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Andrew White 🐦‍⬛

@andrewwhite01 • 32,527 subscribers

Automating science. Cofounder @EdisonSci. Cofounder @FutureHouseSF. Prof of chem eng @UofR (on sabbatical).

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Most chiral molecules arise from carbons being bonded to 4 different atoms, which are called sterocenters. The makes the molecule have a different mirror image that cannot arise from simple rotation. But, you can have chiral molecules not from stereocenters. You can have chirality that doesn't come from a single point in the molecule. It comes from some global property. The classic example is helicene, which doesn't have any stereocenters, but has chirality because of hits helical structure. This means you cannot capture this molecule with a graph, and thus SMILES or a string representation cannot capture this. Of course natural language comes to the rescue (just say in words if it's left-handed or right-handed helix), but it's an interesting failure mode for viewing molecules as just a graph. Another example of a molecule with helical chirality is DNA. DNA is actually chiral in two ways, which is kind of confusing. It has both helical structure and stereocenters. You won't find the stereocenters ever flipped, but left-handed helical DNA can exist (called Z-DNA). Interestingly, making the flipped stereocenter of DNA could be part of an entire mirror organism (mirror RNA, DNA, AAs, sugars) that would then be potentially invisible to our immune systems. This has been recently proposed as a "mechanism" for how a runaway AI system could cause harm to Earth. I find it to be a pretty tedious and difficult way to cause harm, but it is intellectually cool. Anyway - this came up in a PhD defense and I have a lot of arcane knowledge about this I wanted to dump.

Most chiral molecules arise from carbons being bonded to 4 different atoms, which are called sterocenters. The makes the molecule have a different mirror image that cannot arise from simple rotation. But, you can have chiral molecules not from stereocenters. You can have chirality that doesn't come from a single point in the molecule. It comes from some global property. The classic example is helicene, which doesn't have any stereocenters, but has chirality because of hits helical structure. This means you cannot capture this molecule with a graph, and thus SMILES or a string representation cannot capture this. Of course natural language comes to the rescue (just say in words if it's left-handed or right-handed helix), but it's an interesting failure mode for viewing molecules as just a graph. Another example of a molecule with helical chirality is DNA. DNA is actually chiral in two ways, which is kind of confusing. It has both helical structure and stereocenters. You won't find the stereocenters ever flipped, but left-handed helical DNA can exist (called Z-DNA). Interestingly, making the flipped stereocenter of DNA could be part of an entire mirror organism (mirror RNA, DNA, AAs, sugars) that would then be potentially invisible to our immune systems. This has been recently proposed as a "mechanism" for how a runaway AI system could cause harm to Earth. I find it to be a pretty tedious and difficult way to cause harm, but it is intellectually cool. Anyway - this came up in a PhD defense and I have a lot of arcane knowledge about this I wanted to dump.

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Finishing 2024 with one more research result! We’ve trained small language agents to do hard sci tasks: engineering proteins, manipulating DNA, and working with sci literature in a new library called Aviary. We beat humans and frontier LLMs on these tasks!

Finishing 2024 with one more research result! We’ve trained small language agents to do hard sci tasks: engineering proteins, manipulating DNA, and working with sci literature in a new library called Aviary. We beat humans and frontier LLMs on these tasks!

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Normal Friday night FutureHouse. It wants to go in the lab so bad to get to work.

Normal Friday night FutureHouse. It wants to go in the lab so bad to get to work.

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I packed-up a full-text paper scraper, vector database, and LLM into a CLI to answer questions from only highly-cited peer-reviewed papers. Feels unreal to be able instantly get answers by an LLM "reading" dozens of papers. 1/2

I packed-up a full-text paper scraper, vector database, and LLM into a CLI to answer questions from only highly-cited peer-reviewed papers. Feels unreal to be able instantly get answers by an LLM "reading" dozens of papers. 1/2

Andrew White 🐦‍⬛

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