--- Log opened Sun Oct 22 00:00:53 2017
00:14 < ebowden> kanzure http://www.sciencedirect.com/science/article/pii/0005272884902445
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00:31 < fenn> .title
00:31 < yoleaux> Investigation of the apparent inefficiency of the coupling between Photosystem II electron transfer and ATP formation - ScienceDirect
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05:18 < kanzure> .title
05:18 < yoleaux> Investigation of the apparent inefficiency of the coupling between Photosystem II electron transfer and ATP formation - ScienceDirect
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05:37 < ebowden> Not QUITE as simple as the title suggests.
05:37 < ebowden> I suggest you read the paper.
05:38 < ebowden> http://www.joh.cam.ac.uk/energy-hijacking-pathway-found-within-photosynthesis
05:41 < ebowden> I'd like to see this competing pathway stymied within plants.
05:41 < ebowden> Maybe just with some mechanism that stooges oxygen away from the photosystem.
05:41 < ebowden> 10.1038/nchembio.2192
05:42 < ebowden> http://sci-hub.cc/10.1038/nchembio.2192
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06:18 < kanzure> .title
06:19 < kanzure> hmph
06:28 < ebowden> kanzure, it'd be nice to see a modern medicine garden, full of genetically engineered plants produce pharmaceuticals at high yield.
06:38 < ebowden> *medicinal garden, full
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08:10 < kanzure> .title https://github.com/fg-inet/socket-intents
08:10 < yoleaux> GitHub - fg-inet/socket-intents: Augmented socket interface for an application to express knowledge about its communication.
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08:46 < kanzure> .title https://news.ycombinator.com/item?id=15526036
08:46 < yoleaux> Micron now has a 11TB SSD | Hacker News
08:46 < kanzure> https://www.digikey.com/product-detail/en/micron-technology-inc/MTFDHAL11TATCW-1AR1ZABYY/MTFDHAL11TATCW-1AR1ZABYY-ND/7598107
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10:19 < kanzure> nmz787: instead of human hair they should have done FIB + guitar strings
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10:34 < kanzure> crime scene dna analysis software thingy https://github.com/propublica/nyc-dna-software
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11:13 < kanzure> here are most of the papers i've been looking at in 2017 http://diyhpl.us/~bryan/papers2/2017-10-22-kanzure-reading-list-2017.v0.pdf
11:17 < kanzure> .title https://twitter.com/kanzure/status/922164370288898048
11:17 < kanzure> er..
11:17 < kanzure> .tw https://twitter.com/kanzure/status/922164370288898048
11:18 < yoleaux> Here's a gallery of the 1st page of most of the research papers I've been reading in 2017: http://diyhpl.us/~bryan/papers2/2017-10-22-kanzure-reading-list-2017.v0.pdf h/t h/t @laurilove (@kanzure)
11:18 < yoleaux> kanzure: Sorry, that command (.title) took too long to process.
11:35 < poppingtonic> I like this. I've read tons of papers this year but haven't organized the abstracts in any reproducible way.
11:39 < kanzure> "Analytic modeling of starshades" https://arxiv.org/pdf/1106.2127.pdf
11:40 < kanzure> it occurs to me that i am missing all the papers i read that i only linked to abstracts not the pdf link......
11:47 < kanzure> nsh has made one too, http://diyhpl.us/~bryan/papers2/laurilove-reading-2017-frontpages.pdf
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12:01 < poppingtonic> kanzure: have you read Merkle and Freitas's book on kinematic self-replicating machines?
12:02 < poppingtonic> I've been somewhere in the first section for years. The Nanomedicine book as well.
12:09 < kanzure> i've flipped through the online copy.
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12:32 < kanzure> nsh paper dump v2 (now with less lossy image compression, but larger pdf file) http://diyhpl.us/~bryan/papers2/laurilove-reading-2017-frontpages.v2.pdf
12:33 < superkuh> Is the generation of either of those scripted?
12:34 < kanzure> yes
12:34 < kanzure> i pulled from irc logs for myself
12:34 < kanzure> i did a bunch of this: pdftk A=1606.03588v1.pdf cat A1 output thumb_1606.03588v1.pdf
12:34 < kanzure> followed by: pdftk thumb_*.pdf cat output output.pdf
12:34 < superkuh> Thanks.
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12:40 < nmz787> ebowden: pharmagarden is hope/dream of mine
12:44 < kanzure> .tw https://twitter.com/kallerosenbaum/status/922183604024815618
12:44 < yoleaux> @kanzure @laurilove Holy cow! What a paper junkie! The diversity! What did you do on the other 5 minutes of 2017? (@kallerosenbaum, in reply to tw:922164370288898048)
12:44 < kanzure> .tw https://twitter.com/kanzure/status/922186285682429952
12:44 < yoleaux> @kallerosenbaum @laurilove I estimate those are ~10% of the total, actually. As for the other 9,600 hours of my year? Work. (@kanzure, in reply to tw:922183604024815618)
12:46 < nmz787> kanzure: I am unimpressed with the one ResearchGate cover page I saw in yours
12:46 < kanzure> there are many :-(
12:47 < nmz787> but quite intrigued with the protein subnanopore sequencing paper
12:47 < nmz787> .doi 10.1038/NNANO.2016.120
12:48 < nmz787> so even if I can build a whiz-bang nanopore sequencer/discriminator with a nanofluidic handling system... loading it with reagents will still likely require something like an inkjet printer to fill up each input reagent
12:49 < nmz787> while I hope they won't require special gas protection (like argon, etc) because of being 'green' chemistry or enzyme-based... I guess I need to read up on POSAM at least from a mechanical/tech side of things... i.e. what print head did they use
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12:52 < nmz787> also, an idea that came about last night... we could make a single molecule of DNA using nanopore translocation of the growing strand to limit chain-growth, using washes of monomers on the top, along with idk tethered-enzyme, the bottom could just be a collection area, and when you're done synthesizing your one-molecule (to rule them all) maybe you could just PCR the hell out of it to get it up to
12:52 < nmz787> usable scale for macro-handling (pipets) to deal with
12:53 < nmz787> (more for bioengineering than data storage, but I guess it could work for more-archival version of the latter)
12:54 < kanzure> there was a video posted in here a few days ago where someone had a graphene nanopore that had a 'kink' in it or something, and dna could not translocate without an electric field applied to it. so it was more or less monomer control going through the nanopore. is that what you mean?
