James Hawley, PhD
@jrhawley.scholar.social.ap.brid.gy
6 followers 3 following 34 posts
I use math and computers to study cancer biology. Senior Computational Biologist at Roche. PhD in computational biology and cancer epigenetics from the Department […] 🌉 bridged from ⁂ https://scholar.social/@jrhawley, follow @ap.brid.gy to interact
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Reposted by James Hawley, PhD
rebeccasear.bsky.social
Cites this excellent piece: "A university isn’t a town square where anyone has the right to say anything they like... Universities contribute to society not by producing more speech, but by producing better speech. Our business is quality, not quantity"

academicmatters.ca/free-speech-...
Free speech and the battle for the university - Academic Matters
At the University of Waterloo, a controversial talk had the faculty association looking for creative ways to respond. How did the faculty [...]
academicmatters.ca
Reposted by James Hawley, PhD
jonny.neuromatch.social.ap.brid.gy
with regard to Jay of bluesky suggesting they would platform engineer away the dynamics that lead to people demanding jesse singal be banned, reminder to our members that

a) you can report me or any of the members of the social working group and the reported person will not be involved in […]
Original post on neuromatch.social
neuromatch.social
Reposted by James Hawley, PhD
riannawalcott.bsky.social
Hello! I’m Rianna, an assistant professor of communication at university of Maryland.

I research Black (British) identity, community, and communication practices on social media and our relationship to the broader Black diaspora!

I wrote this in April 🔮 just-tech.ssrc.org/field-review...
#RIP Twitter: The Conditions of Black Social Media Platform Migration
ABSTRACT Elon Musk’s acquisition of Twitter on October 31, 2022 has left Black Twitter reeling in the wake of over a year of turbulence, with constantly changing affordances rendering the...
just-tech.ssrc.org
Reposted by James Hawley, PhD
gedankenstuecke.scholar.social.ap.brid.gy
Just made the PR to sign @jaredwhite's open letter for a community fork from #rails, to get away from fascist DHH.

I'm not really using Rails any longer, so I don't know that my voice carries any weight here. But, for 14 years we ran openSNP on Rails, providing the world with an open […]
Original post on scholar.social
scholar.social
jrhawley.scholar.social.ap.brid.gy
I really like this article

https://thenode.biologists.com/the-paradox-of-doctoral-training/careers/

You can see how funding impacts science via grad students and postdocs. Positions may not be available until funding is secured, which then means the new hire will work on a pre-existing idea […]
Original post on scholar.social
scholar.social
Reposted by James Hawley, PhD
futurebird.sauropods.win.ap.brid.gy
Starting today I'm going to become more aggressive about supporting independent media and journalism.

I'm not wealthy enough to make a big difference on my own but I think this is something that could have an impact if enough people with a little handful of disposable income and deep concerns […]
Original post on sauropods.win
sauropods.win
Reposted by James Hawley, PhD
nonilex.masto.ai.ap.brid.gy
#trump #epa tells scientists to stop publishing studies, employees say
Staff from the EPA’s Office of #water were summoned to a “town hall” meeting this week & told to pause the publication of most #research, pending a review.

#publichealth #climate #pollution #science #law […]
Original post on masto.ai
masto.ai
jrhawley.scholar.social.ap.brid.gy
Wow, setting default labels for your data in #rstats using "label" attributes is a good idea. I'd never heard of this before, but I'm glad that #ggplot2 is now supporting it. Manually specifying axis labels was a bit tedious.

I do like that if you transform the data, the default label is not […]
Original post on scholar.social
scholar.social
Reposted by James Hawley, PhD
egonw.social.edu.nl.ap.brid.gy
reading https://liberdon.com/@linux/115163461488053805

What if @zotero had a #fediverse plugin and that plugin would listen to certain hashtags, like #icanhazpdf, and would reply to the requesting account *and* the fediverse account linked to the person of the Zotero account, or just send the […]
Original post on social.edu.nl
social.edu.nl
Reposted by James Hawley, PhD
marekmcgann.sciences.social.ap.brid.gy
The more I learn about history, the more I understand how important learning about history is. This is doubly important in my own professional field.

