--- Log opened Wed Jan 18 00:00:18 2023
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04:20 <+gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f1b1a6e6 Bryan Bishop: add discord link >> http://diyhpl.us/diyhpluswiki/hplusroadmap/
04:20 <+gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=9ab65bb1 Bryan Bishop: add rs2146881 for longevity >> http://diyhpl.us/diyhpluswiki/genetic-modifications/
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06:00 < kanzure> "The inheritance of maze-learning ability in rats" https://psycnet.apa.org/record/1926-08467-001 (1924) showed a loss of maze learning ability in a third generation
06:01 < kanzure> fourth generation seemed to do better (in 1935) https://psycnet.apa.org/record/1935-03228-001
06:03 < kanzure> okay.. and they continued up to a 16th generation (1941) https://www.tandfonline.com/doi/abs/10.1080/08856559.1941.10534590?journalCode=vzpg20
06:05 < nsh> when you think (presumably) before saying something like "fourth generation seemed to do better" are you considering at all any kind of confidence assessment of that assertion?
06:05 < kanzure> hm? according to the abstract, the third generation showed no differences, unless i misread
06:08 < nsh> a result that isn't accompanied by at least a vague sense of how many grains of salt to take it with is not necessary more useful than no results
06:08 < nsh> and in all likelihood most often less useful
06:09 < nsh> *necessarily
06:09 < kanzure> i mean you could just skip ahead to the 16th generation manuscript and read that instead
06:09 < nsh> reading and literacy aren't the same thing, which should be clear in the age of text-to-speech :)
06:12 < kanzure> wonder what happened to this rat population
06:16 < kanzure> also, why only use maze learning as the sole test each generation? why not some sort of combined measurement of multiple different tests.
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08:55 < docl> I wonder if selective ion channels for gold exist in nature? seems like microbes tend to avoid concentrating it inside themselves because it's toxic, actually biomineralization by D acidovorans results from it chelating the gold to keep from being poisoned by it (doi: 10.1038/nchembio.1179)
08:56 < kanzure> "gold bioremediation" was an igem project https://diyhpl.us/wiki/dna/projects/
08:56 < kanzure> er, "gold biomineralization"
08:56 < docl> lol same thing really
08:57 < docl> at least, you'd probably be doing something similar to pull mercury, cadmium, etc. out of the ocean
09:02 < kanzure> fenn how would you do at-sea (cell-)micromanipulator stabilization
09:02 < kanzure> hexastewart?
09:03 < hprmbridge> nmz787> Something like one of those floating spherical keychain compasses, to start, maybe?
09:05 < hprmbridge> nmz787> Hrmm, it seems discord doesn't want to prevent auto-scrolling when the android app is minimized then restored https://support.discord.com/hc/en-us/community/posts/360042591531-Option-to-Disable-Automatic-Scrolling-to-Newest-Message-on-Mobile
09:05 < hprmbridge> nmz787> Which is super annoying for this high volume channel :/
09:11 < L29Ah> enjoy your vendor lock-in
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09:18 < docl> that's kind of how I feel about discord as well. I can kind of see how it got popular but it's not foss
09:20 < L29Ah> it doesn't even need to be FOSS, it's enough not to ban alternative implementations on sight to have better clients
09:21 < docl> yeah
09:23 < hprmbridge> nmz787> not really locked in at all
09:32 < L29Ah> then i hope you're enjoying the rich range of clients available for you to choose from instead of the proprietary abandonware you're experiencing problems with
09:32 < docl> oh nice, the bridge filters out the wave to say hi stuff
09:33 < hprmbridge> nmz787> l29ah yeah this was an experiment, as kanzure stated up-front
09:33 < hprmbridge> nmz787> it would be nice to find something like an modern Android IRC client that auto-handles media upload
09:34 < hprmbridge> nmz787> it's annoying enough to go to imgur, upload, copy link, paste into a chat window
09:34 < L29Ah> you may like Conversations
09:34 < L29Ah> but it's an XMPP client, you'll need a bridge additionally
09:35 < L29Ah> idk if there are public ones these days, i use one on localhost
09:39 < hprmbridge> Luke Parrish> would it be worth dipping a toe in fediverse waters? gitter?
