--- Log opened Tue Feb 04 00:00:29 2020 00:03 < nsh> .t https://twitter.com/jason_koebler/status/1224361402246275072 00:03 < EmmyNoether> Archivists have pirated more than 5,000 studies about coronaviruses and made them open access: "It's a moral imperative," they said. "A copyright on the health of humanity? Fuck off." // https://www.vice.com/en_us/article/z3b3v5/archivists-are-bypassing-paywalls-to-share-studies-about-coronaviruses (@jason_koebler) 00:48 -!- velol [~velol@c-68-55-229-154.hsd1.mi.comcast.net] has joined ##hplusroadmap 01:07 -!- preview [~quassel@2407:7000:8423:b00::2] has joined ##hplusroadmap 01:09 < mrdata> https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf 01:09 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 265 seconds] 01:09 < mrdata> Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag 01:10 -!- dr-orlovsky [~dr-orlovs@194.230.147.144] has joined ##hplusroadmap 01:10 < fenn> they're very short sequences and not unique to HIV at all 01:11 < mrdata> discussed in the paper 01:11 < fenn> also they're not quite the same, which means, if you use "not quite right" as your search criteria, you can find just about anything 01:11 < fenn> do a blastp on those sequences and see what you get and then talk about it 01:12 < fenn> you may have to uncheck 'hide low complexity results' on the algorithm tab, i forget 01:13 < mrdata> no other coronavirus has these four inserts; each insert is short, sure, but all four align to asian strains of HIV-1 01:14 < mrdata> quantify the likelihood 01:14 < fenn> no u 01:14 < mrdata> i'mn not well versed in the tools, but sure i'll give it a go tomorrow 01:15 < mrdata> should be possible to analyze from the basic math 01:16 < mrdata> could run a monte-carlo analysis 01:16 < fenn> HIV mutates quickly and we have a lot of sequence data on it 01:16 < mrdata> it is also an RNA virus, yes. and they mutate very rapidly, true 01:17 < mrdata> the bat coronavirus is 96% similar, so around 1200 bases mutated 01:18 < fenn> for the purposes of bioweapon conspiracy theories, the "2013" bat coronavirus sequence doesn't count because it was uploaded only a few days ago 01:19 -!- velol [~velol@c-68-55-229-154.hsd1.mi.comcast.net] has quit [Ping timeout: 240 seconds] 01:19 < mrdata> that virus was discovered in 2013; are you saying the sequence was kept secret unil a few days ago? 01:20 < mrdata> kept by who 01:20 < fenn> no, i'm saying that if there were a conspiracy, you couldn't trust the sequence data to actually be from a virus from 2013 01:20 < mrdata> ? 01:20 < fenn> they could be using it to cover their tracks 01:20 < mrdata> i dont understand 01:21 < mrdata> anyway i'm off to bed; will crunch on this after that 01:22 < fenn> the bat virus shows evidence of the natural progression from earlier viral genomes to the 2019-nCoV. if someone had actually engineered 2019-nCoV then they would want it to appear natural, but maybe the virus was released early or they never expected their handiwork to be discovered, and so published a misleading fake history as disinformation. so goes the conspiracy theory at least 01:24 -!- preview [~quassel@2407:7000:8423:b00::2] has quit [Ping timeout: 248 seconds] 01:37 -!- raonyguimaraes [~raonyguim@89.101.121.177] has joined ##hplusroadmap 01:47 < nsh> decadent civilisation is the conspiracy and it's entirely open 02:01 < nmz787> watched contagion and world war z tonight, to get up to speed on the coronavirus potential... funny that contagion was also about a bat that pooped into a pig pen, which then started infecting people near china 02:02 < nmz787> contagion came out in 2011, wwz in 2013 02:16 -!- shawwwn [uid6132@gateway/web/irccloud.com/x-jawuxkhberzbayom] has quit [Quit: Connection closed for inactivity] 02:35 -!