@olivia and colleagues driving home the point against the inevitability of AI reminding us of this.
When we engage with the public, we notice people think that AI, as a field or a technology, appeared on the scene in the last three years. And they experience confusion and even dissonance when they discover the field and the technologies have existed for decades, if not centuries or even millennia (Bloomfield 1987; Boden 2006; Bogost 2025; Guest 2025; Hamilton 1998; Mayor 2018). Such ahistoricism facilitates “the AI-hype cycles that have long been fuelled by extravagant claims that substitute fictionforscience.”(Heffernan, 2025,n.p. Duarte etal.2024).
Reposted by James Hawley, PhD
thomas-sandmann.genomic.social.ap.brid.gy
This week I learned how to manage project-specific R libraries with {rv}, a relatively new, declarative alternative to the well-established {renv} R package: https://tomsing1.github.io/blog/posts/rv/ . {rv} is a command line tool, written in rust, and I really like how it leverages repository […]
Original post on genomic.social
genomic.social
Reposted by James Hawley, PhD
jonny.neuromatch.social.ap.brid.gy
#sciop hit a Petabyte (actually a Pebibyte but nobody knows that word) of total proven capacity a week or two ago. That's all the seeders * the size of the things they are seeding. All volunteers, zero dollars in funding, piggybacking off existing resources […]

[Original post on neuromatch.social]
Indexing 233 datasets
with 927 uploads.

13416 peers, 8590 seeders sharing
216.8 TiB in 8514732 files.

Swarm capacity 1.0 PiB
jrhawley.scholar.social.ap.brid.gy
I recently finished "Proofs and refutations" by Imre Lakatos. I went into it thinking that an artificial dialogue between a teacher and students about the philosophy of math couldn't possibly live up to the hype. But honestly, I really enjoyed it!

The students are modelled on real […]
Original post on scholar.social
scholar.social
jrhawley.scholar.social.ap.brid.gy
I encountered a strange problem, trying to transfer my #zotero library from one account to another. I couldn't find a solution to my problem anywhere online, so I wrote up my solution here:

https://jrhawley.ca/2025/08/28/performing-surgery-on-my-zotero-database
Performing surgery on my Zotero database
I love Zotero and use it to manage my academic papers and citations. But I encountered a unique problem with my setup that I couldn’t find a solution for in the Zotero forums or anywhere else online. So, for posterity, I’m going to write out the problem and how I solved it, just in case anyone else runs into a problem like this. # The problem with multiple accounts In grad school, I set up an online account with Zotero using my university email address. I didn’t need to do this, since I didn’t make use of the cloud syncing, but sharing documents between groups does require this, so I made one anyway. Over the course of my degree, I saved thousands of articles in my personal collection. Zotero was simply the best tool I needed for citation management. My problem arose from a few elements: 1. I forgot my password for that account 1 2. After graduating, my university deprecated my email address, switching from `@mail.utoronto.ca` to `@alumni.utoronto.ca` 2 This meant that I could no longer log in to my Zotero online account, and couldn’t use the “Forgot my password” link since I wasn’t receiving emails at my university email account. I wanted to start paying for the cloud storage service 3, but without being able to access my account, I couldn’t do that anymore. # Items don’t transfer easily between accounts I thought the simple solution to this problem would be to make a new online account, and then transfer everything over on my local database. I hadn’t previously made use of the cloud syncing, so I didn’t have anything to lose from the old account. This turned out to be much harder than I expected it to be. If you unlink your account, your data doesn’t necessarily get deleted. However, if you attempt to sync your library to a new account, all the data in your current library that is associated to a different linked account gets removed. I tried exporting my library into the “Zotero RDF” or other formats, but there was always some missing information, such as the annotations, tags, or the PDFs themselves. Manually restoring this library for thousands of items is not feasible, so I needed to find another way. # Exploring the Zotero database One of the things that makes Zotero so powerful is its database and schema. It’s all contained in the `zotero.sqlite` database file, stored within your library location. In my case, I can use You can use any SQLite database explorer to browse through the contents of this database. I like TermDBMS for quick tasks like this, but you may prefer other tools like LazySQL or DB Browser for SQLite. With `termdbms`, you can interactively explore the database by running this in a terminal: termdbms -p ~/Documents/Zotero/zotero.sqlite Navigating to the `settings` table, you should see your username and other account information. The `account.username` and `account.userID` fields contained information for my old account, which I needed to update to my new account. # Switching my database to the new account The quickest way to fix this issue was to perform some digital surgery and manually edit the Zotero database. But before I made manual edits, I backed everything up first. I cannot stress this enough: **back everything up before editing any critical files**. I then looked for all occurrences of the old account’s `username` or `userID` within the SQLite databse by running `strings`. This highlighted the account settings in the `settings` table, as shown above, but it also highlighted the syncing URLs for items in the `itemRelations` and `syncCache` tables, which I was previously unaware of. These tables contain URLs any files synced to Zotero’s cloud storage, which should not point to the old account. I knew the new account’s username, but I did not know what the `userID` should be. To find it out, I created a new local Zotero profile by running: zotero -p This new local profile will create an entirely new Zotero library and SQLite database. Once this process was completed, I linked the empty database to my new account via the settings. I then used `termdbms` to find the new `userID` value from the `settings` table, like above. I then used termdbms to do the following on the old database containing all the files I wanted to transfer: 1. Update `settings.account.username` and `settings.account.userID` to the new account’s username and ID, respectively 2. Truncate the `itemRelations` and `syncCache` tables After re-opening Zotero, I let the library sync with the cloud storage, which took a couple hours. # Conclusions This was a tricky problem to solve, as I have little experience with databases and couldn’t find any relevant information on the Zotero forums. But thanks to Zotero’s use of the SQLite (instead of a proprietary format) and some experience with the terminal, I was able to make the manual changes I needed. This new database has been working perfectly for me ever since. # Footnotes I have no idea where it went and searched everywhere for it, including backups of my password manager database, without any luck. 1. I’ve used a password manager for years, but somehow this password went missing. ↩ 2. Sometime during this process, emails sent to my `@mail.utoronto.ca` address stopped being forwarded to `@alumni.utoronto.ca`. ↩ 3. And to finally support Zotero financially after all the years I used it for free in grad school. ↩
jrhawley.ca
Reposted by James Hawley, PhD
ben.werd.social.ap.brid.gy
If we're thinking about building GitHub alternatives, let's build ones that host not just code but everything involved in building software, including the community work involved in validating assumptions and making sure we're solving real problems, equitably, for the people we're trying to help.
Reposted by James Hawley, PhD
tante.tldr.nettime.org.ap.brid.gy
By now I am basically just a Conscientious objector to "AI".
Reposted by James Hawley, PhD
dx.social.ridetrans.it.ap.brid.gy
Just got contacted by a recruiter for a venture-backed startup looking to replace 911 operators with LLMs to triage emergency calls and boy I can’t express how much A) no I do not want to join your company, and B) how much I do not want to live in the world where 911 calls are handled by LLMs
Reposted by James Hawley, PhD
sundogplanets.mastodon.social.ap.brid.gy
THIS ESSAY IS SO GOOD. I don't know that I've ever read an essay so thoroughly saturated with sarcasm and yet devastatingly accurately shredding someone's stupid ideas. This is the kind of essay our world needs right now […]
Original post on mastodon.social
mastodon.social
jrhawley.scholar.social.ap.brid.gy
I wrote about a list of blogs that I really enjoy reading, and some of them are #math and #science focused that I thought others might appreciate.