09:40 < kanzure> not interested
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10:18 < docl> social network effect is stronger on discord anyway
10:20 < L29Ah> do you think there are more transhumanists using discord than irc?
10:20 < docl> yeah, especially younger ones
10:22 < docl> it's sort of the done thing to have a discord + subreddit for a given niche topic, and there are a lot of those related to transhumanism
10:47 < nsh> now many do you think you need before they type the complete works of shakespeare?
10:47 < nsh> or A Tale of Two Cities
10:48 < nsh> https://www.youtube.com/watch?v=nbqW4RH6SyY
10:48 < hplusbot> nsh: It was the best of times it was the blurst of times - The Simpsons - Played Over 1,048,576 Times - length 3m31s - 40↑0↓ - 5,217 views - Million Madness on 2018.10.10
10:51 < hprmbridge> Synopticz> here's an article! https://www.brainpreservation.org/do-we-need-a-noncryogenic-brain-preservation-prize/
10:51 < hprmbridge> Synopticz> don't know of a super comprehensive, up-to-date review. very complex topic, lots of options.
10:51 < kanzure> is nectome's glutaraldehyde work meant to be room temperature?
10:52 < hprmbridge> kanzure> that might be a question for @Tudor
10:52 < hprmbridge> Synopticz> aldehyde-stabilized cryopreservation certainly isn't room temperature. i don't know if they're interested in pursuing this otherwise.
10:53 < hprmbridge> kanzure> are you familiar with the connectome-by-sequencing work from zador lab?
10:53  * L29Ah stabilizes hprmbridge with an aldehyde
11:06 < fenn> "at-sea (cell-)micromanipulator stabilization
11:06 < fenn> i don't think it would cause much of a problem in the first place. put it on a gravity gimbal mount like for kite photography
11:19 < fenn> https://diydrones.com/profiles/blogs/diy-passive-gimbal might need some damping (magnets and an aluminum plate to make eddy currents)
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11:20 < fenn> there are lots of active gimbal mounts for hand held cameras of course, but they might jerk around unexpectedly and cause sloshing
11:21 < docl> in ASC, glutaraldehyde is mainly used to prevent osmotic damage as you deliver high concentrations of cryoprotectants so it vitrifies. it also stabilizes most components of the tissue but not lipids (which are slower to degrade so less time critical but still matter over enough time). so cryopreserving then lets you preserve whole brains for storage without using osmium tetroxide (which fixes lipids 
11:21 < docl> but is ridiculously toxic). they still use OsO4 to stain the tissues for EM purposes as I understand it
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11:24 < fenn> docl: isn't glutaraldehyde just for cross-linking
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11:27 < docl> yeah. cross linking makes the tissue more stable when you start replacing its water with other small molecules like eg, pg, glycerol, etc. basically turns the tissue into rubber. not alive by traditional criteria
11:30 < docl> so then it's a bit tougher / less likely to rupture from osmotic pressure, and also you arrest life processes like apoptosis so you can take more time to introduce the cpa / do it at warmer temperatures
11:41 < L29Ah> i wonder if talking about ridiculous toxicity makes any sense when you crosslink cell contents
11:59 < docl> it does, but mostly in terms of hazards of working with / expense of proper disposal. arguably could be the safest thing for the patient at that stage. aldehydes you can just neutralize and pour down the sink, not so much the case for a heavy metal compound. it's also a very strong oxidizer and the fumes make you go blind in small quantities
12:11 < docl> interesting wiki someone put together https://github.com/ultrastructural-preservation/chemopreservation/wiki
12:13 < hprmbridge> Synopticz> yeah. i'm not super interested in it because i tend to think that connectome + biomolecule annotation is what is needed for whole brain emulation. but i might be wrong.
