--- Log opened Mon Jan 12 00:00:03 2015
--- Day changed Mon Jan 12 2015
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03:13 < archels> https://github.com/screenfreeze/deskcon-desktop/issues/23
03:13 < archels> (inappropriate lol)
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05:46 < delinquentme> http://motherboard.vice.com/read/silk-road-reloaded-i2p
05:50 < kanzure> isn't this the second "silk road reloaded"
05:50 < kanzure> e.g. not the one that people think?
05:51 < eudoxia> i thought we were at number three now?
05:51 < eudoxia> or is it a tree of silk roads rather than a linear chain?
05:52 < chris_99> yeah there was a silk road 2 wasn't there, so you're probably right about it being the 3rd
05:58 < kanzure> silk road 3 is something else
05:58 < kanzure> see https://news.ycombinator.com/item?id=8871465
05:59 < archels> why does Silk Road get all the credit? there are dozens of thriving darknet markets our there
05:59 < archels> is it anything more than a ripped-off name at this point?
06:00 < chris_99> nope
06:00 < kanzure> "It's not even the first site to be called 'Silk Road Reloaded'. The name is also a blatant effort to fool newbies and claim unearned credit."
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06:26 < kanzure> fenn: what are the options for deep sea network communication?
06:27 < cuba_> very low frequencies are used with km long antennas
06:27 < cuba_> or floating devices with satelite communications
06:27 < cuba_> for subs it is of course not bidirect
06:28 < kanzure> iirc there's no good way for 2 km depth communication other than fiberoptics
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06:32 < cuba_> most likely kanzure
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06:35 < kanzure> well what are the theoretical designs here
06:35 < kanzure> orionsarm doesn't seem to have any deep sea wormhole nonsense
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06:35 < kanzure> haha the merkle gear http://orionsarm.com/im_store/technologymain.jpg
06:37 < kanzure> all they got is http://www.orionsarm.com/eg-article/490b3010a681a
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06:45 < kanzure> "A deep sea telescope for high energy neutrinos" http://arxiv.org/pdf/astro-ph/9907432.pdf
06:46 < kanzure> progress update http://arxiv.org/pdf/0711.0563.pdf
06:49 < kanzure> .wik KM3NeT
06:49 < yoleaux> "KM3NeT, an acronym for Cubic Kilometre Neutrino Telescope, is a future European research infrastructure that will be located at the bottom of the Mediterranean Sea." — http://en.wikipedia.org/wiki/KM3NeT
06:50 < kanzure> "KM3NeT will search for neutrinos from distant astrophysical sources like supernova remnants, gamma-ray bursts, supernovae or colliding stars and will be a powerful tool in the search for dark matter in the universe. Its prime objective is to detect neutrinos from sources in our Galaxy. Arrays of thousands of optical sensor modules will detect the faint light in the deep sea from charged particles originating from collisions of the ...
06:50 < kanzure> ... neutrinos and the water or rock in the vicinity of the detector. The research infrastructure will also house instrumentation for other sciences like marine biology, oceanography and geophysics for long term and on-line monitoring of the deep sea environment and the sea bottom at depth of several kilometres."
06:50 < kanzure> "The full neutrino telescope will contain in the order of 12000 pressure-resistant glass spheres attached to about 600 strings - vertical structures with a height of almost one kilometer. Each glass sphere will contain 31 photomultiplier tubes and will be connected to shore via a high-bandwidth optical network. At the shore of each KM3NeT installation site, a farm of computers will perform the first data filter in the search for the ...
06:50 < kanzure> ... signal of cosmic neutrinos, prior to streaming the data to a central KM3NeT data centre for storage and further analysis by the KM3NeT scientists."
06:50 < kanzure> .wik ANTARES (telescope)
06:50 < yoleaux> "ANTARES is the name of a neutrino detector residing 2.5 km under the Mediterranean Sea off the coast of Toulon, France. It is designed to be used as a directional Neutrino Telescope to locate and observe neutrino flux from cosmic origins in the direction of the Southern Hemisphere of the Earth, a complement to the southern hemisphere  …" — http://en.wikipedia.org/wiki/ANTARES_(telescope)
06:52 < kanzure> "On the other hand, water contains more sources of background light than ice (radioactive isotopes potassium-40 in the sea salt and bioluminescent organisms), leading to a higher energy thresholds for ANTARES with respect to IceCube and making more sophisticated background-suppression methods necessary."