https://jrhawley.ca/2025/08/13/blogroll
Blogroll
I like reading people’s blogs. Not so much the professionally-produced multi-person newsletter with editors and income streams, but the ones by people who tinker on their own websites, academics, creative people, and anyone else who writes with such passion and insight that you can’t help but soak up whatever they publish. I also like writing blog posts. They serve as a space for me to think about personal and professional topics and wrestle with them in a way that is still focused on communicating some interesting idea to someone else. But between being a parent, relationships, work, and re-emerging fascism as a ludicrous attempt to thwart off the effects of climate change, economic inequality, and human rights atrocities, I have been finding it tough to find the time or motivation to write on my blog. It’s hard to have it all 🤷. However, smart people from the past and smart people from the present have written that doing _something_ is better than doing nothing than stewing in the anxiety and dread brought on by the bleak world around you. And _joy_ is something worth finding and sharing. So I have been doing my best at being a parent, leaning into my personal relationships, thinking about cool things at work, reading vociferously about politics and history, and learning from amazing people who write amazing things and put it online. To that end, I’d like to share some of the blogs that bring me joy that I believe others will also appreciate. ## Standouts * Bartosz Ciechanowski This is, hands down, one of the single most impressive blogs I’ve ever seen. Ciechanowski takes generic topics like GPS, mechanical watches, or bicycles, and creates stunningly educational and interactive explainers. Almost everything on the page is his own custom work and the design of the pages and the integration of the text, highlights, colours, and visuals are incredibly cohesive while also being simple and clear. It’s no surprise he only publishes a few posts a year. * “A Working Library” by Mandy Brown Brown is one of those writers you’re always jealous of. In essays long and short, she’s seamlessly able to weave together ideas from multiple writers, and infuse them with a love of humanity and reflection that I’d love to emulate. Some recent favourites of mine are Toolmen, Remote to who?, and Against optimization. * “Miniature Calendar” by Tatsuya Tanaka Unlike every other blog I mention here, Tanaka is an artist, rather than a writer. But his Miniature Calendar collection is astounding both for his creativity and his consistency. Every day, Tanaka publishes a photograph of some miniature scene he has constructed with any materials he can get his hands on. Keychains, bananas, slippers, you name it. And I do mean _every day_ - he’s published a new scene every single day since 2011. ## Canadiana In my opinion, too much of the internet is centred on the United States. Learning about unique aspects of Canadian history and culture is something that I value, both to improve my understanding of the country I live in, and to push back against the monoculturalism that results from (social) media based in the US and other countries. * “Active History” This is a blog run by historians at the University of Saskatchewan and Huron University College that does many things, with publishing essays being one of them. From public housing in Toronto and the everyday politics of Indigenous land and identity to the 1919 wave, there are lots of interesting pieces of Canadian history and politics that you can learn about here. * “Corruptario” by Jordan Roberts Doug Ford is a crook, as are many of the people around him 1. Independent news outlets like The Narwhal and The Local have covered many similar stories (and I highly recommend them both), but Roberts does a good job at highlighting the personal, financial, and political connections to political offices in Ontario. * Sean Boots Boots is a public servant working on technology for the Government of Yukon. I first learned about him from his excellent keynote at FWD50 in 2023, and I like his infrequent yet thoughtful comments on how the Canadian bureaucracy works and how it can better serve the needs of everyday people. ## COVID-19 Many people may be done with COVID, but COVID isn’t done with us. * “The Gauntlet” by Julia Doubleday Doubleday has long COVID, a chronic illness with a myriad of symptoms that can last for months to years after a SARS-CoV-2 infection. This blog is a place where she documents both what it feels like to be put through the gauntlet, and to address the many layers of eugenics, ableism, denialism, and ignorance that pervades public health and healthcare in the US. Her writing is more forceful than many and, given her chronic condition, I can only imagine how much effort each of her insightful essays requires. If you like Doubleday’s writing, I would also recommend Pandemic Accountability Index by J. J. Kogburne and The Disabled Ginger by broadwaybabyto 2. * “Still COVIDing Canada” This is a website that aggregates news articles about COVID and public health in Canada and around the world. The authors work hard to provide information and resources for individuals who want to keep themselves safe and be informed about the lack of protection in healthcare and public settings in Canada. The authors also publish a monthly newsletter, “The COVID Times”. * “The Sick Times” This is a similar publication to Still COVIDing Canada, but based in New York. It was founded by independent journalists and has a strong editorial and advisory board that I’ll also recommend. ## Math & science I love math and science, and I feel privileged to study them both in my career. I read an obscene amount of papers in these areas, but