--- Log opened Sat Oct 28 00:00:59 2017 00:10 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 00:12 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 00:55 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Read error: Connection reset by peer] 00:55 -!- fltrz [4d6d6154@gateway/web/freenode/ip.77.109.97.84] has quit [Ping timeout: 260 seconds] 00:56 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 01:01 -!- aeiousomething [~aeiousome@117.195.133.60] has joined ##hplusroadmap 01:01 < mrdata> "limiting principles for end users are not well developed as end 01:01 < mrdata> user (of a product) was considered minor stake holder" 01:02 < mrdata> if you had life-saving gene therapy, youre all-in, now 01:02 < mrdata> that isnt minor 01:03 * mrdata sleeps 01:03 -!- ebowden [~ebowden@2001:8003:1074:bc00:d1fa:1b2f:3c78:e4ca] has quit [Read error: Connection reset by peer] 01:04 -!- ebowden [~ebowden@2001:8003:1074:bc00:d1fa:1b2f:3c78:e4ca] has joined ##hplusroadmap 01:27 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 01:39 -!- augur [~augur@2601:645:c100:1132:6431:9fa9:8804:1691] has joined ##hplusroadmap 01:44 -!- augur [~augur@2601:645:c100:1132:6431:9fa9:8804:1691] has quit [Ping timeout: 252 seconds] 01:45 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 258 seconds] 02:19 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has joined ##hplusroadmap 02:32 -!- hazzy [6bc258ef@gateway/web/cgi-irc/kiwiirc.com/ip.107.194.88.239] has quit [Ping timeout: 255 seconds] 02:32 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 02:35 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 240 seconds] 03:04 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 03:06 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 260 seconds] 03:29 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 03:32 -!- aeiousomething [~aeiousome@117.195.133.60] has quit [Ping timeout: 240 seconds] 04:23 < archels> mit tech review refuses to serve me content in "private browsing mode" 04:27 -!- sachy [~sachy@nat.brmlab.cz] has joined ##hplusroadmap 04:41 -!- preview [~quassel@2407:7000:842d:4000::3] has quit [Ping timeout: 246 seconds] 04:55 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 05:09 -!- aeiousom1thing [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 252 seconds] 05:10 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 05:22 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 248 seconds] 05:23 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 05:23 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Client Quit] 05:23 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 05:47 < kanzure> http://mouselight.janelia.org/ 05:49 < kanzure> "In vivo RNA targeting of point mutations via suppressor tRNAs and adenosine deaminases" https://www.biorxiv.org/content/early/2017/10/27/210278 https://twitter.com/biorxivpreprint/status/924018133731508225 05:49 < kanzure> "we engineered and optimized two complementary approaches, referred together hereon as tRiAD, based on the use of tRNAs in codon suppression and adenosine deaminases in RNA editing. Specifically, by delivering modified endogenous tRNAs and/or the RNA editing enzyme ADAR2 and an associated guiding RNA (adRNA) via adeno-associated viruses, we enabled premature stop codon read-through and ... 05:49 < kanzure> ...correction in the mdx mouse model of muscular dystrophy that harbors a nonsense mutation in the dystrophin gene. We further demonstrated inducible restoration of dystrophin expression by pyrolysyl-tRNA mediated incorporation of unnatural amino acids (UAAs) at the stop codon. Additionally, we also engineered ADAR2 mediated correction of a point mutation in liver RNA of the spfash mouse model ... 05:49 < kanzure> ...of ornithine transcarbamylase (OTC) deficiency. Taken together, our results establish the use of suppressor tRNAs and ADAR2 for in vivo RNA targeting, and this integrated tRiAD approach is robust, genomically scarless, and potentially non-immunogenic as it utilizes effector RNAs and human proteins." 05:50 < kanzure> nterestingly, this is not the same paper as https://www.nature.com/nature/journal/vaap/ncurrent/full/nature24644.html or http://science.sciencemag.org/content/early/2017/10/24/science.aaq0180 05:50 < kanzure> .title https://www.genomeweb.com/business-news/bgi-launches-george-church-institute-regenesis 05:50 < yoleaux> BGI Launches George Church Institute of Regenesis | GenomeWeb 05:51 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 05:52 < kanzure> "Feasibility of 3d reconstruction of neural morphology using extension microscopy and barcode-guided agglomeration" https://www.frontiersin.org/articles/10.3389/fncom.2017.00097/full https://twitter.com/AdamMarblestone/status/922693623380049920 05:57 -!- augur [~augur@2601:645:c100:1132:6431:9fa9:8804:1691] has joined ##hplusroadmap 05:59 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 06:02 -!