--- Log opened Mon Jan 16 00:00:16 2023
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04:41 < kanzure> "A competitive advantage by neonatally engrafted human glial progenitors yields mice whose brains are chimeric for human glia" https://www.jneurosci.org/content/34/48/16153 (2014)
04:42 < kanzure> not quite interspecies blastocyst complementation:
04:42 < kanzure> "The cells were then delivered to the test mice using a five site intracerebral injection protocol that targeted the corpus callosum and cerebellar peduncle, as we have previously described (Windrem et al., 2008). As graft hosts, we used either newborn rag2−/− immunodeficient myelin wild-type pups or hypomyelinated homozygous shiverer × rag2−/− pups. Each mouse was transplanted with ...
04:42 < kanzure> ...300,000 GPCs delivered at five forebrain sites (Windrem et al., 2008),"
04:42 < kanzure> so they just use "intracerebral injection" against live mouse pups and 1 year later the forebrain shows substantial domination of human glial cells
04:43 < kanzure> ref: Windrem MS, Schanz SJ, Guo M, Tian GF, Washco V, Stanwood N, Rasband M, Roy NS, Nedergaard M, Havton LA, Wang S, Goldman SA (2008) Neonatal chimerization with human glial progenitor cells can both remyelinate and rescue the otherwise lethally hypomyelinated shiverer mouse. Cell Stem Cell 2:553–565, doi:10.1016/j.stem.2008.03.020, pmid:18522848
04:47 < kanzure> "glia replacement therapy" pffft
04:51 < kanzure> no immunosuppression required for early xenotransplantation of neural progenitor cells https://stemcellres.biomedcentral.com/articles/10.1186/s13287-021-02427-1
04:54 < kanzure> and here they do human cortical progenitor xenografts into mice https://www.nature.com/articles/s41586-021-04230-7
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06:17 < kanzure> "[an estimate] puts training GPT-3 at about a TWh, which is about six million years' of power for a single [human] brain"
06:17 < kanzure> .title https://news.ycombinator.com/item?id=34399142
06:18 < kanzure> oh yeah.
07:38 < docl> sounds like biology is more energy efficient. I think we typically consume considerably more than 20-40 watts keeping a brain alive and comfortable though
07:45 < L29Ah> most of energy consumed by an idling human is spent on maintaining the muscle mass iirc
07:48 < docl> makes sense
07:50 < docl> if we do 2d brains-on-electronics it might be closer to the 20 watts per person-equivalent, as artificial csf synthesized from petroleum products
08:20 < docl> .tw https://twitter.com/ruthhook_/status/1614833713136947203
08:21 < docl> "how is everyone not clamoring for dec2 related gene therapy to only need 6 hrs of sleep a night via myod1/orexin
08:21 < docl> jk targeting and delivery idk I am actually going to sleep"
08:23 < docl> is beggars in spain the only sci-fi book about short sleepers?
08:30 < kanzure> nobody knows if dec2 gene therapy would result in any changes for an adult human
08:30 < kanzure> better to do it at the germline level
08:30 < kanzure> even if you did have a dec2 adult gene therapy, what if it doesn't reach all the neurons?
08:33 < docl> does the mechanism need that? maybe microchimerism would be fine... have women found themselves sleeping less after pregnancy with a partner who doesn't need much sleep?
08:34 < docl> .t https://www.pnas.org/doi/pdf/10.1073/pnas.1801693115
08:34 < kanzure> docl: see pm
08:35 < kanzure> yashgaroth: could we do a DEC2 modification in an AAV/lentivirus/something? not expecting it to work, just need it to be 'feasible'
08:36 < kanzure> docl: are there reported cases of cortical microchimerism from a pregnancy?
08:37 < kanzure> "Tissue microchimerism in human autopsy study" https://academic.oup.com/molehr/article/21/11/857/2459808
08:38 < kanzure> "... Male microchimerism was present in the cerebral cortex of all five women whose brain autopsy material was available. In the brain, chimeric cells appeared to be glial cells and possibly neurons and were also found in blood vessel endothelium."
