Titus Brown

great paper by @blekhman.bsky.social

"Because manuscripts reflected real progress towards our field’s goals, our assessment systems began relying on them as primary metrics...which is obviously flawed...Generative AI has broken this already-flawed proxy completely" journals.plos.org/plosbiology/...

woohoo! we've also integrated interledger's webmonetization standard into bridgy fed, so we can bridge this across networks 👀

Here is my pitch for anyone who has worries about rail: I think that building out rail is a necessary (but not sufficient) step in transforming American cities from totally car dependent to slightly walkable, in a way that no other form of transit is.

Status reports that ABC News deleted that explosive story about the Trump kids getting billions in federal contracts for their companies. ABC hasn't explained why they nuked the story, even as Trump has crowed about its deletion, sparking a firestorm behind scenes. www.status.news/p/david-elli...

Thank. You! Someone is following the through-line here.

honestly, who is shipping like this rn? companies like openai need a devday to tell you all the things they've copied from other companies, meanwhile open social web builders are actually innovating and forming communities the biggest orgs in the world wish they could. AND ETHICALLY, AT THAT.

Here’s what I do know. If someone white was doing half the stuff Blacksky has done in the last year, they’d be lauded as one of the most forward thinking and innovative people on the planet. But it just shows how progress is always happening, especially in places where folks don’t want to look

NEW: As gas prices soar amid Trump’s war in Iran, Republican Senate candidates are asking their own supporters to donate money to cover campaign fuel costs.

They started texting with a 16-year-old. After two years, they offered to sell him a gun. They consider that "stopping a terrorist attack." And they are calling it heroic. What an absolute embarrassment.

"Automate the routine work, and the humans are left with the rare, hard cases, with less practice than ever." Lianne Bainbridge, "Ironies of Automation" Automatica 1983. Quoted by Jana Chen, baseten SRE at O11y Day in London, a @honeycomb.io event.

"AI makes writing code cheap. It doesn't make attention cheap." - Jana Chen, baseten SRE, at O11y Day in London.

Throwing away code as part of building. "Falsework", like building architecture - the falsework is the stuff you build when putting up a bridge, that you later remove leaving the actual structure you were building for. Interesting idea at this @honeycomb.io O11y day.

Not sure I’ve ever seen an essay that so precisely hits the mark as this. Read it. Share it.

When I was writing about the System in Gnomon it felt considerably more distant than this. That book came out in 2017/18 and people laughed (if nervously) at the idea of your networked washing machine spying on you for a ubiquitous AI which was just there to improve your life.

Hidden but Expanding Sampling Bias Distorts Prokaryotic Genome Collections www.biorxiv.org/content/10.6... #jcampubs

Our new preprint is out! We show that genomically discrete and ecologically cohesive subspecies are a common feature in the global ocean microbiome, and represent a fundamental level at which ecological and evolutionary forces act to shape microbial diversity www.biorxiv.org/content/10.6...

This is getting a lot of quotes, so I feel I should correct this a bit (sorry @anildash.com!) “AI” was 100% born toxic! The first AI workshop was born from the field of “automata studies”, and…1/ (Pictured: the folks who convened for the first workshop. Notice anything notable here?)

Anand Giridharadas: Cities are very unfairly labeled as these 'problem centers' by Donald Trump. One thing worth remembering is a large chunk of those people who end up in cities were failed in other parts of this country. We are holding a lot of your people who you failed to love and take care of.

Are you interested in learning how genomes of weird fungi and protists evolve and are you looking for an exciting PhD opportunity? Jolien van Hooff and I are looking for an enthusiasic PhD candidate at Wageningen University: www.wur.nl/en/vacancy/p... #TEworldwide #Fungi #Protists #Genome

Any sane academic evaluation policy would forbid mention of Impact Factor

This autumn is the 10th anniversary of the publication of Written/Unwritten: Diversity and the Hidden Truths of Tenure. It came out during a heartbreaking time, my mom’s passing. I worked on copy edits and proofs from her living room, between medical appointments. uncpress.org/978146962771...

