--- Log opened Mon Oct 23 00:00:54 2017
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03:54 < kanzure> ebowden: no i told you that you should go find those papers
04:02 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/twist-bioscience-dna-data-storage-whitepaper.pdf
04:05 < kanzure> (this was from http://www2.twistbioscience.com/dna-based_data_storage_white_paper )
04:06 < kanzure> "Storage media overview: historic perspectives" http://storageconference.us/2016/Slides/BobFontana.pdf
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04:43 < ebowden> kanzure, you think it's practical to replace all earth's plants?
04:46 < ebowden> (With ones that have more efficient photosystems.)
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07:48 < jrayhawk> that's actually a good question: is there a downside to replacing C3 photosynthesis with C4 photosynthesis?
07:59 < kanzure> for practicality, you can get a pretty big chunk of the plant population. maybe not all of them.
08:16 < kanzure> at least all the agriculture.
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08:29 < kanzure> https://medium.com/@SassanoM/lets-enhance-how-we-found-rogerkver-s-1000-wallet-obfuscated-private-key-8514e74a5433
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08:52 < kanzure> https://blog.acolyer.org/2017/10/23/why-neurons-have-thousands-of-synapses-a-theory-of-sequence-memory-in-neocortex/
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09:30 < kanzure> "Turning corners into cameras: Principles and methods" http://people.csail.mit.edu/klbouman/pw/papers_and_presentations/cornercam_iccv2017.pdf
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11:19 < kanzure> https://www.arxiv-vanity.com/ https://news.ycombinator.com/item?id=15534580
11:19 < kanzure> (browser rendering stuff)
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14:03 < fltrz> regarding replacing plant genetics for more efficient photosynthesis, how much energy is wasted when there is 'too much' light? perhaps its easier to use solar panels to provide light for 2 levels of plants and/or buffer the solar energy and spread it out more evenly during the day?
14:08 < fltrz> the corner camera is cool
14:13 < kanzure> "easier" as in, easier to launch giant filters into space? i don't think so-- genetics is easier at this point.
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14:33 < ebowden> kanzure, you know how there are very few noot vendors that properly test their products?
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14:41 < kanzure> "Blender is used by NASA for publicly available 3D models. Many 3D models on NASA's 3D resources page are in a native .blend format.[62]"
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14:53 < fltrz> which giant filters are you referring to? what are noot vendors?
14:53 < kanzure> star shades
14:53 < kanzure> nootropic vendors
14:53 < fltrz> ah
14:54 < ebowden> kanzure, one of the few that did was sued and went under.
14:55 < ebowden> (Powdercity)
14:56 < fltrz> I meant on the ground, i.e. instead of having a single level of plants at ground level, stack 2 layers of plants, with appropriate lighting, and on top a solar panel the surplus energy is stored, and the plants receive a constant amount of light during daytime instead of little, good, too much, good, little
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16:15 < fltrz> kanzure: thanks for posting the sequency memory neuronal model, as far as I have read it, it explicitly models neuronal feedback on cellular level, as opposed to the common whole brain backpropagation feedback without basis in a single neuron model
16:18 < heath> nmz787: useful! thanks for sharing
16:31 < fltrz> the simulation results for the online learning is stunning, it reaches 'perfection' or best possible accuracy after a few thousand tries, the initial learning being steep... this reflects very much human task learning
16:32 < fltrz> but its still obscure to me how the identities of presynaptic cells are chosen for the dendritic segment clustered synapses
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20:07 < kanzure> yashgaroth: be greeted
20:07 < yashgaroth> ah, hello
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20:49 < kanzure> jrayhawk: could we fix the ssl cert issues on diyhpl.us
20:57 < jrayhawk> Okay, done.
20:58 < kanzure> thank you
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22:04 < mrdata_> https://www.nextbigfuture.com/2017/10/darpa-brain-stimulation-can-accelerate-learning-by-40-know-why-it-works-could-be-common-by-2023.html
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22:21 < nmz787> yashgaroth: so this old dude was telling me half-life of enzymes is in the hours
22:22 < yashgaroth> for some of them, yeah
22:22 < nmz787> he was saying even the best
22:22 < nmz787> like even PCR enzymes
22:22 < nmz787> I don't know/remember the max PCR cycles possible
22:22 < yashgaroth> PCR enzymes are running at 95C so that's not too surprising
22:22 < nmz787> and even then I was saying like, isn't that input vs output concentration dependent... not the enzyme dying
22:22 < nmz787> and he was like, no, the enzyme goes bad
22:23 < yashgaroth> well that's just, like, his opinion man
22:23 < nmz787> I can only imagine some room-temp color conversion experiment, with the enzyme in some dialysis tubing, and input reagent dripped in from the top
22:24 < nmz787> what's that immuno color based thing?
