--- Log opened Mon Sep 18 00:00:21 2017
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04:15 < NeddLudd> hi all
04:35 < kanzure> http://www.weareresonate.com/2017/07/chinese-scientists-collect-dna-smart-people-engineer-genius-babies/
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07:39 < kanzure> xkcd has requested nuclear fireworks and neutrino beams to cut through the planet https://xkcd.com/1891/ let's not disappoint.
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07:50 < kanzure> "guns don't kill people. blood loss and organ damage do.  organs are not recommended."
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07:54 < adlai> i've heard that drinking blood helps, though
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08:34 < ybit> .title https://www.youtube.com/watch?v=5767l3MveFY
08:34 < yoleaux> Crawling and swimming in one simulation, attempt #03 - YouTube
08:52 < kanzure> alright here's one way to fix dna synthesis error rates during phosphoramidite chemistry. instead of using TdT to replace one of the steps in the synthesis chemistry, arbitrary enzymes should be used. and you should synthesize DNA that encodes for various proteins/enzymes which are also the enzymes that you add to the reaction chemistry. and you do sequencing to check for which enzymes in ...
08:52 < kanzure> ...which reactions assisted the most with ensuring a low error rate of DNA synthesis. also you can do mutagenesis if you want.
08:53 < kanzure> over time you will be creating enzymes that facilitate phosphoramidite chemistry and the reduction of high error rates.
08:55 < kanzure> you can shoot out these custom enzymes by inkjet, or you could tether them to the surface if you don't want them to get washed away by wash steps.
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08:59 < kanzure> "Paris japonica has the largest genome of any plant yet assayed, about 150 billion base pairs long. An octoploid and suspected allopolyploid hybrid of four species, it has 40 chromosomes. With 150 billion base pairs of DNA per cell (50 times larger than that of a human haploid genome), Paris japonica may possess the largest known genome of any living organism; the DNA from a single cell ...
08:59 < kanzure> ...stretched out end-to-end would be longer than 300 feet (91 m).[2] The flower has 19 billion more base pairs than the previous record holder, the marbled lungfish, whose 130 billion base pairs weigh in at 132.83 picograms per cell.[2] Since then, other organisms have been assayed and reported to have larger genomes; Polychaos dubium may be the current record holder, but the authors of one ...
08:59 < kanzure> ...study suggest treating that measurement with caution because it was taken before the advent of modern genomic methods.[3]"
09:00 < kanzure> "Polychaos dubium has one of the largest genomes known for any organism, consisting of 670 billion base pairs or 670 Gbp,[4]"
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09:00 < kanzure> whatcha doing with all that genome size
09:01 < kanzure> "Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination" http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000552
09:11 < kanzure> other than starting with methylated nucleotides, is there a chemical method of completely methylating a DNA molecule?
09:13 < abetusk> .title https://en.wikipedia.org/wiki/Polychaos_dubium
09:13 < yoleaux> Polychaos dubium - Wikipedia
09:14 < abetusk> "The authors of one 2004 study, however, suggest treating that measurement with caution, because it was taken before the advent of modern genomic methods."
09:33 < kanzure> minion nanopore sequencers seem to be reading at 1kbp/sec but i wonder if that's because of a thousand nanopores each doing 1/sec.  IIRC slowing down the movement of DNA is quite difficult in this context.
09:40 < abetusk> Does anyone here have experience using a nanopore?
09:43 < kanzure> well a few of us know someone who operates a nanopore startup.
09:44 < abetusk> as in using the nanopore as a key technology or part of the nanopore group?
09:44 < kanzure> founder of a nanopore startup
09:46 < archels> ybit: yeah, saw the OpenWorm announcement mail too, good stuff
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09:47 < archels> hard to find details though :)
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10:26 < ybit> archels: did you see the comments for the video?
10:27 < ybit> anyone here happen to know who owns openbio.co?
10:31 < JayDugger> Atomic fireworks! (Seen in Varley's novel Steel Beach.)
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12:06 < ybit> https://codegolf.stackexchange.com/questions/11880/build-a-working-game-of-tetris-in-conways-game-of-life
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12:19 < nmz787> kanzure: so you want to MAGE your way out of this?