12:54 < kanzure> (these were molecular dynamics simulations, IIRC)
13:01 < nmz787> mmm, that sounds interesting, but I think just normal electrophoresis (maybe AC electrophoresis) could be useful
13:02 < nmz787> like, if the growing oligo isn't poking it's head out (like a turtle) from the nanopore, an enzyme can't attach and extend it
13:03 < nmz787> like that old saying... "you can't superglue a funny hat onto a turtle when its head is retracted into its shell"
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13:12 < JayDugger> US$2600 for a farmbot?
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13:18 < nmz787> JayDugger: where?
13:20 < kanzure> biorxiv papers are enormous O_O
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13:21 < JayDugger> Quoting fenn,
13:21 < JayDugger> .title http://farmbot.io
13:21 < yoleaux> Meet FarmBot - Humanity's First Open-Source CNC Farming Machine
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13:22 < JayDugger> Yeah, biorxiv has slowed my reading.
13:22 < JayDugger> Huh...farmbot for beekeeping?
13:23 < kanzure> no i mean physically they are all >1 MB each
13:25 < kanzure> why is "The developing human connectome project" paper over 30 MB in size? https://www.biorxiv.org/content/early/2017/04/07/125526
13:32 < kanzure> ok,
13:32 < kanzure> i have updated my paper reading list with the 1st pages from biorxiv + arxiv papers http://diyhpl.us/~bryan/papers2/2017-10-22-kanzure-reading-list-2017.v0.pdf
13:32 < kanzure> and a bunch of bitcoin papers
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13:35 < nmz787> https://www.aliexpress.com/item/PURSWAVE-ST14DC-DCTiny-Compressor-12V24V48V-MAX-300W-capacity-R134a-for-portable-refrigerator-mini-air-conditioner/32812575090.html
13:35 < JayDugger> Any thing specially clever you're doing to make these reading lists?
13:37 < nmz787> he said just using pdftk and the "cat" function of it
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13:37 < nmz787> I'd guess a ls -la and then grepping by date modified, then piping to xargs and pdftk
13:37 < heath> .title https://www.youtube.com/watch?v=-q82IrNWbKc
13:37 < yoleaux> Cellscape VR Biology Guided Tour - YouTube
13:38 < heath> vr video of human cell
13:39 < heath> on youtube, there are lots of vr videos for different types of cells it seems
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13:41 < JayDugger> Thanks, nmz787. I missed that, and didn't search (lazy me).
13:53 < JayDugger> kanzure, The developing human connectome project" paper over 30 MB in size happens because of the images on pages 8, 15, and 16.
13:54 < JayDugger> page 8 has 4 images at least 1.5 MB each, and page 16 has a 3.6 MB image.
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13:58 < nmz787> "Trimethyl (methylcyclopentadienyl) platinum(IV) (MeCpPtMe3) (SAFC, Sigma-Aldrich) was used as the platinum source (precursor), this compound was housed in a stainless steel bubbler and subjected to 70°C of heating. The resulting vapour was drawn into the chamber by the vapour draw method."
13:58 < nmz787> MeCpPtMe3 is $4000 for 10 grams from Sigma-Aldrich
13:59 < nmz787> I need to calculate how many layers for a small wafer that would be, or how many devices that might be able to produce
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14:04 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=d717d896 Bryan Bishop: mention dCas9-acetyltransferase >> http://diyhpl.us/diyhpluswiki/gene-editing/
14:07 < kanzure> .title https://github.com/rg3/youtube-dl/issues/6246
14:07 < yoleaux> Add support for spherical ("360 degrees") videos · Issue #6246 · rg3/youtube-dl · GitHub
14:11 < nmz787> heath: nice video
14:11 < nmz787> I have a PC good enough for VR... I should get a headset with those controllers
14:16 < nmz787> $15 for a pretty low-res and low-brightness projector, I'd guess it was LCD, not MEMS: http://www.brookstone.com/pd/brookstone-keychain-projector/317994p.html
14:16 < nmz787> (plus $8 shipping)
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14:18 < nmz787> amazon has it for same price, $5 shipping
14:18 < nmz787> grabbed on, it could be useful for something someday
14:18 < nmz787> one*
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15:02 < kanzure> something something fasano CXCR3 antagonists
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15:14 < fltrz> nmz787: the specifications say 320x240 (720p) ? why do they call it 720p?
15:57 < nmz787> fltrz: I can only imagine they get away with it by claiming it supports 720p input (downscaling)
15:58 < fltrz> I guess, but they put the "320x240 (720p)" as Native resolution
15:58 < nmz787> to be honest I didn't even see those specs when I looked through
15:59 < fltrz> 240*3 colors =720 ... so perhaps they pretend to confuse this with 720p?