08:41 < kanzure> "Male microchimerism in the human female brain" https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045592
08:42 < yashgaroth> you could theoretically make a viral vector to deliver base editing of DEC2, but it absolutely wouldn't be worth the risk/cost/low efficacy
08:43 < kanzure> so the fragment lengths would fit in the vector?
08:44 < yashgaroth> in lenti, sure. Not much point in delivering the mutant gene since you don't see much of an effect from heterozygous expression
08:46 < kanzure> apparently microchimerism has also been observed after blood transfusion https://ashpublications.org/blood/article/93/9/3127/266544/Survival-of-Donor-Leukocyte-Subpopulations-in
08:47 < yashgaroth> substantial cost aside, you'd have to bathe the entire brain in repeat rounds of extremely high-purity virus to even consider seeing an effect, which is more likely to cause brain damage than actually improve wakefulness
08:47 < kanzure> yeah i don't need it to actually work
08:48 < yashgaroth> safest bet is to inject saline then, saves on cost too
08:48 < yashgaroth> imagine the placebo effect from a brain injection
08:48 < kanzure> but i'm not injecting anything? it's more of a project to point people to and show them the materials so that they can find us and other people interested in similar projects.
08:48 < kanzure> (and it would have a bunch of warnings about how it's not likely to work and we should pick better targets)
08:49 < yashgaroth> still quite a bit of work involved in designing the vectors and other protocols
08:51 < kanzure> ok ok the search continues then
08:53 < kanzure> "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" https://www.nature.com/articles/s41467-022-32230-2
08:55 < kanzure> "Transfer and integration of breast milk stem cells to the brain of suckling pups" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6155265/
09:02 < superkuh> Disturbing. Slightly less after the explanation that newborn digestive systems just suck.
09:03 < docl> and also that their immune systems aren't fully developed
09:03 < docl> hmm. dogs also have that sexually transmissible cancer thing
09:04 < superkuh> I wonder if the maternal chimerism cells become senescent in the middle of the proginy's life due to cell lifespan issues...
09:05 < superkuh> ... and I should have just kept reading.
09:05 < superkuh> Apparently there is pathology.
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10:23 < docl> .t https://ask.metafilter.com/359228/Sci-Fi-about-people-who-dont-sleep
10:24 < kanzure> jrayhawk: where did the bot go or what buttons do i press to turn it back on?
10:27 < jrayhawk> libera is having a slight issue: 'nickserv: No such nick/channel'
10:28 < kanzure> oh, tomaw's notice. ok.
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10:59 < kanzure> "Blastocyst development after fertilization with in vitro spermatids derived from nonhuman primate embryonic stem cells" https://www.sciencedirect.com/science/article/pii/S2666335X21000665
11:04 < jrayhawk> wow i never knew that 'Maternal microchimerism is quite common in human and may occur more than one fifth of the population, persists for decades and involves multiple organs and tissues. This study supports the idea that breastfeeding may be partially responsible for this high incidence. Based on the experimental data and theoretical calculations, daily viable BMCs transfer to a breastfed human 
11:04 < jrayhawk> baby was estimated to be 4E6 to 17E9, among which there are substantial number of stem cells'
11:04 < kanzure> there seems to be no studies about whether non-sperm cells in semen can cause microchimerism
11:06 < kanzure> (wonder if any of the male fetal microchimerism in women has been mistakenly identified as fetal)
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11:32 < yashgaroth> what, like non-sperm cells getting into the embryo? seems unlikely, they'd have to be able to both swim and burrow into the egg
11:32 < kanzure> non-sperm cells going into the female human
11:33 < kanzure> (and establishing a niche)
11:37 < yashgaroth> seems...tricky. I'd imagine the bulk of microchimerism is from breastfeeding and via the placenta
12:03 < fenn> i wonder if various superpowers have developed prion based bioweapons https://www.wired.com/2011/01/airborne-prions-disease/
12:06 < L29Ah> prion diseases are too slow to be effectively used as weapons, no?