22:24 < nmz787> horseradish peroxidase?
22:24 < yashgaroth> ELISA
22:24 < yashgaroth> but yeah you could test it on HRP
22:24 < nmz787> yeah I mean the common signalling enzyme that is bound to the antibody in ELISA
22:24 < nmz787> that does color change, right?
22:25 < yashgaroth> yeah
22:25 < yashgaroth> anyway it still depends on the enzyme and conditions, if it's running in a cell and/or at high temperatures, eventually it'll degrade in a way that makes it nonfunctional
22:26 < yashgaroth> if you expect it to catalyze reactions for days you'll probably be disappointed, luckily proteins are cheap
22:27 < nmz787> well I was thinking something like a DNA harddrive
22:27 < nmz787> or storage
22:27 < nmz787> or synthesis pipeline
22:27 < nmz787> basically you're saying I need to factor in protein supply and waste stream I guess
22:27 < nmz787> or that's how I'm hearing it
22:28 < nmz787> even how many enzymes per bp DNA synthesized
22:28 < nmz787> or bp per enzyme, rather
22:28 < yashgaroth> mhm, stability is okay but during catalysis I suppose there's a small chance the protein will covalently bind the substrate or something
22:29 < yashgaroth> if you've got reactive chemicals in there they'll attack it as well
22:29 < nmz787> just thinking water and any needed salts at this point
22:29 < nmz787> for i.e. TdT
22:29 < nmz787> so polymerase
22:29 < nmz787> and incoming nucleotide triphosphates
22:30 < nmz787> unless I can think of a way to use these PEDOT:PSS electrodes (which at low enough voltage prevent catalysis of water) then there might be evolution of H2 and O2 at either electrode
22:31 < nmz787> which I am hoping to avoid
22:31 < yashgaroth> yeah O2 is nasty stuff
22:31 < yashgaroth> plus the other free radicals which are infinitely worse
22:33 < yashgaroth> idk if someone's done a study on that, like running a polymerase for a long time and doing mass spec to fingerprint if the enzyme ends up with a phosphate stuck to it
22:34 < nmz787> I was also thinking about possibly implementing a sort of linear motor, so the electrophoresis could be lower voltage along a micro/nanochannel
22:35 < nmz787> like striped electrophoresis electrodes
22:35 < nmz787> and using close pairs of them
22:35 < nmz787> instead of from one end to the other
22:35 < nmz787> sort of like that "digital microfluidics", but nano
22:35 < nmz787> and in channels, instead of an open plane
22:36 < yashgaroth> mm, biomolecules are gonna get fucked up if they actually reach the electrode though
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22:37 < nmz787> yeah idk, I can't remember much about electrochemistry
22:37 < nmz787> I seem to think there is some voltage that they might be OK
22:37 < nmz787> like, that's the reaction energy for a given temperature or something
22:38 < yashgaroth> it's a dangerous game I'd imagine, but yeah I'm not big on electrochem either
22:41 < nmz787> there might be some possibility to add a thin insulating layer, so it's more of a capacitive coupling, so DC can't go through
22:41 < nmz787> then I'd have to do AC electrophoresis
22:41 < nmz787> with a controller to pulse one of the electrodes a bit more than the other
22:41 < nmz787> to get directional control
22:43 < yashgaroth> I'm also not big on electrics, but sure
22:45 < fenn> .title https://m.phys.org/news/2017-10-gene-brain-major.html
22:45 < yoleaux> fenn: Sorry, that doesn't appear to be an HTML page.
22:45 < fenn> huh
22:46 < heath> .wik foldamer
22:46 < yoleaux> "In chemistry, a foldamer is a discrete chain molecule or oligomer that folds into a conformationally ordered state in solution. They are artificial molecules that mimic the ability of proteins, nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets." — https://en.wikipedia.org/wiki/Foldamer
22:47 < fenn> vSLENDR (viral mediated single-cell labeling of endogenous proteins by CRISPR-Cas9-mediated homology-directed repair)
22:53 < nmz787> heath: that reminds me of the ability to take impressions of antibodies with plastic, and the plastic retained some antigen-binding capability -- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874824/figure/F1/
22:55 < nmz787> I got my gleaux plant today (again, after first one was contaminated upon arrival), this time being dirt-rooted
22:55 < nmz787> I potted it earlier, and tried to look at it
22:55 < nmz787> but couldn't see anything
22:55 < nmz787> I have a dSLR I can try setting up
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--- Log closed Tue Oct 24 00:00:08 2017