--- Log opened Thu Oct 08 00:00:51 2015
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00:01 < kanzure> "a visual introduction to venture financing" http://dlopuch.github.io/venture-dealr/
00:05 < kanzure> and obligatory criticism https://news.ycombinator.com/item?id=10346585
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00:34 < kanzure> maybe you could get octopus chromatophore skin display to show information about neural plasticity status in some high-resolution map
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02:49 < delinquentme> ellipsometry. kanzure i found one of your heybryan.org pages on instrumentation on this process.
02:50 < delinquentme> looks novel ... but do you think its called ellipsometry not because of whatever "elliptically polarized light " may be
02:50 < delinquentme> and instead because the light sources rotate around an ellipse to examine the sample?
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06:04 < JayDugger1> kanzure, do have a reference for those Freitas hierarchical ontologies you mentioned?
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06:56 < kanzure> nah just ksrm and stuff
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07:05 < kanzure> that ryan grant person randomly mentioned that he knows clement vidal, i wonder if he stalked me long enough to specifically pick that one
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07:06 < kanzure> .title http://www.foresight.org/nanodot/?p=6774
07:06 < yoleaux> the Foresight Institute » Blog Archive » Review of artificial molecular machines and their controlled motions
07:07 < kanzure> foresight institute video stuff https://vimeo.com/foresightinst/videos
07:08 < kanzure> bah george church was at a foresight institute conference to pimp cadnano, what a bunch of traitors
07:09 < kanzure> ( https://vimeo.com/63008845 )
07:09 < kanzure> .title http://www.foresight.org/nanodot/?p=6765
07:09 < yoleaux> the Foresight Institute » Blog Archive » Addressable molecular machines arranged in a porous crystal
07:09 < kanzure> genehacker would like that because of the stuff about metal organic frameworks....
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07:38 < kanzure> "nasa technology transfer initiative" http://www.technology.nasa.gov/startup
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07:55 < JayDugger1> a quick google search on Freitas hierarchical ontologies names an Alex Freitas, but it seemed more likely you meant R.F.
07:55 < kanzure> yes there is only one freitas
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09:02 < CaptHindsight> kanzure: I more interested in how the proteins bond strands
09:03 < CaptHindsight> have to read over all the work by the three that won the recent Nobel for Chemistry
09:06 < CaptHindsight> why reinvent the wheel http://www.hhmi.org/research/dna-mismatch-repair-and-genetic-stability
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09:13 < kanzure> well most cells don't have a million dna strands that they have to sort between when doing dna repair activities
09:13 < kanzure> in fact, i would say all of them have far less than a few million dna molecules
09:14 < CaptHindsight> it's the simple mechanism for bonding
09:14 < kanzure> dna ligase (an enzyme) has been frequently mentioned as a possible component of doing assembly of longer dna molecules
09:14 < kanzure> https://en.wikipedia.org/wiki/DNA_ligase
09:16 < CaptHindsight> and the errors in synthesis are easily detected since the oligos are so short
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09:19 < CaptHindsight> I'd like to find a group like the three here http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2015/press.html and make some hybrid tech vs brute force like the current synthesis tech
09:20 < kanzure> their work was a study of existing functionality; what we want is not necessarily already existing in cells.
09:20 < CaptHindsight> it is and it isn't
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09:20 < kanzure> you may be interested in https://groups.google.com/group/enzymaticsynthesis
09:21 < CaptHindsight> what's nice about nature is that it's already has it in a compact little package
09:21 < CaptHindsight> we just want to be able to control/program it
09:23 < CaptHindsight> I have some catching up to do
09:23 < CaptHindsight> but it already splices and bonds
09:28 < CaptHindsight> what's a good way to make quick money in DNA synthesis?
09:29 < CaptHindsight> combine that with the plans for the tech, hand it to several co's in China...
09:30 < CaptHindsight> sit back for a bit and watch the prices drop for synthesis tech and custom oligos
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10:18 < maaku> love the AI Now guy
10:18 < maaku> can't tell if it is satire or earnest naiveté
10:19 < Hous> he's serious
10:19 < Hous> just crazy
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12:26 < kanzure> XaTuring: greetings
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13:13 < kanzure> CaptHindsight: another way to do dna is to have combinatorial library of small fragments, then attach the fragments as required to make longer sequences. no synthesis steps required. but.... needs very large library. 4^n where n is number of base pairs. 4^20 is already larger than can realistically fit in most facilities i think.