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12:13 < jrayhawk> and it's not clear that they impact anyone other than metabolically broken people who are unable to do protein cleanup, similar to tau tangles and amyloid plaques
12:14 < jrayhawk> lab mice physiology is bred to collapse at the slightest insult
12:16 < fenn> at a high initial dose, the chain reaction might have enough of a head start that the organism dies before it can react
12:17 < kanzure> to be fair, we have not spent too many brain cycles on bioweapon design in this channel, there's probably lots of low-hanging fruit
12:17 < fenn> yeah it wasn't really my intent to design bioweapons
12:17 < docl> prion therapeutics?
12:18 < kanzure> normal biology is horrifying enough to suffice *shrug* let them suffer by deprecation
12:19 < fenn> apparently destroying the amygdala removes all fear. perhaps it can be temporarily disabled with an implant
12:20 < docl> "canine transmissible venereal tumour" is a thing. I guess technically a form of chimerism, 6000 year old cancer
12:21 < jrayhawk> is henrietta lacks transmissable?
12:21 < kanzure> fenn: well, you could do "designer receptors exclusively activated by designer drugs" (DREADDs) for amygdala.. but you would need to target the amygdala somehow.
12:21 < jrayhawk> i guess not
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12:22 < kanzure> there was some ultrasound technology for microbubble cavitation of gene therapy in human brain tissue if you want to localize a target, but i can't imagine the efficiency or yield is high enough to matter
12:23 < fenn> i was thinking some wires or magnets that disrupt normal activity
12:23 < kanzure> docl: so it's a naturally occuring xenotransplantation or cross-species chimerism?
12:24 < fenn> the amygdala is pretty deep and it would be rather invasive surgery
12:24 < docl> a typical adult has lots of benign lesions, which is almost like a chimeric body part in that it's a mutant cell line. makes me wonder if custom not-cancers in disreet parts of the body could be used for something therapeutic
12:25 < docl> kanzure: the former, it's probably technically a dog (although that far back might have been a wolf?)
12:27 < fenn> "custom not-cancer" sounds like an organoid or tissue engineering
12:27 < fenn> i think you meant "benign growths"
12:27 < fenn> a lesion is destroyed tissue
12:29 < docl> fenn: yeah organoid works as a term if they aren't using it for something else already. maybe make engineer the cell line to be easy to destroy if/when you are done with it
12:31 < docl> fenn: is "lesion" used consistently? I've seen it in contexts where I assumed they meant growths (e.g. "benign skin lesions")
12:31 < kanzure> docl does not know about organoids?
12:31 < kanzure> .wik organoid
12:31 < hplusbot> kanzure: Organoid - An organoid is a miniaturized and simplified version of an organ produced in vitro in three dimensions that shows realistic micro-anatomy. They are derived from one or a few cells from a tissue, embryonic stem cells or induced pluripotent s... - https://en.wikipedia.org/wiki/Organoid
12:35 < docl> kanzure: tbh I had seen that wiki but wasn't sure if it was used only to describe in vitro
12:35 < kanzure> ah
12:36 < fenn> ok lesion is also used to refer to benign tumors apparently :(
12:37 < L29Ah> 21:16:46]<fenn> at a high initial dose, the chain reaction might have enough of a head start that the organism dies before it can react
12:37 < L29Ah> so are you telling us you can think of a discreet way to introduce a high dose of protein into human cells (or at least bloodstream)?
12:37 < fenn> the article was about how prion aerosols can directly infect brain tissue (through the olfactory bulb i presume)
12:38 < docl> fenn: the language people were asleep wrt 'lesion', I found it confusing as well :(
12:38 < fenn> i was imagining something like cluster bombs that spray an aerosol delivery fluid
12:39 < fenn> typical bio/chemical weapon stuff
12:39 < kanzure> .g site:gnusha.org/logs aerosolized nasal stem cells
12:39 < hplusbot> kanzure: no results found
12:39 < kanzure> hmph
12:40 < kanzure> https://diyhpl.us/~bryan/papers2/bio/Intranasal%20delivery%20of%20cells%20to%20the%20brain.pdf
12:40 < kanzure> https://diyhpl.us/~bryan/papers2/bio/Nasal%20absorption%20and%20biodistribution%20of%20plasmid%20DNA.pdf
12:40 < kanzure> https://diyhpl.us/~bryan/papers2/bio/New%20intranasal%20and%20injectable%20gene%20therapy%20for%20healthy%20life%20extension%20-%202021.pdf
12:43 < kanzure> if you snort enough canine olfactory stem cells would your sense of smell change
12:44 < fenn> you'd suddenly find fire hydrants very interesting
12:44 < L29Ah> cool
12:45 < fenn> how is it that mice have a better sense of smell than humans? it must be beneficial for humans to have a reduced sense of smell?
