--- Log opened Sat Sep 02 00:00:06 2017 00:00 -!- cluckj [~cluckj@static-173-59-27-112.phlapa.ftas.verizon.net] has quit [Read error: Connection reset by peer] 00:00 -!- cluckj [~cluckj@static-173-59-27-112.phlapa.ftas.verizon.net] has joined ##hplusroadmap 00:01 < kanzure> ayup.. 00:03 -!- balrog [~balrog@unaffiliated/balrog] has quit [Ping timeout: 240 seconds] 00:04 -!- CRM114 [~urchin@unaffiliated/urchin] has quit [Ping timeout: 258 seconds] 00:04 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 00:50 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 02:33 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Quit: leaving] 02:33 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 02:37 -!- NikopolSohru [~NSohru@s5596eed8.adsl.online.nl] has joined ##hplusroadmap 02:37 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 02:59 -!- NikopolSohru [~NSohru@s5596eed8.adsl.online.nl] has quit [Quit: Leaving] 03:04 -!- augur [~augur@c-73-71-242-163.hsd1.ca.comcast.net] has joined ##hplusroadmap 03:08 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 03:09 -!- augur [~augur@c-73-71-242-163.hsd1.ca.comcast.net] has quit [Ping timeout: 240 seconds] 03:37 < fltrz> kanzure: wow, I sincerely believe array *might* have worked 03:38 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Read error: Connection reset by peer] 03:44 -!- aeiousomething [~aeiousome@183.82.170.54] has joined ##hplusroadmap 04:05 -!- aeiousom1thing [~aeiousome@59.93.89.85] has joined ##hplusroadmap 04:06 -!- Gurkenglas [~Gurkengla@dslb-178-000-222-214.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 04:07 -!- aeiousomething [~aeiousome@183.82.170.54] has quit [Ping timeout: 248 seconds] 04:09 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 248 seconds] 04:13 -!- jaboja [~jaboja@jaboja.pl] has joined 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##hplusroadmap 06:05 -!- aeiousom1thing [~aeiousome@59.93.89.85] has quit [Ping timeout: 246 seconds] 06:08 < kanzure> yeah seems unfortunate. someone should send them a microelectrode array. 06:42 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 06:46 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=c778c929 Bryan Bishop: linkify all the things >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 06:52 -!- cevi_ [~zeb@pool-74-103-254-184.prvdri.fios.verizon.net] has quit [Ping timeout: 240 seconds] 06:57 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 06:58 -!- cevi_ [~zeb@pool-74-103-254-184.prvdri.fios.verizon.net] has joined ##hplusroadmap 07:03 -!- cevi_ [~zeb@pool-74-103-254-184.prvdri.fios.verizon.net] has quit [Ping timeout: 240 seconds] 07:21 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=350d6f63 Bryan Bishop: more hyperlinkz >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 07:27 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5376a707 Bryan Bishop: fix linker typo >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 07:36 -!- Gurkenglas [~Gurkengla@dslb-178-000-222-214.178.000.pools.vodafone-ip.de] has joined ##hplusroadmap 07:42 -!- delinquentme [~delinquen@2602:306:ceb7:990:6827:e35c:ae32:4bb8] has joined ##hplusroadmap 07:44 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 07:47 -!- delinquentme [~delinquen@2602:306:ceb7:990:6827:e35c:ae32:4bb8] has quit [Ping timeout: 255 seconds] 07:59 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 08:12 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 255 seconds] 08:28 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has joined ##hplusroadmap 08:32 -!- poppingtonic [~brian@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] 09:19 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 260 seconds] 09:29 -!- Storyteller [~Storytell@unaffiliated/storyteller] has joined ##hplusroadmap 09:36 -!- Storyteller [~Storytell@unaffiliated/storyteller] has left ##hplusroadmap ["Leaving"] 09:38 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=d542859b Bryan Bishop: more links >> http://diyhpl.us/diyhpluswiki/transcripts/scalingbitcoin/milan/schnorr-signatures/ 09:40 -!- aeiousomething [~aeiousome@61.3.66.190] has quit [Quit: leaving] 09:41 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 09:43 < kanzure> "tacit knowledge is killing the cost structure of experimentation" 09:44 < kanzure> shouldn't that be *lack of* tacit knowledge as the killer? 09:47 < kanzure> "it's taking a team 10 years and 2 mln just to get yeast to make a few closely related cannabinoids in yeast... their problem is not long sequence writing costs" what how is it that possible? if they could try a million things then it would be easier. 