12:20 < nmz787> kanzure: 450 nt/s is a single nanopore on minion this week
12:21 < nmz787> abetusk: I know a guy on facebook that has done at home sequencing a bunch on a minion
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12:31 < kanzure> single nanopore is 450/sec? hmm. how many nanopores/minion?
12:36 < abetusk> nmz787, did he do any postings about it?  And what's the cost?
12:48 < kanzure> fiber optic cable instead of DMD micromirror array, right? why is this not done more often
12:49 < kanzure> https://en.wikipedia.org/wiki/Subwavelength-diameter_optical_fibre
12:49 < superkuh> https://www.eff.org/deeplinks/2017/09/open-letter-w3c-director-ceo-team-and-membership "Effective today, EFF is resigning from the W3C."
12:50 < kanzure> DRM reasons?
12:50 < kanzure> ietf > w3 anyway
12:59 < maaku> I have pre-ordered a series 3 Apple watch, and will be writing a 24/7 audio recording and transcription app, for those who care about this project
13:00 < maaku> I encountered too much difficulty in getting my Pebble Time to work for this use case, and it looks like Apple is now exposing enough API to make this possible without absolutely killing the battery life
13:01 < maaku> I forget whoall else was interested, but ping me and I'll keep you in the loop privately as things develop
13:08 < fenn> i was interested but i don't think i'll be buying an apple watch
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13:28 < kanzure> gotta wear two watches for that juicy audio triangulation data
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13:59 < delinquentme> ok hivebrain I want new portfolio project
14:00 < delinquentme> ideally genomics parallelle processing and stats
14:03 < kanzure> nanopore ablation of methyl groups from dna molecules
14:05 < delinquentme> idk if thats factoring in genomics data =X
14:06 < kanzure> delinquentme: bioinformatics gwas literature mining to make ultimate version of http://diyhpl.us/wiki/genetic-modifications/
14:07 < kanzure> gwas is stats-heavy
14:11 < delinquentme> OSX is a bad OS.
14:12 < delinquentme> Ive had to google for 10+ minutes and havnt found a tool just to monitor total network bandwidth
14:20 < kanzure> "Optimizing distributions over molecular space. an objective-​reinforced generative adversarial network for inverse-​design chemistry"
14:24 < maaku> delinquentme: Activity Monitor doesn't work for that?
14:24 < delinquentme> it gives me packets
14:25 < maaku> data received in/out is on the right-hand side
14:26 < maaku> delinquentme: what metric are you looking for?
14:26 < delinquentme> maaku, im looking for a kb / mb per second
14:37 < maaku> delinquentme: this is what I see in activity monitor : https://imgur.com/a/yJaTx
14:37 < maaku> note the lower-right two numbers which is what you're looking for
14:38 < delinquentme> maaku, oh, sure enough. yeah i didnt parse the "its kilobytes dummy"
14:38 < delinquentme> https://gist.github.com/AKB428/dbdba5f98645e7539d87
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14:39 < delinquentme> is this the asian programmers of this util making a lulz? "iftop_osx_insrall"
14:39 < delinquentme> methinks
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14:50 < kanzure> EEG headset thing https://github.com/OpenBCI/Ultracortex  https://twitter.com/ultracortex
14:50 < kanzure> .tw https://twitter.com/SafeForRobots/status/791768762844319745
14:50 < yoleaux> First Fossilized Dinosaur Brain Found! Let's put an @OpenBCI @ultracortex on it! http://nyti.ms/2dMtlO0 (@SafeForRobots)
14:51 < kanzure> maaku: welp there's your fozzilized dinosaur brain. now your next task is to convince them to not break it until we have molecular nanotechnology.
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15:18 < nmz787> kanzure: $1000 to buy, 450 nt/s per pore with 512 pores per minION but they only guarantee roughly 300 will work (I think that's ~%70)
15:19 < nmz787> kanzure: tons of facebook posts
15:19 < nmz787> kanzure: when I mentioned non-air optical waveguide last week (and showed you my cell phone's display) you scoffed
15:23 < kanzure> LCD instead of micromirror array? yes i would have scoffed.