13:16 < xrr> What determines n?
13:17 < kanzure> physics, limits of the universe and all time and space
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13:18 < kanzure> lower bound of n is limited by practical issues like, need a minimum number of bp for enzymes to attach fragments together correctly, need some dna hybridization of watson-crick base pair binding affinity, need overlapping regions, can't just have n=2 because that's useless. usually needs to be at least n=6 but probably more like n=8.
13:21 < kanzure> nmz787: what about a wacky method like, super long dna molecule that is wound up like magnetic tape, unspool to get to region of interest, each region is 100 billion bp of repeating dna (e.g. 4^n for some n and some combination of bp), use primers to extract and amplify. spooling should be more efficient than attempting pick-and-place at micro-level.
13:21 < kanzure> er, sub-micro level...
13:25 < kanzure> http://www.nytimes.com/2015/10/09/science/rat-brain-digital-reconstruction-human-brain-project.html?_r=0
13:25 < kanzure> .title http://www.cell.com/cell/abstract/S0092-8674%2815%2901191-5
13:26 < kanzure> "Reconstruction and Simulation of Neocortical Microcircuitry"
13:26 < yoleaux> kanzure: Sorry, that doesn't appear to be an HTML page.
13:28 < kanzure> http://www.cell.com/cell/pdf/S0092-8674(15)01191-5.pdf
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13:33 < kanzure> 13:32 <+dpk> "Soviet nuclear submarine. Sailor for scale" http://i.imgur.com/XSUt1wu.jpg
13:34 < CaptHindsight> the inkjet method already makes full custom oligos ~100bp long
13:34 < kanzure> solid state can be way better than chemical synthesis
13:35 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20and%20simulation%20of%20neocortical%20microcircuitry.pdf
13:35 < CaptHindsight> well nobody here has the budget or time here to develop any of this anyway
13:37 < CaptHindsight> the latest nobel winners in Chemistry have figured out how proteins scan, cleave and bind on the nanoscale
13:38 < CaptHindsight> I'd try to work with them or similar to take advantage of that
13:38 < kanzure> those protein details were already known previously; i think the nobel prize there was re: some specific variant of dna repair enzymes. there's lots of them.
13:38 < CaptHindsight> see about hybridizing it
13:38 < kanzure> with what?
13:39 < CaptHindsight> with something you can control on demand
13:39 < kanzure> that's novel research territory
13:40 < CaptHindsight> well you've pretty much proven that there's nobody to copy :)
13:41 < kanzure> i see the chemistry people sorta like machinists-- there's very very few online hanging out on the interwebs, but that doesn't mean nobody knows
13:41 < CaptHindsight> a big pharma doesn't seem to be interested in this
13:41 < CaptHindsight> yeah, they are probably out there
13:42 < CaptHindsight> have to keep looking for them
13:43 < kanzure> so far most of the dna synthesis/genetic engineering people have been selling microbes to the oil industry or to the industrial chemical industry
13:44 < kanzure> big pharma has its own issues to deal with... iterating on a million products doesn't help them, because cost per product to go through all testing stages is so high. but interesting to think about, haven't considered all the ways to pitch to big pharma for super cheap dna synthesis.
13:45 < CaptHindsight> lets say you had a gene printer, what would it cost to go from that point to be able to sell the first gene for human treatment?
13:46 < CaptHindsight> have a doc write a script for you to take to CVS
13:46 < kanzure> probably the same as any other big pharma product- billions. unless you're okay with medical tourism and flying out of the country.
13:47 < kanzure> drug trials are $100M minimum these days, sorta dumb but that's how the FDA rolls. and how the costs work out, apparently...
13:48 < CaptHindsight> lets just say you or I had a DNA printer right now...
13:48 < kanzure> check out these notes i typed when in audience of some big pharma presentation from 2010 http://diyhpl.us/wiki/transcripts/open-science-summit-2010/aiden-hollis-health-impact-fund/
13:49 < kanzure> yeah even with the dna printer, drug trials still cost a ton
13:49 < kanzure> the effects of super cheap dna synthesis don't change the costs of drug trials at all
13:49 < CaptHindsight> you prove it works, what would happen next?