How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...

We are excited to share research, but I want to take some time to share a little about myself. I LOVE science, but I also spend a lot of time advocating for more inclusive science. This work is promoted by my own obstacles in pursuing science which I talk about here: www.cell.com/cell/fulltex...

Hello this is my colleague Jeff.

Enjoyed Corey Robin's essay "On Nikole Hannah-Jones" coreyrobin675129.substack.com/p/on-nikole-...

... and another from Cassie Ettinger and summer student Jennifer Arroyo on comparative genomic analysis of seagrass doi.org/10.1016/j.aq... and conservation of some of the genes involved in symbioses between plants and AMF (Fungi).

Congrats to the NEON Biorepository at Arizona State University for receiving funding from NSF to co-lead a project aimed at creating a national resource for sequencing and analysing the DNA of important species! news.asu.edu/20260924-env...

I can't get the search terms right... how, on Mac OS X, do you click the checkboxes in a Word document? I've been right clicking, going to Properties, and changing the default state to "Checked". But, seriously... there's a way, right??

Yes. (From www.reddit.com/media?url=ht...)

A colleague is looking for a NodeJS-specific hosting service for a relatively low-compute-need academic Web site. Are there good ones that are less flexible than a full VPS/specialized for NodeJS, or realistically does everyone just spin up a VPS and install stuff? Curious. Thank you!

Strongly recommend. I collaborate with several people in this department and they are all wonderful peeps.

Please repost/share We're hiring! UC Davis Plant Pathology seeks a tenure-track Assistant Professor in plant health & microbiomes. recruit.ucdavis.edu/JPF07904 My department is full of great colleagues, and we look forward to recruiting our new colleague!

Assistant Professor of Food Microbiology position here at UC Davis (tenure track) - apply by Dec 1, 2026!

Here's a link to @chrisadami.bsky.social 's book, which I highly recommend: press.princeton.edu/books/paperb...

Interested in airborne monitoring using computer vision? We (@weecology) just released annotated data with bounding boxes and species IDs for over 50,000 individual birds of 6 widely distributed species from our drone work in the Everglades. doi.org/10.1002/ecy....

Colleague just e-mailed asking if I was ready to lecture on Thursday. I'm supposed to lecture on Thursday in a week, per the schedule he sent me a few months back. Now soft-panicking that the schedule changed and he didn't tell me 😆

Focusing in on a new env metatranscriptome analysis project this week, and our collaborators sent us a whole bunch of papers by @nekton4plankton.bsky.social (former pd w/me) as well as others by colleagues here at UC Davis. Kinda funny, I guess I've been in this field for a while, eh?!

It's GENUINELY like this: You cannot "solve" intractability with heuristics. Trust me. I devoted 20 years to this, and really, if you squeeze out intractability in one spot it'll pop up in another. It may look different on the surface, but in essence you're still facing the same epistemic problem.

I really hate the framing of these stories as "an AI agent broke out and hacked something." No, an inadequate sandbox meant that a powerful and unpredictable computer program was set loose on the open internet by the company that designed it. The agency isn't with the "AI agent", it's with the firm

We spend a lot of time asking whether our animals make us happy. Maybe we should ask whether we make them happy, too. Turns out, the two may be more connected than we thought.

"I used to think that the fundamental role of journalism was to produce information. Today, however, I believe there is another responsibility that is just as important: Transforming complex information into information that people can actually use."

Same session but now Better Python Notebooks with Marimo from @tshafer.com (I think this is the right Tom Shafer 🙏🏿) #positconf #positconf26

Now attending Quarto Notebook and Literate Programming in Positron with Jonathan McPherson #positconf26 #positconf

Well this title certainly caught my attention: "Invasion Pythons in the Florida Everglades: History, Ecology, Impact, and Control" How cool! (Talk here at UCD in late Oct.)

Microbial #bioinformatics tweeps (@acritschristoph.bsky.social and others) if I want to critically evaluate how well metagenome ONT is mapping to specific genomes, what are the big technical gotchas I should be checking for? thx! Using minimap2 currently.