--- Log opened Fri May 28 00:00:21 2021
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01:54 < archels> oops https://news.ycombinator.com/item?id=27298529
01:55 < archels> how one could not feel strung out as heck from 600 mg of moda, I don't really understand
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01:59 < jrayhawk> there's a lot of individual dose/response variation for stimulants. some people get prescribed 60mg adderall to have any effect at all.
02:02 < jrayhawk> the concept of "methodological self-blinding" made me laugh
02:03 < shadowLab> Anyone here aware of the electronic brain link network?
02:07 < shadowLab> Big Larry, dream broadcasting? :-)  
02:10 < jrayhawk> no, but we can give you some links to some research papers on schizophrenia if you'd like
02:11 < jrayhawk> i am fond of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755113/ myself
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02:17 < jrayhawk> https://scholar.google.com/scholar?q=quinolinic+acid+kynurenine+schizophrenia is the NMDA agonist i find most interesting
02:20 < jrayhawk> ooh, a 2021 meta-analysis i haven't read yet
02:21 < jrayhawk> why must sci-hub be mothballed :(
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06:27 < kanzure> so scihub still isn't doing new files?
06:27 < kanzure> how has the r/datahoarder efforts been going on that front?
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06:57 < kanzure> "Longitudinal analysis of blood markers reveals progressive loss of resilience and predicts human lifespan limit" https://www.nature.com/articles/s41467-021-23014-1
07:21 < kanzure> .tw https://twitter.com/biorxiv_genomic/status/1397817435089211399
07:21 < saxo> The complete sequence of a human genome https://biorxiv.org/cgi/content/short/2021.05.26.445798v1 #biorxiv_genomic (@biorxiv_genomic)
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07:54 < jrayhawk> wooooow
07:58 < jrayhawk> they got 5mC data off of nanopore, but no 5hmC, 5caC, or 5fC, so not quite as complete as one would hope
07:58 < jrayhawk> still, quite a bit better
08:00 < jrayhawk> so is the industry going to stick with a frankentig reference genome, or what?
08:00 < jrayhawk> does somebody get to be The Canonical Human?
08:02 < jrayhawk> do we get a public vote on who it gets to be?
08:18 < L29Ah> and at what time
08:19  * L29Ah methylates himself
08:19 < L29Ah> #feelsbadman
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13:15 < redlegion> oh dear, don't let NIST know if we do find a "reference human"
13:36 < archels> kanzure: can you explain "bandage string graph visualisation" like I'm 5? (https://www.biorxiv.org/content/10.1101/2021.05.26.445798v1.full.pdf Fig 2 caption)
13:45 < archels> redlegion: looks like the initial honour goes to "CHM13", female, "of European origin, including regions of Neanderthal introgression, with some predicted admixture from other populations (30) (Fig. 1A, Note S2)"
14:05 < kanzure> archels: not immediately no
14:09 < kanzure> last day to register a wuhan team any takers? https://2021.igem.org/Competition/Registration
14:55 < kanzure> https://health.ucsd.edu/news/releases/Pages/2021-05-25-first-clinical-trial-to-assess-alzheimers-gene-therapy-receives-5-million.aspx
14:56 < kanzure> super annoying- are you telling me that we haven't yet tried BDNF overexpression in human alzheimers subjects yet?
14:56 < kanzure> the earlier nerve growth factor trial is somewhat redeeming i guess.
15:19 < kanzure> https://2021.igem.org/Engineering/Webinars
16:12 < fenn> it seems prett obvious doesn't it
16:20 < kanzure> "hey guys, we've decided to finally do a clinical trial to check to see if supplying oxygen is helpful to patients who have breathing problems"
16:23 < kanzure> "next we're planning to try blood donation to people who have lost blood once the IRB committee goes out to lunch"
17:05 < maaku> jrayhawk: The Canonical Human is some guy in Buffalo, New York according to the human genome project
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17:41 < jrayhawk> some guy in buffalo, plus amplicons from whatever grad students happened to be doing labwork that day
17:45 < jrayhawk> the human genome project has always papered over the limitations of PCR and short reads in its public messaging
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18:29 < fenn> i thought it was j. craig venter
18:34 < fenn> "The human reference genome is derived from thirteen anonymous volunteers from Buffalo, New York. Donors were recruited by advertisement in The Buffalo News, ... about 80 percent of the reference genome came from eight people and one male, designated RP11, accounts for 66 percent of the total."
18:36 < fenn> "Watson's genome revealed 3.3 million single nucleotide polymorphism differences, while about 1.4 percent of his DNA could not be matched to the reference genome at all."
18:45 < mrdata-> seems like a small sample
18:46 < mrdata-> but despite that, i hear that humans are 99.9% identical
18:46 < mrdata-> so how does this get as high as 1.4%
18:47 < jrayhawk> https://genome.ucsc.edu/FAQ/FAQreleases.html there are a lot of human reference genomes
18:52 < mrdata-> it takes a million generations for that much variation to occur. what am i missing
18:52 < jrayhawk> there's much, much bigger differences in copy number variations that short reads weren't able to detect
18:53 < mrdata-> hmm...
18:54 < jrayhawk> also copy number variation occurs by lamarckian means, not strictly darwinian means
18:55 < jrayhawk> it's a weird 3-generation epigenetic process, though
19:01 < jrayhawk> http://www.tandfonline.com/doi/full/10.1080/15592294.2015.1062207 
19:11 < jrayhawk> in general you should distrust things geneticists say in public
19:11 < jrayhawk> their field is far, far more uncertain than they let on
19:13 < jrayhawk> i am still mad they managed to annex the field of cancer research
19:13 < jrayhawk> only to do nothing with it
19:13 < jrayhawk> s/do/accomplish/
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19:32 < fenn> long variable repeat regions
19:33 < fenn> it's like telomeres or something, they're hard to align
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19:34 < fenn> "epimutations" sounds like a misleading word
19:34 < jrayhawk> howso
19:35 < jrayhawk> it is epigenetically-controlled mutation
19:36 < fenn> epigenetic state changes
19:36 < fenn> you can't "undo" a mutation
19:38 < jrayhawk> okay? that seems consistent with intended implication and actual result
19:38 < fenn> they are referring to epigenetic state changes as epimutations. the particular changes they are studying in this paper are ones that cause regular old genetic mutations
19:39 < fenn> presumably the epigenetic state changes go back to normal after a generation or two
19:39 < fenn> maybe even after a cell division
19:57 < fenn> < FLHerne> https://media.defense.gov/2021/May/07/2002637461/780/780/0/210507-F-IN231-1004.JPG  <- official Space Force media event (no really,  check the URL)
21:17 < speerfissure> I don't think that pic is gonna be canon.
21:17 < speerfissure> ;)
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23:25 < maaku> Stargate SG1 crossover
--- Log closed Sat May 29 00:00:22 2021