Titus Brown

congrats!

I'd be interested.

Protein language models reveal evolutionary constraints on synonymous codon choice Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Wat

In our ongoing saga of description of new protists, we are happy to introduce Multisulcus malaysiensis, a deep-branching heterolobosean that forms highly unusual multiflagellated cells with multiple ventral grooves. Great work by @kristina-prokina.bsky.social

onlinelibrary.wiley.com/doi/epdf/10....

If this wasn't what you wanted with a theory of change... change the theory of change.

If it oversells the breadth of the replication crisis.. say so.

If it isn't really a universal "gold standard" and there are other paths to rigor....make that clear in the lit.

Most of what I've seen has been #openscience leaders scrambling to

a) Falsely insist that the only alternative to the current status quo rhetoric is to ignore all of sciences problems

b) Litigate blame saying they couldn't have known, or that it would have happened anyway.

In the above figure, there's a government building next to "make it required". The #Openscience community requested this, and got it---of course nothing like they envisioned. It's a great time for #metascience to self reflect, engage with experts in weaponization of science, and re-examine rhetoric.

I think @drugmonkey.bsky.social is right on in that many folks conflate narrow-sense technical reproducibility with generalizability. We have done a great job reducing technical variation, so that we can now focus on the sources of biological variation (and generalizability). This is a good thing.

In my small corner of biology, I’m constantly reassured by how frequently we confirm main findings. And then when differences do show up, they very rarely end up being fraud, but instead tell us something important about differences in experimental design.

Today I'm attending Sustaining Open Source Software in the Research Enterprise (SOSSRF), an NSF, Sloan Foundation & @cziscience.bsky.social workshop

It's interesting that it's on OSS in research institutions, but most people aren't focused on #ResearchSoftware

See sr.ithaka.org/blog/sustain...

taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!

Weekender: New Exhibitions at Manetti Shrem, Buzzing Art Spark Activity and More New Exhibitions Open Aug. 7 at Manetti Shrem Museum ‘OJO’ and ‘Breath(e): Toward Climate and Social Justice. Both exhibitions are on view Aug. 7–Dec. 1, Jan Shrem and Maria Manetti Shrem Museum of Art...

Manetti Shrem opens today with new exhibitions. Go enjoy the art and the AC. www.ucdavis.edu/arts/blog/we... @ucdavis.bsky.social @ucdavisclear.bsky.social @ucdlands.bsky.social

Korem Lab - Microbiome Systems Biology @ Columbia | New York, USA We apply systems biology approaches to decipher the metabolic interactions between the microbiome and its human host in diverse clinical settings, aiming towards personalized microbiome-based therapeu...

We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health!
Message or email me if interested. 🖥️ 🧬

PNW forest near a creek with older, fairly huge Doug fir tree trunks in the foreground and distance, ground covered in lush foliage, duff and rotted wood, fallen wood and a giant root ball with baby trees growing on it too in the center of the picture

I hope this email doesn't find you because you are walking among giants in the forest

Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...

💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥

I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com

@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social

www.cell.com/cell-systems...

🧵...

I think it's really worth noting that this concentration camp was opened one month and three days ago.

This woman saw enough horror in that time to quit and tell the public what she saw.

Which suggests that it's not as bad as we think, or as bad as we can envision from her description—it's worse.

Pleased to report that we've now updated the official databases page for #sourmash with GTDB rs226, all NCBI eukaryotes, and all NCBI viruses.

Part of the Wisconsin Idea is that our teaching and research should reach beyond the classroom and make a public impact. Recent PhD Erin Conley exemplified this Idea, dedicating a chapter of her thesis to communicating her research to non-specialists. Check it out below!
scifun.org/Thesis_Award...

