--- Log opened Fri Apr 07 00:00:19 2017
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04:13 < kanzure> hm.
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04:24 < kanzure> Jen3: hi.
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04:25 < kanzure> hmph
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04:26 < Jen3> hey
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05:36 < JayDugger> Pfui.
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07:40 < archels> OpenCV build started...
07:40  * archels goes for a coffee
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10:18 < kanzure> you guys are boring
10:18 < JayDugger> This week's been a hard act to follow, you know.
10:20 < cevi_> big news - an outline of the third proof attempt (second serious attempt) for the CSP dichotomy conjecture was posted to the arxiv: https://arxiv.org/abs/1704.01914
10:20 < kanzure> .title
10:20 < yoleaux> [1704.01914] The Proof of CSP Dichotomy Conjecture
10:22 < kanzure> hm this seems to be useful for probabilistically checkable proofs
10:23 < cevi_> The other serious attempt was much more technical: https://arxiv.org/abs/1703.03021
10:28 < kanzure> https://www.nasa.gov/press-release/nasa-invests-in-22-visionary-exploration-concepts
10:28 < kanzure> http://ssi.org/ssi-exotic-propulsion-2017-niac-phase-1award/
10:29 < kanzure> "Evacuated Airship for Mars Missions, John-Paul Clarke, Georgia Institute of Technology in Atlanta"
10:29 < kanzure> "Dismantling Rubble Pile Asteroids with Area-of-Effect Soft-bots, Jay McMahon, University of Colorado, Boulder"
10:29 < kanzure> "Direct Multipixel Imaging and Spectroscopy of an Exoplanet with a Solar Gravity Lens Mission, Slava Turyshev, JPL"
10:30 < kanzure> https://www.nasa.gov/directorates/spacetech/niac/2017_Phase_I_Phase_II/
10:34 < cevi_> This one sounds promising: "A Synthetic Biology Architecture to Detoxify and Enrich Mars Soil for Agriculture"
10:37 < cevi_> have people finally stopped caring about contaminating Mars?
10:38 < JayDugger> Also http://ssi.org/ssi-releases-bpw2016-videos/
10:38 < JayDugger> from their Breakthrough Propulsion Workshop.
10:39 < kanzure> cevi_: http://diyhpl.us/~bryan/papers2/space/astrobiology/
10:42 < kanzure> musics https://www.youtube.com/watch?v=ajF2NOuYkjk&t=30m
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10:52 < kanzure> https://www.wired.com/2017/04/hackers-hijacked-banks-entire-online-operation/
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11:07 < cevi_> I'm not sure I trust any of these breakthrough propulsion workshop videos
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11:24 < nmz787_i> mega-dosed on vitamin D last night after getting a low test result back from a blood lab
11:25 < nmz787_i> http://ajcn.nutrition.org/content/87/3/688.abstract
11:25 < nmz787_i> .title
11:25 < yoleaux> Pharmacokinetics of a single, large dose of cholecalciferol
11:25 < nmz787_i> took 100k IU just as I started eating dinner
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11:25 < nmz787_i> feel pretty decent today, even though I got around 6.5 hours of sleep
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11:37 < kanzure> cevi_: also, not mars related, but there was a proposal in here for doing selective breeding of bacteria to survive space conditions
11:38 < nmz787_i> re: complaining about NSF-funded projects that failed to publish all data: "  Please refer your notice regarding the PI and his reporting to the division assigned for the award. They can be reached at the Division of Molecular & Cellular Biosciences  (BIO/MCB) (703) 292-8440  or at biowebmaster@nsf.gov. Thanks.   "
11:41 < nmz787_i> https://www.youtube.com/watch?v=kG1TUhYLAeM
11:41 < nmz787_i> .title
11:41 < yoleaux> $13.5M Moore Grant to Develop Working 'Accelerator on a Chip' Prototype - YouTube
11:41 < nmz787_i> https://www6.slac.stanford.edu/news/2015-11-19-accelerator-on-a-chip-grant
11:41 < nmz787_i> i can't remember if I already posted  on that, sorry if so
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11:48 < nmz787_i> cevi_: so you said your background was math and cs... and you'd heard of a few of those solver tools... so what kind of things are you into, hobby wise... really meaning, what are you up late on nights and weekends working on?
