Protein language models are overly constrained by covariation
Why good performance on one set of goals can lead to poor performance on another
Genes, Minds, Machines
Genes, Minds, Machines: Thoughts about Science, Communication, and AI. A newsletter covering topics in biology, data visualization, effective communication, AI, and higher education.
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The error bar cargo cult
You don't need to understand error bars. You just need to draw them.
Nene Royal—A generational talent
The kids in Thailand are alright.
If the work is good why does it need a story?
I thought we do science here, not fiction or romance
How useful are zero-shot predictions of mutational effects?
Zero-shot predictions are great, except for when it matters
“Tell a story” is not helpful advice
If people knew how to tell a story they wouldn't need the advice in the first place
The Google Scholar preprint bug strikes again
Google is never going to fix this bug, are they?
Creating reproducible data analysis pipelines
There was a discussion recently on Bluesky about reproducible data analysis pipelines.
Protein language models are bad at mutational effect prediction
Biology is hard. Yes, even for AI.
Sociopathic AI agents
AI alignment will likely require creating AIs with genuine empathy
Python is not a great language for data science. Part 2: Language features
It may be a good language for data science, but it’s not a great one.
Python is not a great language for data science. Part 1: The experience
It may be a good language for data science, but it’s not a great one.
LLMs excel at programming—how can they be so bad at it?
My explanation for the mystery of why LLMs can be both exceptionally good and quite terrible at programming.
1000 subscribers feedback and AMA thread
A few days ago I broke 1000 subscribers here on Substack.
Random seeds and brown M&Ms
Your first mistake was assuming people actually understand how random numbers work.
If your random seed is 42 I will come to your office and set your computer on fire🔥
Figuratively. More likely you'll get a stern talking to.
Most graduate students propose to do too much
No thesis proposal has ever been critizied for lack of ambition
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
How to write an NSF GRFP research plan
This is my second post about the NSF GRFP.
How to write an NSF GRFP personal statement
The personal statement can make or break your application.