12:13 < hprmbridge> Synopticz> as opposed to just the connectome graph.
12:14 < hprmbridge> kanzure> there is also a way to get the molecules, receptors, etc such as with antibody labeling, aptamer labeling, and DNA nanoscopy (sequencing + DNA barcoding for sub micron geometry detail reporting)
12:14 < hprmbridge> kanzure> (and whole tissue clearing)
12:15 < docl> muurkha: that wiki has some stuff about hydrogels in the context of brain preservation
12:16 < hprmbridge> Synopticz> i think osmotic stabilization is probably the reason why aldehyde perfusion helps with cryoprotectant perfusion, but i don't think we necessarily know the full mechanism. mechanisms are complicated and we shouldn't be too confident without experiments. could also be blood vessel stabilization, helping with intracellular penetration of cryoprotectants, stabilization during rewarming, all ...
12:16 < hprmbridge> Synopticz> yeah it's a good wiki. molnan has also posted on r/biostasis.
12:17 < hprmbridge> Synopticz> i think cost/practicality is very important since that's the main benefit of higher temperature storage has over cryopreservation.
12:17 < hprmbridge> Synopticz> so right now i'm most interested in liquid storage options because they are very convenient and might work.
12:19 < hprmbridge> Synopticz> interesting. i didn't realize they could get sub micron geometry and biomolecular annotations just from dna sequencing.
12:19 < hprmbridge> Synopticz> my guess is that the level of detail one could get from just looking at the tissue under the microscope (perhaps after expansion) will always be higher, and this is easier, but i could be wrong.
12:19 < hprmbridge> kanzure> DNA nanoscopy https://www.nature.com/articles/s41467-017-00542-3
12:20 < docl> good points, also I've been told (could be wrong) that aldehyde perfusion isn't really doable after death like cryoprotecant perfusion is. (even the latter has decidedly mixed results, depending on vasculature and edema and so on)
12:21 < docl> (after clinical death by natural causes, I mean -> typical cryonics case)
12:23 < hprmbridge> Synopticz> sometimes people say this. i don't think this is true though.
12:29 < docl> I'm unsure. the mental picture I got was the blood vessels end up shut and get sealed that way by the fixative, whereas you could force them open to a limited degree otherwise :/
12:40 < hprmbridge> Synopticz> yeah that's one of the things people say. fixation doesn't really work that fast though. maybe if you used a ridiculously high concentration of fixative and also had a blood clot it could get more viscous and prevent future flow, in a way that wouldn't happen with cryoprotective agents that can act as an extended washout. but i think in practical settings, this isn't that much of a conce...
12:42 < L29Ah> ...
12:53 < docl> kanzure: it's cutting off messages, FYI
12:53 < docl> "...in practical settings, this isn't that much of a concern. the much bigger concern is the no reflow phenomenon preventing perfusion with both fixatives and cryoprotective agents.
12:54 < docl> ah, that makes sense to me
12:57 < docl> well, how quickly does fixation take effect? we're talking very thin layer for it to affect in capillaries
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13:12 < docl> not sure how well this generalizes but "Formaldehyde reacts virtually instantaneously with primary and secondary amines, thiols, hydroxyls and amides to form methylol derivatives." https://www.ncbi.nlm.nih.gov/books/NBK138711/
13:38 < kanzure> docl: well, it's better than not sending long messages at all (previous behavior)
13:41 < fenn> i think it's still dropping messages. last night around "Isn't this decades old idea?" which apparently came out of nowhere, something about lasers
13:42 < fenn> https://gnusha.org/logs/2023-01-17.log (scroll to bottom)
13:43 < kanzure> thta was probably a response to https://www.nature.com/articles/s41566-022-01139-z
13:43 < hplusbot> kanzure: hprmbridge linked that 20 hours, 53 minutes ago.
