AI tells you what you want to hear, statisticians usually tell you what you don't want to hear

I am adding this to my bioinformatics course immediately. mtcars |> yeet(mpg > 20) |> vibe_check(mpg, cyl, hp) |> glow_up(kpg = mpg * 1.6) |> slay(desc(mpg))

I will support any New York mayoral candidate who admits bodegas are just convenience stores and everywhere in the world has them

This is from Autocracy, Inc, about how modern autocratic propaganda works. I consider this every time I decide what to share and how to frame it.

Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:

😱😱😱😱😱

I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it. The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma. tl;dr it's glam-slop & everyone involved should be embarrassed

Interviewer: Oh, nice! I see you've published in Nature Cell and Science. You should really proofread your CV, though - you forgot some commas. Interviewee: Errrr...

WashU in STL just announced, in a university-wide email, that we will NOT be signing The Compact. This statement, I believe, exists thanks to the tremendous energy generated w/in our community by, among others, the Faculty Senate, the revived AAUP, and student journalists. I'm proud of everybody.

The 400 richest Americans are now worth a record $6.6 trillion. The entire bottom 50% of America is worth just $4.2 trillion. Read that back. When 400 people control more wealth than half a country’s population, we have a very serious problem.

he's going to come after you either way, so you might as well act with integrity

PSA: dbGaP authorized access/run selectors seem to be not working. I assume it's the shutdown - either they turned the lights off, or something's busted and no one is there to fix it

These 3-L bottles contain one million tiny colored spheres each. One sphere is black (1 ppm). Finding the black sphere is comparable to detecting a protein present at ~ 6,000 copies in the proteome of a human cell. Quantifying the protein requires analyzing multiple jars.

I have been trying to get this published as an op-ed, but I am going to post it here since I think it is timely in light of the "consent" extortion events. Deafening Quiet from the Scientific Establishment jeremymberg.github.io/jeremyberg.g... 1/14

Today's little mystery involving started simply enough: I was hacking on a web tool that autocompletes gene names, and was surprised when searching for "TP53" didn't return that gene. I checked, and it was definitely in the input data, so I was left scratching my head (1/n)

How do we get @ensembl.org l the infrastructure they need to not be unresponsive like three times a week? Like can we pass the hat? I'm in for twenty bucks.

Immigrants, particularly on H1Bs, are the lifeblood of American innovation. If you wanted to hurt US competitiveness in the next century, I can think of few more effective ways than a move like this Even when found illegal, the mere intent will have irreparably harmed our future

Critical part of the President's new $100,000 charge for H1-B visas: The Administration can also offer a $100,000 discount to any person, company, or industry that it wants. Replacing rules with arbitrary discretion. Want visas? You know who to call and who to flatter.

When you want to do reproducible analysis in R, some packages require you to set a RNG seed. I'm not sure I trust anyone who doesn't immediately run `set.seed(42)`

Zstandard's --long range mode works wonders for assemblies, but needs uninterrupted single line sequences. *AllTheBacteria 661k, multiline fasta* gzip (pigz): 751GB zstandard --long: 641GB (30% original size) *Single line fasta* gzip (pigz): 700GB zstandard --long: 232GB (10% original size)

Everyone has a second full time job being mad at the government now

Good news. The House of Representatives stands behind the NIH budget with no cuts.

These are the words of a lunatic who does not belong in government, much less as our nation's top health official. It is dangerous to allow him to oversee ALL federal health research and public health infrastructure. It is never too late to do the right thing. Fire RFK Jr.

📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp.... Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!

The Genome Informatics conference (@ Cold Spring Harbor Lab, Nov 5 - 8) abstract deadline is **today**. We welcome your submissions! Topics include: - PanGenomes - Genome Assembly & Seq. Algos. - Algorithmic Evo. Bio - Single Cell & Spatial Omics - Microbial Genomics - AI/ML & Integrative Omics 🙏🙏🙏

The Journal of Open Source Software (@joss-openjournals.bsky.social‬) is looking for editors. Come join our team! I've only been an editor for a few months, but I love working with JOSS. Our peer review process is actually collaborative, and we're Diamond Open Access. #AcademicSky 🧪 ⚗️ #CompChem

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.