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06:59 < kanzure> "NEMO-Ovde: a submarine station for real-time monitoring of acoustic background installed at 2000 m depth in the Mediterranean Sea" http://arxiv.org/pdf/0804.2913.pdf
07:01 < kanzure> "The stored data library, consisting of more than 2000 hours of recordings, is a unique tool to model underwater acoustic noise at large depth"
07:03 < kanzure> "Recent Results from the ANTARES Neutrino Telescope"
07:03 < kanzure> "Recent Results from the ANTARES Neutrino Telescope" http://arxiv.org/pdf/1211.5516.pdf
07:03 < kanzure> page 1 figure 1 good diagram
07:10 < kanzure> http://antares.in2p3.fr/Gallery/selected.html
07:13 < kanzure> http://antares.in2p3.fr/Gallery/3D/Aguilar/posterCentralv4_lowquality.jpg
07:13 < kanzure> others http://antares.in2p3.fr/Gallery/3D/index.html
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08:21 < fenn> 09:08 <@SketchCow> Ted Cruz just got in charge of NASA, NOAA, and NSF
08:21 < fenn> 09:08 <@SketchCow> Lot of stuff could be disappearing.
08:23 < kanzure> hmm. well none of that is ncbi, so our genomes are safe.
08:24 < fenn> ok maybe that was inaccurate. he's chair of "ubcommittee on Space, Science, and Competitiveness
08:26 < fenn> they added "competitiveness" just now
08:28 < justanotheruser> paperbot 0131896431
08:28 < justanotheruser> paperbot isbn:0131896431
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08:37 < fenn> ceci paperbot est mort, vive paperbot en direct
08:40 < kanzure> i am trying to figure out if "nobody can remotely operate deep sea mining vehicles (like from the safety of coasts) and this is why nobody is mining sea stuff" is true
08:40 < fenn> it's hard to get permission to do seafloor mining
08:41 < kanzure> from who?
08:41 < kanzure> i meant communication physics stuff
08:41 < fenn> http://szabo.best.vwh.net/miningthevastydeep.html
08:41 < kanzure> god damn it szabo
08:42 < fenn> communication is not the problem; if you're transmitting power you can transmit data too
08:42 < kanzure> i had assumed nuclear deep sea vehicles because everything else is more inconvenient
08:43 < fenn> "Disputes over who owns what in the ocean have been a fact of global politics for decades. For reasons of security, potential resources and sometimes just pride, countries are constantly claiming control over new chunks of underwater property. As an indicator of just how rare it is to be able to mine hassle-free in the ocean, the exploration licence Papua New Guinea granted Nautilus was a world
08:43 < fenn> first."
08:43 < kanzure> was that an oil exploration license? or just a general exploration license?
08:43 < fenn> that was written in 2007; i think nautilus never actually got anywhere
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08:44 < fenn> they were doing manganese nodules i think
08:45 < kragen> I think it is true that nobody can remotely operate deep-sea mininng vehicles from the safety of coasts
08:46 < kragen> I mean, unless you lay a cable to the coast
08:46 < fenn> "seafloor massive sulfides ... Elements of potential commercial interest in both the modern and ancient deposits are copper, zinc, lead, silver, gold and barium."
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08:47 < kragen> seawater strongly attenuates radio waves above ELF and sound above the audible, neither of which have enough bandwidth for a live video feed
08:48 < fenn> well someone has to actually throw the ROV in the water, and since they all require electricity to function (no nuclear reactors yet, unfortunately) that means there must be a ship overhead with generators. and once you have all that, you might as well add a shipping container for a portable ROV control center
08:48 < justanotheruser> kanzure: pls get libgen back up asap
08:48 < kanzure> er, how do the subs work?
08:48 < kanzure> justanotheruser: way ahead of you
08:48 < kanzure> i thought subs had reactors
08:48 < kanzure> or am i remembering warhammer and not reality?
08:48 < fenn> commercial ones dont
08:49 < fenn> there are only like 50 nuclear subs anyway
08:49 < kragen> subs have had reactors since the 1960s, yes
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08:49 < kragen> but building your own nuclear sub would be very challenging because of anti-proliferation
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08:50 < fenn> carring a ton of peroxide and fuel cells is probably feasible though
08:50 < kragen> yeah, you can probably do that.  or even just liquid oxygen
08:50 < kragen> which is both cheaper and less dangerous than peroxide
08:50 < fenn> if you say so
08:50 < kanzure> how long does hte longest storm tend to last
08:51 < kanzure> also it may not make sense to make everything designed to surface for fueling
08:51 < kanzure> or maintenance
08:51 < fenn> sure you could just drop fuel+oxygen tanks
08:51 < kanzure> well i mean pressure/density transition impacts on materials, etc.. there's design issues.
08:51 < fenn> but still, if you're doing mining eventually you want to surface something, and the more refining you do on the seafloor the more expensive it gets
08:52 < kragen> if you had an undersea neutrino telescope maybe you could send a video feed via neutrino beams
08:52 < kragen> kanzure: typically less than a week I think
08:52 < kanzure> that's just detection of neutrinos not neutrino transmission
08:52 < fenn> i dont think the pressure transition is a big problem for machines
08:52 < kragen> making neutrinos is pretty easy
08:53 < kragen> it's detecting them that's hardd
08:53 < kragen> fucking shitty keyboard
08:53 < fenn> i assumed that's why he was reading about neutrino telescopes
08:53 < kanzure> eh mostly because i was confused about why i am not familiar with deep sea communication technologies
08:53 < kragen> yeah
08:54 < justanotheruser> what happened to paperbot?