13:50 < CaptHindsight> is there an anti-synthetic DNA group or lobby?
13:50 < kanzure> ETC group
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13:52 < kanzure> i have been listing out "things to do with a dna printer" here http://diyhpl.us/wiki/dna/projects/
13:53 < CaptHindsight> yeah, industrial uses
13:53 < kanzure> stuff like "gastrointestinal microbe to treat lactose intolerance" would be interesting
13:53 < CaptHindsight> lots of em
13:54 < CaptHindsight> where everything comes out smelling like roses
13:54 < kanzure> after dna printer is working, need rest of lab equipment (which is all relatively simple in comparison, i think), such as for incubation (growth of cells), transfection (insertion of dna), etc.
13:56 < CaptHindsight> somebody asked the other day why anyone would want a 3D printer to print features down to 1um or smaller
13:56 < kanzure> they wouldn't, most people would be okay with any type of printer that made features that small
13:57 < kanzure> 1 micron features are really useful for microfluidics, stuff like "lab on a chip", v. popular for custom analysis of chemicals in random water or whatever.
13:58 < kanzure> (or blood is another popular one there, w/e)
13:59 < CaptHindsight> print synthetic spider silk on demand as you repel down the mountain
14:00 < kanzure> one of the advantages of having a dna printer is that you don't have to convince someone to mail you a physical plasmid, you can just print out the custom genetic circuits you want to include in your organism
14:02 < CaptHindsight> someone needs to go through the list and see what can be more cost effective
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14:03 < CaptHindsight> custom organism vs current method
14:03 < CaptHindsight> polymer production could be a big one
14:04 < CaptHindsight> chemical sensors
14:04 < kanzure> lots of sensors, yes
14:04 < CaptHindsight> thats where the hybridization can come in
14:05 < CaptHindsight> custom organism with low voltage serial bus
14:05 < kanzure> traditionally people have used aptamers for biosensors, which is where you use basically random dna molecules and you keep replicating all the dna molecules until you get some that better bind to the small molecule target of interest that you have. but this doesn't require controlled dna synthesis. (still, there are good reasons to focus on genetic circuit synthesis instead-- like for what you do after the aptamer has latched on to ...
14:06 < kanzure> ... whatever it's supposed to be sensing)
14:06 < kanzure> well, i shouldn't say aptamers are traditional. antibodies are traditional, aptamers are sort of the weird esoteric variant :-).
14:06 < kanzure> (dna usually binds to random crap on its own- so you can hone this by copying dna sequences and using natural copy error rate to try to find versions that better latch on to the random crap)
14:08 < CaptHindsight> silicon on organism
14:08 < kanzure> yea i should go through that list and .. do something. not sure what the something is.
14:08 < CaptHindsight> meatspace to internet interface
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14:08 < kanzure> they have that already ("optogenetics")
14:09 < kanzure> .wik optogenetics
14:09 < yoleaux> "Optogenetics (from Greek optikós, meaning "seen, visible") is a biological technique which involves the use of light to control cells in living tissue, typically neurons, that have been genetically modified to express light-sensitive ion channels." — https://en.wikipedia.org/wiki/Optogenetics
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14:09 < CaptHindsight> something like that
14:10 < CaptHindsight> but just works
14:10 < CaptHindsight> easy to connect
14:10 < CaptHindsight> and standardized
14:11 < CaptHindsight> or it connects itself
14:12 < CaptHindsight> do you put little backpacks with the digital interface in them on cells or ..
14:12 < kanzure> nah, the way optogenetics works is you shoot photons at cells, some of the photons hit the light-sensitive ion channels, then the cells have some reaction to that
14:13 < CaptHindsight> do you keep it separate and have the connections seek out and attach themselves to cell membranes
14:13 < kanzure> that's much harder to create
14:13 < kanzure> you might be overestimating current sophistication of biotech!
14:13 < CaptHindsight> I tend to do that
14:13 < CaptHindsight> I've seen the optogenetics
14:14 < CaptHindsight> I'm just looking further
14:15 < kanzure> probably lots of gene trade over the interwebs
14:16 < CaptHindsight> I'm picturing remote controlled or monitored cells
14:17 < CaptHindsight> the bio parts being the factory or sensor with a network interface
14:17 < CaptHindsight> might be overkill for producing simple things like ethanol in bulk
14:18 < kanzure> speculation goal is "really cool things to do with biology that wouldn't be impossible, and would actually be useful"?
