--- Log opened Thu Aug 21 00:00:16 2025
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01:45 < fenn> enviropig was genetically modified to express phytase to break down the mineral absorbing anti-nutrient phytic acid, which helped prevent phosphorus induced algal blooms in runoff contaminated bodies of water, but also enhances bioavailability of minerals such as magnesium
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02:26 < fenn> i normally eat high oleic sunflower oil, which was a strain produced through selective breeding. something similar could be done with corn and soy and canola cultivars, just like how they bred out erucic acid to make canola
02:27 < fenn> "Canola oil is limited by government regulation to a maximum of 2% erucic acid by weight in the US and EU"
02:27 < fenn> could do the same with PUFAs
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02:56 < hprmbridge> .monokhrome> Is there a test you can get to see if all these pufas are actually ending up in your cell membranes?
02:58 < hprmbridge> .monokhrome> yes there is, Omega-3 Index blood Test, measures stuff in your red blood cell membranes
03:06 < fenn> umm
03:06 < fenn> you know there are more than one kind of PUFA right
03:08 < fenn> it's actually really complicated
03:08 < fenn> fatty acids are difficult to separate so historically have been less studied than other classes of chemicals
03:14 < fenn> the omega-3 / omega-6 ratio is more important than getting loads of omega-3
03:14 < fenn> also it should be DHA (fish oil), not flax oil
03:19 < fenn> there are other pufas that are neither omega-3 nor seed oil omega-6: omega-7 Palmitoleic Acid: This fatty acid is found in macadamia nuts, omega-6 arachidonic acid, found in butter eggs and beef
03:20 < fenn> palmitoleic also in avocado and sardine
03:21 < fenn> in other news, i bought some gouda cheese today, based on its vitamin k-2 content: https://pmc.ncbi.nlm.nih.gov/articles/PMC5946231/
03:22 < L29Ah> even fish oils are different
03:22 < L29Ah> and fishes are vastly different in terms of oil content too
03:22 < fenn> this paper argues that cheese is the main source of vitamin k-2 in the modern diet
03:23 < fenn> i didn't realize gouda had so much mk-4, this fact is not widely discussed
03:24 < hprmbridge> .monokhrome> how aged is it?
03:25 < L29Ah> MuaddibLLM: how much is mk-4 in yogurt?
03:25 < MuaddibLLM> gimme a sec, checking actual MK-4 assays for yogurt
03:25 < MuaddibLLM> L29Ah: Pretty low - yogurt MK-4 is usually undetectable to about ~1 µg/100 g, while K2 in dairy skews to MK-8/9 in aged cheeses and kefir can have a few µg/100 g of MK-7; refs: https://pmc.ncbi.nlm.nih.gov/articles/PMC3941825/ https://onlinelibrary.wiley.com/doi/full/10.1002/fsn3.4474 https://en.wikipedia.org/wiki/Vitamin_K2
03:26  * L29Ah sticks to his 100ug trans-mk7 tablets
03:30 < fenn> @monokhrome 13 weeks is the most popular according to the paper
03:31 < hprmbridge> .monokhrome> but the vitamin k content increases with age?
03:32 < fenn> yes but not as much as you'd think
03:34 < L29Ah> MuaddibLLM: how to tell the natural taste of natto from horrible bacterial contamination that will kill you?
03:34 < MuaddibLLM> L29Ah: Safe natto smells nutty-cheesy with a bit of ammonia, tastes mild-savory, shows tons of sticky “threads” when stirred, and beans look beige with a faint white frost - sketchy natto lacks threads, turns sour/putrid or sulfurous, goes pink/orange/green/black, gets mushy or gas-bloated, so when in doubt yeet it.
03:34 < hprmbridge> .monokhrome> where have humans historically gotten their vitamin k2 from anyway?
