--- Log opened Wed Oct 08 00:00:02 2025
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02:21 < hprmbridge> kanzure> "Imagine being a chemist; but in an alternate-reality fanfiction where the elements that make up the world are wildly different. You literally dump a soup of artificial molecules into a virtual beaker. Then, they collide according to the rules of your made-up world. You can compile Artificial Chemistries (ACs) to actual DNA molecules. Thus, the logic of your fake universe can be executed by real
02:21 < hprmbridge> kanzure> chemical systems via strand displacement." https://www.cs.mun.ca/~banzhaf/AC-home.html
02:27 < hprmbridge> kanzure> some church barcoding lore https://centuryofbio.com/p/manifold
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04:11 < hprmbridge> kanzure> https://huggingface.co/models?other=chemistry
04:12 < hprmbridge> kanzure> sort by trending.
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05:45 < hprmbridge> kanzure> E11-PRISM stuff: https://github.com/e11bio/e11-open-data https://github.com/e11bio/volara https://www.addgene.org/depositor-collections/e11-bio-prism-collection/
05:48 < hprmbridge> kanzure>  https://cdn.discordapp.com/attachments/1064664282450628710/1425464766155067503/image0.png?ex=68e7af04&is=68e65d84&hm=aad94ed0fe2f720a5832916aad4a4a43fee61ea75ebe81a6d67d497559f18eae&
05:49 < hprmbridge> kanzure>  https://cdn.discordapp.com/attachments/1064664282450628710/1425465107768410163/image0.jpg?ex=68e7af55&is=68e65dd5&hm=dff4e4f4ec4134f6837beafee1e6f8b2df988598a3cf1fbe43f39cdf15eab018&
05:50 < hprmbridge> kanzure> the neuroglancer tool is odd, what is this. just a visualizer?
05:51 < hprmbridge> kanzure> https://github.com/e11bio/prism_training
06:00 < hprmbridge> kanzure> srsly why is ben best's page showing up for a neuroanatomy query, isn't that embarrassing? what are all the other non cryonics people doing with their time?
06:00 < hprmbridge> kanzure> https://benbest.com/science/anatmind/anatmd2.html
06:19 < fenn> wearables may be a better route to downloadable immunity: "Preemptive immunity against the microbiota provides a previously unrealized route of vaccination." https://www.science.org/doi/10.1126/science.adz0485
06:19 < fenn> .t https://www.nature.com/articles/s41586-024-08489-4
06:19 < saxo> Discovery and engineering of the antibody response to a prominent skin commensal | Nature
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06:33 < hprmbridge> kanzure> chatgpt draws the human brain https://cdn.discordapp.com/attachments/1064664282450628710/1425476272338767962/brain_connectome.png?ex=68e7b9bb&is=68e6683b&hm=a28e59b3f0fc9ac03c426fe7e1e51f06b74e294cb14b9f17011f9a0368146d1f&
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06:49 < kanzure> it broke graphviz.
07:22 < jrayhawk> in which regard?
07:56 < hprmbridge> kanzure> crashed due to route planning. maybe OOM? can't tell because chatgpt ran it remotely and then hid stderr from me.
07:57 < hprmbridge> kanzure> where is the hippocampus in that diagram?
07:57 < hprmbridge> kanzure>  https://cdn.discordapp.com/attachments/1064664282450628710/1425497387136323687/image0.png?ex=68e7cd65&is=68e67be5&hm=8ac96200d89c156d90ab5fe552a57fe61529d05091f009b440fcc8ea7ef878b1&
08:00 < hprmbridge> kanzure> it just has a fornix arrow from hippocampus to mammillary bodies. but no input fibers? I guess just the insular-hypothalamus pathway?
08:01 < hprmbridge> kanzure> "The perforant path, supramammillary, septohippocampal, and amygdalohippocampal pathways are mesoscopic, not typically shown in tractography-level diagrams. The current .dot diagram was organized around major macroscale tracts (thalamocortical, corticopontine, corticostriatal, etc.). Many hippocampal afferents are short or diffuse (not bundled into large white-matter tracts), and often
08:01 < hprmbridge> kanzure> bidirectional (e.g., fornix, cingulum). That makes them harder to represent in the same “tract-level” language — which is why I only included the fornix efferent."
08:01 < hprmbridge> kanzure> bah!
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10:42 < kanzure> "Building a theory of distributed systems: Work by Nancy Lynch and collaborators" https://arxiv.org/abs/2502.20468 (2025) long overview of 50 years of distributed computing work.
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16:34 < hprmbridge> kanzure> "Applying targeted NanoSeq to 1,042 non-invasive samples of oral epithelium and 371 blood samples from a twin cohort, we report an extremely rich selection landscape, with 46 genes under positive selection in oral epithelium, more than 62,000 driver mutations and evidence of negative selection in essential genes* do we have biopsy somatic mutation selection pressure maps for all the human tissues?
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