15:59 < nmz787> apparently this $90 item is hundreds of times brighter: https://www.amazon.com/dp/B07415LSN9/ref=psdc_300334_t1_B01LZRUY6Q
16:00 < nmz787> I don't see the native res there either
16:04 < fltrz> yeah that makes me instantaneously suspicious too
16:04 < fltrz> no user manual either
16:05 < fltrz> but I do believe such a resolution could be delivered at this price profitably
16:05 < fltrz> it's just I dont really see any projector sellers do it
16:06 < fltrz> the projector market pricing is very steep because beamers still carry the expectation of being expensive...
16:08 < fenn> you can get used 1024x768 DLP projectors on ebay for $50 with some dead pixels
16:08 < fltrz> yeah obviously, you can find good deals
16:09 < fenn> i think these cheap things are just a crappy cellphone screen, a lens, and a led light source
16:09 < fltrz> I actually have 4 or 5 identical DLP projectors of this resolution, all missing the blue laser diodes
16:10 < fltrz> fenn: yes, really old cellphone screens even
16:10 < fltrz> fenn: or a newer one in case you were talking about the projector on amazon
16:14 < fenn> heh that one actually shows you the optics https://m.media-amazon.com/images/S/aplus-seller-content-images-us-east-1/ATVPDKIKX0DER/A1XDUTLPKT3DKH/B07415LSN9/OdzH2pTWO7._UX300_TTW__.jpg
16:16 < fenn> image quality actually looks ok, they hadn't progressed to modern lcd phone screens last time i looked
16:18 < fenn> i don't think it's 1080p though
16:26 < nmz787> .title https://github.com/3dem/relion
16:26 < yoleaux> GitHub - 3dem/relion: Image-processing software for cryo-electron microscopy
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17:36 < kanzure> .wik NGC 5457
17:36 < yoleaux> "The Pinwheel Galaxy (also known as Messier 101, M101 or NGC 5457) is a face-on spiral galaxy distanced 21 million light-years (six megaparsecs) away from earth in the constellation Ursa Major." — https://en.wikipedia.org/wiki/NGC_5457
17:36 < kanzure> .wik NGC 6946
17:36 < yoleaux> "NGC 6946 (provisionally known as the Fireworks Galaxy) is an intermediate spiral galaxy about 22 million light-years away, in the constellations of Cepheus and Cygnus. It was discovered by William Herschel on 9 September 1798." — https://en.wikipedia.org/wiki/NGC_6946
17:45 < nmz787> so with ALD, there was that report of glycine deposition.... so maybe kettner's idea of something gas-phase isn't crazy?
17:45 < nmz787> affix TdT to a surface, then insert that into your ALD machine, and pulse different nucleotides or something
17:46 < nmz787> or maybe not even enzymatic
17:46 < nmz787> maybe some sort of spontaneous polymerization can be used that takes advantage of the vacuum (absence of stuff to react with)
17:53 < kanzure> ALD?
17:54 < fenn> atomic layer deposition
17:55 < nmz787> this is pretty much the only thing I've been talking about in here for like 2 weeks
17:56 < nmz787> fenn: do you know any transistor fab via ALD?
17:56 < nmz787> if I could make at least simple amplifiers, that would/should be very good for chances of detecting single molecules via tunnelling current
17:56 < nmz787> (which is already sensible by the open STM microscope)
17:57 < nmz787> microscopes*
17:57 < fenn> i know almost nothing about silicon fab processes
17:58 < fenn> or transistor fab from other substrates
17:58 < fenn> apparently there are screen printed organic transistors now
17:59 < nmz787> I've definitely seen you post about organic transistors, I think
17:59 < nmz787> .title https://www.youtube.com/watch?v=rsy3-ZfbqW0
17:59 < yoleaux> Family Guy - (S2xE13) oh, you speak english - YouTube
18:00 < nmz787> basically you re: transistors
18:00 < kanzure> "Detection of intact lava tubes at Marius Hills on the Moon by SELENE (Kaguya) Lunar Radar Sounder" http://onlinelibrary.wiley.com/doi/10.1002/2017GL074998/full
18:00 < kanzure> .title https://news.ycombinator.com/item?id=15528048
18:00 < yoleaux> A newly discovered moon tunnel | Hacker News
18:00 < kanzure> wouldn't this be a good place to setup shop?
18:00 < kanzure> or is it too leaky for atmosphere
18:01 < fenn> inflatable liner would be fine
18:01 < kanzure> inflatable housing. ok.
18:03 < fenn> thin enough to bridge micro cracks but otherwise conform to the walls of the lava tube
18:03 < nmz787> I was trying to find modular cleanrooms last night
18:03 < nmz787> something like a tent/shade structure with thick plastic shower curtains draping to the floor
18:03 < nmz787> with HEPA and positive pressure from above
18:03 < nmz787> (for my garage)
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18:11 < nmz787> 47 atoms in ATP
18:11 < nmz787> depending on if you count some protons or not
18:12 < kanzure> and what about atp synthase?
18:13 < fenn> ok this is just a weird news headline https://www.washingtonpost.com/news/worldviews/wp/2017/02/21/terrorists-are-building-drones-france-is-destroying-them-with-eagles/
18:15 < fenn> surely some kind of HERF EMP gun would be more appropriate
18:18 < kanzure> for launching eagles into the air, sure.
