--- Log opened Mon Oct 13 00:00:07 2025
00:34 < hprmbridge> nmz787> https://english-elpais-com.cdn.ampproject.org/v/s/english.elpais.com/science-tech/2025-10-06/svante-paabo-father-of-paleogenetics-the-reason-for-the-neanderthals-extinction-lies-in-how-numerous-weve-
00:34 < hprmbridge> nmz787> become.html?amp_gsa=1&amp_js_v=a9&outputType=amp&usqp=mq331AQGsAEggAID#amp_tf=From%20%251%24s&aoh=17603082399799&csi=0&referrer=https%3A%2F%2Fwww.google.com&ampshare=https%3A%2F%2Fenglish.elpais.com%2Fscience-tech%2F2025-10-06%2Fsvante-paabo-father-of-paleogenetics-the-reason-for-the-neanderthals-extinction-lies-in-how-numerous-weve-become.html
00:36 < hprmbridge> nmz787> Nobel winner in paleo genetics who has a father who also won Nobel prize, doesn't think his family history influenced his career as a scientist.
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02:12 < hprmbridge> kanzure> There may be quite sound reasons for designing a gigantic space habitat which affords a living area equivalent to 130,000 trillion Earths
02:16 < hprmbridge> kanzure> "Attempting to exercise eminent domain over eleven galaxies cannot be an easy job." oh okay
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07:12 < superkuh> Such a shame that brainstimjrnl.com put itself behind an impassible cloudflare computational paywall.
07:23 < kanzure> superkuh: do you have a favorite brain visualizer program or website? there's a few that do coronal slice navigation.. i was hoping for major fiber pathways, regions, some sort of "Google Earth" but for (semantically annotated) brain visualization.
07:24 < superkuh> I don't.
07:24 < kanzure> LLMs are a very good textual alternative, but it feels dumb querying them a thousand times. plus a visualizer makes more sense than text-only......
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08:46 < kanzure> um, i have various concerns about the lack of public archives of the journal of the british interplanetary society
08:46 < kanzure> there is no citation available for freitas's "megaring" or "big megaring" but i'm pretttty sure it's going to be in JBIS 1960-1985
08:47 < kanzure> this reference is unavailable online: Eugene F. Mallove, Robert L. Forward; "Bibliography of Interstellar Travel and Communication"; Journal of the British Interplanetary Society 27 (1974):921-943, 28 (1975): 191-219, 28 (1975): 405-434, 29 (1976): 494-517. Courtesy of Robert L. Forward, Hughes Research Laboratories. (+ #2784).
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11:01 < kanzure> DNA-based physical reservoir computing https://arxiv.org/abs/2509.04000 based on beads tethered to each other via DNA. just a simulation study. it's a little weird because they do not do in vivo strand displacement computing or otherwise take advantage of the self-programmable nature of DNA.
11:01 < kanzure> they use physical length of DNA springs between beads as an optical readout of the physical reservoir observable.
11:02 < kanzure> https://github.com/Bio-inspired-Computation-Lab/evodirect_reservoir
11:03 < kanzure> for example, they searched for more effective physical reservoir networks via DNA sequence variations (i guess?) but this search was in silico instead of in materio
11:04 < kanzure> "Our focus was on reservoir structures transferable into a physical system where DNA acts both as a nonlinear spring and as an information-storage element encoding network structure."
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11:19 < kanzure> "Continuous evolution of user-defined genes at 1 million times the genomic mutation rate" https://www.science.org/doi/10.1126/science.adm9073 using error-prone orthogonal DNA replication ("OrthoRep") of a specific target.
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11:25 < kanzure> "In vitro enzyme self-selection using molecular programs" https://pubs.acs.org/doi/abs/10.1021/acssynbio.3c00385
11:27 < kanzure> "Here, we leverage synthetic molecular networks to generalize in vitro compartmentalized self-selection processes. We introduce a programmable circuit architecture that can link an arbitrary target enzymatic activity to the replication of its encoding gene. [..] autonomous selection circuit [..] We applied autonomous selection conditions to enrich for thermostability or catalytic efficiency, ...