13:44 < kanzure> yeah, nmz787 used the discord "reply to message" feature
13:45 < fenn> ah
13:45 < fenn> i was just looking around in the scrollback for related concepts; i didn't click on the link
13:47  * fenn tests to see if this still works
13:47 < fenn> .t
13:47 < hplusbot> fenn: did you mean twitter, tell, tarot, ts, tag, tags, tagged, title, tv, tv_next, tv_prev, tv_last or translate?
13:47 < fenn> .title
13:47 < hplusbot> fenn: .title <url> -- gets a title from a HTML page
13:47 < fenn> well at least it doesn't fail AND berate me
13:48 < kanzure> does anyone have a good python oneliner for irc max line length splitting
13:50 < fenn> like this? https://stackoverflow.com/questions/36575098/python-split-string-in-a-certain-length#36575139
13:51 < fenn> [long_line[i: i + max_length] for i in range(0, len(long_line), max_length)]
13:55 < fenn> you can use regex too
13:56 < fenn> from textwrap import wrap; wrap(long_line, max_length)
13:58 < fenn> wrap is nicer because it won't split words unless necessary
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14:00 < hprmbridge> kanzure> okay, let's try: "yeah that's one of the things people say. fixation doesn't really work that fast though. maybe if you used a ridiculously high concentration of fixative and also had a blood clot it could get more viscous and prevent future flow, in a way that wouldn't happen with cryoprotective agents that can act as an extended washout. but i think in practical settings, this isn't that much of
14:00 < hprmbridge> kanzure>  a concern. the much bigger concern is the no reflow phenomenon preventing perfusion with both fixatives and cryoprotective agents."
14:00 < fenn> see what happens with a long link at the end
14:00 < kanzure> oh is textwrap a native module?
14:00 < fenn> yes
14:01 < fenn> it strips leading and trailing whitespace by default, if that matters
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14:02 < hprmbridge> kanzure> okay, let's try: "yeah that's one of the things people say. fixation doesn't really work that fast though. maybe if you used a ridiculously high concentration of fixative and also had a blood clot it could get more viscous and prevent future flow, in a way that wouldn't happen with cryoprotective agents that can act as an extended washout. but i think in practical settings, this isn't that
14:02 < hprmbridge> kanzure> https://stackoverflow.com/questions/36575098/python-split-string-in-a-certain-length#36575139 lorem ipsum lorem ipsum"
14:02 < hplusbot> hprmbridge: fenn linked that 12 minutes ago.
14:03 < fenn> can we disable that "fenn linked that 12 minutes ago." feature?
14:04 < kanzure> and highlighting per L29Ah's request, cc jrayhawk
14:04 < fenn> oh i figured you were arm-deep in bot surgery already
14:04 < kanzure> i don't know where this one is
14:04 < kanzure> too many bots
14:04 < fenn> lol
14:04 < fenn> .botsnack
14:05 < fenn> ungrateful bastards!
14:06 < fenn> kanzure just checking but was it supposed to include 'that much of a concern. the much bigger concern is the no reflow phenomenon preventing perfusion with both fixatives and cryoprotective agents."'?
14:08 < fenn> i'm assuming you wanted something just below the cutoff length so you deleted it
14:11 < fenn> atlas should make 3d mario "woohoo" noises https://www.youtube.com/watch?v=-e1_QhJ1EhQ
14:11 < hplusbot> fenn: Atlas Gets a Grip | Boston Dynamics - length 1m21s - 29587↑0↓ - 407,346 views - Boston Dynamics on 2023.01.18
14:36 < kanzure> fenn: i used a long url at the end per your suggestion, and cut off the rest.
14:36 < kanzure> and added lorem ipsum
14:44 < kanzure> really would like to find a good semantic search tool
15:08 < kanzure> .wik multiple trait selection
15:08 < hplusbot> kanzure: No results found.