- orlovsky [~dr-orlovs@xdsl-188-155-1-200.adslplus.ch] has joined ##hplusroadmap 02:37 -!- dr-orlovsky [~dr-orlovs@194.230.147.144] has quit [Ping timeout: 265 seconds] 02:49 -!- EmmyNoether [~EmmyNoeth@oasys.ch0wn.org] has quit [Ping timeout: 268 seconds] 03:14 -!- Netsplit *.net <-> *.split quits: maaku, s0ph1a, midnight, mgxm, pointfree, Solgriffin, srk, namespace, indiebio, justanotheruser, (+3 more, use /NETSPLIT to show all of them) 03:18 -!- 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03:20 -!- Solgriffin [sid282649@gateway/web/irccloud.com/session] has joined ##hplusroadmap 03:20 -!- Solgriffin [sid282649@gateway/web/irccloud.com/session] has quit [Changing host] 03:20 -!- Solgriffin [sid282649@gateway/web/irccloud.com/x-nuvmjnwramltgnum] has joined ##hplusroadmap 03:21 -!- rodarmor [sid210835@gateway/web/irccloud.com/x-pnjcioaooqszugjy] has quit [Ping timeout: 245 seconds] 03:21 -!- justanotheruser [~justanoth@cpe-74-68-57-95.nj.res.rr.com] has joined ##hplusroadmap 03:21 -!- justanotheruser is now known as Guest46475 03:21 -!- pepesza [~pepesza@185.83.218.228] has joined ##hplusroadmap 03:22 -!- superjen96 [jenelizabe@gateway/vpn/privateinternetaccess/jenelizabeth] has quit [Read error: Connection reset by peer] 03:22 -!- rodarmor [sid210835@gateway/web/irccloud.com/x-wnxojtlfptkdcfih] has joined ##hplusroadmap 03:22 -!- bbrittain [~bbrittain@ec2-34-242-76-124.eu-west-1.compute.amazonaws.com] has joined ##hplusroadmap 03:23 -!- jrayhawk [~jrayhawk@unaffiliated/jrayhawk] has joined ##hplusroadmap 03:23 -!- gwillen [~gwillen@unaffiliated/gwillen] has joined ##hplusroadmap 03:23 -!- fenn [~fenn@unaffiliated/fenn] has joined ##hplusroadmap 03:23 -!- otoburb [~otoburb@unaffiliated/otoburb] has joined ##hplusroadmap 03:23 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-szsngmkolbzztedh] has quit [Ping timeout: 272 seconds] 03:24 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-almoronbvyubggpf] has joined ##hplusroadmap 03:28 < mrdata> https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf 03:28 < mrdata> * aeiousomething has quit (Ping timeout: 265 seconds) 03:28 < mrdata> Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag 03:28 < mrdata> * dr-orlovsky (~dr-orlovs@194.230.147.144) has joined 03:28 < mrdata> they're very short sequences and not unique to HIV at all 03:28 < mrdata> discussed in the paper 03:28 < mrdata> also they're not quite the same, which means, if you use "not quite right" as your search criteria, you can find just about anything 03:28 < mrdata> do a blastp on those sequences and see what you get and then talk about it 03:28 < mrdata> you may have to uncheck 'hide low complexity results' on the algorithm tab, i forget 03:28 < mrdata> no other coronavirus has these four inserts; each insert is short, sure, but all four align to asian strains of HIV-1 03:28 < mrdata> quantify the likelihood 03:28 < mrdata> no u 03:28 < mrdata> i'mn not well versed in the tools, but sure i'll give it a go tomorrow 03:28 < mrdata> should be possible to analyze from the basic math 03:28 < mrdata> could run a monte-carlo analysis 03:28 < mrdata> HIV mutates quickly and we have a lot of sequence data on it 03:28 < mrdata> it is also an RNA virus, yes. and they mutate very rapidly, true 03:28 < mrdata> the bat coronavirus is 96% similar, so around 1200 bases mutated 03:28 < mrdata> for the purposes of bioweapon conspiracy theories, the "2013" bat coronavirus sequence doesn't count because it was uploaded only a few days ago 03:28 < mrdata> * velol has quit (Ping timeout: 240 seconds) 03:28 < mrdata> that virus was discovered in 2013; are you saying the sequence was kept secret unil a few days ago? 03:28 < mrdata> kept by who 03:28 < mrdata> no, i'm saying that if there were a conspiracy, you couldn't trust the sequence data to actually be from a virus from 2013 03:28 < mrdata> ? 