--- Log opened Wed Jul 05 00:00:08 2017 --- Day changed Wed Jul 05 2017 00:00 -!- JenElizabeth [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has quit [Ping timeout: 240 seconds] 00:08 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 00:11 -!- RebelCoder [~Yuriy@5.134.222.156] has quit [Ping timeout: 240 seconds] 00:22 -!- RebelCoder [~Yuriy@5.134.222.156] has joined ##hplusroadmap 00:36 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 00:41 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 248 seconds] 00:52 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 00:52 -!- Gurkenglas [~Gurkengla@dslb-178-000-211-218.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 00:58 -!- greymdr [~greymdr@112.192.202.141] has joined ##hplusroadmap 01:01 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 01:34 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 268 seconds] 01:41 -!- augur [~augur@2602:304:cdac:e260:447a:3aa7:6e4b:1502] has joined ##hplusroadmap 01:52 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 01:52 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Quit: sleep] 02:11 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Disconnected by services] 02:14 -!- Urchin [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 02:18 -!- greymdr [~greymdr@112.192.202.141] has quit [Quit: leaving] 02:22 -!- augur [~augur@2602:304:cdac:e260:447a:3aa7:6e4b:1502] has quit [Remote host closed the connection] 02:33 -!- augur [~augur@2602:304:cdac:e260:447a:3aa7:6e4b:1502] has joined ##hplusroadmap 02:37 -!- augur [~augur@2602:304:cdac:e260:447a:3aa7:6e4b:1502] has quit [Ping timeout: 240 seconds] 02:50 -!- JenElizabeth [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has joined ##hplusroadmap 02:53 -!- Jen [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has quit [Ping timeout: 255 seconds] 03:16 -!- Jen [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has joined ##hplusroadmap 03:20 -!- JenElizabeth [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has quit [Ping timeout: 260 seconds] 03:31 -!- Jen [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has quit [Ping timeout: 260 seconds] 04:03 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has joined ##hplusroadmap 04:10 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:e5f7:8545:dbf7:3594] has joined ##hplusroadmap 04:16 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 276 seconds] 04:35 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 04:40 -!- RebelCoder [~Yuriy@5.134.222.156] has quit [Remote host closed the connection] 04:45 -!- RebelCoder [~Yuriy@5.134.222.156] has joined ##hplusroadmap 05:03 -!- strages [uid11297@gateway/web/irccloud.com/x-gpjhewwbujjkvppw] has joined ##hplusroadmap 05:07 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 248 seconds] 05:27 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 05:31 -!- Iriez [wario@distribution.xbins.org] has quit [Remote host closed the connection] 05:34 < archels> wow, so slack went to shit. that was fast 05:34 < archels> "There's more to the conversation in #random! To see and search this channel's full history, upgrade to one of our paid plans." 05:35 < chris_99> yeah slack is annoying in the history aspect thing 05:42 -!- Iriez [wario@distribution.xbins.org] has joined ##hplusroadmap 05:56 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:e5f7:8545:dbf7:3594] has quit [Read error: Connection reset by peer] 06:01 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 06:08 < kanzure> they had paid-history-only for quite a long time now (>1 year) 06:16 -!- TC [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 06:17 -!- TC is now known as Guest81384 06:19 -!- poppingtonic [~brian@154.70.48.22] has joined ##hplusroadmap 06:19 -!- poppingtonic [~brian@154.70.48.22] has quit [Changing host] 06:19 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 06:21 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 248 seconds] 06:57 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 07:01 -!- Gurkenglas [~Gurkengla@dslb-178-000-211-218.