14:19 < CaptHindsight> most of the list looks like things that are just bulk production or materials or sensing
14:20 < CaptHindsight> say 10K cells tweaked to sense some odor
14:20 < CaptHindsight> when you get enough consensus you found it
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14:24 < kanzure> dna synthesis is pretty helpful for iterating over all possible sequences of a protein, to try to find a specific protein shape (since you can't really predict shape at the moment)
14:25 < kanzure> well, i mean, cheap dna synthesis....
14:27 < kanzure> which is more-or-less atomically precise molecular manufacturing
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14:28 < maaku> kanzure: ?
14:28 < kanzure> well, it's not like it's a diamond or anything
14:29 < maaku> oh ok
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14:29 < maaku> some people argue DNA as a pathway to diamondoid mechanosynthesis, I thought that's what you were doing
14:29 < kanzure> well, non-diamond molecular manufacturing is pretty useful too
14:29 < maaku> which would be great but I've yet to see a non-handwavy explanation
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14:30 < kanzure> given the ability to predict protein shape you could just design whatever molecular structures you want, and then synthesize the dna, then have the dna inform the ribosome how to construct that protein
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14:30 < kanzure> since we don't know how to do all protein folding predictions, you can use bruteforcing with direct dna synthesis of a million different variants and then look at the shape of each resulting protein
14:31 < kanzure> variants would each have a segment of amino acids switched out for another, or insertions/deletions and other common mutations, perhaps informed by some heuristic algorithm, or the whim of the user, who cares
14:31 < CaptHindsight> there needs to be more people working on the micro and nanoscale
14:31 < CaptHindsight> and they need the inexpensive tools to do it
14:32 < kanzure> maaku: i think you can get pretty far with non-diamondoid molecular manufacturing.
14:32 < maaku> kanzure: have you looked at modifying / expanding the ribosome itself?
14:33 < kanzure> maaku: kinda, yeah https://groups.google.com/d/msg/enzymaticsynthesis/3YEEv0OULo0/zJZPETWDbMIJ
14:33 < maaku> kanzure: there may be research here that is useful : https://astrobiology.nasa.gov/nai/teams/can-5/gatech/
14:34 < maaku> GATech spent five years investigating the origins of the ribosome and mapping variations
14:34 < CaptHindsight> if you could buy a desktop molecular fabricator for a few $K would there just be a zillion nanoscale Yoda heads?
14:34 < CaptHindsight> or would people make useful things?
14:34 < maaku> actually this link may be better: http://astrobiology.gatech.edu/
14:35 < kanzure> "An Atomic Level Description of the Specific Interactions Between Nascent Peptide and Ribosome Exit Tunnel" hmm
14:35 < kanzure> https://astrobiology.nasa.gov/nai/reports/annual-reports/2013/gatech/an-atomic-level-description-of-the-specific-interactions-between-nascent-peptide-and-ribosome-exit-tunnel/
14:35 < maaku> CaptHindsight: uh, there's no shortage of ineresting things to do with a nanofactory
14:35 < kanzure> "extremophile ribosomes" https://astrobiology.nasa.gov/nai/reports/annual-reports/2013/gatech/extremophile-ribosomes/
14:36 < CaptHindsight> reprap and now SLA are pretty depressing to watch
14:36 < kanzure> that's because they are awful
14:36 < kanzure> "resurrection of an ancestral peptidyl transferase" https://astrobiology.nasa.gov/nai/reports/annual-reports/2013/gatech/resurrection-of-an-ancestral-peptidyl-transferase/
14:36 < CaptHindsight> maaku: well you're the exception
14:37 < kanzure> please list out interesting things to do with nanofactories, because why not
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14:37 < CaptHindsight> what he said ^^
14:37 < kanzure> https://github.com/kanzure/nanoengineer/tree/master/cad/partlib
14:40 < CaptHindsight> yes more of this http://wordlesstech.com/wp-content/uploads/2013/03/Nanoscale-3D-printed-Microstructures-3.jpg
14:40 < CaptHindsight> vs this http://www.asdn.net/asdn/nanotools/images/fig2.jpg
14:40 < kanzure> well there's http://diyhpl.us/~bryan/papers2/mems/
14:44 < CaptHindsight> kanzure: how do the teams using repurposed virus for cancer detection get around the millions needed for approval?