09:53 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has joined ##hplusroadmap 09:55 -!- augur [~augur@c-73-71-242-163.hsd1.ca.comcast.net] has joined ##hplusroadmap 09:57 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=aea02909 Bryan Bishop: include olfactory receptor genes mention >> http://diyhpl.us/diyhpluswiki/genetic-modifications/ 09:58 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=83b9dadd Bryan Bishop: update index relevant links >> http://diyhpl.us/diyhpluswiki/index/ 09:59 -!- augur [~augur@c-73-71-242-163.hsd1.ca.comcast.net] has quit [Ping timeout: 240 seconds] 10:03 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 240 seconds] 10:07 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 10:13 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b01897e4 Bryan Bishop: even more links! >> http://diyhpl.us/diyhpluswiki/transcripts/scalingbitcoin/milan/schnorr-signatures/ 10:26 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 264 seconds] 10:28 < kanzure> 10:28 <+asciilifeform> i recommend to kanzure to study the postwar memoirs of heisenberg. he managed to stay off the nuremberg bench by arguing 'none of my shit worked, really', maybe you can too. 10:29 < kanzure> 100% fan fiction. 10:34 -!- JayDugger [~jwdugger@47.185.237.246] has joined ##hplusroadmap 10:51 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap 10:54 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 248 seconds] 10:55 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 10:58 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f1ebe4c4 Bryan Bishop: yep, is correct link >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 11:04 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=04bb8fe9 Bryan Bishop: fix errors, add link >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 11:11 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap 11:24 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=87323128 Bryan Bishop: lotta typo fixes and other deets >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 11:25 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=177d5e69 Bryan Bishop: correctly spell AMD Ryzen >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 11:41 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=6b2b71d2 Bryan Bishop: discardfee link >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 11:41 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 11:44 -!- YenLegion [~YenLegion@2601:281:ca00:1586:4826:12f7:7a69:dc8d] has joined ##hplusroadmap 11:45 < kanzure> YenLegion: greetings 11:49 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 260 seconds] 11:51 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has joined ##hplusroadmap 11:55 -!- YenLegion [~YenLegion@2601:281:ca00:1586:4826:12f7:7a69:dc8d] has quit [Quit: Leaving] 11:59 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=200c863d Bryan Bishop: fix openssl comment >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 11:59 -!- balrog [~balrog@unaffiliated/balrog] has quit [Ping timeout: 240 seconds] 12:03 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 12:10 -!- pepesza [~pepesza@185.83.218.228] has joined ##hplusroadmap 12:36 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:37 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=ad775879 Bryan Bishop: include link for compact client side filtering BIP >> http://diyhpl.us/diyhpluswiki/transcripts/gmaxwell-2017-08-28-deep-dive-bitcoin-core-v0.15/ 13:07 -!- balrog [~balrog@unaffiliated/balrog] has quit [Quit: Bye] 13:10 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 13:16 -!- balrog [~balrog@unaffiliated/balrog] has quit [Quit: Bye] 13:20 -!- balrog [~balrog@unaffiliated/balrog] has joined ##hplusroadmap 13:39 < ybit> missed this one 13:39 < ybit> https://www.thingiverse.com/thing:159052 13:39 < kanzure> .title 13:39 < ybit> .title 13:39 < yoleaux> Laboratory Pipette by lewisite - Thingiverse 13:39 < yoleaux> Laboratory Pipette by lewisite - Thingiverse 13:41 < ybit> pretty sure i've seen this one though: 13:41 < ybit> https://www.thingiverse.com/thing:64977 13:41 < ybit> .title 13:41 < yoleaux> Adjustable Volume Straw Pipette by kwalus - Thingiverse 13:52 -!