--- Log opened Sun Feb 04 00:00:43 2018
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00:38 < kanzure> apoe for metablism?
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01:11 < jrayhawk> Yeah, and there's a lot less metabolic flexibility for ApoE4 carriers due to overactive inflammatory signaling.
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06:15 < kanzure> MTHFR rs1801131 is on the page listed as a power/strength marker http://diyhpl.us/wiki/genetic-modifications/
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10:15 < kanzure> legalese mode go!
10:16 < kanzure> bodily harm as results of your human AAV gene therapy: totes not my problem. <--- sufficient right?
10:16 < kanzure> kthx
10:19 < redlegion> looks good
10:28 < JayDugger> I see no problems.
10:30 < kanzure> great
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11:52 < kanzure> dna photolithoraphy mask stuff:
11:52 < kanzure> "Plasmonic nanostructures through DNA-assisted lithography" http://advances.sciencemag.org/content/4/2/eaap8978 https://twitter.com/physorg_com/status/959501691040206849
11:54 < kanzure> woodpeckers and brain damage https://twitter.com/physorg_com/status/959501693649113091
11:55 < kanzure> in situ tomography stuff http://www.cell.com/cell/fulltext/S0092-8674(17)31510-6 https://twitter.com/ruferbus/status/959362937713512449
11:56 < nmz787> "does not rely on costly patterning methods" except to synthesize currently-costly DNA
11:56 < nmz787> I guess once you debug your DNA though, you should be able to replicate en-masse for cheaper
11:56 < kanzure> elsewhere: "we tested transcription-factor-like effectors (TALE)-based designer transcriptional factors (dTFs),"
11:56 < kanzure> nmz787: probably they mean a small repeating pattern not a lot of novel patterns
11:59 < nmz787> "We observed that when 37.5 mM Mg2+was used in the deposition buffer, ~80% of the plain CDL origamis tend to adsorb onto the Si surface with the S-shaped orientation. However, at 70 mM or higher Mg2+ concentration, the deposition yielded equal amounts of S- and Z-shaped orientations"
12:01 < kanzure> something about testing population genetics and mutation rate https://www.biorxiv.org/content/early/2018/02/02/259507 https://twitter.com/biorxivpreprint/status/959592459553640451
12:01 < nmz787> kanzure: I am taking 'plasmonic nanostructures' to basically mean a fluorescense amplifier... which is definitely something decently cool
12:03 < kanzure> "Generating wikipedia by summarizing long sequences" https://arxiv.org/abs/1801.10198 https://twitter.com/deeplearning4j/status/959883112066048000
12:03 < kanzure> "We show that generating English Wikipedia articles can be approached as a multi- document summarization of source documents. We use extractive summarization to coarsely identify salient information and a neural abstractive model to generate the article. For the abstractive model, we introduce a decoder-only architecture that can scalably attend to very long sequences, much longer than ...
12:03 < kanzure> ...typical encoder- decoder architectures used in sequence transduction. We show that this model can generate fluent, coherent multi-sentence paragraphs and even whole Wikipedia articles. When given reference documents, we show it can extract relevant factual information as reflected in perplexity, ROUGE scores and human evaluations."
12:04 < nmz787> "Steps of the fabrication procedure.
12:04 < nmz787>  Step 1: A transparent sapphire (Al2O3)/silicon nitride (Si3N4) chip is freshly cleaned by acetone and isopropanol.
12:04 < nmz787>  Step 2: An amorphous silicon layer is grown on top of the substrate by PECVD.
12:04 < nmz787>  Step 3: The substrate is treated by oxygen plasma, after which the DNA origami nanostructures (BO shown here as an example) are drop-casted on the chip.
12:04 < nmz787>  Step 4: The silicon dioxide (SiO2) layer is selectively grown on the bare silicon by CVD, leaving DNA origami–shaped silhouettes in the layer.
12:04 < nmz787>  Step 5: Using the grown SiO2 layer as a mask, the silicon underneath is etched away by RIE. Step 6: The metal is deposited onto the chip using PVD in ultrahigh vacuum.
12:04 < nmz787>  Step 7: The SiO2 layer is removed in a liftoff process using hydrogen fluoride–based wet etching. Step 8: The remaining silicon is removed by RIE, thus leaving the DNA origami–shaped metal nanostructure on the substrate."
12:05 < nmz787> damn, left two steps on the same line
12:05  * nmz787 has ruined this portion of the backlog
12:05 < kanzure> how does chemical vapor deposition not deposit stuff under the dna origami?