- augur [~augur@2601:645:c100:1132:6431:9fa9:8804:1691] has quit [Ping timeout: 258 seconds] 06:22 -!- jtimon [~quassel@164.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 06:24 < kanzure> https://twitter.com/patcherbot 06:33 < kanzure> "We here introduce and study the properties, via computer simulation, of a candidate automated approach to algorithmic reconstruction of dense neural morphology, based on simulated data of the kind that would be obtained via two emerging molecular technologies—expansion microscopy (ExM) and in-situ molecular barcoding. We utilize a convolutional neural network to detect neuronal boundaries ... 06:33 < kanzure> ...from protein-tagged plasma membrane images obtained via ExM, as well as a subsequent supervoxel-merging pipeline guided by optical readout of information-rich, cell-specific nucleic acid barcodes. We attempt to use conservative imaging and labeling parameters, with the goal of establishing a baseline case that points to the potential feasibility of optical circuit reconstruction, leaving open ... 06:33 < kanzure> ...the possibility of higher-performance labeling technologies and algorithms. We find that, even with these conservative assumptions, an all-optical approach to dense neural morphology reconstruction may be possible via the proposed algorithmic framework. Future work should explore both the design-space of chemical labels and barcodes, as well as algorithms, to ultimately enable routine, ... 06:33 < kanzure> ...high-performance optical circuit reconstruction." 06:34 < kanzure> .tw https://twitter.com/EricTopol/status/923236965155082240 06:34 < yoleaux> A big #CRISPR DNA and RNA genome editing day @nature & @sciencemagazine https://www.nature.com/polopoly_fs/1.22884!/menu/main/topColumns/topLeftColumn/pdf/550439a.pdf summed up well by @ElieDolgin @NatureNews https://pbs.twimg.com/media/DM_-vXmUEAAfusg.jpg https://pbs.twimg.com/media/DM_-x1RVQAA7BEW.jpg https://pbs.twimg.com/media/DM_-0xAUQAUX_DV.jpg (@EricTopol) 06:34 < kanzure> .tw https://twitter.com/kanzure/status/924258031818461184 06:34 < yoleaux> @EricTopol @nature @sciencemagazine @ElieDolgin @NatureNews @broadinstitute @zhangf @Harvard Also this one https://twitter.com/biorxivpreprint/status/924018133731508225 (@kanzure, in reply to tw:923236965155082240) 06:34 < kanzure> "CRISPR hacks allow for pinpoint repairs" https://www.nature.com/polopoly_fs/1.22884!/menu/main/topColumns/topLeftColumn/pdf/550439a.pdf 06:38 < kanzure> from which, 06:38 < kanzure> "In the base-editing method pioneered by Liu’s team last year, the researchers engineered a naturally occurring enzyme and tethered it to a dud Cas9, which allowed them to convert C to T. But there is no equivalent enzyme found in nature for the opposite conversion in DNA. So the researchers started with an RNA-editing enzyme similar to the one Zhang’s group used. The team guided the ... 06:38 < kanzure> ...evolution of bacterial cells through seven generations, and used some protein engineering in the lab, to produce an enzyme that would recognize and manipulate DNA. The enzyme was able to rearrange atoms in adenine to change it into an inosine, which the cell reads as a guanine. The system then tricked the cell into inserting a cytosine into the unmodified DNA strand (see ‘Changing ... 06:38 < kanzure> ...bases’)." 06:40 -!- sachy [~sachy@nat.brmlab.cz] has quit [Ping timeout: 255 seconds] 06:48 -!- sachy [~sachy@nat.brmlab.cz] has joined ##hplusroadmap 07:21 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 258 seconds] 07:23 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 07:34 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 08:10 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 08:14 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 246 seconds] 08:17 -!- saturn2 [~visitant@unaffiliated/clone-of-saturn/x-2509460] has quit [Read error: Connection reset by peer] 08:21 -!- hazzy [6bc258ef@gateway/web/cgi-irc/kiwiirc.com/ip.107.194.88.239] has joined ##hplusroadmap 08:25 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 260 seconds] 08:34 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 08:38 -!- NikopolSohru [~NSohru@89.38.98.76] has joined ##hplusroadmap 08:43 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 08:46 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has joined ##hplusroadmap 09:15 < kanzure> here are my draft notes for upcoming gp-write phone call (deep dive on current/future dna synthesis techniques) https://docs.google.com/document/d/1djRRVpBqHb-okJWSBAA_DoRDiFFcQBezO1xvb4oHnV4/edit# 09:18 -!- c0rw1n_ [~c0rw1n@cpc109847-bagu17-2-0-cust223.1-3.cable.virginm.net] has joined ##hplusroadmap 09:20 < kanzure> heath: ^could use your help on that 09:20 < kanzure> nmz787: yashgaroth: ^you too 09:21 -!- ebowden [~ebowden@2001:8003:1074:bc00:d1fa:1b2f:3c78:e4ca] has quit [Read error: Connection reset by peer] 09:23 -!