- p0nziph0ne [~p0nziph0n@p200300E10BE1790055E98277A45A25B6.dip0.t-ipconnect.de] has quit [Quit: Leaving] 14:15 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 14:38 < kanzure> 14:37 <+kanzure> asciilifeform: how fast can you run an inkjet valve, you foresee any problem with 1 MHz? 14:38 < kanzure> 14:38 <+kanzure> other than overheating 14:38 < kanzure> 14:38 <+asciilifeform> kanzure: if it's veeery small, use a saw resonator, there's your valve, 100Mhz easy 14:38 < kanzure> you could laser ablate drops in mid-air that you don't want to touch the surface 14:39 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Ping timeout: 264 seconds] 14:40 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 14:47 < kanzure> 14:45 <+mircea_popescu> kanzure at some point someone came up with "charge the droplets, move elctrostatically, send them out with a quarz pump" 14:47 < kanzure> 14:45 <+asciilifeform> if your fluid's triple point is close to room temp, can do exotic, e.g. vapourize it and condence on a cold pin point 14:50 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 14:53 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Ping timeout: 252 seconds] 14:57 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 14:58 < kanzure> 14:56 <+asciilifeform> btw seekrit : 100% of tecan internals are rebranded 'cavro', if you get a hold of the orig. documents from the latter, you have ~all of it. 14:58 < kanzure> 14:57 <+asciilifeform> the hydraulics ain't even rebranded, pop the cover and there it is, cavro. 15:06 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 248 seconds] 15:09 < kanzure> 15:09 <+asciilifeform> regardless, kanzure , why is it necessary for the droplets to fly through the air onto the target? why not let'em diffuse through a sheet of mylar through small hole burned by laser, say 15:09 < kanzure> 15:09 <+asciilifeform> layerwise. 15:10 < kanzure> 15:10 <+asciilifeform> also POSaM (linked device design) is a little antiquated, yes '04 but fpga already existed, why require megabux pci i/o card 15:10 < kanzure> 15:10 <+kanzure> because they are biologists and don't understand technology 15:12 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Read error: Connection reset by peer] 15:14 < kanzure> 15:14 <+mircea_popescu> think of a long sheet of substrate, with prepper and as many prinbter machines as passes needed downstream. 15:14 < kanzure> he means n printheads where n = 100 for 100 bp 15:15 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 15:15 < kanzure> he wants charged drumroll + laser 15:17 < kanzure> 15:16 <+asciilifeform> though incidentally might be interesting to use a decapped sram as a 'printhead' 15:23 < mrdata_> printing what? 15:24 < kanzure> mrdata_: http://diyhpl.us/wiki/dna/synthesis/notes/ 15:28 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 240 seconds] 15:29 < mrdata_> hmm 15:33 < kanzure> also he wants magnetohydrodynamics but i'm not sufficiently a materials person 15:34 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 15:38 -!- aeiousomething [~aeiousome@gateway/vpn/privateinternetaccess/aeiousomething] has quit [Ping timeout: 240 seconds] 15:42 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Read error: Connection reset by peer] 15:48 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 15:52 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 16:01 < kanzure> nmz787: wow these slides are *BAD* 16:01 < kanzure> SUPER bad. these are biologists and they don't know engineering. 16:02 < kanzure> they go to the temple throne room of the semiconductor industry, and they talk about statistical modeling of biological systems, instead of "here's the CMOS chips you need to build for us in order to advance science". 16:03 < kanzure> s2-brisk.pdf is interesting; it's vlsi for microfluidics. 16:03 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 252 seconds] 16:09 < kanzure> yashgaroth: can you remind me about the semiconductor synthesis method that twist and others are using? the deets. 16:09 < yashgaroth> no idea 16:09 < kanzure> we knew at one point 16:09 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 16:09 < kanzure> yeah this is baaad 16:10 < yashgaroth> well you see, robots, semiconductors, algorithms, uhh deep learning 16:10 < kanzure> no 16:11 < kanzure> god damn it 16:12 < kanzure> ?? http://www.google.com.ag/patents/US8716467 16:12 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 16:12 < kanzure> there was a company that was acquired 16:13 < kanzure> CustomArray 16:13 < kanzure> 19:43 < kanzure> so 15 million bp for $6000. hmm. 16:13 < kanzure> 19:43 < kanzure> "CustomArray uses advanced CMOS semiconductor technology to enable it to synthesize thousands of oligonucleotides simultaneously. Each array contains thousands of individually addressable electrodes, which electrochemically synthesize a unique oligonucleotide at each electrode. The oligonucleotides are cleaved from the surface to create custom oligo pools." 