12:06 < nmz787> "selective"
12:06 < kanzure> pffft that could mean anythin
12:06 < kanzure> g
12:07 < nmz787> meaning they got the chemistry such that the depositable stuff won't attach to DNA (probbaly carbon) and only silicon
12:07 < nmz787> .wik atomic layer deposition
12:07 < yoleaux> "Atomic layer deposition (ALD) is a thin-film deposition technique based on the sequential use of a gas phase chemical process. ALD is considered a subclass of chemical vapour deposition. The majority of ALD reactions use two chemicals, typically called precursors." — https://en.wikipedia.org/wiki/Atomic_layer_deposition
12:07 < nmz787> self-limiting reaction in ALD's case, such that you get step-wise growth single atomic/molecular layers at a time
12:08 < kanzure> the dna is just sittin there it's not bound to the surface. it could be dozens of picometers off the surface.
12:08 < nmz787> the other techniques are rate-limited, and things that affect the deposition rate are usually: temperature, pressure, voltage or power
12:08 < kanzure> +g
12:08 < nmz787> and you can't realistically have a step-function in the thermal rate
12:09 < nmz787> so you get some side-effects versus ALD
12:09 < nmz787> kanzure: well there'd need to be something in those picometers
12:09 < nmz787> salt (metal) ions, etc
12:09 < nmz787> they mentioned Mg2+
12:12 < nmz787> kanzure: as long as whatever is underneath doesn't evaporate during the next growth step, the DNA shouldn't move (unless thermal effects cause some brownian motion that is greater than the bond stiffness)
12:12 < nmz787> I guess you could make nanopores like that
12:12 < nmz787> instead of DNA origami, just use single or 2bp oligos
12:15 < nmz787> kanzure: for a lot of novel features in the same pattern, you might be able to design a mega-origami that holds onto the smaller ones, then deposit that and use a nuclease to chew off anything that isn't inaccessible (oh, nevermind, that would require a solution, which means the origami wouldn't be locked onto the silicon surface_
12:15 < nmz787> )
12:15 < nmz787> maybe you could FIB off the mega origami
12:16 < kanzure> mega origami with high entropy is cost limited by dna synthesis
12:16 < nmz787> yeah
12:16 < nmz787> def
12:21 < JayDugger> That Wikipedia paper seems nifty.
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12:28 < nmz787> coupling that with scihub would be like a living wikipedia
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13:16 < kanzure> "In early-modern times, child mortality was very high; in 18th century Sweden every third child died, and in 19th century Germany every second child died."
13:16 < kanzure> born2ndie
13:16 < kanzure> er, born2die
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17:39 < kanzure> what is this, a list for ants? it needs to be at least 10x bigger: https://en.wikipedia.org/wiki/Vectors_in_gene_therapy#Non-viral_methods
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17:46 < kanzure> "The consultant recognizes that any adverse medical effects (including, but not limited to, immune reactions, acquired immunity, acquired immunodeficiency, explosion, severe injury, severe long-term disability, or death) are fully the consultant's responsibility"
17:46 < kanzure> too weak?
17:58 < JayDugger> explosion?
17:58 < JayDugger> What yield?
17:58 < JayDugger> I think you should quantify that.
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18:00 < kanzure> explosions of many possible yields including but not limited to 1, 2, 3, 4, 5, and 6, but not limited to numbers less than or equal to 6.
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18:01 < JayDugger> Hm, seems to have the right flavor, but perhaps with more legalese.
18:01 < kanzure> oh i forgot about dismemberment
18:01 < JayDugger> I think it was wise to omit any units from the statement.
18:02 < JayDugger> Implicitly covered by explosion, I think.
18:02 < kanzure> also going to add defenestration disclaimer
18:03 < yashgaroth> dismemberment falls under disability, but cancer and/or sterility are less defined
18:03 < JayDugger> And burning at the stake, and angry mobs with pitchforks and torches
18:03 < JayDugger> Alright, I can tell you've put more thought into this than I have.
18:03 < JayDugger> What about irresistible charisma? that worth mentioning? It could happen.
18:04 < kanzure> sent it to you by pm
18:04 < yashgaroth> he's right, we should include unwanted or unintended enhancements as well
18:05 < JayDugger> Got it.
18:11 < kanzure> yashgaroth: we should disclaim against unintended enhancements?
18:12 < yashgaroth> a third arm is great, but if you don't want one then legally it's a grey area
18:13 < yashgaroth> not really a disability per se, but it's not for everyone
18:13 < yashgaroth> or heightened senses, or telepathy, what have you
18:13 < kanzure> telepathy... back in my day we just called that schizophrenia.
18:16 < yashgaroth> best to get these things ironed out before we let the eyeball lasers out of the box
18:18 < kanzure> sshhh don't tell them about the eye lasers
18:30 < kanzure> https://hackaday.com/2017/01/03/ditch-openscad-for-c/
18:36 < kanzure> "llvm for grad students" http://www.cs.cornell.edu/~asampson/blog/llvm.html
18:41 < kanzure> "Tiny->Super: You devote the extra 5 hours you get every day to the study of your unique genetics, after ten years you are able to modify your genetics to eliminate sleep completely. By twenty years you and a group of sleepless colleagues leave your unevolved ancestors behind on earth and set out on your next great adventure."