11:50 < cevi_> puzzle solving, mostly
11:52 < cevi_> for instance, http://www.chiark.greenend.org.uk/~sgtatham/puzzles/js/unequal.html on 10x10 size with difficulty set to recursive
11:52 < cevi_> one of those can take me up to a week
11:55 < cevi_> it's kind of a waste of time though, so recently I've switched to doing other things
12:01 < cevi_> I've also been reading up on AI and probabilistic graphical models
12:02 < cevi_> but I'm far from being an expert
12:14 < kanzure> http://diyhpl.us/~bryan/papers2/ai/
12:15 < kanzure> although personally i think more relevant to agi is http://diyhpl.us/~bryan/papers2/neuro/ and connectomes and stuff.
12:16 < cevi_> I've mostly taken up the strategy of following the recent deep learning trends passively - waiting for them to either run out of incremental innovations or come up with something amazing
12:16 < kanzure> (and brain emulation)
12:16 < cevi_> the arxiv postings make great bedtime reading
12:17 < cevi_> each is like 8 pages with pretty pictures and some simple mathematical model
12:18 < kanzure> i was working on a tensorflow/keras implementation of speech recognition for automatic conference talk transcription http://diyhpl.us/~bryan/papers2/ai/speech-recognition/
12:18 < kanzure> so that i don't have to manually produce this stuff anymore http://diyhpl.us/wiki/transcripts/
12:21 < cevi_> I'm sceptical of whole brain emulation
12:22 < cevi_> mostly because of what I've heard about the state-of-the-art with C. elegans
12:22 < kanzure> "it's a lot of work" is the complaint?
12:23 < cevi_> more that I don't think there is any chance of significant progress before 2030
12:24 < cevi_> or even 2050
12:25 < cevi_> but 2030 is generally the point where I stop trying to make predictions
12:25 < cevi_> I expect we should have quantum computing by then
12:26 < cevi_> that should change a lot of things
12:27 < cevi_> hopefully it makes both nanotech and biology much easier (but I've never seen anyone crunch the numbers on exactly how much quantum simulations will help with those - it's always just "a lot")
12:28 < kanzure> i don't recommend waiting around for that kind of speedup
12:29 < kanzure> protein folding simulation stuff just isn't going to be ready for a very long time
12:29 < kanzure> better to stick with known proteins, e.g. make a lego library of protein parts that are already known
12:29 < kanzure> connected by ligands and reprogrammable binding domains
12:30 < cevi_> sure, but if we want to know how the brain works we are sort of forced to do high-accuracy simulation of all the proteins that show up in nature
12:31 < kanzure> dna origami might be a better approach because the dna origami structures are more easily computationally predicted. also, some dna molecules are catalytically active similar to proteins (dnazymes).
12:31 < kanzure> also we can already create dna origami from polyhedral meshes
12:32 < kanzure> no you don't need protein simulation for brain emulation;   mostly we need more "modeldb" entries and the general network of neurons in the brain
12:32 < kanzure> someone manually did a large-scale neuroanatomy study but it's incomplete http://diyhpl.us/~bryan/papers2/neuro/cognitiveconsilience/stitched-diagram.png (warning: 3 MB image)
12:33 < kanzure> generally most of the neuron types in the human brain have already been physiologically characterized and turned into sets of algorithms
12:34 < kanzure> and for missing pieces you could substitute simpler neuron types..   i am not claiming this leads to a 100% realistic brain emulation, but we might not need that anyway.
12:34 < cevi_> I was under the impression that every few weeks a new paper comes out destroying the previous models of how individual neurons worked
12:35 < kanzure> for some parts of the brain, there are models that seem to work, although these are often uninteresting aspects, like audio encoding
12:35 < kanzure> i was about to say visual cortex things but it would be unfair to call that uninteresting..