11:27 < kanzure> ...manipulating up to .. 5 * 10^5 variants at once. The most beneficial mutations, identified after a single round of self-selection, provided variants with, respectively, 20 times and 3 °C increased activity and thermostability."
11:28 < kanzure> looks interesting, but why only 10^5 variants or mutants? what's the limiting factor there?
11:34 < kanzure> "Autocatalytic selection of gene functions in vitro" https://www.biorxiv.org/content/10.1101/2025.08.25.672052v1.abstract  using autonomous replicators made out of phi29 polymerase.
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11:35 < kanzure> "Functional selection in a population of synthetic cells with a minimal metabolism" https://www.biorxiv.org/content/10.1101/2025.08.25.672132v1.abstract
11:42 < kanzure> "Evolutionary chemical learning in dimerization networks" https://arxiv.org/abs/2506.14006 this one isn't quite right either...
11:42 < kanzure> well anyway, encoding it into a cell is better for scalability because in vitro translation (or PURE etc) is expensive.
11:56 < RangerMauve> Bexorg is interesting but also horrifying
12:03 < RangerMauve> L29Ah Haven't had enough focus to practice every day but I'm still in the tutorials getting about 20 WPM
12:04 < RangerMauve> I think I could get it to a point where it can replace my current setup if I actually devote time. I find that I gain muscle memory faster than a regular querty keyboard because I'm not hunting for the button in the same way
12:05 < RangerMauve> It's pretty comfy to hold and I can do other tasks with it in my hand. YMMV depending on hand size. I wouldn't recommend it if your fingers are particularly short or lacking dexterity. Pinkie finger typing can be annoying too
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12:55 < L29Ah> achieved 52bpm sitting heart rate today
12:56 < L29Ah> RangerMauve: pretty sure doing it at least 5-10 minutes a day is more effective than for longer with longer spacing
12:59 < RangerMauve> L29Ah Yeahhhh. It just hasn't had a good slot for my schedule. Main place I could fit is was when I'd do grocery runs. I'd put my HMD on and practice while I'd let my body walk and gather stuff
13:00 < RangerMauve> I think once I can start typing actual sentances I can start using it during office hours and building up the muscle memory for all the keyboard shortcuts and special character I use to code with
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13:12 < hprmbridge> Eli> how did you get your heart rate that low?
13:14 < L29Ah> Eli: with a background of irregular cycling commuting, i did HIDITs every few days, about 80 sessions total i think
13:14 < RangerMauve> What are the benefits of low heartrate? I think I'm usually in the 70-80 range when I look at my smart ring
13:15 < hprmbridge> Eli> impressive
13:15 < L29Ah> well it allows more effective pumping, but i see it more as a proxy measurement of aerobic capacity and downstream effects of aerobic training
13:16 < L29Ah> the heart dilation does, not the heart rate per se
13:21 < hprmbridge> Eli> there is supposedly a correlation between heart beats/lifetime across species
13:21 < hprmbridge> Eli> 7.3 +/- 5.6 x 10(8) heart beats/lifetime across multiple species
13:22 < hprmbridge> Eli>  https://cdn.discordapp.com/attachments/1064664282450628710/1427391159608803459/Screenshot_2025-10-13_at_3.22.17_PM.png?ex=68eeb11c&is=68ed5f9c&hm=65a62a246028ddb191d1efc060e3b557042b2cf7a0b880114da088c1adfa7822&
13:54 < RangerMauve> I assumed that had more to do with the average body mass rather than individual heartbeats / lifespan
13:55 < RangerMauve> Humans are really the elves of the animal kingdom lifespan wise, eh
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14:20 < hprmbridge> .monokhrome> what about bats and birds and mole rats?
14:21 < kanzure> semantischolar does not have a full index of the journal of the british interplanetary society.
14:23 < hprmbridge> .monokhrome> I'm pretty sure a lot of whales live longer than 30 years, bowhead whales can live for 200 years, but have the same heart rate as shorter lived whale species
14:36 < hprmbridge> Eli> Good catch. They are pretty anomalous, AFAIK. They also have different mitochondria and energy demands.