- ebowden [~ebowden@110.141.11.39] has joined ##hplusroadmap 09:36 < kanzure> phil asks: when does it become more cost effective to do editing vs de novo genome synthesis? 09:57 -!- augur [~augur@2601:645:c100:1132:6431:9fa9:8804:1691] has joined ##hplusroadmap 10:02 -!- augur [~augur@2601:645:c100:1132:6431:9fa9:8804:1691] has quit [Ping timeout: 255 seconds] 10:32 < kanzure> so if they want constant aerial surveillance drones recording all spectrum to dna then what if we do it first.. why should i let them win that race. 10:48 -!- fltrz [4d6d6154@gateway/web/freenode/ip.77.109.97.84] has joined ##hplusroadmap 11:02 -!- strages [uid11297@gateway/web/irccloud.com/x-ogqxpsjdeglodfcr] has joined ##hplusroadmap 11:32 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 258 seconds] 11:33 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 11:35 < kanzure> fltrz: sup 11:35 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 11:37 -!- preview [~quassel@2407:7000:842d:4000::3] has joined ##hplusroadmap 11:39 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has quit [Ping timeout: 264 seconds] 11:40 < fltrz> hi, yeah looking up some more op amp noise calculations, theres plenty of plugin equations for the simplest circuits, but I'm looking more for fundamental general circuit of linear elements noise calculations 11:42 < kanzure> there are many people in ##electronics who might know this 11:43 < fltrz> yeah that channel requires identification stuff 11:43 < kanzure> then do identification stuff 11:43 < kanzure> /query nickserv register 11:43 < fltrz> :) not really a fan very much 11:46 < fltrz> it sounds horrible but I would prefer a system of custom ignore lists, which can be shared, so thered be some popular ignore lists, but then people would also share custom whitelists to avoid suppression of nonconformist ideas/interpretations/beliefs 11:46 < kanzure> more on adenosine deaminases and tRNA stuff http://mali.ucsd.edu/uploads/3/1/0/0/31002267/biorxiv_2017.pdf 11:46 < fltrz> now people are forced to accept the moderators censorship 11:47 < kanzure> (updated manuscript) 11:47 < kanzure> fltrz: http://lesswrong.com/lw/c1/wellkept_gardens_die_by_pacifism/ 11:49 < fltrz> kanzure: there would be defense, i.e. the gossiped blacklists and whitelists... i.e. suppose i go to physics, and suppose relativity was not discovered yet, then a bunch of people most whove been blacklisted for talking relativity 11:49 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has quit [Ping timeout: 240 seconds] 11:50 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 11:50 < fltrz> perhaps some of them would be less outspoken, and start a private chat in response to a question, and if the person considered you open minded enough they would dare send you a whitelist for people discussing relativity 11:50 < fltrz> but this way its all still ##physics 11:51 < fltrz> no channel control fights 11:53 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 11:53 < fltrz> a person upon joining a topic channel, could choose to use a default blacklist he found on a site or whomever invited him to the channel, but he might choose to disregard the blacklist too 11:53 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Quit: leaving] 11:55 < fltrz> imho the question is not defense vs pacifism, but delegate/centralize defense vs decentralized individual freedom to filter/censor what you see 11:57 < kanzure> .tw https://twitter.com/BWJones/status/845121891576664064 11:57 < yoleaux> Lungs make blood.. I had to read this twice. I'm gobsmacked. So much more about basic biology that we don't know. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature21706.html (@BWJones) 11:58 < kanzure> fltrz: go make a decentralized chat or whatever.. freenode is free to run their system however they please. 11:59 < kanzure> "The lung is a site of platelet biogenesis and a reservoir for haematopoietic progenitors" http://www.nature.com/nature/journal/v544/n7648/full/nature21706.html 11:59 < fltrz> kanzure: someday I might, but its not my priority, also textbooks and papers tend to be more focussed than some people in ##electronics 11:59 < fltrz> kanzure: did I ever tell you about my theory of the female orgasm? 11:59 < kanzure> "The contribution of the lungs to platelet biogenesis is substantial, accounting for approximately 50% of total platelet production or 10 million platelets per hour" 11:59 < kanzure> fltrz: no 12:00 < fltrz> kanzure: not sure how NSFW we Im allowed to go here 12:00 < kanzure> eh keep it scientific and you'll be fine 12:01 < fltrz> I will just blort it out: I believe that in nature the female orgasm for most mammals serves for childbirth 12:02 < fltrz> the big mystery of what the female orgasm is for is more the result of taboo than lack of data 12:02 < fltrz> the contractions of the uterus push the baby into the vagina, and the contractions of the vagina push the baby out into the world 12:03 < fltrz> the contractions of the uterus are described, the contractions of the vagina during female orgasm are described in scientific literature 12:04 < fltrz> but nobody seems to explicitly connect the dots, many of the founding discoveries were made in a time where most of sex and sexuality was immensely taboo 12:04 -!