12:45 < kanzure> or odor spectrum did not confer enough of an advantage to really matter
12:45 < kanzure> compared to other traits
12:45 < fenn> oh so maybe we can breed super sniffer humans
12:46 < fenn> of course it would really suck to be one, with all the chemical perfume nonsense out there
12:46  * L29Ah still wishes for a systematic exploration of human sense of smell and creation of a library of basic smells mapped to different chemical functional groups
12:46 < L29Ah> and maybe protocols for using smell for chemical analysis
12:47 < kanzure> there are some human super sniffers like smelly cancer lady
12:47 < fenn> that's not already a thing?
12:47 < fenn> organic chemists surely must be familiar with smell vs functional group on an informal basis
12:47 < kanzure> (joy milne is smelly parkinsons lady)
12:48 < L29Ah> my organic chemist friends tell me they don't have much usable sense of smell
12:49 < L29Ah> but those have access to HPLC/LC-MS/NMR spectrometers, so i guess no big pressure on them to learn discerning stuff
12:49 < kanzure> https://www.sciencealert.com/humans-may-be-gradually-losing-their-sense-of-smell
12:50 < kanzure> from https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009564
12:50 < fenn> part of the problem is that there's no language for smell primitives in the first place
12:50 < L29Ah> fenn: not really, as there's already a language for chemical groups
12:50 < L29Ah> and you can already tell things like "proton-rich" instead of "sour"
12:51 < L29Ah> and compare things to pure substances you smelled/tasted before
12:51 < fenn> do humans even have a universal shared set of smell responses? colors are the result of shared color receptor sensitivity to a specific wavelength range; is there something like that where most people have the same set of smell receptors that respond to the same stimulus the same way?
12:51 < kanzure> "Any two people, on average, will have functional differences in over 30 percent of their odorant receptor genes, a 2013 study found. Which explains why some people might find some smells pungent or pleasant that the next person can't even detect."
12:52 < L29Ah> fenn: why would you think they don't?
12:52 < superkuh> "there's no accounting for taste"
12:52 < fenn> because it would explain why there's not a shared language for smells
12:52 < L29Ah> all the people i've asked to smell my sucralose powder noticed they have sweetness receptors deep in their noses
12:54 < L29Ah> (well that'd be >10 russians)
12:54 < kanzure> i have never quite figured out L29Ah's profession but perhaps better to not ask
12:55 < fenn> i think experimenting on humans is his hobby
12:55 < L29Ah> kanzure: i have no formal education beyond the high school
13:09 < kanzure> "Cell-based therapy restores olfactory function in an inducible model of hyposmia" https://www.sciencedirect.com/science/article/pii/S2213671119301468
13:10 < kanzure> "Isolating nasal olfactory stem cells from rodents or humans" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217619/
13:12 < kanzure> this one uses nasal stem cells to fix hearing loss problems? https://www.liebertpub.com/doi/abs/10.1089/scd.2013.0274
13:13 < kanzure> "Isolation and characterization of olfactory stem cells from canine olfactory mucosa" https://www.vetdergikafkas.org/uploads/pdf/pdf_KVFD_L_1886.pdf
13:15 < kanzure> [elsewhere] "it has been estimated that dogs can smell anywhere from 1,000 to 10,000 times better than people."