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 260 seconds] 07:14 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 07:19 < kanzure> .wik doxycycline 07:19 < yoleaux> "Doxycycline is an antibiotic that is used in the treatment of a number of types of infections caused by bacteria and protozoa. It is useful for bacterial pneumonia, acne, chlamydia infections, early Lyme disease, cholera and syphilis. It is also useful for the treatment of malaria when used with quinine and for the prevention of malaria." -- https://en.wikipedia.org/wiki/Doxycycline 07:21 < kanzure> "CRISPR/Cas9-APEX-mediated proximity labeling enables discovery of proteins associated with a predefined genomic locus in living cells" http://www.biorxiv.org/content/early/2017/07/04/159517 07:22 < kanzure> context: "The engineered ascorbate peroxidase (APEX2) has been effectively employed in mammalian cells to identify protein-protein interactions. APEX2 fused to a protein of interest covalently tags nearby proteins with biotin-phenol (BP) when H2O2 is added to the cell culture medium. Subsequent affinity purification of biotinylated proteins allows for identification by MS. BP labelling occurs ... 07:22 < kanzure> ...in 1 min, providing temporal control of labelling. The APEX2 tool enables proteomic mapping of subcellular compartments as well as identification of dynamic protein complexes, and has emerged as a new methodology for proteomic analysis." https://www.ncbi.nlm.nih.gov/pubmed/27274088 i guess. 07:24 < kanzure> they are using a dcas9-apex2 fusion protein to label (by biotinylation) proteins that are attached to genomic loci near the dcas9 sgRNA target sites. 07:25 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Quit: Leaving.] 07:31 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 07:37 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 246 seconds] 07:42 -!- JenElizabeth [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has joined ##hplusroadmap 08:40 -!- Jen [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has joined ##hplusroadmap 08:42 -!- JenElizabeth [~Jen3@cpc76794-brmb10-2-0-cust542.1-3.cable.virginm.net] has quit [Ping timeout: 240 seconds] 08:48 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[~ebowden@2001:8003:1074:bc00:88aa:cb85:5c62:2db6] has joined ##hplusroadmap 13:18 -!- ebowden [~ebowden@2001:8003:1074:bc00:88aa:cb85:5c62:2db6] has quit [Changing host] 13:18 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 13:23 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 240 seconds] 13:25 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 13:34 -!- Gurkenglas_ [~Gurkengla@dslb-178-000-211-218.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 13:47 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 13:48 -!- juri_ [~juri@205.166.94.194] has quit [Ping timeout: 258 seconds] 13:58 < kanzure> .title https://news.ycombinator.com/item?id=14704906 13:58 < yoleaux> Global Foundries discloses 7nm process detail | Hacker News 14:03 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection] 14:04 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-nldsennfhdbiqwow] has joined ##hplusroadmap 14:08 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 14:13 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 14:13 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote host closed the connection] 14:14 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 14:17 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Ping timeout: 246 seconds] 14:18 < emeraldgreen> yoleaux I wonder what the electromigration/lifespan issues will be for 7nm 14:23 < kanzure> yoleaux is bot 14:23 < kanzure> .botsnack 14:23 < yoleaux> :D 14:24 < emeraldgreen> kek *sleepy* 14:28 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 14:31 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 14:38 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Remote 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closed the connection] 16:50 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 17:46 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-nldsennfhdbiqwow] has quit [Quit: Connection closed for inactivity] 17:59 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 18:02 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 18:03 -!- ebowden [~ebowden@2001:8003:1074:bc00:88aa:cb85:5c62:2db6] has joined ##hplusroadmap 18:03 -!- ebowden [~ebowden@2001:8003:1074:bc00:88aa:cb85:5c62:2db6] has quit [Changing host] 18:03 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 18:14 < kanzure> "A genome-wide association study for extremely high intelligence" https://www.nature.com/mp/journal/vaop/ncurrent/full/mp2017121a.html 18:15 < kanzure> "Three variants in locus ADAM12 achieved genome-wide significance, although they did not replicate with published GWA analyses of normal-range IQ or educational attainment. A genome-wide polygenic score constructed from the GWA results accounted for 1.6% of the variance of intelligence in the normal range in an unselected sample of 3414 individuals, which is comparable to the variance explaine... 