03:28 < mrdata> they could be using it to cover their tracks 03:28 < mrdata> i dont understand 03:29 < mrdata> anyway i'm off to bed; will crunch on this after that 03:29 < mrdata> oops; sorry pastefail 03:29 < mrdata> i mean to write, 03:29 < mrdata> wouldnt it be a funny coincidence if, 03:29 < mrdata> (a) it only infects asians; (b) it only kills old people; and (c) it confers immunity to HIV to the survivors? 03:35 < mrdata> and yes i realize this idea is outlandish to the point of ridicule, so i expect it will be disproved pretty quick 03:35 -!- jenelizabeth [jenelizabe@gateway/vpn/privateinternetaccess/jenelizabeth] has joined ##hplusroadmap 03:46 < mrdata> 20 amino acids; average 7 in each of these short sequences, 20^7 combinations = 1.28x10^9 03:46 < mrdata> chance of random match of any one of these inserts with a sequence in asian HIV-1 03:46 < mrdata> 9749 bases in HIV / 1.28e9 = 7.6e-6 03:46 < mrdata> co-ordinate all four of these inserts to govern host specificity, but account for 03:46 < mrdata> inexact match, O(10^-10) = chance of this being a mere coincidence 03:46 -!- jtimon [~quassel@22.133.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 04:10 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Ping timeout: 268 seconds] 04:16 < fenn> there is more than 10kb of HIV sequence data 04:18 < fenn> also i think your calculation is wrong, but i'm not really confident in my ability to correctly do statistics 04:18 < fenn> blast gives very different E-values (number of times you'd expect to get a random match by chance) 04:19 < fenn> i'm tired of talking about this so i will bow out 04:23 -!- Urchin [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 05:20 -!- eliod [~eliod@2a02:2788:1028:d2c:2411:c8d0:e40:b7b4] has joined ##hplusroadmap 05:28 -!- Urchin [~urchin@unaffiliated/urchin] has quit [Ping timeout: 268 seconds] 05:30 -!- eliod [~eliod@2a02:2788:1028:d2c:2411:c8d0:e40:b7b4] has quit [Quit: Leaving] 06:00 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 06:04 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Ping timeout: 246 seconds] 06:20 -!- mauz555 [~mauz555@2a01:e35:8ab1:dea0:ccd1:3bbd:616d:3d67] has joined ##hplusroadmap 06:26 -!- superjen96 [jenelizabe@gateway/vpn/privateinternetaccess/jenelizabeth] has joined ##hplusroadmap 06:29 -!- jenelizabeth [jenelizabe@gateway/vpn/privateinternetaccess/jenelizabeth] has quit [Ping timeout: 268 seconds] 06:30 -!- jenelizabeth [~jenelizab@cpc155793-brmb11-2-0-cust474.1-3.cable.virginm.net] has joined ##hplusroadmap 06:30 -!- superjen96 [jenelizabe@gateway/vpn/privateinternetaccess/jenelizabeth] has quit [Read error: Connection reset by peer] 06:40 < lsneff> maaku: was trying to build a light-field display, but I cant really afford the microlenses for it apparently 07:22 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 07:53 -!- yashgaroth [~ffffffff@2606:6000:ca84:b300:9807:d438:e18a:1165] has joined ##hplusroadmap 08:03 -!- Guest46475 [~justanoth@cpe-74-68-57-95.nj.res.rr.com] has quit [Quit: WeeChat 2.6] 08:04 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 08:23 < kanzure> mrdata: the combinatorics of sequences is not how you figure out probability. the question is horizontal transfer in infected hosts, not combinatorics. 08:23 < kanzure> we need a much more biologically-informed populace. 08:29 -!- mauz555 [~mauz555@2a01:e35:8ab1:dea0:ccd1:3bbd:616d:3d67] has quit [] 09:15 -!- raonyguimaraes [~raonyguim@89.101.121.177] has quit [Ping timeout: 265 seconds] 10:12 -!