Sign in

chris macdonald

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

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

PostsRepliesMedia
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/
215759
Reposted by chris macdonald
jamelle @jamellebouie.net · 09/05/2026
the most anti free speech administration in this country’s history
180120223660
Reposted by chris macdonald
Simon Willison @simonwillison.net · 28/04/2026
Available as a TTF font here bsky.app/profile/dftb...
0231
Reposted by chris macdonald
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
023
Reposted by chris macdonald
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.
34211
Reposted by chris macdonald
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.
0166
Reposted by chris macdonald
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
04217
Reposted by chris macdonald
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.
430777
Reposted by chris macdonald
jproney @jproney.bsky.social · 13/03/2026
I'm excited to announce some major updates to our ProteinEBM paper with Chenxi Ou @sokrypton.org!
14111
Reposted by chris macdonald
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
18698420
Reposted by chris macdonald
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
9376153
Reposted by chris macdonald
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
9560219
Reposted by chris macdonald
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
29546230
Reposted by chris macdonald
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
2315
Reposted by chris macdonald
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
0221
Reposted by chris macdonald
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...
44722
Reposted by chris macdonald
joycecaroloates.bsky.social @joycecaroloates.bsky.social · 21/08/2025
Quality time in the catio reading & napping
0431
Reposted by chris macdonald
Mrs. Detective PikaBOO, Esq. @clapifyoulikeme.favrd.social · 06/07/2025
They finally made the milk from that hotel
a ½ gallon of neutral milk
149134562572
Reposted by chris macdonald
Tim Stearns @stearnslab.bsky.social · 07/07/2025
UCSF Asilomar retreat t-shirt, 1990
0362
chris macdonald @ccmm.bsky.social · 01/07/2025
this whole album smacks of gender
010
Reposted by chris macdonald
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.
2222
chris macdonald @ccmm.bsky.social · 25/06/2025
In a fugue state years ago I guess I got David Pajo to do a cameo to congratulate me on getting my PhD and I just saw it now
110
chris macdonald @ccmm.bsky.social · 24/06/2025
I’m patenting a constant anti-unit of temperature called the Bernard. 1 B = 10^30. Then 30 °F is just 1.92 B and 100 °F is 2.19 B. The beautiful thing is then 1 = 1 B/B.
120
chris macdonald @ccmm.bsky.social · 22/06/2025
Not sure if this is anything
110
Reposted by chris macdonald
lastpositivist.bsky.social @lastpositivist.bsky.social · 14/06/2025
Paper is finally up and open access (www.journals.uchicago.edu/doi/10.1086/...), it's a sequel to an earlier paper where we'd argued that there's not good evidence that pre-publication peer review is a net benefit (www.journals.uchicago.edu/doi/10.1093/...). So in this one we suggest an alternative.
Jury Theorems for Peer Review
Marcus Arvan, Liam Kofi Bright, and Remco Heesen

Abstract:

Peer review is often taken to be the main form of quality control on academic research. Usually journals carry this out. However, parts of maths and physics appear to have a parallel, crowd-sourced model of peer review, where articles are posted on the arXiv to be publicly discussed. In this article we argue that crowd-sourced peer review is likely to do better than journal-solicited peer review at sorting articles by quality. Our argument rests on two key claims. First, crowd-sourced peer review will lead on average to more reviewers per article than journal-solicited peer review. Second, due to the wisdom of the crowds, more reviewers will tend to make better judgements than fewer reviewers will. We make the second claim precise by looking at the Condorcet jury theorem as well as two related jury theorems developed specifically to apply to peer review.
1523586
Reposted by chris macdonald
Nathan Kalman-Lamb @nkalamb.bsky.social · 15/05/2025
"The testimony the authors collected... should be enough to call for a national inquiry into the sport’s violently destructive nature, though it is highly unlikely that any such inquiry will be launched." @silkyweineck.bsky.social in @mid-theory.bsky.social on our @uncpress.bsky.social book.
mid-theory.com
What’s Love Got To Do With It?: A Review of ‘The End of College Football’
It is the love that is troubling: the love of violence (which fans prefer to call “physicality”), the love of an institution that invariably, though to variable degrees, maims its participants in p…
23620
Reposted by chris macdonald
Simon Lewis @simonlewis.bsky.social · 03/05/2025
Pretty shocking: the snake YouTuber designed the experiment to obtain the antibodies, and did the experiment on himself (carefully dosing himself with snake venom for 20 yrs!), and is not a co-author on the paper.
23612
chris macdonald @ccmm.bsky.social · 16/04/2025
Pretty cool stuff en.wikipedia.org/wiki/Bonnet_...
en.wikipedia.org
Bonnet theorem - Wikipedia
000
Reposted by chris macdonald
On This Day in Simpsons History @dailysimpsons.bsky.social · 14/04/2025
#OnThisDay April 14, 1996, Skinner purchased fast food to disguise as his own cooking at an unforgettable luncheon with Superintendent Chalmers, when “22 Short Films About Springfield” first aired on Fox. @thatbilloakley.com #TheSimpsons #SteamedHams
11883282314
chris macdonald @ccmm.bsky.social · 22/03/2025
010
chris macdonald @ccmm.bsky.social · 20/03/2025
seems bad. www.lbc.co.uk/world-news/d...
lbc.co.uk
Diplomatic row erupts after French researcher expelled from US for expressing 'a personal opinion' on Trump
A diplomatic row has erupted between France and the US after a French researcher was expelled from the country for expressing "a personal opinion" on Trump.
000
Reposted by chris macdonald
Chris Hayes @chrislhayes.bsky.social · 18/03/2025
This is a PhD student in *epidemiology*
17446791098
Reposted by chris macdonald
KLAB - finding a cure for GI dysmotility at #HarvardStrong @klab.bsky.social · 12/03/2025
UMASS IS RESCINDING ALL GRAD POSITIONS FOR THIS YEAR
14425651264
Reposted by chris macdonald
Tristan Yates @tristansyates.bsky.social · 11/03/2025
Last year, I was overjoyed to receive an NIH NRSA fellowship to study toddler brains and caregiving effects on memory at Columbia. Last night, my grant was terminated.
821002370
Reposted by chris macdonald
Mark Copelovitch @mcopelov.bsky.social · 08/03/2025
Here is UW - Madison's budget. Our <largest> funder is the federal government. 25%. It used to be the state. Either way, the university in its current form ceases to exist if these federal cuts really happen. But The. Public. Doesn't. Know. This. And our leaders are absent from the public debate.
221290523
Reposted by chris macdonald
David M. Perry @lollardfish.bsky.social · 04/03/2025
no one who went to an ivy league should write about american higher ed without spending a couple years working at a public university, ideally a community college or branch public. maybe he has!
516817
Reposted by chris macdonald
Albert Vilella, PhD. @albertvilella.bsky.social · 04/03/2025
China on Tuesday announced 10 US firms as 'unreliable entities': TCOM Limited, Stick Rudder, Teledyne Brown Engineering Inc., Huntington Ingalls, S3 AeroDefense, Cubic Corporation, TextOre, ACT1 Federal, Exovera, and Planate Mgmt, as well as Illumina $ILMN, all banned from exporting to China.
5157
Reposted by chris macdonald
depths of wikipedia @depthsofwikipedia.bsky.social · 19/02/2025
Slashed zero (0̸), a representation of the number 0 (zero) to distinguish it from the letter O
Slashed letter 'O' (O̸), a representation of the letter O to distinguish it from the number 0 (zero)
192140882690
Reposted by chris macdonald
Derek Lowe @dereklowe.bsky.social · 18/02/2025
Here’s the latest in the Continuing Crisis series - there will, unfortunately, be more:
science.org
The Continuing Crisis, Part IV
14214
Reposted by chris macdonald
Luis Zaman @luiszaman.bsky.social · 14/02/2025
Our Evolution of Evolvability work is finally* out! *technically it has been out for a bit, but all of ~this~ bullshit was happening www.pnas.org/doi/abs/10.1...
pnas.org
Evolution takes multiple paths to evolvability when facing environmental change | PNAS
Life at all scales is surprisingly effective at exploiting new opportunities, as demonstrated by the rapid emergence of antimicrobial resistance an...
25230
chris macdonald @ccmm.bsky.social · 17/02/2025
I wish you could still get posters like this.
000
Reposted by chris macdonald
Reconstructionist @unavaleable.bsky.social · 15/02/2025
we are gutting out competitive advantages and the stakeholders of our democracy don't care? what the fuck is wrong with america's elites?
541691188
Reposted by chris macdonald
Robert Kelchen @robertkelchen.com · 13/02/2025
It's time to start a thread on higher ed budget cuts announced due to actual and potential cuts to federal funding. Northwestern is placing additional scrutiny on all spending and trying to cut non-personnel spending by 10% this year.
dailynorthwestern.com
University leadership announces 10% non-personnel spending reduction, other immediate measures in response to political and financial uncertainty
A slew of executive orders and directives from President Donald Trump that put higher education funding on shaky ground has led Northwestern leadership to announce several immediate measures in respon...
37314181
Reposted by chris macdonald
Joanna Masel @joannamasel.bsky.social · 15/02/2025
Now seems a good time to mention that I haven't yet filled a postdoc position in phylogenetic methods. If you just lost your job, need something temporary, and know something about bioinformatics/statistics/evolution, talk to me.
37698
chris macdonald @ccmm.bsky.social · 14/02/2025
in positive news, I've discovered that calculus of variations makes a lot more sense with just a smidge of differential geometry...
000
Reposted by chris macdonald
Willem van Schaik @wvschaik.bsky.social · 11/02/2025
Heterologous protein over-expression in E. coli is now woke because of 'inclusion bodies'
918242