15:09 < kanzure> .wik index selection
15:09 < hplusbot> kanzure: Index selection - Index Selection is a method of artificial selection in which several useful traits are selected simultaneously.[1] First, each trait that is going to be selected is assigned a weight - the importance of the trait. I.e., if you were selectin... - https://en.wikipedia.org/wiki/Index_selection
15:11 < kanzure> "Theory of index selection" https://www.gwern.net/docs/www/web.archive.org/d97f9c503c769efa9eb56a45f908597cd1214ab1.pdf
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15:19 < kanzure> mouse selection over 140 generations for >20 pups per litter https://www.biorxiv.org/content/10.1101/2021.05.28.446207v1.full
15:22 < kanzure> "South Korea deploys cloned drug-sniffing dogs" https://abcnews.go.com/Technology/story?id=8131708&page=1
15:24 < kanzure> "Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory" https://www.nature.com/articles/s42003-018-0078-7
15:28 < kanzure> .wik phenomic selection
15:28 < hplusbot> kanzure: No results found.
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16:14 < kanzure> "Speed breeding results in ~3 to 9 generations per year compared to 1 to 2 generations per year achieved with conventional selection approaches" https://onlinelibrary.wiley.com/doi/full/10.1111/pbr.12909
16:31 < hprmbridge> docl> I wonder what organisms have the greatest ratio of lifespan to maturation rate? probably something weird like naked mole rats
16:55 < docl> .tw https://twitter.com/Robotbeat/status/1615859371040473088
16:55 < hplusbot> docl: error: invalid username
16:55 < hplusbot> docl: 2023-01-18 23:51:09 Robotbeat: Booo… engineer the coffee to have MORE caffeine, maybe put some adderall in there while we’re at it. https://twitter.com/agbioworld/status/1615398326538469391
17:00 < fenn> .tw
17:00 < hplusbot> fenn: .twitter <user>/<user> <n>/<id>/#<search>/#<search> <n> -- get <user>'s last/<n>th tweet/get tweet <id>/do <search>/get <n>th <search> result
17:00 < fenn> .tw https://twitter.com/agbioworld/status/1615398326538469391
17:00 < hplusbot> fenn: error: invalid username
17:00 < hplusbot> fenn: 2023-01-17 17:19:08 AgBioWorld: Scientists are editing out the caffeine genes using CRISPR genome engineering to develop a "natural" decaf coffee, to avoid the messy chemical process to remove the caffeine in use now. Will you drink it?  https://slate.com/technology/2023/01/decaf-coffee-genetic-engineering.html?via=rss_socialflow_twitter
17:01 < fenn> i figured caffeine extraction was the goal, and decaf coffee was a byproduct
17:05 < docl> I wonder if bacterial biosynthesis of caffeine is cheaper
17:17 < docl> Ok I checked online and caffeine powder is $60/kg, folgers is $10 for a can advertised as 270 6oz "cups" worth. it's 130 mg/6oz, which gives about 35 grams in the whole can. $60 would be 210 grams at that ratio. So apparently the ground coffee is a 5x markup compared to crystalline caffiene powder
17:19  * nsh sighs
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18:31 < forsol> hello
18:32 < forsol> what is transhumanism?
18:36 < docl> https://diyhpl.us/wiki/transhumanism/
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18:56 < L29Ah> it still refers freenode
19:03 < fenn> i totally fixed that during the move to libera
19:04 < fenn> oh this is some random page
19:07 <+gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=3fbba0ef fenn: channel moved to libera >> http://diyhpl.us/diyhpluswiki/transhumanism/
19:08 < docl> this page also needs fixed in 2 places https://diyhpl.us/wiki/diybio/faq/
19:10 < fenn> #biopunk and #biohack aren't here; what should i do? delete the mention of them?
19:12 < L29Ah> #biohack was very dead back on freenode
19:16 <+gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5457cbba fenn: #biopunk and #biohack didn't make it during the move to libera >> http://diyhpl.us/diyhpluswiki/diybio/faq/
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21:34 < hprmbridge> nmz787> Presumably there's other stuff in coffee tho that's good, right?
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--- Log closed Thu Jan 19 00:00:19 2023