08:54 < justanotheruser> did he die?
08:54 < fenn> there's VLF radio and acoustic modems and fiber optics and electric cables, and that's it
08:54 < kragen> typical deep-see communication technology is "three-hundred-mile-long ELF antennna to broadcast an encrypted command to surface for higher-bandwidth communication"
08:54 < kragen> sea
08:54 < kragen> I can't blame that one on the keyboard
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08:54 < kragen> or ultrasound
08:55 < kragen> but sound is not stealthy, so nuclear subs don't like it, and ultrasound is short-range
08:55 < fenn> acoustic can get pretty good bitrates at less than a few km range
08:55 < kragen> yes
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08:55 < fenn> there's a lot of impedance mismatches in seawater due to thermal and saline gradients
08:56 < kragen> and acoustic has this massive advantage around the thermocline
08:56 < kragen> it's self-focusing
08:56 < fenn> sure, if you're transmitting sideways
08:56 < kragen> right
08:56 < kragen> so you don't get inverse-square falloff
08:56 < fenn> a sonobuoy is super cheap though, for a stationary mining operation
08:56 < jrayhawk_> window 4
08:56 < jrayhawk_> whoops
08:57 < kanzure> justanotheruser: libgen.org person died, paperbot was using libgen a bunch, nobody has fixed paperbot
08:57 < jrayhawk_> died?
08:57 < fenn> will someone please think of the robots
08:57 < justanotheruser> oh really? I thought they just moved to .info
08:57 < fenn> lonely hungry orphan robots
08:57 < justanotheruser> and .info is down now
08:58 < kanzure> there are many libgen mirrors
08:58 < kanzure> hard to tell
08:58 < kanzure> they may or may not be mirrors operated by other people
08:58 < justanotheruser> well I went to .org, it was down, thought I had the wrong tld, googled libgen and found libgen.info and it 404d
08:58 < kanzure> your method is silly
08:58 < kanzure> there's a fairly exhaustive list of mirrors in hplusroadmap logs, though
08:58 < fenn> a link to the list, not the list itself
08:58 < justanotheruser> what happened to the libgen.org runner?
08:59 < kanzure> he died
08:59 < kanzure> what's so hard to understand about htis
08:59 < fenn> he was assassinated by a crack team of elsevier commandos
08:59 < kanzure> he ceased to be among the living. he is no more. he is as dead as a parrot watching monty python sketches.
08:59 < justanotheruser> I mean, was it an aaron swartz type thing?
08:59 < kanzure> aaron swartz is also dead, that's certainly true...?
09:00 < justanotheruser> please
09:00 < kanzure> .title https://www.youtube.com/watch?v=Oj8RIEQH7zA
09:00 < yoleaux> Pet Shop (Dead Parrot) - Monty Python - YouTube
09:01 < justanotheruser> kanzure: when did he die?
09:01 < justanotheruser> I used it like 3 months ago
09:02 < justanotheruser> I can't find anything on google on libgen.org shutting down
09:02 < fenn> libgen is run by a group but the domain name was the weak link because only one person had "the legal right" to the domain (or so i am informed)
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09:02 < fenn> and that person died
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09:02 < fenn> that's all the info i have
09:03 < justanotheruser> fenn: yeah, that's mostly what I was confused about, how the domain could go away so easily when they died
09:03 < jrayhawk_> iomobil was the name, apparently
09:05 < justanotheruser> hmm
09:05 < jrayhawk_> libgen.in looks to still work
09:07 < kanzure> huh that video looks all wrong to me
09:07 < kanzure> .title https://www.youtube.com/watch?v=npjOSLCR2hE
09:07 < yoleaux> The Parrot Sketch - Monty Python's The Flying Circus - YouTube
09:07 < kanzure> there we go. what the hell was that other thing?
09:07 < fenn> libgen.in shows these mirrors: gen.lib.rus.ec - 1M (only search) bookfi.org libgen.net - 1M bookzz.org (bookza.org, bookos.org) http://u76v7ha6j4jmtz3k2lseaso5qy36lxs77klhovmptufwcodovatq.b32.i2p/
09:07 < kanzure> there are others
09:08 < justanotheruser> thanks
09:08 < justanotheruser> too bad about iomobil
09:11 < kanzure> anyway you guys should just fix paperbot instead of complaining like this
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09:11 < fenn> cancer apparently. too bad he couldn't share the dns password before dying
09:11 < fenn> anyway it's just a domain name
09:14 < fenn> IP address of libgen.in is 95.31.43.252
09:16 < kanzure> does it have the same php endpoints that paperbot was using
09:16 < kanzure> go get the one that ParahSailin checked the other day
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09:33 < kanzure> "don't think of it as work, just as happy fun paper coding time"
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09:44 < the8thbit|work> archels: Is it possible to cross compile the neuroML2 NEURON plugin using nrnocmodl? nrnocmodl depends on make, and my target does not have make.