15:23 < nmz787> no
15:23 < nmz787> LED matrix
15:23 < kanzure> we've talked about LCD resolution limits for photolithography before
15:23 < nmz787> with direct optical coupling
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15:24 < nmz787> QHD display is 3.6 million pixels
15:24 < kanzure> elaborate
15:24 < nmz787> without the LCD, I bet they could pack smaller
15:25 < nmz787> I guess that'd be OLED density at that point
15:25 < nmz787> my point is... we can make photons and direct them without MEMS or air
15:26 < kanzure> you mean LED matrix + lenses?
15:29 < kanzure> oh you mean raw LED matrix
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16:06 < nmz787> sure you can make lenses too, in planar fab terms they might just call them waveguides, but same idea
16:07 < nmz787> what's the smallest LED that we can make?
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16:33 < JayDugger> Thanks, maaku. As with fenn, not likely to buy one, but remain interested.
16:34 < maaku> JayDugger: I was turned off by price, but most of the alternatives I was investigating were creeping up to be comparable
16:35 < maaku> kanzure: amazing! i wonder how likely it is that connectome is preserved in any way though, even at atomic level of detail
16:36 < JayDugger> maaku: That's good to know.
16:36 < kanzure> yea i guess you really need frozen dinosaur brain, not fossilized dinosaur brain
16:37 < maaku> JayDugger: although if you could convince these people to open their HW api, it'd be perfect : https://kaptureaudio.com
16:37 < kanzure> maaku: maybe email them and tell them it's for a demo/prototype
16:37 < maaku> I failed at convincing them to do so about a year ago. Maybe they're more despirate now (I can't imagine they have a market)
16:38 < kanzure> ah.
16:39 < maaku> Also not sure if it has the battery or the onboard hardware for 24/7 usage
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16:44 < maaku> Haven't raised money since their seed 3 years ago, and product currently out of stock ... I suspect they are more desparate now. I'm writing another email now.
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17:23 < kanzure> http://t.sophon.ai/product/view.html?product_id=00020170322101346GOQ0dTAFIlnTv3S&template=alien-bot
17:23 < kanzure> wtf
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17:37 < kanzure> reminds me of the 1980s household robot craze https://www.youtube.com/watch?v=3qdXkJVQUfM
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17:52 < kanzure> vr particle physics sandbox thing https://www.reddit.com/r/Vive/comments/61n768/announcing_chroma_lab_a_vr_particle_fluid/
17:57 < kanzure> chroma lab video thing https://www.youtube.com/watch?v=ysziAwtT6ko
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18:15 < nmz787> http://www.sciencedirect.com/science/article/pii/S1550413117305028
18:15 < nmz787> .title
18:16 < yoleaux> A Predictive Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural Product
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19:28 < kanzure> hmm well...
19:28 < kanzure> it would have been nice if that paper got finished
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19:41 < kanzure> "An oligonucleic acid synthesizer may comprise material deposition devices that can move in the X-Y direction to align with the location of the substrate. The oligonucleic acid synthesizer can also move in the Z direction to seal with the substrate, forming a resolved reactor ... plurality of clusters... seal with a capping element.. A resolved reactor is configured to allow for the transfer ...
19:41 < kanzure> ...of fluid, including oligonucleic acids and/or reagents, from the substrate to the capping element and/or vice versa."
19:42 < kanzure> "may comprise a plurality of material deposition devices, for example from about 1 to about 50 material deposition devices" AKA "we are doing obvious things yo"
19:42 < kanzure> "In some cases, each material deposition device has a plurality of nozzles, where each nozzle is optionally configured to correspond to a cluster on a substrate. For example, for a substrate having 256 clusters, a material deposition device has 256 nozzles and 100 μm fly height. In some cases, each nozzle deposits a reagent component that is different from another nozzle"
19:42 < kanzure> so they say it's not inkjet... but they're talking about 256 nozzles... sounds like it's inkjet to me.
19:42 < kanzure> if they lie about their technology, then does that invalidate their patent?
19:43 < kanzure> figure 10a sure as hell looks like inkjet to me https://patentimages.storage.googleapis.com/9d/e4/e8/ea4caf1aa8bdfe/US20160310927A1-20161027-D00010.png
19:53 < kanzure> not even sure this is worth considering; what would be faster than a piezo-triggered liquid? what's going to have a faster switching time? wat?
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--- Log closed Tue Sep 19 00:00:22 2017