7. So keep your head up the best that you can. Every scientist has succeeded via raw persistence and dog headedness. Discouragement is the intent. We are not at that point yet, and people are in the trenches every day fighting to keep it that way. 8/n

There is, I think, a compelling case to be made that the American political tradition thinks of free speech not as the basis of a free press but as an instance of it. A newspaper is not a giant person; a person is more like a little newspaper. If this is so, then the vast majority of Americans have low budgets, limited circulation, and few dedicated readers, even in the age of social media. In other words, speech is a resource, not an inalienable property, and as such it is subject to the same regimes of theft, privatization, and accumulation that have swallowed up the labor of workers and the fruits of the earth. We have heard much lately about when free speech ends: the moment when protesting for Palestine becomes grounds for detention or deportation in the eyes of the police state, for instance. Less often asked, but equally important, is when speech begins. Did

instance. Less often asked, but equally important, is when speech begins. Did Cotton's speech begin the moment that the Times published his op-ed? During the editorial process? When Bennet's deputies pitched the idea? At what point, in other words, did the ordinary flow of money, labor, and influence through civil society stop? Well, never. To say that Cotton was too important not to publish is to say that he enjoyed a certain social position that deserved the paper's famously discriminating attention. From the start, Cotton had more than free speech: He had actual speech, the very thing that protesters were being denied all across the country.

One of the principal goals of the protests of 2020 was therefore to seize the means of expression: protesters were not exercising their right to speak freely so much as they were trying to amass a form of social influence that could meaningfully compete at a national level. In other words, they were starting a newspaper; what Williams hates is that people started reading it. The fact is that telling a voiceless person they have free speech is like telling a poor person they have freedom of money: Nice work if you can get it! Williams might respond that a person who finds their ability to speak curtailed does not thereby lose their capacity to think.

"Expression is the exterior form and, if I can express myself so, the body of thought, but it is not thought itself, writes Tocqueville. It is seductive, I know, and highly flattering to those of us who write for a living, to suppose that thought "makes sport of all tyrannies," as Tocqueville puts it. (At least the slave, Buckley had the gall to imply, had retained his freedom of thought under the whip.) But a thought without expression, like a soul without a body, is just as good as dead. Surely we cannot comfort ourselves with the idea that the brutal neck restraint that kept George Floyd from breathing nonetheless could not keep him from thinking. For in the end, we know it did.

Obviously yes you should read Andrea Long Chu’s latest for all the usual reasons (thrillingly blistering assessment of worthy target) — but these two somewhat standalone paragraphs exploring the true nature of American free speech left me absolutely gobsmacked www.vulture.com/article/post...

Since the interviewee must remain anonymous, we are now calling this Moynihan's Law:
"The easier a governmental task looks to an outsider, the more likely it has been found to be impossible by many smart people in the past."

In the search business model, three parties come out ahead: user, website, and advertisers (where G takes their cut) and it’s a non-linear relationship.

In chatbots, there’s no incentive to pay the content provider. Even with a mechanism like Cloudflare’s Pay-Per-Click, I just do not see it.

MRG: use auto-generated database list by ctb · Pull Request #3754 · sourmash-bio/sourmash This PR integrates the database pages built by https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ into the sourmash docs. The revised databases page is here. The revised legacy d...

(PR is here: github.com/sourmash-bio...; template generation code is here: github.com/sourmash-bio...; it was tedious to do but finally reached the point of being more useful than annoying yesterday :))

Beloved #bioinformatics tool users, we are redoing our database download pages for #sourmash with automated templates; see sourmash--3754.org.readthedocs.build/en/3754/data... for an example. What extra/advanced info would be helpful??

"Those who neglect struggles around immigration, gender, and race fail to recognize how our potential and our strength comes from combinations of the many. They’re asleep at the wheel, dreaming of a past forty years of neoliberalism has put behind us. But we’ll wake them up."

At #PlantHealth2025, check Ralstonia research at Lowe-Power lab posters.

At P-614 (Tuesday!), I'm presenting Vienna Elmgreen and Tessa Pierce-Ward's work to develop an interactive dashboard for Ralstonia isolation around the world.
ralstoniadashboard.shinyapps.io/RalstoniaWiltDashboard

Terence Tao (@teorth.bsky.social) has written a thread on Mastodon about the impact of the federal grant freeze to UCLA, particularly to his own field of Mathematics. UCLA's IPAM (Institute of Pure and Applied Mathematics) could shut down entirely

mathstodon.xyz/@tao/1149568...

we asked a simple question:
What does it take to learn the rules of RNA base pairing?

using standard deep-learning technics, got a simple answer:
don't need structures, nor alignments or many parameters
only a few RNA sequences and 21 parameters;
doi.org/10.1101/2025...

it’s a real testament to the intellectual traditions of these centuries-old institutions, folding to authoritarian pressure like paper in a storm and kneeling to naked financial extortion