13:15 < docl> recently bought some lab grade oleic acid off amazon. aftertaste is a bit like that of walnuts (I guess because of the oleic acid content of walnuts)
13:16 < kanzure> but this one argues that humans are suffering from a false olfactory inferiority complex https://www.smithsonianmag.com/science-nature/you-actually-smell-better-dog-180963391/ 
13:16 < kanzure> "Poor human olfaction is a 19th century myth" https://www.science.org/doi/10.1126/science.aam7263
13:16 < superkuh> http://erewhon.superkuh.com/pictures/table-of-organic-compounds-and-their-smells2.jpg
13:17 < superkuh> re: oleic
13:17 < superkuh> There is a trend towards wax/nut at the end of the column but it ends at 15 and oleic is 18.
13:17 < fenn> https://biology.stackexchange.com/questions/88954/what-is-the-human-energy-consumption-by-organ/88955#88955 Liver and spleen : 27%, Brain: 19%, Skeletal muscle: 18%, Kidneys: 10%, Heart: 7%, Other tissues (lungs, intestine, skin, bone, fat tissue, glands...): 19%
13:18 < fenn> oh i remember that smell chart
13:23 < kanzure> "In fact, McGann writes, studies have found little evidence to suggest that olfactory bulb size predicts smelling ability. Bigger animals might need larger brains to control more muscles or process more sensory information, he explains. “However, a larger animal would probably not have more odors it needed to detect and interpret just because it was bigger, so maybe it wouldn't necessarily ...
13:23 < kanzure> ...need a larger olfactory center.”
13:23 < kanzure> but i thought it was receptor types
13:23 < kanzure> "In the 19th century, neuroanatomist Paul Broca was searching for what he believed made humans special: free will. He didn’t find a free will center, but he did find that the large frontal lobes that enabled complex cognition and language in humans were absent in species with smaller frontal lobes. Bigger must be better, he surmised. Therefore, Broca deduced that humans' olfactory ...
13:23 < kanzure> ...bulbs—which are small relative to our total brain size—would enable a far weaker sense of smell than the relatively larger ones found in other animals. [...] Philosophers and psychologists also relied on this assumption; even Sigmund Freud [...]"
13:24 < kanzure> we are so doomed
13:26 < fenn> um i have personally seen many animals react to smells that their caretaker humans were completely unaware of
13:26 < kanzure> these studies reported in the article seem to be for <10 distinct odors, pretty small sample size
13:29 < fenn> i've noticed that methylfolate supplementation increases my smell sensitivity, although this is not necessarily a life improvement
13:31 < L29Ah> 22:16:53]<superkuh> http://erewhon.superkuh.com/pictures/table-of-organic-compounds-and-their-smells2.jpg
13:31 < L29Ah> i would submit that 18-COOH is waxy
13:37 < kanzure> e/acc discovers genetics https://milkyeggs.com/?p=296
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14:21 < hprmbridge> kanzure:
14:21 < kanzure> hmph
14:21 < kanzure> well it's a one-way bridge at least
14:22 < hprmbridge> kanzure:
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14:28 < jrayhawk> fenn: that would presumably be inductive confidence rather than receptor activity, same colors becoming more vibrant when taking stimulants
14:29 < jrayhawk> er, same as colors
14:30 < jrayhawk> and, i guess, widened confidence interval as well
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14:40 < kanzure> hplusroadmap discord bridge https://discord.gg/s3zg3GAh
14:59 < kanzure> .title https://github.com/MaximeBeasse/KeyDecoder
14:59 < hplusbot> kanzure: GitHub - MaximeBeasse/KeyDecoder: KeyDecoder app lets you use your smartphone or tablet to decode your mechanical keys in seconds.
15:02 < L29Ah> is there a Lignux version?