18:15 < kanzure> ...d by GWA studies of intelligence with substantially larger sample sizes. The gene family plexins, members of which are mutated in several monogenic neurodevelopmental disorders, was significantly enriched for associations with high IQ" 18:16 < kanzure> "The primary single-variant findings from our GWA association analysis with high IQ were three intronic SNPs in high LD, r2greater than or equal to0.90: rs4962322 (P=8.05 x 10-9) and rs4962520 (P=1.18 x 10-8), and rs10794073 (P=2.02 x 10-8), all genome-wide significant and located in ADAM12 on chromosome 10. " 18:16 < kanzure> "there is no available replication cohort with extremely high IQ." 18:21 < kanzure> https://timelines.issarice.com/wiki/Timeline_of_Carl_Shulman_publications#Full_timeline 19:04 < kanzure> hrm. 19:04 < kanzure> .title http://www.biorxiv.org/content/early/2017/06/21/153338 19:04 < yoleaux> The experimental design and data interpretation in 'Unexpected mutations after CRISPR Cas9 editing in vivo' by Schaefer et al. are insufficient to support the conclusions drawn by the authors | bioRxiv 19:04 < kanzure> .title http://www.biorxiv.org/content/early/2017/06/30/157925 19:04 < yoleaux> Questioning unexpected CRISPR off-target mutations in vivo | bioRxiv 19:04 < kanzure> .title http://www.biorxiv.org/content/early/2017/07/05/159707 19:04 < yoleaux> "Unexpected mutations after CRISPR-Cas9 editing in vivo" are most likely pre-existing sequence variants and not nuclease-induced mutations | bioRxiv 19:06 < kanzure> off-target effects still happen, but yea testing the same mouse before/after seems like a relevant precondition before sounding alarm bells. 19:08 < kanzure> "Oblique light-sheet tomography: fast and high resolution volumetric imaging of mouse brains" http://www.biorxiv.org/content/early/2017/07/05/132423 19:08 < kanzure> oh that was from may. but the date says june. they are liars. 19:29 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Remote host closed the connection] 19:54 < kanzure> "In vivo magnetic recording of neuronal activity" http://www.biorxiv.org/content/early/2017/06/26/092569 19:54 < kanzure> "... we report on in vivo magnetic recordings of neuronal activity from visual cortex of cats with magnetrodes, specially developed needle-shaped probes carrying micron-sized, non-cooled magnetic sensors based on spin electronics. Event-related magnetic fields inside the neuropil were on the order of several nanoteslas" 19:56 < superkuh> Is this diamond nitrogen vacancy stuff? 19:57 < kanzure> doesn't seem so 19:57 < kanzure> no 19:58 < superkuh> Ah. GMR like HDD. 20:01 < kanzure> "Fluidic microactuation of flexible electrodes for neural recording" http://www.biorxiv.org/content/early/2017/06/26/155937 20:01 < kanzure> "A method to deliver thin, ultra-flexible electrodes deep into neural tissue without increasing the stiffness or size of the electrodes will enable minimally invasive electrical recordings from within the brain. Here we show that specially designed microfluidic devices can apply a tension force to ultra-flexible electrodes that prevents buckling without increasing the thickness or stiffness of... 20:01 < kanzure> ... the electrode during implantation. Additionally, these fluidic microdrives allow us to precisely actuate the electrode position with micron-scale accuracy." 20:01 < kanzure> "Compared to syringe injection, fluidic microdrives do not penetrate the brain and prevent changes in intracranial pressure by diverting fluid away from the injection site during insertion and actuation" 20:13 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 20:28 -!- ebowden [~ebowden@2001:8003:1054:a100:25d5:1188:1de1:3f79] has joined ##hplusroadmap 20:28 -!- ebowden [~ebowden@2001:8003:1054:a100:25d5:1188:1de1:3f79] has quit [Changing host] 20:28 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 20:32 -!- darsie [~darsie@84-113-55-42.cable.dynamic.surfer.at] has quit [Ping timeout: 248 seconds] 20:41 < fenn> are GWAS good science in general? 