14:44 < kanzure> they aren't using living humans, just living human tissue matter, or even non-human cell lines
14:44 < CaptHindsight> I know that they are in the early trial stages and didn't get millions
14:45 < CaptHindsight> oh no they have cured a few patients already
14:45 < CaptHindsight> let me find a link
14:45 < kanzure> clinicaltrials.gov
14:46 < maaku> CaptHindsight kanzure: uh, diamond. everything you can buy at an industrial supply store, but made with diamond
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14:46 < kanzure> can't you already do shape-specific chemical vapor deposition growth of diamonds?
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14:46 < maaku> just in terms of material properties (e.g. strength/weight ratios) it'd be orders of magnitude better
14:47 < CaptHindsight> http://www.cancer.duke.edu/btc/modules/research3/index.php?id=41
14:47 < maaku> kanzure: not fast or cheaply enough
14:47 < maaku> I have an affinity for space travel, so: space elevator and/or <$1k per flight single stage to orbit vehicle
14:48 < maaku> using just 1st generation dumb diamandoid materials
14:48 < CaptHindsight> rocket boots
14:49 < kanzure> "Poliovirus Vaccine for Recurrent Glioblastoma Multiforme (GBM) (PVS-RIPO)" https://clinicaltrials.gov/ct2/show/NCT01491893
14:50 < maaku> computation: Babbage rod-and-gear computers with enough processing power to match all extant computers combined in a cubic centimeter
14:50 < kanzure> just says "Brain Tumor Research Charity Grant"
14:50 < kanzure> maaku: wouldn't that overheat
14:50 < CaptHindsight> kanzure: how long and how much will it cost if the trials are found to be very successful?
14:51 < maaku> kanzure: only exotic tech is reversible computers
14:51 < kanzure> i'm not the right person to ask at the moment, i am also not familiar with cheapest fda-approved clinical trials
14:51 < CaptHindsight> just wondering
14:52 < kanzure> lots of big pharma people say clinical trials cost >$500M into the billions, but that might be because of how many middlemen they use
14:52 < CaptHindsight> if anyone else cares to chime in
14:52 < kanzure> or because of insurance costs
14:52 < kanzure> https://en.wikipedia.org/wiki/Drug_development#Clinical_phase
14:52 < kanzure> https://en.wikipedia.org/wiki/Clinical_trial#Economics
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14:53 < maaku> of course the real benefit of atomicly precise diamond is probably quantum computation: https://en.wikipedia.org/wiki/Nitrogen-vacancy_center
14:53 < pasky> priceless http://www.dailymail.co.uk/sciencetech/article-3264341/How-live-till-150-JANE-FRYER-meets-eccentric-scientist-thinks-s-secret-Just-one-problem-ll-sex.html
14:53 < CaptHindsight> kanzure: vs be available in Thailand for $995 and a plane ticket
14:55 < kanzure> sure
14:55 < fenn> CaptHindsight: some bacteria extrude a "wire" made of iron (?) to reduce minerals as part of their metabolism; this can probably be hijacked to do some electrical interfacing between a chip and a genetic regulatory network
14:56 < fenn> https://en.wikipedia.org/wiki/Bacterial_nanowires
14:57 < CaptHindsight> neat
14:59 < CaptHindsight> maaku: also nanoscale cutting tools
15:00 < fenn> i think the right strategy is to skip the protein folding problem entirely by using rationally engineered proteins instead of giant blobs of shit
15:00 < CaptHindsight> nanomilling
15:00 < kanzure> "rationally engineered proteins" is hard to do when you can't predict what the protein is going to look like
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15:01 < kanzure> .wik protein design
15:02 < yoleaux> "Protein design is the rational design of new protein molecules to fold to a target protein structure, with the ultimate goal of designing novel function and/or behavior. Proteins can be designed from scratch (de novo design) or by making calculated variations on a known protein structure and its sequence (known as protein redesign)." — https://en.wikipedia.org/wiki/Protein_design
15:02 < kanzure> "Rational protein design approaches make protein-sequence predictions that will fold to specific structures"
15:02 < kanzure> so....
15:04 < kanzure> probably will just end up with some bland molecular building blocks made out of proteins, and then change binding affinity between those proteins using specific addressing, then just throw the parts together and get self-assembling lego stuff.