16:14 < kanzure> http://gnusha.org/logs/2015-07-08.log 16:14 < kanzure> 19:45 < kanzure> "CustomArray's chips use electrochemical detritylation to control DNA synthesis. Electrochemical detritylation can be a much-more-efficient method to synthesize oligonucleotides than light-based synthesis processes. This means the oligonucleotides are of highest quality, and the sensitivity of the microarray is maximized. Since physical photolithographic masks or pre-built ... 16:14 < kanzure> ...collections of oligos are NOT involved in the process, all probes ... 16:14 < kanzure> 19:45 < kanzure> pfft physical photolithography masks 16:14 < kanzure> http://customarrayinc.com/faq_main.htm 16:15 < kanzure> is twist bioscience using same technique or what? 16:17 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 260 seconds] 16:21 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 16:21 < kanzure> ~~advanced CMOS semiconductor technology~~ 16:22 < kanzure> ~THOUSANDS~ simultaneously. morans. 16:22 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Read error: Connection reset by peer] 16:28 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 16:30 < kanzure> Topics of greatest interest to the organizers are: 16:30 < kanzure> •What new technical approaches have the greatest potential to improve synthesis throughput and reduce cost for data storage applications? And for life sciences applications? What is the current level of maturity of each approach? 16:30 < kanzure> •How do we minimize the biosecurity risks associated with improved DNA synthesis tools? 16:30 < kanzure> •Where and how should the US government invest to accelerate synthesis R&D? 16:31 < kanzure> "biosecurity risks" ahahaha 16:42 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Read error: Connection reset by peer] 16:44 < kanzure> "Male microchimerism in the human female brain" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045592 16:45 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 16:51 < kanzure> fenn: should i be pimping electrochemical detritylation or what? 16:56 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Read error: Connection reset by peer] 17:02 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 17:11 < kanzure> "On your question, it is absolutely fine to take notes. I really appreciate your offer to share your notes with us. It would be a great help in writing the meeting report, which will be available for all participants." 17:11 < kanzure> bwahahah 17:13 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Read error: Connection reset by peer] 17:14 < kanzure> grant submitted. (not really, just slides.) 17:19 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 17:27 < kanzure> semisynbio proposals due in october 2017 https://www.src.org/app/proposal/submit/semisynbio/ although strangely this does not seem to include dna synthesis technologies (wat? maybe i am bad at reading?) 17:44 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Ping timeout: 255 seconds] 17:51 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 18:03 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Ping timeout: 255 seconds] 18:05 < kanzure> "Inter-homologue repair in fertilized human eggs?" http://www.biorxiv.org/content/early/2017/08/28/181255 18:05 < kanzure> "The development and application of methods to prevent the inheritance of damaging mutations through the human germline could have significant health benefits, and currently include preimplantation genetic diagnosis and carrier screening. Ma et al. take this a step further by attempting to remove a disease mutation from the human germline through gene editing (1). They assert the following ... 18:06 < kanzure> ...advances: (i) the correction of a pathogenic gene mutation responsible for hypertrophic cardiomyopathy in human embryos using CRISPR-Cas9 and (ii) the avoidance of mosaicism in edited embryos. In the case of correction, the authors conclude that repair using the homologous chromosome was as or more frequent than mutagenic nonhomologous end-joining (NHEJ). Their conclusion is significant, if ... 18:06 < kanzure> ...validated, because such a self-repair mechanism would allow gene correction without the introduction of a repair template. While the authors analyses relied on the failure to detect mutant alleles, here we suggest approaches to provide direct evidence for inter-homologue recombination and discuss other events consistent with the data. We also review the biological constraints on ... 