- Urchin [~urchin@unaffiliated/urchin] has joined ##hplusroadmap 10:26 -!- sektor [~sektor@95.87.234.241] has joined ##hplusroadmap 10:38 < kanzure> "Expert programmers have fine-tuned cortical representations of source code" https://www.biorxiv.org/content/10.1101/2020.01.28.923953v1 11:00 -!- Netsplit *.net <-> *.split quits: midnight, justanotheruser 11:02 -!- Netsplit over, joins: justanotheruser, midnight 11:02 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Max SendQ exceeded] 11:02 -!- bbrittain [~bbrittain@ec2-34-242-76-124.eu-west-1.compute.amazonaws.com] has quit [Ping timeout: 240 seconds] 11:03 -!- filipepe [uid362247@gateway/web/irccloud.com/x-mobmkvhhiddlrezg] has joined ##hplusroadmap 11:03 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 11:05 -!- bbrittain [~bbrittain@ec2-34-242-76-124.eu-west-1.compute.amazonaws.com] has joined ##hplusroadmap 11:34 -!- velol [~velol@c-68-55-229-154.hsd1.mi.comcast.net] has joined ##hplusroadmap 11:39 -!- velol [~velol@c-68-55-229-154.hsd1.mi.comcast.net] has quit [Quit: Leaving] 11:50 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has quit [Quit: leaving] 11:50 -!- preview [~quassel@2407:7000:8423:b00::2] has joined ##hplusroadmap 12:02 -!- aeiousomething [~aeiousome@unaffiliated/aeiousomething] has joined ##hplusroadmap 12:08 -!- preview [~quassel@2407:7000:8423:b00::2] has quit [Ping timeout: 265 seconds] 12:08 -!- spaceangel [~spaceange@ip-89-177-23-46.net.upcbroadband.cz] has joined ##hplusroadmap 12:18 < mrdata> kanzure, my combinatorics only rules out a spurious match. basically it says there *must* have been horizontal transfer for these inserts to be in this virus 12:18 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 268 seconds] 12:18 < mrdata> but how those came to be is anyone's guess 12:19 < mrdata> HIV does not infect bats; so this would have occurred in an intermediate host 12:19 < kanzure> oh wait, shared lineage is another option 12:19 < kanzure> i guess horizontal transfer is a subset of shared lineage 12:20 < mrdata> these sequences were not in any other coronavirus 12:28 < heath> related to the bioarxiv link above:https://www.youtube.com/watch?v=uEFrE6cgVNY "Evidence-Oriented Programming" by Andreas Stefik 12:28 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 12:36 -!- jtimon [~quassel@22.133.134.37.dynamic.jazztel.es] has quit [Remote host closed the connection] 13:02 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 265 seconds] 13:02 -!- justan0theruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 13:13 -!- filipepe [uid362247@gateway/web/irccloud.com/x-mobmkvhhiddlrezg] has quit [Quit: Connection closed for inactivity] 13:16 -!- filipepe [uid362247@gateway/web/irccloud.com/x-gooukqlyiiuwchxh] has joined ##hplusroadmap 13:24 -!- Human_G33k [~HumanG33k@62.147.242.8] has quit [Remote host closed the connection] 14:23 -!- spaceangel [~spaceange@ip-89-177-23-46.net.upcbroadband.cz] has quit [Ping timeout: 248 seconds] 15:26 < lsneff> .title https://scitechdaily.com/room-temperature-superconductor-breakthrough-at-oak-ridge-national-laboratory/ 15:27 < lsneff> maybe emmy is down 15:28 < lsneff> "Room Temperature Superconductor Breakthrough at Oak Ridge National Laboratory" 15:28 < lsneff> Not quite there, but it seems they're getting close 15:29 < lsneff> hydrogen-hydrogen bond spacing in zirconium vanadium hydride appear to be significantly closer together than predicted 16:24 -!- sektor [~sektor@95.87.234.241] has quit [Ping timeout: 265 seconds] 17:13 -!- preview [~quassel@2407:7000:8423:b39:fa6e:247:9ac4:2e12] has joined ##hplusroadmap 17:23 -!- filipepe 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