academic writing is often stale and robotic 3. Blogs by people who work in these areas are a happy medium - interesting tidbits that were left out of papers, perennial problems that keep people thinking, and a relaxed attitude are all things I find in these blogs and in conversation with colleagues that I don’t get from journal articles. * “Not Even Wrong” by Alex Woit Woit is a Senior Lecturer in the Mathematics department at Columbia University. He writes a lot about quantum theory, issues with string theory as the dominant player in the space of grand unified theories of physics, and other topics in math and physics. While I’m not familiar enough with the topic to assess its validity, I’ve been entertained by his ideas on Euclidean twistor unification. Most recently, he has been writing about The Situation at Columbia, with respect to the US federal government’s mob-style shakedown of the university. He provides an interesting insider’s perspective about events as they unfold. There are also links to many interesting math and physics blogs on the blog, if you want to browse those, too. * “Statistical Modeling, Causal Inference, and Social Science” This is a blog from a number of different researchers, with Andrew Gelman being the most frequent. These academics have decades of experience in Bayesian statistics, and many of them are behind the Stan programming language for statistical computing, which makes use of Hamiltonian Monte Carlo. I like the behind-the-scenes perspective on statistical research and applications in a variety of fields, and this is one of the few blogs that I read where I find the comments insightful! I’ve learned a lot of applied statistics from this blog and have used it as a starting point for some statistical research in my work. * “Notes from a data witch” by Danielle Navarro Navarro is a self-described “recovering academic” who writes a lot about R, data science, and Bayesian statistics. She’s a co-author on the 3rd edition of the ggplot2 book with Hadley Wickham and Thomas Lin Pedersen, and has recently worked with scientists as Genentech to publish a book about Bayesian analysis of drug response data. Her blog posts are humorous and densely packed with information, and she also does generative art! And by “generative art” I mean using randomness and programming languages to create art, not the soulless JPEGs produced by “generative AI”. There’s lots to learn from here. * Heng Li Li is a superstar in the field of genomics, as far as “stardom” counts for anything in academia. He’s an Associate Professor of Biomedical Informatics at the Dana-Farber Cancer Institute and Harvard Medical School, and is a superstar because he’s the lead author on the BWA short read aligner, samtools, and many other tools and specifications that are the foundation for the entire field of genomics. He blogs infrequently, but when he does, you get to see how many ideas that we take for granted in genomics are far more complicated than you might think. I’d recommend his posts about where BWA came from, the early history of the SAM/BAM format, and what goes into correcting Illumina sequencing errors. * Terence Tao Tao is another academic superstar, but this time in math. He is a Professor in the Department of Mathematics at University of California: Los Angeles, a director of the Institute for Pure & Applied Mathematics, and he won the Fields Medal in 2006 for his contributions to partial differential equations, combinatorics, harmonic analysis and additive number theory. He’s a prolific mathematician and still manages to blog a few times a month. He has career advice for different stages of one’s life, tips for writing math papers, and publishes regularly about his work. This blog is one of the things I love about the internet - you get the read the thoughts of world-class experts in their fields in a way that is almost impossible to, otherwise. * n-Category cafe This is a group blog written by mathematicians that focuses on category theory. As someone who doesn’t know that much about category theory 4, I find this blog just delightful. There are so many connections between category theory and other areas of math, and some of the authors, like John Baez just seem to have so much fun in geeking out on all manner to topics. Some posts are technically challenging, others are very introductory, all are informative. There’s a lot to choose from here, with posts going back to 2006. ## Computers & technology As a computational biologist and some who has loved computers since he was 10, I read, write, and use a lot of computers and software. I like reading about novel ways that people use computers and the bigger sociopolitical ecosystem around computers as a technology. Here are a few people who writes interesting things in this area. * Julia Evans Evans is the kind of person I wish everyone had as a computer programming teacher. She just does such an incredible job of taking programming novices’ concerns seriously, distilling computer quirks into understandable zines, and making computers fun. Seriously, go check out her zines. They’re amazing. * Ethan Marcotte Marcotte is a web designer who literally wrote the book on “Responsive Web Design”, as well as a few other important ones that I’ve enjoyed. He used to work at 18F, the US government organization that focused on procurement, design, and building web services that worked, before the Trump administration murdered the organization. Not only is his website gorgeous, he writes short things about important topics that I really enjoy 5. * Erin Kissane Kissane spends a lot of time thinking and writing about networks. How do computer networks coexist with networks of people and how do those dual networks interact with each other in good and