18:18 < fenn> for disabling the drone electronics
18:18 < kanzure> fenn: https://xkcd.com/1842/
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18:37 < superkuh> I've now spent more time automating this first page of pdf from 2017 than it would've taken by hand. pdftk is so anal about spaces.
18:39 < nmz787> .title http://pdb101.rcsb.org/motm/72
18:39 < yoleaux> PDB-101: ATP Synthase
18:39 < kanzure> superkuh: find -name "* *" -type f | rename 's/ /_/g'
18:39 < kanzure> er, on a copy of course
18:40 < nmz787> based on the 4 linked PDBs, there appears to be 79 + 510 + 22 + 61 == 672 amino acids
18:40 < superkuh> find /home/superkuh/library/ -type f -mtime -295 -not -name "comments.html" -not -name "*.swp"  -not -path "/home/superkuh/library/Biology/ncbigenomes/*" -not -path "/home/superkuh/library/AmSci/*" -not -path "*/Fiction/*" -not -path "*/.Trash-1000/*" > 2017files.txt; pdftk $(<  2017files.txt) cat A1 output thumb_%04d.pdf
18:40 < superkuh> Except none of the $() stuff actually works with pdftk.
18:40 < kanzure> give me 2017files.txt
18:40 < superkuh> So instead I made a perl script. And no matter how many '' or "" I throw in the mix it always can't find th...
18:40 < superkuh> Okay.
18:40 < superkuh> http://superkuh.com/2017files.txt
18:47 < fenn> i don't see the point of concatenating all the first pages
18:47 < superkuh> I guess that could use a -iname '*.pdf' too.
18:48 < fenn> the list of urls is more useful
18:48 < superkuh> I already have a script that does that.
18:48 < kanzure> superkuh: try this http://diyhpl.us/~bryan/irc/superkuh2017.sh
18:49 < kanzure> oh nooo i'm missing quotes
18:49 < kanzure> ok fixed
18:50 < kanzure> superkuh: please confirm the first ~two lines before running the whole script
18:50 < superkuh> http://superkuh.com/recentlib.pl.txt , I'd just need to add the current day of year to @daysback.
18:51 < superkuh> Seems to work.
18:51 < kanzure> there's also a line at the bottom
18:51 < kanzure> also i learned about this vim trick to do this, :%s/^/\=printf('%-4d', line('.'))
18:52 < kanzure> fenn: well it turns out nsh was doing this to provide a character reference for himself to the court.   ((i thought he was doing it because it was interesting data.))
18:53 < superkuh> I'm just following the crowd because it looks fun.
18:54 < superkuh> http://superkuh.com/2017-so-far.pdf
18:54 < superkuh> (9.5 MB)
18:58 < kanzure> rehosted  http://diyhpl.us/~bryan/papers2/2017-10-22-superkuh-reading-list-2017.pdf
18:58 < kanzure> page 5, why is walking so bright?
18:59 < nmz787> average atoms for amino acids is 15.35 atoms, so 672 atoms at that avg == 10315 atoms in ATP synthase
19:00 < superkuh> I'd guess (and it is a complete guess) because walking requires more vision than backing up or chasing females (touch based).
19:00 < kanzure> how you gonna chase without knowing where to go
19:01 < kanzure> oh, you stay low distance
19:02 < kanzure> fenn: make a version of this that pulls out all the "figure 1"s
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19:11 < fenn> well you could do something with pdfimages but it would need a temp directory to store the images
19:14 < kanzure> nsh did imagemagick downsampling into jpeg but everything was blurry-worry http://diyhpl.us/~bryan/papers2/laurilove-reading-2017-frontpages.pdf
19:14 < kanzure> blurry-worly, even.
19:15 < fenn> a lot of papers have stupid crests and logos at the top
19:16 < fenn> so you can't just extract the first image in the file, or the image on the first page
19:16 < kanzure> crest of enlightenment, crest of higher learning, crest of the sacred order of the royal society of journal b, et cetera.
19:17 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=4b4a02f1 Nathan McCorkle: added info on amino acid masses and atom count, along with projected # atoms in ATP synthase (~10315) >> http://diyhpl.us/diyhpluswiki/proteins/faq/
19:18 < kanzure> [[!table Error: cannot find file]]
19:19 < kanzure> nmz787: you probably need to specify the full path to the file
19:19 < kanzure> so proteins/aminos_data_weights_atoms.csv
19:19 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=09efcd6d Nathan McCorkle: path fix for amino acid table >> http://diyhpl.us/diyhpluswiki/proteins/faq/
19:20 < kanzure> nmz787: yep works
19:20 < kanzure> http://diyhpl.us/diyhpluswiki/proteins/faq/
19:20 < kanzure> er, http://diyhpl.us/wiki/proteins/faq/
19:20 < fenn> kewl
19:21 < nmz787> I should be ashamed that I didn't parse the 4 PDBs and get accurate atom counts instead of averaging atoms/amino
19:22 < kanzure> well are you (ashamed)?
19:22 < fenn> can't you just look at the mass of the protein in kDa
19:23 < fenn> .wik kilodalton
19:23 < yoleaux> "The unified atomic mass unit or dalton (symbol: u, or Da) is a standard unit of mass that quantifies mass on an atomic or molecular scale (atomic mass). One unified atomic mass unit is approximately the mass of one nucleon (either a single proton or neutron) and is numerically equivalent to 1 g/mol." — https://en.wikipedia.org/wiki/Kilodalton
19:23 < fenn> oh atoms not nucleons
19:27 < kanzure> might as well put your dna numbers somewhere
19:27 < nmz787> kanzure: I was just forming an email to shop out the job to someone asking for remote assistance contribution on diybio... but realize that I might get it done myself much in a few times what it'll take me to write this email
19:29 < kanzure> nmz787: the super lazy way to do it is to go file -> print on the pdf version of the document, then print out the last 2-3 pages (your appendix) to pdf, then upload the pdf. lazy wins the day again!