15:03 < kanzure> you could use android-x86 or whatever
15:03 < L29Ah> seems marginally more useful than gimp tho
15:03 < hprmbridge> Luke Parrish:
15:03 < L29Ah> can't even generate STL for printing
15:04 < kanzure> bridge seems to be a little buggy
15:04 < kanzure> (it interpreted a join message as a message from "luke")
15:06 < L29Ah> > discord
15:10 < kanzure> just trying it out
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15:51 < kanzure> https://forum.effectivealtruism.org/posts/nSwaDrHunt3ohh9Et/cause-area-short-sleeper-genes
15:51 < kanzure> "For example, with DEC2, one could check (first in mice) if administering orexin (which can be done with nasal spray[4]) at the right dose and schedule has the same effect as having mutant DEC2; if so, that could be the drug.  If not, then you look for something that sensitizes the orexin receptor—or something, this isn't my field.  Ying-Hui and her team have plenty of ideas about how to ...
15:51 < kanzure> ...proceed; that's not the bottleneck here (though it is fun to think of ideas)."
15:52 < kanzure> "The big problem is funding.  Ying-Hui was saying on Reddit in 2015 that funding was insufficient, and it seems to have gotten worse since then; she has said she's "pretty much given up on trying to get NIH to fund my research" and she's had to lay people off from her sleep lab.  The cost to run the lab is in the low millions per year.  Compared to the expected value of the research, the cost ...
15:52 < kanzure> ...is laughable"
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16:09 < hprmbridge> potatodemon:
16:10 < kanzure> welcome, potatodemon
16:10 < hprmbridge> potatodemon: Howdy!
16:10 < hprmbridge> nmz787:
16:10 < hprmbridge> nmz787: Yo dawg
16:11 < hprmbridge> kanzure: @potatodemon I am testing this as a new interface. Curious to hear from folks if this helps them connect to the channel. Or maybe it's just garbage.
16:12 < hprmbridge> potatodemon: I am embarrassed to say I have not had a irc client setup in years 😳. So this is great for me thanks!
16:12 < kanzure> your shame will be our secret
17:02 < maaku> bridge to where?
17:06 < kanzure> discord
17:12 < kanzure> .g breeder's equation
17:12 < hplusbot> kanzure: https://www.nature.com/scitable/knowledge/library/the-breeder-s-equation-24204828/ -- The Breeder's Equation | Learn Science at Scitable: "Evolutionary biologists routinely employ the breeder's equation with only partial information. If divergence (ΔΖ) has been estimated and the accumulated effects..."
17:18 < kanzure> quantitative breeding has been using "genomic selection" recently: "A genomic estimated breeding value (GEBV), expressed as a linear function of [SNP] marker effects, is calculated for each breeding candidate. GS combines genotypic and phenotypic data from a training population (TRN) in a training set (TRS) to obtain the GEBVs of a testing set (TST) which has been genotyped but not phenotyped. ...
17:19 < kanzure> ...The GS model will be then employed to predict breeding values of not phenotyped individuals in the next selection step[...]"
17:19 < kanzure> quite the claim: "Genomic screening of breeding populations can accelerate the genetic gain obtained at each cycle, reducing up two-third the time required for selection [21]"
17:20 < kanzure> the reference is https://acsess.onlinelibrary.wiley.com/doi/abs/10.2135/cropsci2008.08.0512 "In simulations, the correlation between true breeding value and the genomic estimated breeding value has reached levels of 0.85 even for polygenic low heritability traits."
17:21 < kanzure> "Such selection would substantially accelerate the breeding cycle, enhancing gains per unit time. It would dramatically change the role of phenotyping, which would then serve to update prediction models and no longer to select lines."
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17:22 < kanzure> here they use machine learning "using DNA modeled as a natural language" for a genomic selection pipeline (this one combines a few different modalities) https://arxiv.org/abs/2211.05986
17:23 < kanzure> genomic selection review article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8640095/ comparing planet breeding vs dairy cattle breeding programs
17:43 < hprmbridge> nmz787: Planet breeding, sexy
17:43 < kanzure> whoops
17:45 < hprmbridge> nmz787: This could be a "far side" cartoon. "Herbert, this breeder reactor isn't what you've been thinking it was!"
17:48 < kanzure> "Is continued genetic improvement in livestock sustainable?" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788124/
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18:14 < fenn> can we change the bot's prefix to nick> rather than nick: because otherwise it looks like "hprmbridge" is addressing someone
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18:18 < hprmbridge> kanzure: alright, try now
18:18 < kanzure> hmph!