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10:09 < kanzure> "3 Letter Agency - Volume 114 - Stolen Mkultra Mix" electronic music sure has got weird
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10:12 < archels> good question, don't know
10:13 < archels> can you use anything other than NEURON?
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10:27 < the8thbit|work> archels: I just want to run and interact with the openworm neuroML2 files from the command line. I didn't know there were alternatives to NEURON for doing that
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10:30 < FAMAS> greetings
10:34 < the8thbit|work> hello FAMAS
10:35 < archels> I think there are some alternatives
10:35 < FAMAS> anyone here who built their own serology lab?
10:35 < archels> although the OpenWorm team use NEURON themselves, that might be the easiest to bootstrap
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10:37 < archels> cross-compiling should be possible with NEURON
10:39 < the8thbit|work> archels: I can crosscompile NEURON itself, and have done so, but I don't know about the plugin files
10:40 < the8thbit|work> archels: nrnocmodl only seems to have three flags, -i, -f, and -r... nothing about setting a host file for configuration\
10:40 < the8thbit|work> er
10:40 < the8thbit|work> *host machine
10:43 < FAMAS> anyone here who built their own serology lab?
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10:44 < kanzure> FAMAS: you should wait longer for a reply
10:44 < archels> you might need to look into nrnivmodl instead
10:44 < archels> and cross-compile nrnivmodl for the target platform
10:44 < archels> (at least I think that's right)
10:53 < the8thbit|work> archels: I believe everything with iv in it depends on X, which I dont have on the target, and would rather not pull in
10:54 < the8thbit|work> archels: Oh, nevermind
10:54 < the8thbit|work> I have the iv version installed on the target too, and it runs
10:54 < the8thbit|work> but
10:54 < the8thbit|work> I get the same 'make: command not found' error
10:58 < the8thbit|work> same flags availible...
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11:20 < the8thbit|work> archels: I tried building nrnivmodl for amd64 , and running it with my cc envs sourced... wasn't surprised that it didnt work lol
11:21 < the8thbit|work> libtool: compile: unable to infer tagged configuration
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11:38 < heath> more random input from myself: i don't think it's possible to implement Know Your Customer without violating a user's privacy
11:50 < kanzure> .title https://www.mail-archive.com/qemu-devel@nongnu.org/msg273404.html
11:50 < yoleaux> [Qemu-devel] [RFC PATCH v7 00/21] Deterministic replay core
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13:55 < kanzure> http://www.cato-unbound.org/2014/12/01/david-brin/seti-meti-paradox-extraterrestrial-life-there-libertarian-perspective
13:55 < kanzure> http://www.cato-unbound.org/2014/12/03/robin-hanson/should-earth-shut-hell
13:55 < kanzure> http://www.cato-unbound.org/2014/12/24/robin-hanson/adapted-aliens
13:58 < the8thbit|work> oh lol
13:59 < the8thbit|work> The anti-robot question in NEURON's forum registration form is "The _______ equation relates the equilibrium potential of an ionic species to its intracellular and extracellular concentrations"
14:01 < the8thbit|work> and copying and pasting that into google gives you the answer as literally the first result
14:01 < the8thbit|work> its more of an anti-human question
14:19 < the8thbit|work> kanzure: I dont want cato in my browser history
14:19 < jrayhawk_> Robin Hanson is a pretty cool guy and you should not feel ashamed for reading him.
14:20 < jrayhawk_> david brin less so
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15:01 < delinquentme> http://www.computerworld.com/article/2867040/new-service-wants-to-rent-out-your-hard-drives-extra-space.html
15:01 < delinquentme> kanzoo
15:01 < delinquentme> are you caffinated?
15:01 < delinquentme> GOOD.
15:03 < kanzure> taking a while for the adderall to kick in
15:05 < delinquentme> turkey baste it?
15:05 < delinquentme> LEL!
15:16 < delinquentme> kanzure, so the code wasnt horrible
15:16 < delinquentme> &nbsp simply because I wanted to keep styling min. as its all 1 page
15:23 < kanzure> weren't you using jquery
15:29 < delinquentme> yeap
15:29 < delinquentme> suggestions?
15:29 < delinquentme> im about to drink moar coffee
15:29 < delinquentme> kanzure, can we devote a singular prayer to Xenu
15:30 < delinquentme> 3d robotics. They must make offer !
15:33 < kanzure> jquery is pretty bloaty
15:33 < kanzure> consider zepto.js or something
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15:38 < delinquentme> OH GREAT XENU GOD OF THOM CRUZ
15:38 < delinquentme> WE PRAY IN THE NAME OF SPATULA
15:38 < delinquentme> TABERNACLE.
15:38  * delinquentme removes snip of fetlock
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16:00 < ElGalambo_> since coenzyme q10 is quite expensive, what is the lowest effective dose I should take?