15:06 < fenn> you make it out of parts that you can predict
15:06 < fenn> more like building a machine than trying to fold origami out of meat
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15:07 < kanzure> yep sure
15:07 < kanzure> thing i just proposed is minor abstraction on top of proteins, to hide the unpredictable useless parts
15:08 < fenn> you don't need binding affinity addressing so much because the parts are attached as a single strand
15:08 < kanzure> single strand of what?
15:09 < fenn> obivously you can't use the same connector for every part of the protein
15:09 < fenn> single strand of amino acids
15:09 < kanzure> yeah, just have generic cube-shaped proteins, before synthesizing the dna you assign some 20-letter-specific gate/key locking mechanism for binding to another protein
15:09 < kanzure> the more amino acids you add to a strand, the harder it gets to predict shape
15:09 < kanzure> better to just have lots of small blocks floating around
15:10 < fenn> you can link them with glycine chains that don't do anything
15:10 < kanzure> doesn't that lose out on structural precision?
15:11 < fenn> the problem with blocks floating around is your stoichiometry can be wildly off (100% concentration pockets of one part forms a crystal of that part)
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15:11 < fenn> and the "reaction kinetics" of the folding process are orders of magnitude slower than if they're linked together
15:11 < fenn> being linked together is like having a catalyst for the folding process
15:12 < fenn> you just have to make sure that the individual pieces fold fast enough that it never mis-folds
15:13 < fenn> i'm probably doing a bad job explaining this
15:13 < fenn> think lego not limerick
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15:14 < maaku> CaptHindsight: if you have a atomicly precise manufacturing, what may I ask is the purpose of nanoscale cutting tools?
15:14 < fenn> to cut things that are not manufactured
15:15 < maaku> guess I'd need a use case
15:15 < fenn> the energy input per gram of atomically precise stuff will be way higher than any other manufacturing process (and so price will be higher per gram also)
15:15 < kanzure> maaku: digging for dinosaurs
15:16 < Jawmare> kanzure, just thought of something today... what if we functionalize the slide
15:16 < kanzure> doable, solid supports are often functionalized
15:16 < maaku> fenn: ... what's the energy per gram of potatos?
15:16 < kanzure> maybe with biotin or streptavidin
15:17 < fenn> maaku: plants are about 3% efficient max so way less than that
15:17 < Jawmare> and have cartridges with chemicals you need
15:17 < kanzure> tubes pointed into the cartridges, actually
15:17 < kanzure> but yes
15:17 < poppingtonic> what's the difference between cadnano & nanoengineer?
15:17 < kanzure> some of those details are where we need help- like, using the wrong materials will contaminate everything
15:18 < kanzure> poppingtonic: nanoengineer was abandoned, cadnano seems to still be developed (haven't looked)
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15:19 < Jawmare> kanzure, find out what kind of tubes commerical dna machine uses
15:19 < Jawmare> I bet its tygon
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15:20 < kanzure> yea this says tygon on page 244 http://diyhpl.us/~bryan/papers2/DNA/abi391/ABI%20391-manual.pdf
15:20 < kanzure> but mostly polypropylene
15:22 < fenn> maaku look at the graph about halfway down: http://www.lowtechmagazine.com/2009/06/embodied-energy-of-digital-technology.html
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15:22 < CaptHindsight> maaku: cutting a giant silicon crystal to size
15:22 < fenn> i saw a graph where the x axis was "feature size" but doubt i will ever be able to find that again
15:22 < fenn> the curves were similar
15:23 < CaptHindsight> maaku: first sawing then milling to size
15:23 < kanzure> CaptHindsight: you've seen nanofactory stuff before, right? like https://www.youtube.com/watch?v=zqyZ9bFl_qg
15:23 < CaptHindsight> maaku: before you fabricate whatever on top of it
15:23 < kanzure> poppingtonic: that video mentions that nanorex funded making that animated video (nanorex was the one that wrote nanoengineer)
15:24 < maaku> CaptHindsight: for what purpose? what would you use crystal silicon for in bulk that diamond substrate would not suffice?