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18:19 < hprmbridge> kanzure> one more time.
18:19 < fenn> looks good now, thanks!
18:23 < fenn> since genomics has been around forever, why hasn't iterated embryo selection become a thing in livestock breeding yet?
18:23 < fenn> you want genes X Y and Z, and it's a non trivial cost to bring say a cow to breeding age
18:25 < kanzure> chatgpt says: "IES requires the ability to obtain high-quality embryos at a early stage of development, which can be challenging and expensive."
18:25 < kanzure> "IES can lead to a rapid loss of genetic diversity in the breeding population, as only a small number of embryos are selected for each generation"
18:26 < kanzure> "[...] and the genetic improvement rate could be similar to what's obtained by traditional selection or GS at a lower cost."
18:26 < fenn> pff when has loss of genetic diversity ever stopped a breeder
18:26 < fenn> what's "GS"
18:26 < kanzure> genomic selection (see above)
18:27 < kanzure> "a linear function of SNP marker effects, calculated for each breeding candidate"
18:27 < fenn> oh, just polygenic scores?
18:27 < fenn> sure, that too
18:28 < kanzure> sounds like it; not sure why they would focus on SNPs though. why not copy number variations? why not promoter efficiency scoring? etc
18:28 < fenn> one step at a time
18:28 < fenn> it's easy to write computer programs for SNPs i guess
18:29 < kanzure> chatgpt is convinced that genomic selection and polygenic scoring are unrelated, it's kind of cute
18:29 < kanzure> ah wait, it relented: "Both methods are based on the same underlying principle, which is the use of genomic data to predict the genetic merit of individuals. However, they differ in their specific implementation and the type of traits they are used for. GS is mainly used in animal breeding, while PS is mainly used in human genetics and population genetics."
18:30 < fenn> *eyeroll*
18:30 < fenn> you wouldn't DOWNLOAD and embryo
18:31 < kanzure> "Genomic selection uses linear or mixed linear models (BLURP), bayesian models, and machine-learning models such as random forests and neural networks. In contrast, Polygenic Scoring (PS) mainly uses a specific type of statistical model called a "polygenic risk score" (PRS) model. This type of model combines the effect of multiple genetic variants associated with a trait into a single score, ...
18:31 < fenn> it must be due to "bioethics" dancing around the "eugenics" aspect of "selection" of "humans"
18:31 < kanzure> ...and is based on the assumption that a trait is controlled by a large number of genetic variants of small effect. The PRS model can be calculated using different methods such as Lasso, Ridge, Elastic net or Random Forest, but the general idea remains the same."
18:31 < kanzure> okay well it seems to admit random forest is used in both techniques
18:32 < fenn> let's just translate everythin into loglan and get rid of the historical connotations
18:33 < yashgaroth> not sure if anyone's developed the protocols for cow embryo culture, or sequenced enough cows for good data. We've had a few centuries of selection for dairy and meat production (separately, mostly, though there's some breeds that strike a balance)
18:34 < fenn> there's lots of cow IVF stuff and genetic engineering, it can't be that different
18:35 < yashgaroth> usually just turkey baster and sperm sorting but I haven't looked into it. You're probably still more limited by cows nearly maxing out production already. Active engineering for year-round milk production might be useful
18:35 < kanzure> they are not doing year-round currently?
18:36 < yashgaroth> it's pretty close, I think holsteins max out at 10 months but that's a 20% improvement if doable
18:36 < fenn> so like A12 milk suddenly becomes popular, but the cows that produce it are all weird breeds and it would take forever to make an A12 guernsey milk cow. IVF and embryo selection can accelerate the scale-out of your A12 herd
18:36 < yashgaroth> and requires breeding them which might be counterproductive in dairy cattle
18:37 < fenn> (please forgive my ignorance of cow breeds)
18:37 < yashgaroth> A12 would be a good target too
18:38 < fenn> oh it's actually A-2, my bad
18:38 < fenn> anyway. agile cow sprints
18:39 < fenn> or there could be some swine flu resistance allele that's suddenly very important
18:39 < yashgaroth> oh nice A2 is only a single point mutation
18:40 < yashgaroth> might be able to argue it like they do with plant engineering, where a point mutation "could have occurred naturally" so is subject to less stringent regulation
18:41 < fenn> the A-12 was a reconnaissance aircraft prototype preceding the SR-71
18:41 < yashgaroth> now more famous as elon's kid's namesake
18:47 < kanzure> "Undesirable correlated effects have included increased leg and feet weakness in broilers as they bear a heavier load, but strong selection pressure applied to these traits has been effective in reversing these correlated changes (Kapell et al. 2012)."
