I'm convinced large labs are a survival mechanism in a hypercompetitive funding environment. You need the critical mass to write the big papers that allow you to get the next round of funding. 1/2

Reminder that similar mistakes can easily arise in Python.

It is 2025 and this error is still a thing. Biggest software company in the world. 🤦

Become a colleague in my department! Applications close in four days, December 15.

Python people, please embrace missing values. I want the output with all the observations, not only the filtered ones without missing values. If I need filtering, I will do it myself.

The peptide discussion highlights how little people know about chemistry. Peptides are such a huge group of chemicals treating them as one thing is absurd. Many peptides are perfectly safe. (Your food is full of peptides.) Others are toxic. Every peptide needs to be evaluated as its own thing.

The statistical test you would run in this situation to ask whether there was a difference in outcomes is called a chi-square test. And it will tell you in no uncertain terms that you can absolutely not distinguish between 17 and 21 deaths among 22,000 people. It's noise. P = 0.6267.

Preliminary NTSB report, UPS Flight 2976. Left engine separated due to fatigue cracks. www.ntsb.gov/investigatio...

This seems important. Current AI models can't read graphs. They "see" what they expect to see, even if the data shows something else.

As much as I'm loathe to enter into "language wars" style commentary, I think I agree with @clauswilke.com here. The lack of NSE and native missing values is really bad for Python as a data science language (as, in fairness, is the unhinged OOP situation in R)

Part 2 of my deep dive into Python as a language for data science. blog.genesmindsmachines.com/p/python-is-...

Could somebody remind me what if anything of consequence Anthropic has done in the biology space?

Happy to announce that the sicegar package for sigmoidal curve fitting, which my lab developed many years ago, has a new maintainer and a new release with bug fixes and new features. cran.r-project.org/web/packages...

My department at UT Austin is looking to hire an Assistant Professor in Evolutionary Biology, broadly defined. Feel free to reach out to me with any questions you may have. apply.interfolio.com/177547

I, for one, welcome our new trash panda overlords. But for real, fascinating science on how we might be seeing the very early stages of domestication in action in wild animals. 🧪 By @marinacoladas.bsky.social for @sciam.bsky.social

. @clauswilke.com is correct. blog.genesmindsmachines.com/p/python-is-... #Rstats

We are hiring in Evolutionary Biology — apply to join our department!

I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python? blog.genesmindsmachines.com/p/python-is-...

I have realized over the last few days that I'm not executive-tier material. We all have to be honest about our limitations.

My department at UT Austin is looking to hire an Assistant Professor in Evolutionary Biology, broadly defined. Feel free to reach out to me with any questions you may have. apply.interfolio.com/177547

Also important to remember that while Nowak doesn't have a social media presence he's one of the most famous scientists alive. He has more Science and Nature papers than most people have as their career total, across all publication venues. He has an h index of 180 and ~170k citations.

I see @hadley.nz write "I was lucky to have deep conversations about relational database design and Codd’s third normal form much earlier in life than usual" and wonder at what age most people have these conversation. I'm in my fifties and haven't had them yet. hadley.github.io/25-tidyverse...

I see @hadley.nz write "I was lucky to have deep conversations about relational database design and Codd’s third normal form much earlier in life than usual" and wonder at what age most people have these conversation. I'm in my fifties and haven't had them yet. hadley.github.io/25-tidyverse...

Interesting thread. Read the whole thing, till the end. Yes, all 41 posts.

I think I understand how it can be that LLMs are both exceptionally good and quite terrible at programming. It's because there are two entirely different skillsets that we both call "good at programming." LLMs have only one of them. blog.genesmindsmachines.com/p/llms-excel...

This! I am continuously surprised to hear fellow colleagues say that LLMs are trash/useless for programming, while they have radically changed the way I work over the last years. Tasks that used to take a day can now be done in minutes while I fetch a drink.

I think I understand how it can be that LLMs are both exceptionally good and quite terrible at programming. It's because there are two entirely different skillsets that we both call "good at programming." LLMs have only one of them. blog.genesmindsmachines.com/p/llms-excel...

If engine fell off it's most likely a maintenance problem. Look up American Airlines Flight 191, which was a DC 10 (closely related aircraft to the MD 11).

The 21st Century version of corvée work for academics is reviewing papers or grants, writing letters of recommendation, giving public outreach lectures.

If LLMs were actually intelligent—and not just stochastic parrots—they could read all the literature on random number generation, synthesize it, and conclude that always setting the seed to the same number is probably not a good idea. Alas, they don't have that kind of awareness.

Wait, set.seed(42)? What's that? I've never heard of it. 😉

Excellent idea to demonstrate the effect of color-palette choice on visualizations.

if you see this post, your actions are: - if you have a spare buck, give it to Wikipedia, then repost this - if you don't have a spare buck, just repost your action is mandatory for the world's best source of information to survive

My default assumption is all my grants will get rejected so a rejected grant doesn't particularly bother me.

LinkedIn accounts can be stolen easily. This now has happened to two people I know personally, most recently this morning. There appears to be no viable way to protect your account from this attack, as the attack goes through LinkedIn support. nazmul-ahsan.medium.com/your-linkedi...

A response to all the people who say "if your results depend on your random seed you have bigger problems." blog.genesmindsmachines.com/p/random-see...

My NIH panel that was scheduled for tomorrow and Friday is now officially cancelled. Just received the notification. I was expecting this, but would have been nice to know with a bit of advance notice.

Just so we're clear about the scale of the problem: Half a million occurrences of `random_state=42` on github, and another almost 200k occurrences of `random.seed(42)`. (And that's just Python. There are also ~20k cases in R.) 1/2

Not sure if this is in response of my blog post of today. In case it is, I wrote clearly that the choice of random seed is arbitrary. Problems can arise when you're always using the same seed, or even worse, when everybody is. There are 160k occurrences of random.seed(42) on github.

We need to have a conversation about random seeds. Don't use 42. blog.genesmindsmachines.com/p/if-your-ra...

Don't trust a bed with a monthly subscription plan. www.dexerto.com/entertainmen...

"The internet of things will be great" they said. "Connect your cat feeder to the internet and it'll automatically order refills" they said. "Imagine a world where everything is connected and one AWS outage causes 100 million people to starve" they didn't say.

It's still down for me. Has been down since this morning.

My department at Emory is a hiring a tenure-track neuroscientist! Anyone who's talked to me in the last 4 years knows I cannot say enough good things about my dept and the neuroscience community here. My colleagues are so wonderfully supportive. Postdocs, please apply! apply.interfolio.com/174371

Super useful new feature! I've started to recommend plotnine to everybody who does data analysis in python and needs a plotting solution, so this is very welcome.

Excellent realistic assessment of what AI is likely going to be able to do in the short to medium term, from somebody who truly understands this stuff. “Agents don’t work.” “I don’t know why AI companies make these promises, maybe it’s to raise money.” www.youtube.com/watch?v=lXUZ...

Also, don't watch a bunch of knife sharpening videos on YouTube and then go around and sharpen all the knives in the house without telling your spouse about it...

The various people trying to shame me for using large language models to do actual research and produce detailed teaching materials on their harms, instead of simply preaching against them on a street corner—they provide a perfect illustration of wank.