12:35 < cevi_> audio encoding is uninteresting?
12:36 < cevi_> well, sure, compared to the language centers it probably is
12:36 < kanzure> audio signal processing is low on my priority list :P
12:37 < kanzure> maybe there are other stages of audio processing that are interesting, of course.
12:37 < kanzure> like later semantic stages or whatever. who knows.
12:37 < cevi_> I'd like to understand the mechanism behind "brain plasticity"
12:38 < cevi_> it doesn't seem essential for AI, but it seems awfully cool
12:38 < kanzure> there are many kinds of plasticity, but perhaps the most well studied is the one with AMPA receptors and its feedback cycle
12:40 < cevi_> maybe brain plasticity isn't the right phrase for what I'm thinking of
12:41 < cevi_> I mean the ability to hook up new types of sensory input and have them just become a part of you
12:41 < cevi_> or the ability to learn to control a robotic limb
12:42 < cevi_> I'd want some similar capability in an AI
12:45 < cevi_> possibly in a more abstract sense - you hand it a way to call a subroutine that can do gaussian elimination, and it makes that subroutine a part of itself in some automatic, subconscious way
12:46 < kanzure> this one is sorta-emulation sorta-not http://nengo.ca/
12:47 < kanzure> http://nengo.ca/build-a-brain/spaunvideos
12:47 < kanzure> if maaku was around then he would tell you he's more interested in goertzel's ideas for agi
12:48 < cevi_> this nengo thing seems farther along than I expected
12:49 < cevi_> I'm not sure what goertzel is doing - he seems awfully fixated on "weighted hypergraphs", but there doesn't seem to be any good reason to choose that particular architecture
12:49 < kanzure> maaku_: ping
12:49 < kanzure> maaku is probably busy at http://fc17.ifca.ai/bitcoin/schedule.html
12:50 < kanzure> and is therefore a slacker
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13:52 < NikopolSohru> Hello
13:55 < fenn> i'm surprised nasa funded "Mach Effects for In Space Propulsion" which is probably some kind of anti-gravity scheme
13:59 < cevi_> wikipedia's take: "Woodward also gave a video interview[78] for the TV show Ancient Aliens, season 6, episode 12.[79] However doubters do exist.[6]"
14:05 < fenn> i read a lot of woodward's papers and they never got below the level of uncertainty of whether the thrust effect was due to the purported thrust effect or if it was due to a heat differential like in a crookes radiometer
14:06 < fenn> yeah it would be great if it worked but he's been trying for 30 years
14:08 < chris_99> apparently the crookes radiometer only works because of air interestingly i always thought it was a vacuum
14:09 < chris_99> if you carry on pumping air out the effect doesn't work
14:11 < heath> would be nice to have a copy of this https://www.reddit.com/r/Scholar/comments/639q0r/article_categories_of_models_for_concurrency/
14:26 < fenn> nmz787_i: my brother is working on that project at SLAC, he says they already have a 1 meter long "plasma cell" that raises electron energy from 10GeV to 25GeV
14:26 < nmz787_i> fenn: awesome!
14:26 < fenn> presumably completely different technology though
14:27 < nmz787_i> I like the Thai saying 'same same, but different'
14:27 < fenn> i didn't get as much information as i would have liked, we were just talking in the car on the way back from visiting the computer history museum
14:28 < fenn> i think this is it https://portal.slac.stanford.edu/sites/ard_public/facet/research/Pages/rpwa.aspx
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14:39 < fenn> "I've never had a sense of smell, ever. I can't imagine what it would feel like to smell things, so I don't miss what I've never experienced."