19:30 < fenn> fwiw e. coli atp synthase has 4926 residues (in 8 chains) for a total weight of 535 kDa
19:30 < nmz787> hmm, these PDBs seem to show there might be a lot more atoms in just one mid sized subunit
19:30 < nmz787> not sure if this is including water and salt or something
19:31 < nmz787> fenn: hmm, one of the PDBs I looked at were from bovine, and another e.coli...
19:31 < nmz787> maybe I didn't consider some multimers/dimers/copies
19:32 < fenn> there were a lot of search results
19:32 < fenn> i picked one that looked like atp synthase
19:33 < kanzure> it's well studied
19:33 < fenn> http://www.rcsb.org/pdb/explore/explore.do?structureId=5T4Q
19:35 < kanzure> also we should look at taq polymerase or terminal deoxyribonucleo transferase
19:35 < kanzure> or er, was it nucleotidyl transferase
19:37 < kanzure> for some reason i don't like the heterodimer polymerases
19:39 < nmz787> kanzure: you prefer homodimers, or monomers?
19:39 < kanzure> monomers. taq polymerase.
19:40 < nmz787> fenn: that link says "length 513"
19:40 < nmz787> I assumed that meant 513 amino acids
19:40 < nmz787> 'residues'
19:41 < nmz787> 513*8 == 4104
19:41 < fenn> that's one chain
19:41 < fenn> i think 6 of the chains are duplicates
19:42 < kanzure> pdb crystals aren't always "clean"
19:42 < nmz787> yeah that's what I am thinking
19:42 < nmz787> like maybe some water
19:42 < nmz787> or even subspecies (or species) variation
19:43 < fenn> water was removed from the structure
19:43 < kanzure> with dna-associated enzymes sometimes i see dna or rna stragglers in the pdb files
19:44 < JayDugger> kanzure, if you've an old NSS.org archive, you can probably find the chapter (Oregon, maybe?) that did work on lunar lava tubes such as the one described in the recent news.
19:45 < kanzure> i think fenn is more likely to have nss.org content
19:47 < fenn> i don't
19:49 < JayDugger> I don't have any handy, so if that's of interest, it'll take some digging.
19:50 < fenn> .title http://www.OregonL5.org/lbrt/l5lbrt01.html
19:50 < yoleaux> Oregon L5 Society - Lava Tubes from Clementine
19:51 < fenn> from 1998
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19:51 < kanzure> why is there an oregon legrange 5 society
19:52 < fenn> .title http://www.OregonL5.org/lbrt/l5isru1.html
19:52 < yoleaux> Oregon L5 - Utility of Lava Tubes on Other Worlds
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19:54 < fenn> .title http://www.OregonL5.org/lbrt/l5aaa88b.html
19:54 < yoleaux> Oregon L5 - Lava Tubes of the Pacific Northwest
19:54 < fenn> http://www.OregonL5.org/lavatube/
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19:56 < fenn> there are a lot of space dreamers in oregon
19:57 < fenn> NSS was set up before internet access was widespread
19:57 < fenn> it made sense to have local chapters
19:58 < fenn> http://www.OregonL5.org/lavatube/images/moontube.jpg
20:02 < heath> if you're looking for small dnaps, the a and x family seem to be the smallest
20:02 < heath> i'm guessing x is the smallest
20:03 < nmz787> it was more like kanzure's first response after I mentioned 47 atoms in ATP
20:03 < nmz787> how many atoms in ATP synthase
20:04 < heath> but if i recall reading correctly, the x family usually more produces transcription errors
20:04 < heath> nmz787: guess i can investigate
20:04  * nmz787 just opened https://ocw.mit.edu/courses/chemical-engineering/10-626-electrochemical-energy-systems-spring-2014/study-materials/MIT10_626S14_S11lec29.pdf
20:04 < heath> s/more produces/produces more
20:05 < nmz787> "Lecture 29: Electrokinetics"
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20:14 < kanzure> .tw https://twitter.com/MIRIBerkeley/status/921574637384892416
20:14 < yoleaux> "Reality held a more extreme position than I did on the Yudkowsky-Hanson spectrum." -@ESYudkowsky http://intelligence.org/?p=16754 (@MIRIBerkeley)
20:16 < fenn> a more reasonable thing would be to say "we were both wrong"
20:18 -!- preview [~quassel@2407:7000:842d:4000::3] has quit [Read error: No route to host]
20:19 < kanzure> .tw https://twitter.com/BugsInYourGuts/status/921424488788582400
20:19 < yoleaux> Vast majority of viral genomes are now from uncultivated viruses #viromicsworkshopOSU https://pbs.twimg.com/media/DMmOq8TW4AEVBjx.jpg (@BugsInYourGuts)
20:20 < kanzure> .tw https://twitter.com/PDBeurope/status/921381099640586240
20:20 < yoleaux> We're 46 🎂! PDB archive was announced #OTD in 1971. We've always been #openaccess (but the announcement isn't 🙁) http://www.nature.com/nature-newbio/journal/v233/n42/pdf/newbio233223b0.pdf https://pbs.twimg.com/media/DMlkoclX0AARRuK.jpg (@PDBeurope)