03:35 < L29Ah> perhaps the same place they got aspirin from
03:40 < fenn> here's the same data in visual form https://fennetic.net/irc/vitamin_k2_in_cheese_radar_linear.svg
03:41 < fenn> so-called safe natto wants to kill me
03:43 < fenn> we are mainly interested in the yellow line which is MK-4
03:46 < hprmbridge> lordkek__> Natto smells Like beans mushy cheese so when bit ammonia yeet goes pink
03:57 < fenn> now with all the labels https://fennetic.net/irc/vitamin_k2_in_cheese_radar_linear_zoomed.svg
04:01 < fenn> "Jersey milk is the Cadillac of all milk, with higher protein, calcium, butterfat and A2 beta-casein"  then why do they even have other cows
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04:05 < L29Ah> about the reason they have non-hard wheat
04:05 < L29Ah> and non-cherry tomatoes
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04:06  * L29Ah loads another batch of milk into his yogurt fermenter
04:07 < fenn> beefsteak tomatoes are good though
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04:22 < fenn> more k2 cheeses https://fennetic.net/irc/vitamin_k2_in_cheese_radar_european_cheeses.svg
04:25  * L29Ah locks fenn up in a polar coordinate system
04:30 < Hooloovoo> what are the units? what do the different line colors mean?
04:31 < fenn> sorry, i still haven't figured out how to do legends in gnumeric
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04:33 < fenn> the units are ng/g and the colors are the different species of vitamin K2 which are just different side chain lengths. MK4 is the pink line around 100, MK-9 is the green line, MK-10 is the blue line and only really present in emmenthaler
04:34 < fenn> L29Ah: i don't understand the aspirin comment
04:36 < L29Ah> fenn: the point is that they didn't necessarily have it at all or enough
04:37 < fenn> eel is a thing
04:55 < fenn> munster is a soft french cheese and is what is shown on the graph; muenster is an american cheese with an orange color dabbed on the outside and probably more similar to mozzarella
04:57 < L29Ah> i doubt eel was ever accessible to a large fraction of humanity
04:58 < fenn> maybe the concentration was higher in beef fat when the cows are eating leaves and grass
05:00 < fenn> "two to four eggs a day from pasture-raised hens may provide adequate K2"
05:00 < fenn> that's a lot of eggs for a caveman
05:02 < L29Ah> MuaddibLLM: was pleistocene megafauna rich in vitamin K2?
05:02 < MuaddibLLM> Let me quickly check reliable data on MK-4 in animal organs and wild/grass-fed animals to not hand-wave this.
05:03 < MuaddibLLM> Grabbing solid refs on MK-4 in animal organs/fat and wild/grass-fed meat to answer the megafauna angle without guessing.
05:03 < fenn> kielbasa???
05:04 < MuaddibLLM> Short answer: probably yes in organs and fat but not in lean muscle - MK-4 concentrates in mammalian extrahepatic tissues (pancreas, brain, fat) and is higher when animals eat green forage, so nose-to-tail megafauna would’ve given K2 even though we lack direct mammoth assays; refs: https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2017.4780 https://pmc.ncbi.nlm.nih.gov/articles/PMC11276079/
05:05 < fenn> yes i am seein a lot in brain but it's not often measured
05:09 < fenn> "Absorption of menaquinones produced by gut bacteria in the distal intestine remains uncertain"
05:10 < fenn> so maybe a different microbiome?
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05:14 < fenn> k-1 the precursor is "mainly found in green leafy vegetable plants and Brassica" which tracks with my leafy cow diet hypothesis
05:19 < fenn> "no evidence of adverse effects associated with supplementation up to 10 mg/day for 1 month" "no adverse effect after daily administration of 2,000 mg/kg body weight for 30 days [in animals]"
05:24 < fenn> "phylloquinone in plant foods is tightly bound to chloroplasts in plant cells thus not easily available for absorption when plant foods are ingested"
05:27 < fenn> perhaps some sort of fermented leafy greens was eaten?
05:43 < fenn> like the goop in the cow stomach
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07:14 < hprmbridge> kanzure> https://huggingface.co/collections/ByteDance-Seed/seed-oss-68a609f4201e788db05b5dcd
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07:28 < hprmbridge> kanzure> "DeltaDB uses CRDTs to incrementally record and synchronize changes as they happen. It's designed to interoperate with Git, but its operation-based design supports real-time interactions that aren't supported by Git's snapshots. For async interactions, fine-grained change tracking also enables character-level permalinks that survive any code transformation, so we can anchor our interactions to
07:28 < hprmbridge> kanzure> arbitrary locations in the codebase, not just to snapshots of recently-changed code."