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16:19 < kanzure> bloop
16:26 < kanzure> stalk mode https://twitter.com/readcoor/status/850464216284790784
16:26 < kanzure> i can only identify the ghost
16:26 < kanzure> hah where can i get the t-shirt
16:30 < kanzure> i guess i'll have to make my own, i'll put gmaxwell on one side and george church on the other
16:33 < kanzure> "Predicting properties of molecules with machine learning" https://research.googleblog.com/2017/04/predicting-properties-of-molecules-with.html?m=1
16:34 < kanzure> "Macrophages: micromanagers of antagonistic signaling nanoclusters" http://jcb.rupress.org/content/early/2017/03/21/jcb.201702028?papetoc https://twitter.com/JCellBiol/status/850432246117003265
16:40 < kanzure> http://www.eusynbios.org/blog/2017/4/3/building-a-genome-from-scratch-an-interview-with-dr-leslie-mitchell https://twitter.com/Dny_Q/status/850414539346726912
16:41 < kanzure> "Leslie Mitchell: The Sc2.0 consortium is certainly a unique collaboration. Each team agrees to work on an Sc2.0 chromosome of specific sequence, but has nearly total autonomy in devising a scheme for assembly. While the final product--the yeast cell encoding the designed chromosome--is open source to the research community, new ideas associated with DNA synthesis and chromosome assembly are...
16:41 < kanzure> ... completely owned by the partner group."
16:41 < kanzure> http://syntheticyeast.org/build-a-genome/course-description/
16:42 < kanzure> "With the decreasing cost of DNA synthesis, however, the commercial production of synthetic DNA in this size range became more cost effective in late 2012. The Spring 2013 B-A-G classundertook a new workflow to build 'minichunks', or ~3kb segments of synthetic DNA, from building blocks previously constructed in B-A-G or delivered from a synthesis company. In this workflow, students use '...
16:42 < kanzure> ...in yeasto' assembly, exploiting the native homologous recombination machinery in yeast to assemble minichunks. The minichunk assembly protocol was developed in collaboration with students of the Tianjin University "B-A-G China" course. In the spring semester of 2014, the Johns Hopkins B-A-G students started building ~10kb chunks from minichunks, also using yeast homologous recombination ...
16:42 < kanzure> ...as a cloning tool."
16:42 < kanzure> great, people are already using homologous recombination for assembly
16:47 < cevi_> hm, according to http://science.sciencemag.org/content/sci/suppl/2016/06/01/science.aaf6850.DC1/Boeke.SM.pdf the cost of ssDNA synthesis is significantly smaller than dsDNA???
16:52 < cevi_> I'm having a hard time understanding why you can't just fill in the other strand
17:00 < fenn> they used homologous recombination for assembling mycoplasma laboratorium
17:01 < fenn> i thought it was larger though, like 50kb
17:01 < kanzure> cevi_: they probably mean dsDNA synthesis and not ssDNA-then-dsDNA
17:02 < kanzure> i'm not sure why they call dsDNA synthesis "gene synthesis"
17:02 < kanzure> but i'll be going to their conference in may and i'll be sure to heckle them about tihs.
17:03 < fenn> .title http://www.pnas.org/content/105/51/20404.full
17:03 < kanzure> and yashgaroth is speaking, if anything he is now responsible for this type of shit they do
17:03 < yoleaux> One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome
17:07 < fenn> 17-35kb
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17:14 < kanzure> too big
17:14 < kanzure> we need closer to 100 bp
17:18 < cevi_> how often do you get several copies of the same 50 bp sequence in dna?