18:06 < kanzure> ...inter-homologue recombination in the early embryo. (1) Ma, H. et al. Correction of a pathogenic gene mutation in human embryos. Nature, doi:10.1038/nature23305 (2017)." 18:07 < kanzure> https://motherboard.vice.com/en_us/article/vbb8ey/prominent-geneticists-question-the-results-of-human-embryo-editing-experiment 18:07 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 18:08 < kanzure> .tw https://twitter.com/antonioregalado/status/903048940488204293 18:08 < yoleaux> Statement from CRISPR embryo editor Mitalipov to critics. http://www.biorxiv.org/content/early/2017/08/28/181255 https://pbs.twimg.com/media/DIhGNx4VYAAPuLA.jpg (@antonioregalado) 18:13 < kanzure> https://ipscell.com/2017/08/doubts-raised-on-key-points-of-nature-paper-on-crispr-gene-editing-of-human-embryos/ https://twitter.com/pknoepfler/status/902913425214406657 18:13 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 18:15 < kanzure> .tw https://twitter.com/BoredSynBio/status/732929182225797120 18:15 < yoleaux> Sorry for not tweeting, I was at a secret meeting on building Jurassic Park from scratch. Oh, wrong secret meeting... (@BoredSynBio) 18:28 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 260 seconds] 18:34 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 18:40 -!- jaboja [~jaboja@jaboja.pl] has quit [Ping timeout: 248 seconds] 18:48 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 252 seconds] 18:53 -!- jaboja [~jaboja@jaboja.pl] has joined ##hplusroadmap 18:54 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 19:09 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 240 seconds] 19:12 < fenn> TIL tritiated != tritylated 19:14 < fenn> "At each step of synthesis, acid is produced in confined regions by application of current to individual electrodes, directing patterned removal of protecting groups on the adjacent substrate." 19:15 < fenn> so it's just like light-directed but with electrical conductors instead 19:15 < kanzure> yes 19:15 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 19:15 < fenn> does it have better yields than light-directd synthesis or something? 19:16 < kanzure> possibly it can have easier high density than light-directed, due to small size per electrode + ... er. i guess you would need a (even digital) photomask to make the microelectrodes anyway.... 19:17 < fenn> it could make for a more compact machine overall 19:17 < fenn> like a usb stick 19:17 < kanzure> yea but that's not what these people are into, they like the idea of a synthesis "facility" that you can't lug around 19:17 < fenn> well you could have more of them per square meter of facility 19:17 < fenn> less power consumption etc etc 19:17 < kanzure> sorry, did you find them doing usb form factor things? 19:17 < fenn> no 19:18 < fenn> but it's just a chip right? 19:18 < kanzure> it's a chip plus other undisclosed chemical reagent delivery i suppose 19:18 < kanzure> i think we discussed this before, 'acid generation' 19:19 < kanzure> http://gnusha.org/logs/2015-07-13.log 19:19 < kanzure> 'photogenerated acid' 19:21 < kanzure> 07:32 < kanzure> so wouldn't it be better to isolate each reaction in a drop instead ofj ust hoping the acids don't brownian motion themselves over to the other electrode areas 19:21 < kanzure> 07:36 < ParahSailin> "In contrast, in the electrochemical case reagent generated by the electrode is able to diffuse into the PRL but is prevented from excessive diffusion by the presence of a buffering agent in the surrounding solution." 19:21 < kanzure> 07:36 < ParahSailin> " Near the electrode, the buffer is overwhelmed, allowing reaction of the ECG reagent with the PRL bound substrate; but further away, the concentration of the diffusing reagent is insufficient to overcome the concentration of the buffering agent, and no reaction occurs." 19:23 < kanzure> "Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762329/ 19:23 < fenn> dont you need to wash the whole chip with nucleotide solution 19:25 < fenn> ugh its too hot to think 19:25 < kanzure> i think semiconductor people will respond more positively to "give us a billion electrodes" 19:25 < fenn> i'd like to see some comparison chart of various metrics for different synthesis processes, like error rate, yield, size, cost per run, cost per machine etc 19:26 < kanzure> and scaling dimensions 19:26 < fenn> a couple points on each variable dimension should be fine 19:26 < fenn> i.e. chemically POSAM is the same as IDT's bundle of valves and tubes 19:26 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Read error: Connection reset by peer] 19:27 < Jenda`> I still don't understand the printer stuff. So it is adding different chemicals to the drops -- and the drops keep growing? Or are the old chemicals somehow washed/removed? 