16:02 < kanzure> https://news.ycombinator.com/item?id=8873250
16:02 < kanzure> "GPU cores are tiny because the problems they deal with are "embarrassingly parallel", trivially solved by throwing more cores at the problem. You make the cores as simple as possible so you can have thousands of them on a chip. Modern GPUs don't even have SIMD units per core any more; both NVidia and AMD are completely scalar now. You'd think that graphics would be the perfect scenario for SIMD, since shaders spend so much time dealing ...
16:03 < kanzure> ... with 3 and 4D vectors, transformation matrices, colors, and so on, but it worked out that the gain in throughput and instruction density per-core was outweighed by the power, heat, and die cost of having parts of those thousands of SIMD units sitting idle while working on data that doesn't take up a whole SIMD register. And because context switches are much rarer on GPUs than CPUs, they can have extremely deep pipelines that push ...
16:03 < kanzure> ... compute efficiency even further, at the expense of context switch latency."
16:03 < kanzure> "CPU cores are, if I may, "fuckhuge", because by and large they can't solve their problems by throwing more cores at them. They take on problems that are inherently serial and branch heavy, like compiling a program or optimally compressing a large file, and throw bigger cores at them (out-of-order execution, branch prediction, speculative execution, multiple ALUs per core, instruction schedulers that exploit the parallelism hidden in the ...
16:03 < kanzure> ... serial instruction stream, large register files only visible to the microarchitecture, etc) while maintaining a fairly short pipeline so that branch prediction failures and context switches don't take too long to recover from. SIMD fits in well here, because the cost of bigger and bigger ALUs is pretty much insignificant compared to all the other hardware that goes into a high-end CPU core. It can be a pain to optimize for, but it's ...
16:03 < kanzure> ... great for middle-ground tasks that need both heavy parallel and serial/branch-heavy computing resources with little latency between the two, like video compression."
16:03 < the8thbit|work> halp im drowning in all this text
16:03 < the8thbit|work> halp
16:03 < delinquentme> ElGalambo_, Munkholm H, Hansen HH, Rasmussen K:Coenzyme treatment in serious heart failure. Biofactors 9(2-4): 285-289, 1999.
16:04  * delinquentme throws ramen at the8thbit|work 
16:04  * delinquentme ( only 1 packet )
16:04  * delinquentme ( and its stale )
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16:05 < the8thbit|work> mmmm dry stale noodles...
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16:05 < delinquentme> steep for 4-6 minutes
16:05 < kanzure> the8thbit|work: you wouldn't happen to know how the magic of mRNA display works, eh?
16:05 < the8thbit|work> mRNA display?
16:06 < the8thbit|work> I dont even know wtf that is
16:06 < ElGalambo_> kanzure, look up nvidia tesla. also this explains why brute force computing like bitcoin mining is much faster on gpus
16:06 < kanzure> so you're saying there's a chance?
16:06 < kanzure> bitcoin mining is not significantly faster on gpus than asics
16:06 < the8thbit|work> kanzure: Hes comparing CPUs to GPUs
16:06 < ElGalambo_> kanzure, no I mean in comparison with cpus
16:06 < delinquentme> kanz is making 4k displays by using controlled flourescence synthesis for RGB
16:07 < kanzure> you mean nmz787
16:07 < delinquentme> biological TVs
16:07 < kanzure> no that's anselm
16:07 < kanzure> well, biological TVs and less smelly vaginas
16:07 < kanzure> i assume the vagina yeast thing is a side project
16:07 < the8thbit|work> so can I have sex with it then
16:07 < delinquentme> I dont care so long as I have a flexible HD display embedded in my thigh by next christmas
16:08  * delinquentme tests his butthole biome
16:08 < delinquentme> tastes a little sweet ?
16:08 < delinquentme> should I get that tested?
16:08 < the8thbit|work> you should get that tweeted
16:10 < kanzure> yashgaroth: so why in principle should cells be more difficult to work with anyway.. just kill off the offenders?
16:11 < kanzure> like http://diyhpl.us/~bryan/papers2/microfluidics/Ultrahigh-throughput%20screening%20in%20drop-based%20microfluidics%20for%20directed%20evolution%20-%202010.pdf
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16:11 < delinquentme> I *truly* love fixed-width fonts
16:13 < kanzure> "In total, we screen ∼10^8 individual enzyme reactions in only 10 h, using <150 μL of total reagent volume; compared to state-of-the-art robotic screening systems, we perform the entire assay with a 1,000-fold increase in speed and a 1-million-fold reduction in cost."
16:18 < kanzure> here's someone doing it with a cell-free protein synthesis reaction http://pubs.rsc.org/en/content/articlelanding/2012/lc/c2lc21035e#!divAbstract
16:19 < kanzure> i forgot about http://diyhpl.us/~bryan/papers2/paperbot/Cell-free%20protein%20synthesis%20from%20a%20single%20copy%20of%20DNA%20in%20a%20glass%20microchamber.pdf
16:21 < kanzure> evaporative cooling to freeze biological samples in microfluidic devices http://scitation.aip.org/content/aip/journal/rsi/86/1/10.1063/1.4905184
16:21 < kanzure> hmm.