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07:30 < hprmbridge> kanzure> "We aim for an evolution beyond version control that incorporates not just the code itself, but also the background information of how and why the code got into a particular state—context that AI agents can query to make more informed edits, understanding the assumptions, constraints, and decisions that shaped the existing code." ehh, that context isn't always written down....
07:30 < hprmbridge> kanzure> what is the autocomplete prediction subfield called? like cursor warping prediction.
07:33 < hprmbridge> kanzure> "a new kind of version control that tracks every operation, not just commits."
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08:56 < kanzure> "a gene-delivery system to generate CAR-T cells in vivo by dosing of a CD8-targeted lipid nanoparticle carrying anti-CD19 CAR mRNA" https://www.science.org/doi/10.1126/science.ads8473 (2025)
09:20 < kanzure> "Programmable macromolecule delivery via engineered trogocytosis" https://www.biorxiv.org/content/10.1101/2025.03.12.642522v1
09:29 < kanzure> if those are autologous cells or reprogrammed CAR T cells for trogocytosis-based gene therapy, then maybe you can avoid immune reactivity
09:30 < kanzure> and if you are delivering natural human proteins (especially if they were already present in the human before) then immunogenicity of the delivered proteins could be lower
09:30 < kanzure> a few years ago there was a paper in here about reducing the immunogenicity of foreign proteins delivered in gene therapies by protein engineering to make the modified proteins look very similar to other existing immunogenic proteins, but obviously still retaining the desired functional improvemnet.
09:31 < kanzure> and that sort of thing can be screened in cell culture before injection
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12:27 < hprmbridge> kanzure> https://www.astralcodexten.com/p/my-responses-to-three-concerns-from
13:24 < kanzure> kimi k2 is such the jokester: "YOUR_COMMAND | sed '2,$s/^\( \)*/\1/; 1!s/^\( \)*/\1/' | sed '1s/^\( \)*/\1/' | sed '0,1s/^\(   \)*/\1/' … Just kidding. Just pipe everything into this: ...." actually the output was non-terminating and it started puking random garbage.
13:25 < kanzure> "I have rewritten everything here. Here's the correct expression: … & … & … & & & ... & … & … & … & & … & ... … … ... … … & & & & … … ... & …"
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15:10 < kanzure> "iPSC-derived cells lack immune tolerance to autologous NK-cells due to imbalance in ligands for activating and inhibitory NK-cell receptors" https://stemcellres.biomedcentral.com/articles/10.1186/s13287-023-03308-5 (2023)
15:10 < kanzure> cell surface ligand ratios, even when all surface expressed objects are of an allogenic or autologous origin, need to be tweaked to minimize immune activation. ugh.
15:13 < kanzure> "Synthetic immune checkpoint engagers protect HLA-deficient iPSCs and derivatives from innate immune cell cytotoxicity" https://www.cell.com/cell-stem-cell/fulltext/S1934-5909%2823%2900365-X
15:14 < kanzure> "Stretch growth of integrated axon tracts: Extremes and exploitations" https://pmc.ncbi.nlm.nih.gov/articles/PMC3019093/ (2011)
15:15 < kanzure> "Tissue-engineered grafts exploit axon-facilitated axon regeneration and pathway protection to enable recovery after 5-cm nerve defects in pigs" https://pmc.ncbi.nlm.nih.gov/articles/PMC9635828/ (2022)
15:18 < kanzure> https://pmc.ncbi.nlm.nih.gov/articles/PMC8610031/ "have previously developed tissue engineered nerve grafts (TENGs) through the process of axon stretch growth. TENGs consist of living, centimeter-scale, aligned axon tracts that accelerate axon regeneration at rates equivalent to the gold standard autograft in small and large animal models of PNI, by providing a newfound mechanism-of-action ...
15:18 < kanzure> ...referred to as axon-facilitated axon regeneration (AFAR). To enable clinical-grade biomanufacturing of TENGs, a suitable cell source that is hypoimmunogenic, exhibits low batch-to-batch variability, and able to tolerate axon stretch growth must be utilized. To fulfill these requirements, a genetically engineered, FDA-approved, xenogeneic cell source, GalSafe® neurons, produced by Revivicor, ...