18:49 < kanzure> .wik somatic fusion
18:49 < hplusbot> kanzure: Somatic fusion - Somatic fusion, also called protoplast fusion, is a type of genetic modification in plants by which two distinct species of plants are fused together to form a new hybrid plant with the characteristics of both, a somatic hybrid.[1] Hybrids ... - https://en.wikipedia.org/wiki/Somatic_fusion
18:50 < kanzure> "Uses of somatic fusion include making potato plants resistant to potato leaf roll disease.[2] Through somatic fusion, the crop potato plant Solanum tuberosum – the yield of which is severely reduced by a viral disease transmitted on by the aphid vector – is fused with the wild, non-tuber-bearing potato Solanum brevidens, which is resistant to the disease. The resulting hybrid has the ...
18:50 < kanzure> ...chromosomes of both plants and is thus similar to polyploid plants."
18:51 < kanzure> and this one:
18:51 < kanzure> "Cybridization is the fusion of the nucleus from one parent and the cytoplasm of both parents. The product formed is called a cybrid and the process is known as cybridization."
18:51 < fenn> what if the mitochondria fight
18:52 < kanzure> "When human and mouse cells (or cells of any two mammalian species or of the same species) are mixed, spontaneous cell fusion occurs at a very low rate (10-6). Cell fusion is enhanced 100 to 1000 times by the addition of ultraviolet inactivated Sendai (parainfluenza) virus or polyethylene glycol (PEG).
18:53 < kanzure> don't know what this is
19:08 < yashgaroth> what part, PEG can be used to fuse cells and the virus acts as a donor source of syncytin-like proteins that also fuse membranes
19:08 < hprmbridge> kanzure> yeah but why do it
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21:25 < hprmbridge> nmz787> Like it said, tongst hybrids
21:27 < hprmbridge> nmz787> To get hybrids
21:28 < hprmbridge> nmz787> Also electrofusion is a thing
21:29 < fenn> "tongst"?
21:29 < hprmbridge> nmz787> "to get"
21:29 < hprmbridge> nmz787> I guess the bot doesn't push edits through
21:29 < fenn> good
21:29 < hprmbridge> nmz787> Bad?
21:30 < hprmbridge> nmz787> It's inconvenient at least
21:30 < hprmbridge> nmz787> Or less so
21:30 < fenn> it's really annoying when matrix people edit constantly and there's repeated lines all over the place
21:30 < hprmbridge> nmz787> I did just check the logs on that, right before you asked for clarification
21:30 < hprmbridge> nmz787> Well the alternative is the same without being a matrix people... Just retyping the same line with the fixes
21:31 < hprmbridge> nmz787> Or doing the whole perl regex thing
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22:56 < stipa> EEVblog 1524 - The 10 CENT RISC V Processor! CH32V003 https://www.youtube.com/watch?v=L9Wrv7nW-S8 
22:56 < hplusbot> stipa: EEVblog 1524 - The 10 CENT RISC V Processor! CH32V003 - length 19m55s - 1967↑0↓ - 33,317 views - EEVblog on 2023.01.16
22:56 < Muaddib> [L9Wrv7nW-S8] EEVblog 1524 - The 10 CENT RISC V Processor! CH32V003 (19:55)
23:07 < hprmbridge> nmz787> But can it run DOOM?
23:11 < stipa> it cam rim DOOM and Crysis at the same time
23:11 < stipa> run*
--- Log closed Tue Jan 17 00:00:17 2023