Joe Thornton

A general substitution matrix for structural phylogenetics. Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

Hey #Chicago science folks. It's time to get out there with everyone else fighting. @standupforscience.bsky.social stands together with @indivisiblechicago.bsky.social for No Kings Day this Saturday June 14.
Find your rally at
www.nokings.org #nokings 👑❌

Harvard will not comply.

“No government — regardless of which party is in power — should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue.”
— Harvard President Alan M. Garber

www.thecrimson.com/article/2025...

Opinion | This Is How Universities Can Escape Trump’s Trap, If They Dare (Gift Article) It’s been tried in other countries facing authoritarian crackdowns. It works.

www.nytimes.com/2025/04/14/o...

Science Under Threat in the United States: Feeling abandoned but energized Many individual researchers are frustrated by the response - or the lack of a response - from universities to a growing crisis.

My OpEd in @elife.bsky.social

“It feels as if we are trying to fight a series of attacks on science with one arm tied behind our back and our lips half sewn shut.”

“Yet we are not beaten, and some of us are downright energized.”

elifesciences.org/articles/106...

Adapted from @lizneeley

The government’s attack on Columbia University has nothing to do with addressing antisemitism. The goal is to force universities to police and punish students and faculty to Trump’s liking — to use our universities against us to obliterate political protest and chill discourse.

This attack on Columbia University is patently illegal, but the bully could still succeed by making other universities cower and pre-submit to the White House's climate of fear. Solidarity!

Message from SMBE Leadership

Letter from the SSE/SSB/ASN councils on the scientific understanding of sex and gender, pls RT

I usually reserve this account for my personal views; but today I want to represent my position as President of @asn-amnat.bsky.social to post a message that will shortly go out to the membership of the American Society of Naturalists from the ASN Executive Council

I see no other institution that has taken a position as unnecessarily restrictive of research, and as submissively precompliant, as that taken by the University of Chicago. bsky.app/profile/jere...

Guidance from Stanford leadership on the OMB memo.

Trump Administration Live Updates: White House Orders Federal Grants Pause (Gift Article)

The sword has now been brandished over civil society, including scientists, universities, and other NGOs. Who, including university presidents, will have any backbone in defending their jnstitutions’ missions? Or will they take on the Zuckerberg/ Bezos pose? www.nytimes.com/live/2025/01...

If a university increases the stipend by 15k per year with no compensation to labs, it also gives itself a big raise in overhead costs (~10k per year per student), which it takes from our grants, too. Does it really cost the university more to administer a higher stipend?

I have been told that Caltech reduced the tuition they charge to lab budgets to compensate for increased stipends. (But this has not been independently verified.) See link: lh3.googleusercontent.com/u/2/drive-vi...

Have they reduced the graduate tuition they take from your grant budgets? Reduced the overhead charges (typically 55-80%) that they impose on student stipends? Reduced the overhead they take on your salary as PI? Other ideas?

Scientists at universities that have raised graduate student stipends: What have your administrations done to mitigate the costs to lab budgets so that the science itself doesn’t have to be curtailed? Examples of best practices would be appreciated.

Dan, I’m so sorry about the loss of your dad. What a rich and inspiring life he led. May his memory be a blessing.

Midwest seasonal update

The Human Genetics and Genetics, Genomics & Systems Biology PhD programs at UChicago are hosting our second annual info session for prospective applicants.

Sign up at bit.ly/GeneticsInfo20… for application tips from a diverse panel of current PhD students and faculty!

And please repost! 🧪🧬🖥️

Here’s a powerful and insightful critique of “protecting science from woke-ism” rhetoric and policy. Written for a UK context, it’s very relevant in the US and elsewhere. Please read and consider signing.