18:46 < kanzure> yashgaroth: do you think these two are okay at bioinformatics things, like genome assembly and hunting for SNPs and missing chromosome fragments?
18:46 < yashgaroth> not really, no
18:46 < kanzure> this is re: my needle-haystick situation with only a mother and son genome with the interesting trait
18:46 < kanzure> ok.
18:48 < yashgaroth> should be possible to find/modify/write a program that does most of it automagically
18:49 < kanzure> actually i haven't collected the samples yet sooooo i should wait
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19:23 < kanzure> .tw https://twitter.com/Beluosa/status/960349850511532032
19:23 < yoleaux> Someone told me this weekend "I used to be lactose intolerant". #CRISPR #genetherapy #BDYHAX2018 (@Beluosa)
19:24 < kanzure> .tw https://twitter.com/janemetcalfe/status/960305855542583296
19:24 < yoleaux> CEO injects himself with live #Herpes vaccine in grand finale at #bdyhax2018 #genetherapy as performance art. https://pbs.twimg.com/media/DVOxENRVoAAU4AH.jpg https://pbs.twimg.com/media/DVOxENUVoAAjD3D.jpg https://pbs.twimg.com/media/DVOxENSU8AAimHV.jpg (@janemetcalfe)
19:25 < kanzure> .tw https://twitter.com/emilylmullin/status/960276354909589505
19:25 < yoleaux> Aaron Traywick, CEO of Ascendance Medical, just injected himself with an untested gene therapy for herpes in front of an audience at #BDYHAX2018. Video here: https://www.facebook.com/N2Sreports/videos/1668713259903223/. Our previous story on DIY gene therapy and the FDA: https://www.technologyreview.com/s/609568/biohackers-disregard-fda-warning-on-diy-gene-therapy/ (@emilylmullin)
19:25 < kanzure> ah didn't know he was in town.
19:26 < kanzure> .tw https://twitter.com/biohackinfo/status/960265567805440000
19:26 < yoleaux> As Ascendance Biomedical & @ProphaseBio's herpes cure test is about to go live at #BdyHax2018 Bodybacking Convention, biohacker Josiah Zayner denounces them as scammers that do not represent biohackers. https://twitter.com/4LOVofScience/status/960260735254188032 (@biohackinfo)
19:26 < kanzure> .tw https://twitter.com/4LOVofScience/status/960260735254188032
19:26 < yoleaux> Interview with Ascendance Bio CEO starts at ~1:27 Talks about his nanorobotic(has to be a joke right?) herpes cure he is going to test on himself. Earlier a guy says they are making @US_FDA compliant gene therapy while using bare hands in a flow hood 😂😂 https://m.facebook.com/story.php?story_fbid=342472759563087&id=100014010967687 (@4LOVofScience)
19:27 < kanzure> here are the people to murder: https://pbs.twimg.com/media/DVOKEhKVMAEpOdy.jpg:large (note their faces for murderings later)
19:28 < kanzure> .tw https://twitter.com/BDYHAX/status/960256221315059712
19:28 < yoleaux> What if your insulin device could not only deliver your insulin for you, but know exactly how much you needed, when you needed it? Go reactive to proactive with your insulin, with @DanaMLewis and #OpenAPS. We want to rewright the standard at #BDYHAX2018. #JoinTheFuture https://pbs.twimg.com/media/DVOD8WaVMAA7KX-.jpg (@BDYHAX)
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19:30 < kanzure> .tw https://twitter.com/kristenvbrown/status/960237790758830080
19:30 < yoleaux> “If there is anybody out there who is in the first trimester of pregnancy and wants abortion pills, I will give them to you.” At #BDYHAX2018, @MichaelSLaufer offering to give someone an abortion on stage ... I’m all for more access to options for women, but eek. (@kristenvbrown)
19:35 < kanzure> zayner says "Andreas strumer just told me that he thinks they will cure cancer"
19:37 < kanzure> hmm okay we need to isolate these people
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20:01 < kanzure> omg having a fresh keyboard is really liberating
20:07 < kanzure> "i can tell when you do your twitter run when i get a bunch of crazy biohacker retweets in my timeline"
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23:13 < kanzure> .tw https://twitter.com/4LOVofScience/status/959246388075753472
23:13 < yoleaux> Aaron Traywick and Ascendance Biomedical running Facebook ads and promoting another live gene therapy type injection. Claims it's a cure for herpes... Wondering how long till FDA cracks down on them. Any bets? https://pbs.twimg.com/media/DU_tfw6VMAAhAbW.jpg (@4LOVofScience)
23:17 < kanzure> https://www.facebook.com/josiah.zayner/posts/10103180183663617
23:35 < kanzure> hm well anyway.
23:38 < kanzure> "Also I'm confused why you think that consulting on a project is sufficient to damn the entire breadth of work of the researchers involved" well... because of the clowns.
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23:40 < mrdata> send in the clowns
23:49 < kanzure> clownicide.
--- Log closed Mon Feb 05 00:00:43 2018