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20:20 < kanzure> .tw https://twitter.com/pathogenomenick/status/921664854838169600
20:20 < yoleaux> Useful guide to current Nanopore tool chain from @j_perkel http://blogs.nature.com/naturejobs/2017/10/16/techblog-the-nanopore-toolbox/ (@pathogenomenick)
20:21 < kanzure> .tw https://twitter.com/SynBioAlex/status/921275658713616386
20:21 < yoleaux> I'm curious if anyone's ever reproduced <10 min doubling time with V. natriegens? The 1962 paper is the only place I've seen such data. (@SynBioAlex)
20:22 -!- mindsForge [~nak@174-26-21-211.phnx.qwest.net] has quit [Remote host closed the connection]
20:22 < kanzure> "vSLENDR (viral mediated single-cell labeling of endogenous proteins by CRISPR-Cas9-mediated homology-directed repair)"
20:23 < nmz787> PoreCamp - a training bootcamp based on the Oxford Nanopore MinION -- Welcome to PoreCamp 2017 -- Monday 3 - 7 July 2017 University of Birmingham Birmingham, UK
20:23 < nmz787> how is a camp at a school :/
20:23 < nmz787> I guess ToorCamp has stretched my expectations of professional things with "Camp" in the name
20:23 < kanzure> "Virus-mediated genome editing via homology-directed repair in mitotic and postmitotic cells in mammalian brain" http://www.cell.com/neuron/fulltext/S0896-6273(17)30933-9
20:23 < kanzure> "Precise genome editing via homology-directed repair (HDR) in targeted cells, particularly in vivo, provides an invaluable tool for biomedical research. However, HDR has been considered to be largely restricted to dividing cells, making it challenging to apply the technique in postmitotic neurons. Here we show that precise genome editing via HDR is possible in mature postmitotic neurons as ...
20:24 < kanzure> ...well as mitotic cells in mice brain by combining CRISPR-Cas9-mediated DNA cleavage and the efficient delivery of donor template with adeno-associated virus (AAV). Using this strategy, we achieved efficient tagging of endogenous proteins in primary and organotypic cultures in vitro and developing, adult, aged, and pathological brains in vivo. Thus, AAV- and CRISPR-Cas9-mediated HDR will be ...
20:24 < kanzure> ...broadly useful for precise genome editing in basic and translational neuroscience."
20:24 < rpifan> hello
20:24 < kanzure> "Phage-assisted continuous evolution of proteases with altered substrate specificity" https://www.nature.com/articles/s41467-017-01055-9 https://twitter.com/rosscloney/status/921742620866502656
20:24 < rpifan> how do u even do this gene editing stuff
20:24 < rpifan> is it a shot
20:24 < rpifan> or do u snort it
20:24 < rpifan> or what
20:25 < kanzure> .tw https://twitter.com/Pipette_Ninja/status/921472816540680192
20:25 < yoleaux> Genetic Constructor #synbio software from @Autodesk: http://pubs.acs.org/doi/abs/10.1021/acssynbio.7b00236 Congrats Max, Flo, Deepak, Eli, and others! (@Pipette_Ninja)
20:25 < kanzure> rpifan: yes it's both snort + shot
20:26 < ebowden> kanzure, you somewhat interested in noots?
20:26 < kanzure> ebowden: i have some plans for how to make 1000x more powerful nootropics
20:26 < kanzure> however, it involves brain pathogens
20:26 < ebowden> lol
20:26 < ebowden> For... delivery?
20:26 < ebowden> Of genes?
20:27 < ebowden> kanzure, ^
20:28 < kanzure> see page 15 http://diyhpl.us/~bryan/irc/2017-02-03-beacon.pdf#page=15
20:29 < ebowden> OR.
20:29 < ebowden> Use a potent TrkB agonist.
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20:31 < ebowden> kanzure, I would never bother pursuing that idea unless I was doing research for no other reason than to determine if the plot of a movie was plausible.
20:31 < kanzure> is this entertainment to you
20:32 < kanzure> https://www.youtube.com/watch?v=t_3VZDb7pj4
20:32 < nmz787> .title
20:32 < yoleaux> AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHHH - YouTube
20:33 < rpifan> but how
20:33 < rpifan> i mean how can a snort or a shot
20:33 < rpifan> get inside u
20:33 < rpifan> and edit parts of u
20:33 < rpifan> seems impossible
20:33 < kanzure> ok
20:34 < nmz787> rpifan: think modified virues
20:34 < nmz787> viruses
20:34 < rpifan> ah
20:34 < kanzure> http://diyhpl.us/wiki/transcripts/diy-human-gene-therapy-with-crispr/
20:34 < ebowden> Kanzure, BDNF can, under some circumstances cause apoptosis.
20:34 < kanzure> "Intranasal delivery of cells to the brain" http://diyhpl.us/~bryan/papers2/bio/Intranasal%20delivery%20of%20cells%20to%20the%20brain.pdf
20:35 < rpifan> ebowden, wait r u telling me u can make me skinny
20:35 < rpifan> gimme gimme
20:36 < rpifan> kanzure, can u gimme some crispr to fix my diseases
20:36 < ebowden> *causes apoptosis.