17:18 < kanzure> at the ends it's just lots of repeats
17:19 < cevi_> I could see having lots of repeats as an obstruction to being able to do dna assembly even in principle
17:20 < cevi_> if the repeated sequences are long enough
17:20 < kanzure> yes you need to specifically design homology sequences so that recombinases can match the ends of your dna fragments
17:20 < kanzure> (my above statement was about the ends of chromosomes)
17:21 < kanzure> thankfully it does not seem like repeated sequences are mandatory inside protein sequences
17:21 < kanzure> for regulatory elements like promoters and the surrounding dna, i'm less sure, that's a good question for yashgaroth
17:23 < kanzure> even if a repeating sequence is required in some random poor protein, you can either reposition it so that it's not near the end of a dna fragment, or you can probably engineer the repeating sequence out of it, like switching out which triplet code to use
17:23 < kanzure> one of the human genome project presentations last year was about removing a few of the triplet codes from the ecoli genome so that viruses are unable to infect the cells
17:24 < kanzure> http://diyhpl.us/wiki/transcripts/hgp-write/2016-05-10/recoding-ecoli-to-57-codons/
17:26 < cevi_> oh, that's a fun idea
17:27 < cevi_> what if we take it a step further, and completely rewrite the codon-to-protein translation system?
17:27 < kanzure> synthetic tRNAs have been done before, sure
17:27 < kanzure> they usually call that "expanding the genetic alphabet"
17:29 < cevi_> seems like - modulo a huge host of issues - this would give you instant immunity to all viruses
17:29 < cevi_> issues I'm imagining include dna folding incorrectly
17:29 < kanzure> in fact i proposed a method of using synthetic tRNAs for protein synthesis without requiring de novo DNA synthesis: https://groups.google.com/d/msg/enzymaticsynthesis/3YEEv0OULo0/zJZPETWDbMIJ
17:30 < kanzure> cevi_: yes that was george church's plan, he was calling it "multi-virus resistance"
17:30 < kanzure> ( http://diyhpl.us/wiki/transcripts/hgp-write/2016-05-10/ultra-safe-cell-line/ -- this presentation was by jef beoke, but it's an idea from george church)
17:31 < kanzure> ah wait here is where george talked about virus resistance http://diyhpl.us/wiki/transcripts/hgp-write/2016-05-10/from-recoli-to-1-million-genomes/
17:40 < cevi_> seems like an awful lot of work just to cure the common cold
17:41 < kanzure> just the common cold?
17:41 < cevi_> and all other viral diseases, as a side-effect
17:42 < kanzure> it's a good excuse to get genome synthesis costs down :)
17:43 < cevi_> I'm imagining a brief golden era of no viral disease before someone has the bright idea of porting some of the old viruses to the new genetic code
17:44 < cevi_> maybe we ought to give every child their own unique genetic code
17:46 < kanzure> a researcher will port viruses immediately, that's how you would test
17:46 < kanzure> well, one virus, not all of them at least.
17:47 < kanzure> i dunno about switching it up for everyone.  maybe not all the possible codon sequences will produce the same effects.  there's already some weird stuff about guanine bias or whatever.
17:49 < cevi_> ...a hundred years down the line, every virus comes with a collection of proteins which reverse engineer the genetic code used in this particular cell and translates itself into the new code...
17:50 < kanzure> perhaps instead the viruses will have their own bootstrapping proteins, like some ribosomes and other materials. the trick would be packaging all the required proteins into the virus capsid.
17:50 < cevi_> it would definitely make the virus do more work
17:51 < cevi_> maybe enough that being a virus is just no longer profitable
17:52 < fenn> hurr what
17:52 < fenn> "Our team is happy to announce that Elton Nixon donated 74,888 acres of land situated in west of Blythe, California." crowdmars.com
18:05 < cevi_> another side effect of switching up the genetic code differently for everyone: no more unwanted pregnancies!
18:06 < fenn> .wik xenogenesis
18:06 < yoleaux> "Disambiguation: Xenogenesis" -- https://en.wikipedia.org/wiki/Xenogenesis
18:08 < fenn> take a bite out of virology
18:09 < fenn> in the meanwhile there's still https://en.wikipedia.org/wiki/DRACO
18:10 < fenn> eCD4Ig is a generally applicable vaccine concept as well
18:11 < fenn> you could rotate the codons such that AT/GC ratios remained constant
18:11 < fenn> you'd only rotate coding regions anyway, because promoters etc recognize dna sequences, not amino acid sequences
18:13 < kanzure> ah.