Only 35% of the dictionary? Yes, it might require some tortile posts from us nonathletes to get it done, but we're no tambourinists, we can do this! www.avibagla.com/blueskydicti...

"It gives one that too-familiar mixture of rage, despair, and embarrassment that is peculiar to the Trump era, and for which the English language does not have an appropriate word."

As stressful as it is to run a laboratory in the US right now, my thoughts are often with the NIH staff living in the awful chaos trying to preserve the whole enterprise. I’m grateful for every moment they choose not to give up. These people are the only thing keeping it from entirely collapsing.

In 1951, Harry S. Truman laid the cornerstone of the NIH clinical center, stating, "Research to prevent disease" was a better investment for federal dollars than "providing unlimited hospitalization to treat it."

Shout out to the WSJ journalists who reported on Vought’s impoundment by footnote, causing the White House to walk it back. Impact journalism!!

NEW The White House is blocking the NIH from awarding new research grants for the rest of the fiscal year Chokes off billions in research funding Gift link www.wsj.com/politics/pol... with @nidhisubs.bsky.social

Similar story over here. Yes, getting funding has always been hard, but this means 96% of NCI grant applications are getting nothing. So much wasted time. It's going to destroy so many labs, and so much promising research. Just absolutely brutal.

However hard to read it might be, it'd probably be a more accurate way to represent science. "Try this experiment on page 9 - antibody failed, dead end" "Try this experiment on page 24 - data inconclusive, dead end"

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field? That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience A 🧵 1/n

No you cannot determine which drugs are safe and effective with machine learning. You cannot. It will not work. People will die.

People outside tech starting to realize how quality software and typing/generating code fast are not correlated

I frequently take comfort in the fact that the Universe is vast and beautiful and entirely unaffected by petty human foolishness

If you see this, I want your answer to this question from @alz_zyd_ on twitter: "What is the largest scope/time project, of any kind, you've accomplished in your life so far?"

A major danger of LLMs is that humans are SO predisposed to attribute knowledge to any entity that uses natural language fluently. We cannot imagine that a machine that outputs natural-seeming speech/text doesn't have cognition. Brilliantly articulated by @emilymbender.bsky.social et al. (2021).

🧪Good News! A key committee in the House of Representatives rejected the administration’s plan to make deep cuts to research programs at the USDA; the leader of the Senate’s appropriations panel called the 40% cut to the NIH’$47 billion budget “disturbing.” www.science.org/content/arti...

Atul Butte died yesterday. The world lost a giant. A big bear of a man. With a huge smile. With love for everyone. With energy that could power a room. I loved everything about Atul. I loved how he was always happy. I loved how excited he was about science and helping people.

Worth considering that one reason Bluesky doesn't always feel super fun is that current events are relentlessly horrifying and bad

12/ Bioinformatics isn’t about blindly analyzing big matrices. It’s about asking: “What’s the signal? What’s the noise? And what can I ignore to see the truth?” That’s the real art of dimension reduction.

I wrote a new piece on how much progress has been made in treating childhood leukemia. The answer is: quite a lot! Before the 1970s, fewer than 10% of children diagnosed survived 5 years after diagnosis. Now most are cured and around 85% survive that long. ourworldindata.org/childhood-le...

must be incredibly frustrating and disheartening to have federal funding that was promised to you for important work suddenly and arbitrarily ripped away

This is heartbreaking. Americans don't support this.

We thank Reviewer 2 for their helpful feedback which has greatly improved the paper

One problem we face today is how few people understand the science that helps us all. Some scientists are able to explain the importance of their work. @baym.lol of Harvard University is one of them. Science is for everyone, and benefits us all more than most people know.