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16:21 < kanzure> why would they only run that for just 10 hours anyway?
16:31 < delinquentme> current best website for PDF text books?
16:31 < delinquentme> libgen << DOWN
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16:42 < kanzure> hmm if my "use cells as reagents in oligonucleotide synthesis" thing (+ directed evolution) has a chance of working then you might as well also do extracellular cell-assisted pcr too
16:43 < AmbulatoryCortex> i understood some of those words
16:43 < kanzure> pcr is just "use some polymerase and reagents to copy dna molecules"
16:44 < kanzure> but you have to buy and maintain mastermix
16:44 < kanzure> and.. stuff..
16:44 < kanzure> anyway it's just inconvenient
16:45 < delinquentme> dj kanzoo
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16:48 < kanzure> https://www.youtube.com/watch?v=9OnIXIVBUMc
16:48 < kanzure> eh nevermind
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16:53 < kanzure> "Cell extract - or lysate-derived systems for protein synthesis - continue to be exploited and optimized, with the traditional wheat germ, rabbit reticulocyte and E. coli lysates being extended with Leischmanii (Kovtun et al. 2011), Thermus (Zhou et al. 2012) and even human (Mikami et al. 2008) cell-free systems."
16:54 < kanzure> "Ribosomal protein synthesis (both cellular and cell-free) is characterized by exceptionally high fidelity, with an amino acid misincorporation frequency of approx. 0.01%, even at high elongation rates (20 residues/s)(Yadavalli and Ibba 2012). This makes it possible to accurately produce extremely large proteins (up to 3.5 MDa)(LeWinter and Granzier 2010) by these biochemical methods. ‘Cell factories’ are able to perform the complete ...
16:54 < kanzure> ... metabolic transformation of simple nutrients (inorganic salts and carbon fuels) into protein products. Cell-free systems require input of pre-formed amino acids, but provide other advantages described above. Solid phase chemical synthesis of proteins can in principle be used to produce polypeptides with a virtually unlimited range of building blocks and stereochemistry, but requires protected amino acid derivatives, is relatively ...
16:54 < kanzure> ... slow (approx. 15 min per coupling cycle) and the relatively high error rate (maximum coupling efficiency approximately 99% per cycle) (Merrifield 1997) places a practical limit on the size of the protein product that can be formed (Table 1)."
16:54 < kanzure> from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553302/
16:57 < kanzure> .title http://www.pnas.org/content/106/10/3865.short
16:57 < yoleaux> Directed evolution of adeno-associated virus to an infectious respiratory virus
16:57 < kanzure> yikes "We used directed evolution in an organotypic human airway model to generate a highly infectious adeno-associated virus. This virus mediated gene transfer more than 100-fold better than parental strains and corrected the cystic fibrosis epithelial Cl− transport defect. Thus, under appropriate selective pressures, viruses can evolve to be more infectious than observed in nature, a finding that holds significant implications for ...
16:58 < kanzure> ... designing vectors for gene therapy and for understanding emerging pathogens."
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17:11 < kanzure> huh apparently my idea of cell-mediated chemical reactions is not very well studied http://diyhpl.us/~bryan/papers2/bio/directed-evolution/Combining%20bio-%20and%20chemo-catalysis:%20from%20enzymes%20to%20cells,%20from%20petroleum%20to%20biomass.pdf
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18:01 < bbrittain> current status: pretending that I'm a large hardware company to get a datasheet for an LCD monitor :/
18:01 < bbrittain> where is the underground market for this shit?
18:01 < kanzure> bbrittain: big co and associates
18:02 < kanzure> shenzhen
18:02 < kanzure> it's above ground though
18:02 < kanzure> bbrittain: does ginkgo do much "directed evolution" stuff?
18:03 < bbrittain> goddamn, I love china. It's so easy to get hardware there
18:03 < bbrittain> they totes try to scam me though :?
18:03 < bbrittain> :/
18:03 < bbrittain> kanzure: very little I think.
18:03 < kanzure> hm ok
18:03 < bbrittain> why?
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18:04 < kanzure> trying to figure out why nobody has bothered investigating cell-mediated chemical reactions
18:04 < kanzure> probably because nobody has single cells isolated well enough to try
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18:07 < bbrittain> hmmm. I found a similiar LCD, I just gonna pretend they kept the interface the same
18:07 < bbrittain> we'll see if I blow it up :D
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18:30 < AmbulatoryCortex> maybe if you got your hands on one of those gigantic amoebas from the seafloor
18:32 < AmbulatoryCortex> those would be pretty easy to isolate, if you could keep them alive
18:32 < kanzure> why those amoeba?