18:14 < fenn> only a problem when a promoter sequence is embedded in a coding sequence
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18:43 < kanzure> "Integrated computational guide design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments" http://biorxiv.org/content/early/2017/04/07/125245 https://twitter.com/biorxivpreprint/status/850408082509352960
18:43 < kanzure> ".. using arrayed or pooled lentiviral libraries of single guide RNAs (sgRNAs)"
18:44 < kanzure> https://twitter.com/CRISPR_papers
18:47 < kanzure> "Delivery technologies for genome editing" http://www.nature.com/nrd/journal/vaop/ncurrent/full/nrd.2016.280.html
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19:01 < kanzure> yashgaroth: why is dsDNA synthesis called "gene synthesis" by the hgp-write people?
19:02 < yashgaroth> mostly arbitrary, but generally when people want DNA synthesized it's for a gene, and there ain't much use for ssDNA by itself
19:05 < kanzure> but why are they synthesizing dsDNA and not ssDNA?
19:05 < yashgaroth> you can synthesize ssDNA but it's much easier to work with when it's double-stranded, since there's much less secondary structure...loops, hairpins etc
19:06 < kanzure> so they are synthesizing dsDNA?
19:06 < kanzure> i mean... i can't tell if they are doing ssDNA first and then making dsDNA and calling it "dsDNA synthesis".
19:06 < yashgaroth> depends on the method; also it needs to be dsDNA for cloning and stuff
19:07 < yashgaroth> "gene synthesis" is the generic term that everyone uses, not just gp-write
19:08 < yashgaroth> mostly to contrast with oligo synthesis, since primers are also a popular product, so "DNA synthesis" is ambiguous
19:09 < kanzure> well, i never saw a phosphoramidite oligonucleotide synthesis method that makes dsDNA directly..
19:09 < yashgaroth> yeah pamidite is all ssDNA, not sure how much secondary structure there is in that reaction since it's got all kinda chemicals in there
19:10 < yashgaroth> once you're done with a fragment you can just slap on a primer and polymerize the second strand, so there's not too much point
19:45 < kanzure> "Delivery technologies for genome editing" http://diyhpl.us/~bryan/papers2/gene-therapy/Delivery%20technologies%20for%20genome%20editing%20-%202017.pdf
19:53 < kanzure> this is a nice review.
19:56 < kanzure> "Cas9 from Staphylococcus aureus (SaCas9) is ~1kb shorter than SpCas9 and can edit the mammalian genome[96]."
20:03 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=42d1e1b3 Bryan Bishop: mention meganucleases >> 
20:04 < kanzure> boom http://diyhpl.us/wiki/gene-editing/
20:06 < kanzure> what was that other review paper i was looking at
20:06 < kanzure> ah,
20:06 < kanzure> "Programmable genome editing tools and their regulation for efficient genome engineering" http://www.sciencedirect.com/science/article/pii/S2001037016300770
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20:10 < kanzure> "targetrons: Group II introns: mobile ribozymes that invade DNA"
20:10 < kanzure> wtf.
20:11 < gnusha_> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=db34e8df Bryan Bishop: also mention targetrons, apparently >> http://diyhpl.us/diyhpluswiki/gene-editing/
20:12 < kanzure> "... The LAGLIDADG family of meganucleases have been extensively studied and applied as genome editing tools [43,44,45,99-101]." who names this stuff
20:13 < yashgaroth> looks like an amino acid sequence, but at least they didn't give it some cutesy name
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21:21 < kanzure> other review i was looking at was "Non-viral nucleic acid delivery strategies to the central nervous system" i guess.
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23:33 < nmz787_> kanzure: do you know any MEMS/microfluidics engineers/consultants for hire? that you could pay to help me? since you can't find a chemist at the moment.
23:34 < nmz787_> I need to talk shop with someone who knows valves
23:35 < nmz787_> like which of the 10+ varieties to use (or start with), etc
--- Log closed Sat Apr 08 00:00:20 2017