce some major updates to our ProteinEBM paper with Chenxi Ou @sokrypton.org!
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chris macdonald @ccmm.bsky.social · 12/03/2026
common misconception. he does have a ranger tab though
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chris macdonald @ccmm.bsky.social · 07/03/2026
didn’t realise it was by mark herman. that boy gets around
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Joshua Weitz @joshuasweitz.bsky.social · 07/03/2026
The data is in: the NIH goalposts have shifted. What were once almost certain fundable scores have become coin flips and what used to be likely grants have become aspirational, leading to fewer awards. Another manifestation of how HHS policies have led to fewer awards and less science.
Graph of award probability of R35 and R01 from NIH factbook as a function of review rank percentile. As is apparent, 2025 is a significant departure, with lower award probabilities at all scores <40 and significant departures from norm, where even being in the top 10% is no longer a nearly certain indicator of success.

Data source: https://report.nih.gov/nihdatabook/report/302
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chris macdonald @ccmm.bsky.social · 06/03/2026
gulf strike?
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Andrew Straw @andrewstraw.bsky.social · 06/12/2025
Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too! preprint (with videos!) + thread 🧵 Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking www.biorxiv.org/content/10.6... 1/9
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Marsh's Library @marshslibrary.bsky.social · 17/12/2025
A break from Christmas content to enjoy this capybara eating a banana. From François Froger's 'A relation of a voyage ...' (London, 1698).
17th century engraving of a capybara under a palm tree eating a banana
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Yamuna Krishnan @krishnanyamuna.bsky.social · 17/12/2025
Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
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chris macdonald @ccmm.bsky.social · 04/12/2025
they’re opening the john jones underground warfare school of excellence soon
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chris macdonald @ccmm.bsky.social · 04/12/2025
chud ops
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John Ganz @lioneltrolling.bsky.social · 16/11/2025
The weekly Reading, Watching post.— www.unpopularfront.news/p/the-maga-m...
unpopularfront.news
The MAGA meltdown; Mamdani's Rainbow Coalition; Remembering Tatsuya Nakadai
Reading, Watching 11.16.25
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The Flenser @theflenser.bsky.social · 03/10/2025
Agriculture’s new album The Spiritual Sound is available everywhere today. The record is a study in joy and intensity, carrying forward the ecstatic spirit of their debut while pushing deeper into grief, transcendence, and renewal. Listen: youtu.be/k9yMIboriEY @agriculturemusic.bsky.social
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chris macdonald @ccmm.bsky.social · 14/09/2025
try woodman’s before you decide
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chris macdonald @ccmm.bsky.social · 12/09/2025
toothbrush
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chris macdonald @ccmm.bsky.social · 10/09/2025
labor discipline
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Matt Barber @biobarber.bsky.social · 22/08/2025
Excited to share the latest work by outstanding PhD student @kdc509.bsky.social. This was one of our first forays into experimental evolution and uncovered some cool connections between potassium transport and antimicrobial resistance in S. aureus. Major kudos to Killian!
journals.asm.org
Evolution of polyamine resistance in Staphylococcus aureus through modulation of potassium transport | mSphere
Staphylococcus aureus is a leading cause of infectious disease-related deaths globally. Understanding factors that govern adaptation and survival of S. aureus and other pathogens in the host environme...
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joycecaroloates.bsky.social @joycecaroloates.bsky.social · 21/08/2025
Quality time in the catio reading & napping
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Mrs. Detective PikaBOO, Esq. @clapifyoulikeme.favrd.social · 06/07/2025
They finally made the milk from that hotel
a ½ gallon of neutral milk
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Tim Stearns @stearnslab.bsky.social · 07/07/2025
UCSF Asilomar retreat t-shirt, 1990
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chris macdonald @ccmm.bsky.social · 01/07/2025
to be fair the vast majority of drug discovery pre-AI has also ended up with toxic compounds
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chris macdonald @ccmm.bsky.social · 01/07/2025
this whole album smacks of gender
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The Quietus @thequietus.com · 28/06/2025
Members of #Senyawa and Emptyset join forces with Sam Slater and Oscar-winning composer Hildur Guðnadóttir for an exploration of machine learning that sounds thrillingly alien Osmium - Osmium buff.ly/5jLhEs4 @invadarecords.bsky.social
Osmium - Osmium album cover. A kind of runic mark made of 6 double headed fork shapes against a black background.
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