18:32 < AmbulatoryCortex> they're macroscopic
18:32 < AmbulatoryCortex> considerably so
18:32 < kanzure> but why does that matter?
18:33 < AmbulatoryCortex> you were wondering about isolating single cells
18:35 < kanzure> cell isolation is not problem
18:35 < kanzure> quite common procedure
18:35 < kanzure> you can shove them into a narrow channel and force them to separate, for example
18:39 < AmbulatoryCortex> ah, nevermind then
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19:11 < yashgaroth> kanzure: re that paper you linked me earlier, assuming all that stuff works well then sure, but there's still the issue of what peptides you're displaying, like where would you start
19:14 < yashgaroth> horseradish peroxidase is absurdly easy to screen as well, but I won't fault them for that
19:14 < kanzure> i dunno if you need to start anywhere in particular except something like "the cell does in fact leak some stuff once in a while"
19:14 < kanzure> and "the cell in fact does know how to express shit on its surface, although not necessarily the stuff you want yet"
19:17 < yashgaroth> it's certainly possible that they could evolve some sort of beneficial effect, I just have a hard time imagining it; now something like active membrane-bound TdT selection, that I can see
19:17 < kanzure> heh
19:17 < kanzure> well, hm
19:17 < kanzure> would cell-membrane-expression of tdt be more useful than mRNA display of tdt
19:17 < kanzure> or rather, i mean, easier
19:18 < yashgaroth> assuming you can get it to stay active...I imagine being attached to an enormous cell would make it difficult to extend a bound oligo chain
19:18 < kanzure> i feel like "cell display" would be a more well known technique (listed right next to "phage display" and "mRNA display") if that was a truly uesful technique, and afaik nobody lists "cell display" anywhere near those two?
19:19 < yashgaroth> well, we use "nature's cell display" i.e. b-cell affinity maturation, all the time
19:20 < yashgaroth> I imagine it can work a lot better in microfluidics, like the linked paper
19:21 < kanzure> i like the idea of abusing cells because i only have to feed them rather than purify expensive reagents and shit
19:23 < yashgaroth> purification is kind of a racket anyway, but cells do have an appeal; it's just a black box you have to deal with
19:23 < kanzure> yields are definitely going to be lower with cells. hmm.
19:23 < kanzure> well, i guess there's no real reason they have to be that much lower
19:24 < kanzure> like you can imagine cells that can be grown to release lysozymes of enzymes
19:26 < yashgaroth> lysozymes?
19:27 < kanzure> er... there's some sort of vesicle thing. there are many such things.
19:27 < yashgaroth> oh lysosomes
19:29 < kanzure> most of these directed evolution projects look like a few rounds of selection
19:29 < kanzure> i don't see any indication of replication periods or growth phases
19:30 < kanzure> and meiosis/mating seems like a good thing to encourage for gene pool reasons...
19:32 < yashgaroth> if you're working with variants in a single gene, meiotic recombination isn't gonna be too reliable, esp. if you want one variant per cell
19:32 < kanzure> hm i don't know if i want one variant per cell
19:32 < kanzure> i just care about phenotype only, right?
19:32 < yashgaroth> ah, true
19:33 < yashgaroth> in that case yes, yeast orgies in between selection rounds are advisable
19:33 < kanzure> ah
19:34 < kanzure> sounds easy enough
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19:36 < yashgaroth> just sayin', since cell-aided synthesis implies you'll be using TdT, at least start with that... otherwise you'll get bogged down funneling yeast into tiny tubes
19:37 < kanzure> also thinking of this method just for more general reasons too
19:37 < kanzure> there are many good reasons to have a cheap selection system for doing various interesting things, like fluorescent protein optimization stuff
19:37 < yashgaroth> well in that case go ahead
19:38 < kanzure> and you meant, above: start with tdt surface expression cheats?
19:40 < yashgaroth> well, tdt stuff in general
19:41 < yashgaroth> surface expression by itself is already a large challenge
19:42 < kanzure> i think that cells are probably randomly expressing stuff on their surface by accident in many cases, the trick is to select for those mistakes
19:43 < yashgaroth> a little bit, though it wouldn't be hard to insert a construct that'll make them do that
19:43 < kanzure> yeah i seem to recall lots of random protein tags that tend to make things show up on the membrane surface?
19:44 < kanzure> never used them though
19:45 < kanzure> heh you can selectively pick cells to for meiosis
19:46 < kanzure> ah here is a paper on microbial surface display things http://openwetware.org/images/1/18/Wu_SurfaceDisplay.pdf
19:49 < kanzure> "A viable solution to address the limitations is through surface display of various cellulases, combined with fermentation genes in a robust organism, such as Saccharomyces cerevisiae. A recent paper comparing cellobiose usage by surface expressed versus secreted b-glucosidase demonstrated that expression on the yeast cell surface stabilized and increased specific activity of the enzyme [36]."