- gene-hacker [~tetrapod@c-24-131-17-249.hsd1.pa.comcast.net] has quit [Quit: Leaving] 12:04 < fltrz> so probably many realized it, but didn't dare or were discouraged from making the connection 12:04 < fltrz> or their brain simply refused to see the forrest through the trees 12:05 < fltrz> because of being raised in puritanism 12:05 < fltrz> oxytocin is released during sex 12:06 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 12:07 < fltrz> the discovery of oxytocin: some dude put a human brain in a blender, analyzed it into seperate chemical substances, and administered them to cats. For the substance we now know as oxytocin, the cat behaved in a way the researcher somehow realized was like a cat having contractions for birth 12:07 < fltrz> now oxytocin is used to induce delivery 12:08 < fltrz> would it be so strange for animals in discomfort of getting ready to deliver, to try and soothe their pain somehow? 12:09 < fltrz> also, the subjective experience of orgasm is so powerful (compared to say sugar rush) that it is bound to be reward for a very profoundly important part in survival 12:10 < fltrz> for the male the orgasm is reward for succeeding to ejaculate, for the female it is reward for succeeding to put child on earth 12:10 < fltrz> the contractions are like squeezing tube of toothpaste 12:11 < fltrz> so in short, there is no mystery of the female orgasm, only a taboo 12:11 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:12 < fltrz> so females also can have an orgasm during sex, which is then exercise to develop the muscles for childbirth later 12:14 < fltrz> the result of taboo is that for many women these muscles are never properly trained, and that in the hospital (an animal tends to look for a psychologically calm and quiet and dark place, not with a load of strangers, and spotlights) 12:14 < fltrz> that in the hospital they dont even consider easing their pain with masturbation 12:15 < fltrz> oxytocin is injected, the women is sexually excited 12:15 < fltrz> contractions of the uterus start 12:16 < fltrz> now the clitoris, internally has 2 large protrusions hugging/surrounding the vagina. the clitoris, now erect can also be stimulated from within the vagina, the g spot as well 12:17 < fltrz> so the baby is pushed by the uterine contractions into the vagina, and this triggers the vaginal contractions 12:18 < fltrz> its weird how people accept that female orgasm can be initiated by a penis, but somehow not by a much larger baby passing through 12:19 < fltrz> this taboo also makes it impossible for the female to properly consent to an orgasm, without a taboo the female consents the moment she decides to have a baby 12:19 < fltrz> but in a world of taboo, it is too late to not consent if the baby will be delivered 10 minutes from now 12:20 < fltrz> in a sense the taboo rapes them. many women report flashbacks to earlier traumas of rape during child birth 12:20 < fltrz> because they unexpectedly find themselves having an orgasm in a situation where everyone pretends it has nothing to do with sex 12:21 < fltrz> and find themselves unable to stop the situation 12:22 < fltrz> postpartum depression 12:23 < fltrz> who can they confide in? did anyone notice? perhaps family members were present? will their husband think? 12:24 < fltrz> will the husband think she is a bad wife if she explains what happened and if her interpretation is crazy or true? 12:25 < fltrz> is there some weird for profit conspiracy of the medical world? 12:25 < fltrz> all these thoughts together with rape traumas probably explain postpartum depression imho 12:26 < fltrz> if the muscles are not well developed due to taboo about sex, the complication risk also increases 12:26 < fltrz> brazil 90% of childbirth involves _elective_ caesarian sections.. i.e. not even necessary 12:27 < fltrz> meanwhile "primitive" tribes have no problem procreating... 12:27 < fltrz> or rather little 12:29 < fltrz> at some point pompei was excavated, and it was a direct contact from antiquity (i.e. not handed down and filtered by previous generations) 12:29 < fltrz> it was full of obscene statues 12:29 < fltrz> pan copulating with a goat 12:29 < fltrz> in the middle of the square 12:30 < fltrz> the archaelogists had to hide all the artefacts from public view 12:32 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 12:32 < fltrz> I saw the pompei things in a documentary called "the history of pornography" or smth, only the first 1 or 2 episodes are interesting 12:33 < fltrz> as its about the oldest artefacts. there was this Venus like women (in clay I think), obviously highly pregnant, but also apparently pleasuring herself 12:33 < fltrz> with visibly excited vagina 12:34 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:34 < fltrz> almost an ancient form of documentary, describing natural childbirth. 