15:18 < kanzure> ...Inc., have been selected to advance TENG biofabrication for eventual clinical use."
15:19 < fenn> why were they able to do it in pigs but not humans?
15:21 < fenn> pigs need hypoimmunogenic cells too right?
15:34 < fenn> that kimi-k2 error looks like the provider is over-quantizing
15:39 < hprmbridge> kanzure> where do you see "not humans" just curious
15:42 < hprmbridge> kanzure> i assume it wasntt a clinical trial so how would they get approval to do humans?
16:30 < hprmbridge> kanzure> "Proof of concept for multiple nerve transfers to a single target muscle" https://pmc.ncbi.nlm.nih.gov/articles/PMC8530510/
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17:42 < hprmbridge> kanzure> they put humpty dumpty back together wrong https://www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2017.00072/full "A 15-year-old boy, with traumatic avulsion of nerve roots C5–C7 and a non-rupture of C8–T1, was operated 3 weeks after the injury with nerve transfers: (a) terminal part of the accessory nerve to the suprascapular nerve, (b) the second and third intercostal nerves to
17:42 < hprmbridge> kanzure> the axillary nerve, and (c) the fourth to sixth intercostal nerves to the musculocutaneous nerve. A second operation—free contralateral gracilis muscle transfer directly innervated by the phrenic nerve—was done after 2 years due to insufficient recovery of the biceps muscle function. One year later, electromyography showed activation of the biceps muscle essentially with coughing through the
17:43 < hprmbridge> kanzure> intercostal nerves, and of the transferred gracilis muscle by deep breathing through the phrenic nerve."
18:37 < hprmbridge> kanzure> "Rules of motor innervation in chick embryos with supernumerary limbs" https://pubmed.ncbi.nlm.nih.gov/7298909/ (1981)
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19:11 < hprmbridge> kanzure> "Targeted muscle reinnervation for real-time myoelectric control of multifunction artificial arms" https://pmc.ncbi.nlm.nih.gov/articles/PMC3036162/
19:29 < hprmbridge> kanzure> contralateral C7 (cC7) transfer for traumatic brachial plexus injury is pretty cool! C7 carries ~17–40k myelinated fibers, which is more than enough motor signal throughput for our purposes. possibly requires neurorrhaphy with a recipient nerve or other coaptation to join the two nerves together and allow the donor to regenerate axons for the recipient nerve fiber.
19:31 < hprmbridge> kanzure> apparently motor signal is distributed across the ventral roots, so in cc7 transfer the humans report a slight weakening in the original muscle target of the donor nerve but not paralysis, or likewise for sensory data
19:55 < hprmbridge> kanzure> "The control and training of single motor units in isometric tasks are constrained by a common input signal" https://elifesciences.org/articles/72871
19:55 < hprmbridge> kanzure> "The volitional control of individual motor units is constrained within low-dimensional neural manifolds by common inputs" https://www.jneurosci.org/content/44/34/e0702242024.abstract
20:05 < hprmbridge> kanzure> geeze only 17 wpm (handwriting), or 1 gesture/sec captured, by wrist EMG https://www.biorxiv.org/content/10.1101/2024.02.23.581779v2.abstract why not use a keyboard typing task instead? you can get direct keypress data...
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20:21 < hprmbridge> kanzure> oh facebook published a keyboard typing EMG dataset with a few hundred hours of data https://arxiv.org/abs/2410.20081v3
20:21 < hprmbridge> kanzure> https://github.com/facebookresearch/emg2qwerty
20:30 < hprmbridge> kanzure> hrm. why require qwerty? it should be neurofeedback training and personalized to each user. you should be able to get very high dimensionality and very high wpm.
22:04 < fenn> neurofeedback on what?
22:04 < fenn> repost: https://ai.meta.com/research/publications/brain-to-text-decoding-a-non-invasive-approach-via-typing/
22:06 < fenn> https://winbuzzer.com/wp-content/uploads/2025/02/Meta-Brain2Qwerty-AI-model-brain-decoding-magnetoencephalography-via-Meta.jpg
22:07 < fenn> despite steno achieving much higher word rates, almost nobody uses it
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22:53 < hprmbridge> kanzure> that's their MEG dataset
--- Log closed Fri Aug 22 00:00:17 2025