20:42 < yashgaroth> it generates papers if that's your qualifier...otherwise no, not really 20:43 < kanzure> for neuroscience i think there's a lot of people throwing up their hands and saying well we can attempt to do shitty correlation studies with gwas 20:44 < fenn> 1.6% of variance is not very much. it might be interesting if it were a single gene 20:45 < fenn> surely they could come up with some statistics fuckery that has a stronger effect 20:45 < fenn> so i don't understand what's going on 20:46 < kanzure> i think we will remain screwed until we get bulk hypercheap dna synthesis, and then we can start making proteins to help sort things out and report on actual internal biological environments. 20:47 < fenn> we still won't be able to do the experiments we want to do because of "ethics" boards 20:47 < fenn> also humans take a long time to grow 20:47 < fenn> but maybe mouse studies will have some use 20:48 < fenn> is it "unethical" to use human neurons in mice? 20:48 < fenn> i forget what the party line is 20:49 < kanzure> there needs to be a cambrian explosion style event that radically refactors a lot of this crap into something other than spaghetti, because this is intolerable and not usable 20:49 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Remote host closed the connection] 20:50 < kanzure> the party line is "we reserve the right to carefully consider whatever we want, and fuck you for frontloading everything with ethics instead of prudently considering each case" 20:50 < fenn> i meant the incumbent party 20:50 < kanzure> oh those guys? 20:53 < kanzure> also: i am upset with science focusing mostly on debilitative disease, and there should be more focus on positive outliers. trying to individually study each of the shit "dice rolls" in genetic disease seems like a losing game to me. 20:54 < kanzure> herd immunity, i know, i know. 20:55 -!- ebowden [~ebowden@110.141.40.86] has joined ##hplusroadmap 20:55 -!- ebowden [~ebowden@110.141.40.86] has quit [Changing host] 20:55 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 20:55 < fenn> ah you skipped the important part: "with cases consisting of 1238 individuals from the top 0.0003 (~170 mean IQ) of the population distribution of intelligence ... The single-nucleotide polymorphism heritability for the extreme IQ trait was 0.33 (0.02), which is the highest so far for a cognitive phenotype" 20:56 < kanzure> biological complexity would be more tolerable if debugging would more quickly lead to relevant reuslts. 20:56 < kanzure> what is 0.33 and what is 0.02 20:59 -!- ebowden [~ebowden@unaffiliated/ebowden] has quit [Remote host closed the connection] 20:59 < kanzure> 33% and what. 21:02 < kanzure> biological complexity reduction: offload more features into semiconductors in the larger cells, and the smaller cells... ok i have no idea. 21:04 < kanzure> big cells (with semiconductors that increasingly handle load that was once handled by spaghetti in the cell) could monitor mutiple small cells, and then you just need these cells to grow in the right proportion or whatever. everywhere. 21:05 < fenn> if you're going that route, why not protein based computers 21:06 < kanzure> i think we will need protein-based computers but so far we have onlny demonstrated silicon computers in cells, other than recombinase-stuff basic dna manipulation string operations in cells. 21:10 -!- ebowden [~ebowden@110.141.40.86] has joined ##hplusroadmap 21:10 -!- ebowden [~ebowden@110.141.40.86] has quit [Changing host] 21:10 -!- ebowden [~ebowden@unaffiliated/ebowden] has joined ##hplusroadmap 21:16 < kanzure> maybe just ultracentrifuge lots of cell cultures, at least then you get protein systems that are mass targeted, better than mere spaghetti.... 21:27 < fenn> ok i'm giving up on trying to understand this GWAS paper 21:27 < fenn> apparently there are 3 genes responsible for most of the variation in IQ in their sample 21:28 < fenn> or at least, 3 genes are significant at all (maybe not most of the variation) 21:28 < fenn> there are two schools of thought on heritability, one looks at regression, and the other looks at covariance 21:28 < fenn> i'm not sure what 0.33 and 0.02 represent exactly 21:30 -!- augur [~augur@2602:304:cdac:e260:b9ea:6fbd:2331:f784] has joined ##hplusroadmap 22:18 -!- mrdata_ [~mrdata@unaffiliated/mrdata] has joined ##hplusroadmap 22:22 -!- mrdata [~mrdata@unaffiliated/mrdata] has quit [Ping timeout: 240 seconds] 22:48 -!- jtimon [~quassel@102.30.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 23:10 -!- gnusha [~gnusha@unaffiliated/kanzure/bot/gnusha] has joined ##hplusroadmap 23:10 -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - 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