12:35 < fltrz> but they don't make that connection in the documentary, they just mention the controversy, because its an important artefact due to its age, and appears indecent to current norms, 12:36 < fltrz> but the archaeologists disagree if its just a pregnant women, or if she is masturbating, as if they are mutually exclusive 12:36 < fltrz> was that scientific enough? 12:36 < fltrz> I can add some references, but most can be found on wikipedia, say discovery of oxytocin, the problem is not the data, its that nobody dares to connect the dots 12:37 < fltrz> whoever does is basically saying they mother orgasmed them into the world, marks themself for ridicule 12:38 < fltrz> I can imagine a lot of doctors having the insight, and internally they rationalize it as "sheeple just want children, and they expect this to be a nonsexual event, so we just start the whole process with drugs, and pretend nothing is happening" 12:39 < fltrz> the venus like women was from south america, I think peru 12:41 < kanzure> about liu lab thing https://www.washingtonpost.com/news/speaking-of-science/wp/2017/10/25/scientists-announce-new-gene-editing-techniques-aimed-at-common-mutations/ 12:41 < fltrz> also keep in mind that there is a group of people who decide to give birth at home (possibly with a doctor closeby in case of emergency), so there is a possibility that a fraction of them is aware 12:42 < kanzure> .tw https://twitter.com/markusgershater/status/921322972698300416 12:42 < yoleaux> We're hiring lab people! Looking for passion, hard work, intelligence, eloquence and persistence. RTs = gratitude https://synthace.com/careers-biological-scientist/ (@markusgershater) 12:42 < fltrz> kanzure: can you imagine that if I made these claims in a channel for midwives, that I would be banned? 12:42 < kanzure> .tw https://twitter.com/EBItraining/status/922470089353564160 12:42 < yoleaux> David from @PDBeurope gets participants exploring structural to ID these #3Dprinted protein structures! https://pbs.twimg.com/media/DM1FpV1X0AE43Wz.jpg (@EBItraining) 12:42 < kanzure> fltrz: uh whatever 12:43 < fltrz> its just an example why I think centralized channel control is not desirable 12:45 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 12:48 <@nmz787> kanzure: have to go to ATM now, will read all your notes, etc... also did you make SRC doc edits? I saw some typos and such I wanted to fix, in addition to adding a bit more enzmye info if still needed 12:50 < kanzure> i don't remember 12:51 < kanzure> .tw https://twitter.com/BiochemPhD/status/922603793090535425 12:51 < yoleaux> Thx to friends @LABiohackers, @ChiTownBio now has an electrophoresis power supply! We can now separate/visualize DNA of diff. sizes! #DIYBio https://pbs.twimg.com/media/DM2_QklUIAAooC6.jpg (@BiochemPhD) 12:52 < kanzure> .tw https://twitter.com/4LOVofScience/status/922855956907671552 12:52 < yoleaux> Heartbreaking and beautiful story about DIY Immunotherapy a bunch of us have been working on by @kristenvbrown https://gizmodo.com/when-hope-runs-out-cancer-patients-are-making-their-ow-1819405332 (@4LOVofScience) 13:25 < heath> https://gist.github.com/heath/3390ba7d7e27f0805636b8fc4310cac4 13:26 < heath> is TdT the only completely template independent polymerase? 13:28 < heath> .title 13:28 < yoleaux> Eukaryotic DNA Polymerase · GitHub 13:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 13:37 < kanzure> there are many TdTs 13:37 < kanzure> heath: homodimers/monodimers/whatever would be a good column for that document 13:39 < kanzure> geeze i forgot about telomerase 13:39 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f23e75c8 Bryan Bishop: forgot about telomerase >> http://diyhpl.us/diyhpluswiki/gene-editing/ 13:40 < heath> moved to https://docs.google.com/spreadsheets/d/1WseqP3zjdRoWp5Qge8BuxFPXaIRWOi3IOv2v60P_ync/edit?usp=sharing 13:45 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 13:55 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 13:55 -!- NikopolSohru [~NSohru@89.38.98.76] has quit [Ping timeout: 240 seconds] 13:59 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has joined ##hplusroadmap 14:06 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 14:07 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 14:16 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Quit: Leaving.] 14:46 <@nmz787> heath: poly A polymerase 14:46 <@nmz787> wik poly A polymerase 14:46 <@nmz787> .wik poly A polymerase 14:46 < yoleaux> "Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA (mRNA) for translation." — https://en.wikipedia.org/wiki/Polyadenylation 14:46 <@nmz787> kanzure: oh yeah, telomerase... hmm 14:53 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 14:53 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Client Quit] 15:01 < heath> http://pdb101.rcsb.org/motm/106 15:01 < heath> .title 15:01 < yoleaux> PDB-101: Poly(A) Polymerase 15:02 < heath> "the end of (almost) every messenger RNA strand is composed of a long string of repeated adenosine nucleotides. These long poly(A) tails are not encoded in the genome. Instead, they are added after RNA polymerase finishes its normal process of transcription." 