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19:53 < kanzure> "Flagella are cell-surface appendages that serve the purpose of providing motility. The E. coli flagellar filaments, such as the FliCD proteins, have been exploited for the expression of foreign proteins and peptides [15,51]. The five FliD molecules that make up the capping structure at the end of the flagellum were used to display fibronectin, the collagen-binding YadA and the surface-layer (S-layer) protein, SlpA, of Lactobacillus ...
19:53 < kanzure> ... brevis simultaneously [51]. The display of multiple degradative enzymes is advantageous for targeting sequential pollutant degradation or cellulose hydrolysis."
19:55 < kanzure> "E. coli cells simultaneously expressing GFP intracellularly and streptavidin-binding peptide extracellularly with CPX were immobilized onto a microfabricated electrode array using positive dielectrophoresis (DEP), thus enabling each sensor element to be measured electrically for multiple ligand-display technology [59]."
19:57 < kanzure> "Spores can survive indefinitely in a metabolically inactive state, stay intact for millions of years and resist temperatures as high as 90 8C [62]. B. subtilis spores displaying the tetanus toxin fragment C and using the spore outer coat protein CotB were used as live vaccines [62,63], as well as for screening of tetrameric streptavidin [64]. Another approach is the use of chemically pretreated and boiled L. lactis as a matrix to bind ...
19:57 < kanzure> ... heterologous proteins externally [65]. The protein peptidoglycan hydrolase, AcmA, displays a-amylase and b-lactamase, as well as epitopes of the Plasmodium berghei malaria circumsporozoite protein antigen. Nasally immunized mice with the non-living, non-recombinant vaccine showed higher levels of immunoglobulin G (IgG)-specific serum antibodies after the second dosing than the subcutaneously immunized mice."
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19:58 < yashgaroth> haha man my internet is shit
19:58 < kanzure> http://gnusha.org/logs/2015-01-12.log
20:01 < yashgaroth> anyway yes cell surface display is fairly trivial, though a lot easier and more predictable in eukaryotes
20:02 < kanzure> why's that?
20:03 < yashgaroth> more reliable and better-understood pathways, though I suppose you can use bacteria if you want
20:04 < kanzure> yeast sounds pretty damn convenient
20:04 < kanzure> there might be some benefits to using multi-cellular eukaryotes
20:04 < kanzure> related to specialization... maybe.
20:05 < yashgaroth> whoa there buddy don't get carried away
20:05 < yashgaroth> yeast are nice, if only because I don't think anyone can really sort bacteria
20:06 < kanzure> the reason why cells were proposed is because they are pretty good at continuing to exist (whereas my supply of reagents.. is less good at this).. among other things.. and selection reasons. so things that are already using multiple cells might be even better at coming up with insane solutions to my insane problems.
20:08 < yashgaroth> reagents mostly come from cells though, slap some tags on there and the purification's practically done
20:09 < yashgaroth> also my connection is at the point where I have to read your message on the logs, then type in here and check the logs again to see if it went through
20:10 < kanzure> eh then you should know that i'm gonna brb for a bit
20:11 < yashgaroth> also generational rates of multicellular organisms are gonna be a lot lower than unicellular
20:12 < yashgaroth> probably for the best, I'm gonna go light some votive candles
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20:18 < kanzure> i know there's atmospheric bacteria but is there atmospheric dna that people have studied?
20:29 < yashgaroth> probably only what's inside the bacteria
20:29 < kanzure> hmph
20:31 < yashgaroth> though if we've learned anything about weird environments, there's sure to be viruses they prey on atmospheric bacteria
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20:36 < maaku> kanzure: I sent a certain JoshNH4H this way, I don't know if he's logged in to chat yet
20:37 < maaku> he wants to work on self-replicating machines for space colonization
20:37 < maaku> von neuman replicators and all that
20:38 < kanzure> awesome i will be sure to brainwash him
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20:40 < maaku> heh :)
20:41 < maaku> last I checked up on him he was a chemistry undergrad, although that was >4 years ago. not sure what he's up to now, but he's very proactive
20:42 < kanzure> is this the irc type or the type that i have to convince to idle arounc
20:42 < kanzure> *around
20:47 < maaku> yeah he still needs to be convinced to use a bouncer :\
20:47 < fenn> i love when you plug a hard drive in, intending to make a backup, and it goes totally bonkers. very reassuring.
20:47 < maaku> he's more of a web forum guy (that's how i met him)
20:48 < maaku> fenn: ddrescue ftw
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20:50 < fenn> the internal sata connector came loose i think
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21:03 < nmz787> .title http://articles.journalmtm.com/jmtm.3.1.3.pdf
21:03 < yoleaux> nmz787: Sorry, that doesn't appear to be an HTML page.
21:03 < nmz787> '3D PRINTED SMARTPHONE INDIRECT LENS ADAPTER FOR RAPID, HIGH QUALITY RETINAL IMAGING'
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--- Log closed Tue Jan 13 00:00:22 2015