20:36 < nmz787> rpifan: just get a gut microbiome swap, might make you skinny (as long as your donor is skinny)
20:36 < rpifan> u mean one of them fecal matter transplants
20:37 < nmz787> yeah
20:37 < rpifan> seems complicated
20:37 < rpifan> and idk about diy
20:38 < rpifan> unless
20:38 < rpifan> its as easy as eatting ass
20:38 < rpifan> which might make sense really
20:38 < nmz787> there's a DIY protocol
20:39 < nmz787> https://www.theverge.com/2016/5/4/11581994/fmt-fecal-matter-transplant-josiah-zayner-microbiome-ibs-c-diff
20:39 < rpifan> hmm
20:39 < rpifan> well ive done all kinds of crazy stuff
20:39 < rpifan> so that probably woulnt be the worst
20:39 < rpifan> now where do i get some twink poop
20:40 < nmz787> basically dose yourself with a few weeks of antibiotics, then eat some good poop
20:40 < rpifan> why the antibotics
20:40 < rpifan> wont that kill the good stuff too
20:40 < nmz787> yeah, but you gotta decimate the previous community
20:40 < rpifan> ah
20:40 < rpifan> that makes sense
20:41 < nmz787> basically replacing all the citizens
20:41 < rpifan> well ill tell u this
20:41 < rpifan> when i lived in south america
20:41 < rpifan> i could not stop losing weight
20:41 < rpifan> like seriously it was dangerously low
20:41 < rpifan> now im almost dangerously high
20:43 < ebowden> Kanzure, if you want to induce such absurd levels of brain growth and plasticity you could use a mixture of small molecules.
20:43 < rpifan> ill say this my stomach hurt all the time tho in south america
20:43 < rpifan> and i was eating real food supposedly
20:43 < rpifan> now that i eat all the bad american food
20:43 < rpifan> my stomach is fine
20:45 < nmz787> rpifan: wow, sorry to hear you're in near-dangerous conditions. I might go on a kimchee diet or something for a few weeks :O
20:46 < rpifan> the worst part is i am workign out now
20:46 < rpifan> lifting weight and such
20:46 < rpifan> but obviously im not builidng much muscle
20:46 < rpifan> its all frustrating
20:46 < rpifan> so can these gene therapies regrow shit
20:46 < rpifan> cuase ive had some stuff removed
20:46 < rpifan> that id like returned
20:46 < nmz787> ah
20:46 < ebowden> kanzure, are you looking not get them to produce as much BDNF as possible, but get them to make very, very specific changes to brain structure to achieve the goal>
20:46 < ebowden> *goal?
20:47 < rpifan> i was hoping for 3d printed parts
20:47 < rpifan> but if we can get my body to just mke another one
20:47 < rpifan> thatd be great
20:52 < nmz787> .title https://youtu.be/HDQ8ct4md-8
20:52 < yoleaux> Mütek PCD Tutorial - Electrochemical Doublelayer - YouTube
20:53 < rpifan> i heard about this tooth regrowing shit
20:53 < rpifan> u got any of that
20:53 < rpifan> i got bad teeth
21:00 < nmz787> that stuff is still in the works from what I know
21:00 < nmz787> a lot more mouse data than anything
21:01 < rpifan> well
21:01 < rpifan> how about the hiv one
21:10 < nmz787> fenn: that laser cutter design, could it be pushed to be a wafer prober, capable of say 10 nm resolution?
21:11 < rpifan> so do viruses modify are dna already?
21:12 < nmz787> yes
21:13 < rpifan> so ur telling me the flu has left little chunks inside me?
21:18 < nmz787> depends on the virus
21:18 < mrdata_> hork them out with garlic
21:19 < rpifan> seems incredible
21:19 < rpifan> but then again
21:19 < rpifan> apparently syphilis which is a bacteria stays in u forever basically
21:19 < mrdata_> rpifan, if the virus has a DNA reverse transcriptase, then it copies itself into your genome
21:19 < ebowden> After a certain progression, yes.
21:19 < mrdata_> idk if flu does tho
21:19 < mrdata_> i think ebola has that
21:19 < superkuh> Mammals wouldn't even exist if viruses hadn't lent the proteins needed for membrane fusion to make the placenta possible.
21:19 < ebowden> Though there is a way to kill syphilis even after that,
21:19 < ebowden> *that.
21:19 < rpifan> yea
21:19 < rpifan> i mean i know
21:20 < rpifan> ive had it
21:20 < rpifan> 3 times lol
21:20 < rpifan> and its dead but ill still show up positive for life bascially
21:20 < ebowden> You've had syphilis thrice?
21:20 < rpifan> yea
21:20 < ebowden> How the fuck is that?
21:20 < rpifan> cause u can keep getting it
21:20 < rpifan> syphilis is on the rise
21:20 < ebowden> As in, what on earth are you doing to catch it so frequently?
21:21 < rpifan> im a gay
21:22 < ebowden> Are you having unbelievable amounts of unprotected anal or something?
21:22 < rpifan> yes
21:22 < rpifan> well they are normal in my communtiy LOL
21:22 < nmz787> .wik hydrogen evolution reaction
21:22 < yoleaux> nmz787: Sorry, that command (.wik) crashed.
21:23 < ebowden> Unbelievable amounts of unprotected anal sex is normal where you live?
21:23 < rpifan> in the gay world yes
21:23 < nmz787> rpifan: gay != irresponsible
21:23 < rpifan> but what u consider unbelieve is likely normal
21:23 < rpifan> which is why im saying my ocmmunity
21:24 < ebowden> What about HIV?
21:24 < rpifan> ive got that too
21:24 < rpifan> ive got lots of things
21:25 < fenn> nmz787: i doubt it, usually things in that precision range use crossed roller linear bearings
21:25 < ebowden> Well shit.