15:02 < heath> it requires a blunt end? 15:02 * heath needs to read more 15:03 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 15:03 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Client Quit] 15:04 < kanzure> yashgaroth: do you know which ones require blunt ends. and is changing this a hard thing. 15:08 < heath> http://www.sciencedirect.com/science/article/pii/S1097276505013912 15:08 < heath> Our data argue that pol μ, like TdT, is able to add nucleotides to unpaired primer termini (3′ overhangs) and that this activity is primarily attributable to the loop 1 element these polymerases share. However, unlike TdT, pol μ does not frequently generate template-independent N additions in the context of cellular NHEJ (Table 1; Bertocci et al., 2003). 15:09 < heath> Indeed, sequencing of junctions from in vitro end-joining reactions using substrates with noncomplementary 3′ overhangs also argues that the majority of nucleotide addition by pol μ in this context is template dependent. 15:10 < heath> maybe useful for the notes, not really relevant to the current conversation, apologies 15:17 <@nmz787> .wik non homologous end joining 15:17 < yoleaux> "Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair, which requires a homologous sequence to guide repair." — https://en.wikipedia.org/wiki/Non-homologous_end_joining 15:18 < heath> i don't think it's a show stopper, though, my guess is that complete template independence has a small reduction in the total number of steps. i need to study engineering methods as well 15:18 < heath> thanks nathan 15:19 <@nmz787> yashgaroth is a protein (production) engineer by day 15:19 <@nmz787> so he is pretty steeped in knowledge 15:20 < heath> oh! i didn't realize 15:20 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 15:20 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Client Quit] 15:22 < yashgaroth> blunt end? the RNA is single stranded 15:22 -!- berndj-blackout [~berndj@mail.azna.co.za] has joined ##hplusroadmap 15:23 -!- berndj [~berndj@mail.azna.co.za] has quit [Ping timeout: 240 seconds] 15:23 <@nmz787> yashgaroth: I think that was re: pol μ 15:24 -!- berndj-blackout is now known as berndj 15:24 < heath> i did use the phrase "blunt end" in reference to poly(a) 15:25 < heath> yashgaroth: are you aware of any other dna polymerase that is completely template independent similar to TdT? 15:26 < yashgaroth> no, they're quite rare 15:30 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 15:30 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Client Quit] 15:31 < yashgaroth> at least there's a breadth of different species with variants of TdT though 15:40 <@nmz787> so a friend has an idea about using robots that can move themselves in 3D (swimbots, or balloon bots, UAVs, etc), each representing amino acids, and having light emitters+sensors at each atom, with their drive/response representative of the charge on the atom (something like a transfer curve of distance vs repulsion/attraction) 15:41 <@nmz787> and that a swarm of these bots, representing the aminos of a protein, could programmed to maximize the amount of light-signal detected on all inputs 15:41 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 15:41 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Client Quit] 15:41 < kanzure> i don't get it. UAVs are making dna? 15:41 <@nmz787> and that this sort of signal-maximizing algorithm of moving the bot swarm around, might have the same effect as protein folding would 15:41 < maaku> nmz787: what are those bots made of such that the components for all that can be smaller than the amino acids they're carrying around? 15:41 <@nmz787> not actual aminos, just models 15:42 <@nmz787> like each bot could be the size of a fist 15:42 <@nmz787> i.e. have the shape of each amino acid in the cartoon sphere drawing type 15:42 < maaku> oh what is this an educational thing or something? 