bad ways? Her talk at the 2024 XOXO festival emphasizes that collectively we need to “fix the fucking networks”, she makes interesting observations about governance models of Mastodon and the fediverse, and compiled a lot of information to show just how involved many people at Meta were complicit in the genocide of the Rohingya people in Myanmar. * Alex Kladov Kladov is a software engineer who was intimiately involved in one of my favourite bits of software: the rust-analyzer language server. A lot of his writing has focused on the Rust programming language, but he writes about lots of other interesting topics as well. One of my favourite posts is his resilient LL parsing tutorial. It helped me understand what goes into language servers, what differentiates parsers from compilers, and other topics that come up in computer science classes that I never took. * Yoshua Wuyts Wuyts is another person who writes a lot about the Rust programming language, as he’s a member of multiple working and project groups within the Rust development team 6. But where most programmer blogs focus on building things and writing about the process, Wuyts focuses on different ways of building a language and how that impacts what you can do with it. It’s tough to describe the quality of technical writing here without getting too deep into the weeds, but his posts about the syntax of match statements, the difficulties with `Pin`s, and how asynchronous programming interacts with generics, performance, and ergonomics. If this type of material is your thing, I would also highly recommend “Without boats, dreams dry up” by Saoirse. ## Conclusions There you have it, some of my favourite blogs on the internet. I left out lots of others I do read and listen to, like authors, journalists, podcasters, and musicians because I wanted to focus on individuals and blogs where I could. Reach out to me if you found someone new you like, or have any recommendations for me. ## Footnotes 1. This is not news. The Ford brothers’ history with drug dealing is well-documented and has been known for over a decade. I also happen to know one of these associate crooks personally. It’s always fun to see losers from high school use their family connections to fail their way upwards into positions of authority that they then abuse for personal gain. ↩ 2. All three of these writers publish on Substack and I largely don’t point people to Substack because Substack has a Nazi problem. Substack’s leaders refuse to do anything meaningful about it despite far right extremists openly using the platform to promote fascism and white supremacy. It’s almost like these tech executives are making too much money by supporting reactionary viewpoints. But Doubleday and others like her started publishing via Substack before the company’s moderation issues came to light. I don’t want to sit here and admonish them for not having the ability or financial security to adjust their infrastructure on-the-fly without acknowledging how high transition costs can be. Switching platforms can cause short term headaches and long term financial problems if all of one’s patrons aren’t able to make the switch seamlessly. Some of these writers have enough to deal with already, like chronic illnesses, without sanctimonious people like me piling on with “you’re using the wrong platform”. In short, solidarity over moral purity. ↩ 3. Mine included. I’m working on it. ↩ 4. My biggest exposure to category theory is from The Joy of Abstraction by Eugenia Cheng, which is just an amazing book. I’ve never seen a love of math expressed in such a way that so closely mirrors my own feelings on the topic. Please go read it. ↩ 5. In fact, his recent post about newsletters is finally what pushed me over the edge to write this blogroll post I’ve been meaning to write. ↩ 6. One of the things that I have loved about the Rust programming language is their teams structure and governance model. No single governance model is perfect, but they have had an excellent track record of building an amazing language and programming community over the course of a decade. I have yet to see any other language reach the same level of performance, robustness, effectiveness, and adoration from people within and without the Rust community. I believe this governance structure and the people behind it are a big reason why. ↩
jrhawley.ca
Reposted by James Hawley, PhD
hrbrmstr.mastodon.social.ap.brid.gy
yay? it seems BH/DC was a covid superspreader combo event.

just a reminder that long covid rly sucks and covid itself changes the body and brain in pretty terrible ways.

i guess we're never gonna learn.
Reposted by James Hawley, PhD
gedankenstuecke.scholar.social.ap.brid.gy
Between #GiveUpGitHub and #inaturalist jumping the "AI" shark, I'm extra grateful for infrastructures like @Codeberg that have democratic governance mechanisms to give contributors a real vote and power in decision making.

I hope more folks use those opportunities to find infrastructures that […]
Original post on scholar.social
scholar.social
Reposted by James Hawley, PhD
Reposted by James Hawley, PhD
himself.bsky.social
An amicus brief from LessWrong warning that the existence of 10^46 putative future sentient beings depends on the class action being denied.
jjaron.bsky.social
I believe they call this "finding out" arstechnica.com/tech-policy/...
Reposted by James Hawley, PhD
petrichor.digipres.club.ap.brid.gy
Tentatively announcing that I expect to be available for consultancy 1-2 days a week from mid-September onward.

I have 15 years experience bridging the gap between people and technology through:
👨🏻‍🏫 Training
📝 Technical writing
🌐 Community building
📑 Research & analysis
🏗️ Service development […]
Original post on digipres.club
digipres.club