19:27 < kanzure> microelectrodes are much more solid state than a bunch of inkjet valves.. but it sounds like there's various black magic related to buffering solution. 19:27 < kanzure> Jenda`: both! 19:27 < kanzure> Jenda`: re-printing over same spot/droplet with new droplets. chemicals mixx together and react. then you have a wash step eventually, and repeat. 19:27 < fenn> jenda you wash the protecting group off so you can add a new base with the next printed drop 19:27 < fenn> otherwise you get repeated bases 19:28 < kanzure> or no more growth 19:28 < Jenda`> hmm, how is the washing implemented? 19:28 < fenn> a hose 19:28 < kanzure> acetonitrile 19:28 < kanzure> http://diyhpl.us/wiki/dna/synthesis/notes/ 19:30 < Jenda`> yeah, I have seen that, but somehow concluded that you are only adding various stuff 19:30 < kanzure> alright why do we not have a billion electrode dna synthesizer already 19:32 < kanzure> i guess i should just ask them 19:32 < Jenda`> http://playground.tensorflow.org/ "Tinker With a Neural Network Right Here in Your Browser." 19:34 < fenn> "CustomArray's chips use electrochemical detritylation to control DNA synthesis. Electrochemical detritylation can be a much-more-efficient method to synthesize oligonucleotides than light-based synthesis processes. This means the oligonucleotides are of highest quality, and the sensitivity of the microarray is maximized." 19:34 < fenn> maybe they have a patent and are blocking development 19:34 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 19:35 < fenn> oh they sell oligos http://www.customarrayinc.com/oligos_main.htm 19:37 < kanzure> "Electrochemical solid phase synthesis" (1999) https://www.google.com/patents/US6280595 this one is from combimatrix 19:42 < kanzure> some sort of generic dna synthesis patent granted to church in ~2005 https://www.google.com/patents/US20060127920 19:42 < kanzure> customarray patents https://www.google.com/search?num=100&safe=off&hl=en&tbm=pts&tbm=pts&q=inassignee:%22Customarray,+Inc.%22&biw=1920&bih=901 19:48 -!- Gurkenglas [~Gurkengla@dslb-178-000-222-214.178.000.pools.vodafone-ip.de] has quit [Ping timeout: 240 seconds] 20:09 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 260 seconds] 20:10 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 20:16 -!- jaboja [~jaboja@jaboja.pl] has quit [Remote host closed the connection] 20:23 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Read error: Connection reset by peer] 20:33 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 20:48 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 248 seconds] 20:55 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 21:03 -!- drewbot [~cinch@54.211.56.9] has joined ##hplusroadmap 21:09 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 248 seconds] 21:16 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 21:22 < fenn> electrochemical implies the strands are stuck to the chip, meaning you can't do electrowetting or optical electrowetting based manipulation to assemble the oligos 21:25 < fenn> once you release them from the chip they are all mixed together in solution in one pot 21:32 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Read error: Connection reset by peer] 21:38 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 21:53 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Ping timeout: 246 seconds] 21:59 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 22:12 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Read error: Connection reset by peer] 22:20 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has joined ##hplusroadmap 22:29 -!- yashgaroth [~yashgarot@2606:6000:cd4d:3300:f5e0:f867:a11d:8d52] has quit [Quit: Leaving] 22:34 -!- delinquentme [~delinquen@2602:306:ceb7:990:4567:ed39:da91:d349] has quit [Ping timeout: 264 seconds] 22:38 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 22:54 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 240 seconds] 22:56 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has joined ##hplusroadmap 23:14 -!- delinquentme [~delinquen@108-235-112-153.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 260 seconds] --- Log closed Sun Sep 03 00:00:07 2017