15:42 < kanzure> whoops, i mean proteins obviously, since you said amino acids 15:43 < kanzure> yeah same question 15:43 < heath> http://biomatrica.com/dnastable.php 15:43 < heath> "Compositions for stabilizing DNA and RNA in blood and other biological samples during shipping and storage at ambient temperatures" https://patents.google.com/?q=dna&assignee=Biomatrica%2c+Inc. 15:43 <@nmz787> not really educational, just his idea of "would a swarm of such bots running a simple maximizing program based on the LEDs/photosensors be faster than computer simulations" 15:44 < heath> "Stabilization of non-denatured polypeptides, nucleic acids, and exosomes in a blood sample at ambient temperatures" https://patents.google.com/patent/WO2015191633A1/en?q=dna&assignee=Biomatrica%2c+Inc. 15:44 <@nmz787> and thus solve protein folding problems 15:44 <@nmz787> aide protein engineering 15:44 <@nmz787> obv there are things like ions that would affect the transfer/response curve of the LEDs/sensors 15:45 < heath> "Compositions and methods for biological sample storage" https://patents.google.com/patent/US20110081363A1/en?q=dna&assignee=Biomatrica%2c+Inc. 15:45 < kanzure> what was the dnascript method? tdt? 15:46 < heath> yes 15:46 < heath> the patents are me remembering this sentence 15:46 < heath> "The 15:46 < heath> sample treated with DNAstable held at 65°C behaved similarly to the sample held at -20°C (1,691 15:46 < heath> vs 1,641, with 89 sequences missing from one but not both samples)." 15:46 < heath> from "Scaling up DNA data storage and random access retrieval" https://www.biorxiv.org/content/biorxiv/early/2017/03/07/114553.full.pdf 15:48 < kanzure> anselm levskaya is cited in there 15:54 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 16:05 < heath> 2017 mamallian dna repair conference https://www.grc.org/mammalian-dna-repair-conference/2017/ 16:05 < heath> 2009 dna repair and mutagensis conference https://www.asm.org/ccLibraryFiles/FILENAME/000000004897/Program%20Abstract%20Book.pdf 16:06 < kanzure> .wik recq4 16:06 < yoleaux> "ATP-dependent DNA helicase Q4 is an enzyme that in humans is encoded by the RECQL4 gene." — https://en.wikipedia.org/wiki/RECQL4 16:06 < kanzure> .wik tls polymerase 16:06 < yoleaux> "DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day." — https://en.wikipedia.org/wiki/DNA_repair 16:08 < heath> i've seen translesion synthesis abbreviated to TLS 16:11 < heath> not a lot of information on pol sigma 16:17 < kanzure> the greek lettering is silly... there's more than 20 types of polymerases or whatever. 16:18 < kanzure> but biologists gotta be biologist 16:23 -!- Gurkenglas [~Gurkengla@dslb-094-223-135-191.094.223.pools.vodafone-ip.de] has joined ##hplusroadmap 16:53 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 16:53 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Client Quit] 16:58 < fltrz> nmz787: I don't understand why this person thinks physically moving a robot with mass around would be faster than numerical simulation? even simulating the swimming robots would be faster than having real robots swim... 17:12 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has joined ##hplusroadmap 17:16 <@nmz787> fltrz: something about many-body problem being faster to just solve with physics/real-system rater than computationally 17:17 <@nmz787> fltrz: also the guy is not a programmer and has told me he pretty much knows nothing about computers or how they work or how programming works 17:25 <@nmz787> fltrz: however, I will say it seems building some (30 or 100) swim-bots with 14-27 LEDs/photosensors each (atoms per amino) (or less, if you wanted to ignore very uninvolved-in-bonding atoms) and finding a swimming pool to throw them in would be pretty cheap 17:25 <@nmz787> especially if you could market them like a toy, to get Chinese toy manufacturers to produce them for cheap 17:25 < fltrz> Im quite skeptical about many-body problems being faster to solve with "physics/real systems", in the end computers are physical systems too. I can imagine certain restricted problems being faster to solve with analog electronics and/or optics (like 4F correlators), but I would be lying if I had any idea of how to efficiently translate protein folding to analog electronics for example 17:25 <@nmz787> they already have those microbe plush dolls 17:26 <@nmz787> amino-bots seems like the next-best thing 17:26 < fltrz> to think in the opposite direction: if physical then automatically faster than computer is really misguided imho 17:26 <@nmz787> fltrz: sure, computers are real systems... but it's a different architecture, I guess 17:26 < fltrz> what are microbe plush dolls? 17:27 < fltrz> I can imagine this to be useful for art/education in the sense of motivating and captivating interest for newcomers 17:27 <@nmz787> I think these https://en.wikipedia.org/wiki/GIANTmicrobes 17:28 <@nmz787> some bio club sold them at my college I think, or the bio department for a fundraiser 17:28 <@nmz787> I didn't buy any 18:05 -!- mindsForge [~nak@174-26-123-39.phnx.qwest.net] has quit [Remote host closed the connection] 18:34 -!