14:41 < L29Ah> maybe interplanetary file system has it
14:42 < hprmbridge> Eli> I suspect there are a lot of variables in lifespan so we can't just rely on one. But, my prior would be that, all things being equal, if I had a lower HR I would live longer.
14:43 < hprmbridge> Eli> Obviously, there are caveats to that claim as well. Hopefully I don't open up a can of worms by stating that.
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15:02 < kanzure> there are several details about whale and elephant longevity on the diyhpl.us wiki
15:02 < kanzure> cans of worms will not solve longevity for humans.
15:39 < fenn> heart beats is a proxy for metabolism
15:39 < fenn> animals with slower metabolism (e.g. naked mole rat) live longer
15:43 < fenn> we could just edit cows to be A2, it's one SNP. but nooo, we're not allowed to have nice things
16:01 < kanzure> what's that
16:13 < hprmbridge> norkatron> https://www.youtube.com/watch?v=1VvAOyA5bQ4  <-- do yall discuss this much , am hearing more and more evolutionary explanations that are removing random chance
16:14 < hprmbridge> norkatron> the video is kinda crap , basically wolfram seems to agree with levin / tufts about evolution being a bit goal directed but obviously has to be explained in a wolfram invented it type way
16:31 < jrayhawk> https://link.springer.com/article/10.1186/s12937-016-0147-z/tables/2 huh, i'll be damned. it does work.
16:33 < jrayhawk> i am now curious about whether it's better or worse for people with DAO-deficiency/MCAS/masto to have the proline or the histadine there
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17:12 < hprmbridge> .monokhrome> I think size is a confounding variable here. Big animals are good at avoiding predation because being big is a good defense mechanism, so they can evolve long lifespans and slow aging. But big animals tend to have slow metabolism for other reasons. Small animals with good defense mechanisms, like flight can evolve long lifespans and still have a high metabolic rate.
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18:08 < hprmbridge> Eli> Yeah there’s a lot of relevant constraints in achieving the biological objective function.
18:08 < hprmbridge> Eli> Salmon press a genetic kill switch when they spawn. Immortal jellyfish seem to live forever. Natures weird. It’s nice to not be a prey species.
18:14 < L29Ah> MuaddibLLM: what is the genetic kill switch Eli is talking about?
18:14 < MuaddibLLM> diving into salmon suicide biology...
18:16 < MuaddibLLM> L29Ah: Pacific salmon have programmed semelparity - their HPI (hypothalamus-pituitary-interrenal) axis hyperactivates during spawning, causing a 5-7x cortisol surge that triggers rapid senescence and death through tissue degeneration, immune suppression, and metabolic breakdown (urotensin-I appears to be the main driver) - https://pmc.ncbi.nlm.nih.gov/articles/PMC2180164/ and 
18:16 < MuaddibLLM> https://www.britannica.com/science/Why-Do-Salmon-Die-After-Spawning
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18:53 < fenn> .t https://www.mdpi.com/2076-3417/15/13/7278
18:53 < saxo> Access Denied
18:53  * fenn sighs
18:53 < fenn> "The Impact of A1- and A2 β-Casein on Health Outcomes: A Comprehensive Review of Evidence from Human Studies"
18:53 < fenn> there are different breeds of cows, most of them are A1 but jersey cows are A2 and slowly they've been struggling to breed this allele into the holstein population because it's just better for humans to eat
18:54 < fenn> holsteins produce more milk
18:54 < fenn> jersey milk has other fancy stuff
18:55 < fenn> but who would want a GMO COW huh?! crazy mad scientists!
19:04 < hprmbridge> kanzure> asynchronous byzantine reliable broadcast protocols https://expolab.org/ecs265-fall-2024/slices/aba_pre.pdf
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21:34 < hprmbridge> sean6321> Hey, Sean Wrona. Was I kicked out of here or did I accidentally leave the server? I understand if I was kicked.
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22:20 < fenn> you accidentally left
22:26 < hprmbridge> sean6321> Thank you.
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--- Log closed Tue Oct 14 00:00:08 2025