21:25 < ebowden> You got drugs to control it?
21:25 < rpifan> i got all kinds of drugs
21:25 < rpifan> lol
21:25 < ebowden> So, antiretrovirals>
21:26 < ebowden> So, antiretrovirals?
21:26 < fenn> i call bullshit
21:26 < fenn> name some drugs you're taking
21:26 < rpifan> truvada
21:26 < rpifan> and isentress
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21:28 < rpifan> ive got other genetic issues tho
21:28 < rpifan> and ive just had cancer
21:29 < fenn> and brain damage
21:29 < rpifan> maybe a little
21:29 < rpifan> but nothing major
21:30 < rpifan> thye did just put me on adderal
21:30 < fenn> you said earlier that you had brain damage from a TMS treatment
21:31 < rpifan> u remember wow
21:31 < rpifan> well the mri that i got recently
21:31 < mrdata_> TMS shouldnt be invasive enough to do that
21:31 < rpifan> did show some kind of non specific brain thing
21:31 < rpifan> thats literally what they said
21:31 < mrdata_> you have some kind of non specific brain thing?
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21:32 < fenn> i agree with this assessment
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21:32 < mrdata_> syphilis can do this
21:32 < rpifan> yea thats literally what they said
21:32 < rpifan> well this was before the syphilis
21:32 < ebowden> HIV can cause brain damage.
21:32 < mrdata_> playing soccer can cause brain damage
21:33 < mrdata_> just look at how david icke turned out
21:33 < fenn> the UFO guy?
21:33 < rpifan> thats true
21:33 < rpifan> ive had hiv for a long time
21:34 < ebowden> How long was it uncontrolled for?
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21:34 < rpifan> since 2009
21:34 < rpifan> until about 3 years ago
21:34 < mrdata_> so about 5 years
21:34 < mrdata_> youre lucky to be alive
21:35 < rpifan> well
21:35 < rpifan> it wasnt uncontrolled
21:35 < rpifan> just unmedicated
21:35 < ebowden> That's uncontrolled.
21:35 < rpifan> it was monitored
21:35 < ebowden> Without medication, the virus will rip and tear through your body.
21:36 < rpifan> depends on the body and the strain
21:36 < ebowden> Who in the fuck would monitor someone with that deadly disease and not medicate them?
21:37 < rpifan> it was within the parameters
21:37 < rpifan> also my choice
21:38 < ebowden> You just didn't want to take medication?
21:38 < fenn> mrdata_: i'm reading the brief bio on wikipedia, david icke had psychological issues all through childhood
21:39 < rpifan> yea
21:39 < mrdata_> fenn, and here i thought the problem was getting knocked in the head too many times
21:39 < fenn> it could be due to multiple factors
21:40 < mrdata_> a buddy of mine met him
21:40 < mrdata_> in vancouver, during a book signing, a decade or so ago
21:40 < mrdata_> has some insights about him
21:40 < ebowden> rpifan, and how is your immune system now?
21:42 < rpifan> well i had cancer
21:42 < rpifan> so idk
21:48 < ebowden> What happened to your cognition whilst you were unmedicated and HIV positive?
21:53 < rpifan> i dont think anything changed
21:53 < rpifan> but how can i be sure
22:08 < rpifan> speaking of which tho
22:08 < rpifan> most mental stimulants
22:08 < rpifan> dont work for me
22:18 < nmz787> .title http://onlinelibrary.wiley.com/doi/10.1002/elps.201000617/full
22:18 < yoleaux> Electrolysis-reducing electrodes for electrokinetic devices - Erlandsson - 2011 - ELECTROPHORESIS - Wiley Online Library
22:19 < nmz787> "The ease-of-manufacture and small size of EOPs [electroosmotic pumps] are obvious advantages for their use in LOC systems; however, EOPs usually produce H2 and O2, H2O2 and/or H1 and OH at the electrodes [1–7]. All of these reactions are undesirable, as gases can quickly break the connection between the aqueous sample and an electrode, and H1, OH, and H2O2 can disturb sensitive materials (e.g.
22:20 < nmz787> proteins) being studied. Still, it is beneficial to integrate the electrodes intimately with the fluidic system as the plug-like electroosmotic flow (EOF) associated with EOPs exists only between the electrodes."
22:21 < nmz787> "By taking advantage of the electrochemical (EC) functionality of materials such as conjugated polymers (CPs) used in organic electronics, we have created EOPs that nearly eliminate the oxidation/reduction of solvent, without electroplating e.g. Ag from one electrode to another, and hence the production of EC byproducts or release of materials that could interfere with biological and chemical
22:21 < nmz787> samples. Using a blend of oxidized and reduced CP at each electrode means that electrochemistry, and hence fluid transport, begins at small applied potentials, as opposed to 2 V required for the case of Pt electrodes, making low-voltage battery-operated LOC devices easier to construct. It should also be noted that metal electrodes such as Pt, which often are considered to be inert, can undergo
22:21 < nmz787> chemical changes and even dissolve when used as electrodes to drive EOF [8]. The polymers used here have the additional advantage of being solution processable, that is to say that they can be cast from solution using, e.g., inkjet printing [9]. This combination makes these integrated pumps ideal for LOC applications, and also useful in a wide range of laboratory-scale systems."
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23:58 < ebowden> kanzure, got a list of papers on improving the photosystem?
--- Log closed Mon Oct 23 00:00:54 2017