- jaboja [~jaboja@jaboja.pl] has quit [Remote host closed the connection] 18:56 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 19:16 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Quit: Leaving] 19:51 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has quit [Quit: Leaving] 19:51 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has joined ##hplusroadmap 19:54 < heath> https://ampliqon.com/en/ordering/storage-and-shipping-conditions-pcr-enzymes/stability-test-taq-dna-polymerase/ 19:57 < heath> http://www.gwent.org/presentations/aetstab_08.pdf "Most contract research has led to the generation of stable enzyme formulations from between 50 days to over 18 months at temperatures of up to 50 ° C" 19:58 < heath> "Extended stability of restriction enzymes at ambient temperatures." https://www.ncbi.nlm.nih.gov/pubmed/10997268 20:13 <@nmz787> is that 50 das to 18 months in storage, or in use? 20:14 <@nmz787> days* 20:25 -!- thxffo [SMD@gateway/shell/elitebnc/x-ysnvikkbyyupwhbn] has quit [Ping timeout: 255 seconds] 20:26 < heath> i assumed storage, but it isn't clear 20:27 <@nmz787> yeah, seems so 20:27 <@nmz787> at least the last paper you posted 20:30 <@nmz787> the second to last paper is good so far 20:30 <@nmz787> slides really 20:31 <@nmz787> fltrz: well computers are pretty good these days, and computers still aren't solving protein folding problems quickly or well 20:31 <@nmz787> (the last I checked, which wasn't recently) 20:47 -!- darsie [~username@84-114-73-160.cable.dynamic.surfer.at] has quit [Ping timeout: 248 seconds] 20:48 < heath> .title http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005084 20:48 < yoleaux> A Database of Domain Definitions for Proteins with Complex Interdomain Geometry 20:52 <@nmz787> .title dx.doi.org/10.1021/nl100999e 20:52 < yoleaux> nmz787: Sorry, that doesn't appear to be an HTML page. 20:52 <@nmz787> .title https://dx.doi.org/10.1021/nl100999e 20:52 < yoleaux> nmz787: Sorry, that doesn't appear to be an HTML page. 20:52 <@nmz787> :/ 20:52 <@nmz787> Sub-10-nm Nanochannels by Self-Sealing and Self-Limiting Atomic Layer Deposition 20:53 < heath> for future ref: dx.doi.org will return a 303 redirect 20:54 <@nmz787> yoleaux could learn to handle that 20:54 * heath nods 20:54 < maaku> nmz787: a more reliable approach would be quantum computing 20:55 < maaku> it's actually what quantum computing was invented for, when feynman tried to design a computer that would be able to efficiently simulate quantum effects 21:00 <@nmz787> sure 21:00 <@nmz787> we're still years away from doing that kind of simulations/experiments with qbits 21:04 <@nmz787> this could be useful, it seems interesting: "Semantic Techniques for Quantum Computation" www.cs.mcgill.ca/~prakash/Pubs/DKPP-chap-final.pdf 21:05 < heath> https://github.com/hohlraum/gdsCAD A simple but powerful Python package for creating photolithography masks in the GDSII format. 21:06 <@nmz787> https://www.allaboutcircuits.com/news/microwave-qubit-creation-method-large-scale-quantum-computers/ 21:07 <@nmz787> heath: that really doesn't seem any better than the Python tooling I've got for BRLCAD 21:07 <@nmz787> heath: feel free to challenge that 21:09 < heath> "Very Efficient Template/Primer-Independent DNA Synthesis by Thermophilic DNA Polymerase in the Presence of a Thermophilic Restriction Endonuclease" http://pubs.acs.org/doi/abs/10.1021/bi0489614?journalCode=bichaw 21:09 < heath> 2004 21:11 <@nmz787> hmm, apparently GDSII is some sort of standard 21:11 <@nmz787> .wik GDSII 21:11 < yoleaux> "GDSII stream format, common acronym GDSII, is a database file format which is the de facto industry standard for data exchange of integrated circuit or IC layout artwork. It is a binary file format representing planar geometric shapes, text labels, and other information about the layout in hierarchical form." — https://en.wikipedia.org/wiki/GDSII 21:13 <@nmz787> apparently BRL-CAD doesn't have a GDSII converter 21:13 <@nmz787> I guess in that case, I could probably use that package heath :) 21:15 < heath> .wik dna clamp 21:15 < yoleaux> "A DNA clamp, also known as a sliding clamp, is a protein fold that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand." — https://en.wikipedia.org/wiki/DNA_clamp 21:16 < heath> .title https://www.youtube.com/watch?v=qf8_tn7lBIc 21:16 < yoleaux> The Best Of Clamps! From Futurama! - YouTube 21:19 * nmz787 turns the TV on for this one 21:20 <@nmz787> ah, audio only 21:36 < heath> .title https://www.ncbi.nlm.nih.gov/pubmed/19631767 21:36 < yoleaux> DNA polymerase family X: function, structure, and cellular roles. - PubMed - NCBI 22:07 < heath> did anyone happen to download the video on primer exchange reactions linked previoulsy? https://vimeo.com/231591472 22:53 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 23:01 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has quit [Ping timeout: 248 seconds] 23:26 -!- ebowden [~ebowden@110.141.11.39] has quit [Remote host closed the connection] 23:37 -!- ebowden [~ebowden@110.141.11.39] has joined ##hplusroadmap 23:37 -!- rpifan [~rpifan@207-244-191-189-dhcp.mia.fl.atlanticbb.net] has joined ##hplusroadmap 23:47 < maaku> .title https://foresight.org/from-de-novo-protein-design-to-molecular-machine-systems/ 23:47 < yoleaux> From de novo protein design to molecular machine systems - Foresight Institute --- Log closed Sun Oct 29 00:00:17 2017