15:24 < CaptHindsight> maaku: silicon is cheap and easy to get or grow currently
15:25 < poppingtonic> hmmm kanzure, I thought it was you
15:25 < kanzure> nah i only rescued nanoengineer from oblivion
15:26 < kanzure> my source code looks way better :-)
15:26 < fenn> poppingtonic: nanoengineer allows you to put arbitrary molecules together and them simulates the structure, and it has some tools to do DNA origami structures; cadnano only lets you string DNA together and has many more macros specific for DNA origami
15:27 < fenn> it used to be spelled caDNAno
15:28 < fenn> s/arbitrary molecules/arbitrary atoms/
15:28 < kanzure> fenn: had surprisingly hard time convincing CaptHindsight of cool things to do with dna synthesizer (above in recent backlog) (not his fault- just hard to pick the right example projects)
15:28 < fenn> the iGEM projects list wasn't enough?
15:28 < poppingtonic> Foresight Institute's vimeo channel has a talk by George Church about caDNAno among other things
15:29 < kanzure> "mostly lousy sensors" :D
15:30 < poppingtonic> well, he mentions it...
15:30 < fenn> i would hope so
15:32 < fenn> well, i don't know what to say to "why would anyone want a DNA synthesizer" it's like asking "why would anyone want a computer" or "why would anyone want a cnc machining center" etc
15:33 < kanzure> not really like a computer- you have very limited input, very limited output, can't see the state, and it fails almost constantly because cells are finnicky
15:34 < fenn> yeah yeah
15:34 < CaptHindsight> kanzure: the most interesting applications for a DNA synthesizer to me is for medical cures
15:34 < kanzure> well, then designer baby stuff
15:34 < kanzure> but that's not something like "1 day after the dna synthesis machine proven works"
15:34 < fenn> not saying it's like a computer, but the lack of imagination is hard to penetrate
15:35 < CaptHindsight> unfortunately the guberments have put of roadblocks to prevent that from happening cheaply and easily
15:35 < CaptHindsight> of/up
15:35 < kanzure> nah, frame as "save all the babies"
15:35 < kanzure> pro-lifers will be convinced
15:35 < fenn> there are a lot of DNA vaccines that would be good to be able to experiment with widely during a pandemic
15:36 < fenn> or even regular vaccines
15:36 < fenn> or serum or whatever
15:36 < CaptHindsight> kanzure: sounds similar to a windoze machine
15:37 < kanzure> i think i should write a one paragraph indoctrination hype piece to convince people "holy shit i totally want a dna synthesis machine so i can go do those things"
15:37 < CaptHindsight> but what color do cells turn when they die?
15:37 < fenn> you only need one DNA synthesizer in the world, but access to its output is hard to arrange for some reason, so more is better
15:37 < kanzure> and also scheduling problems
15:37 < kanzure> and also, you need parallelism to work on a single project... need to make many variants and see which ones work.
15:38 < fenn> .wik trypan blue
15:38 < yoleaux> "Trypan blue is a vital stain used to selectively colour dead tissues or cells blue. It is a diazo dye." — https://en.wikipedia.org/wiki/Trypan_blue
15:38 < kanzure> printing out 30% of a genome is useful, but you need 10,000 variants to see which ones are metabolically efficient
15:39 < CaptHindsight> why aren't the Chinese all over DNA synthesis?
15:39 < kanzure> what was it you had against bruteforce, again?
15:39 < CaptHindsight> it's inefficient
15:39 < fenn> well 10000 is not a large number of permutations
15:39 < drethelin> why would anyone NOT want a dna synth
15:39 < CaptHindsight> yeah
15:40 < fenn> .wa length of a human genome
15:40 < yoleaux> size of the human genome: 3.08×10⁹ bp (base pairs); Unit conversion: 3.08 Gbp (gigabase pairs); Comparisons: ~(0.023 ~1/43) × estimated number of base pairs in the lungfish genome (~1.33×10¹¹ bp); ~(0.18 ~1/6) × estimated number of base pairs in the genome of wheat (~1.7×10¹⁰ bp); ~8.4 × estimated number of base pairs in the pufferfish genome (~3.65×10⁸ bp)
15:40 < CaptHindsight> everyone should have the right to have one
15:40 < fenn> .wa 4^(3.08*10^9)
15:40 < yoleaux> fenn: Sorry, no result!
15:40 < fenn> .wa 4^(3080000000)
15:40 < yoleaux> fenn: Sorry, no result!
15:41 < fenn> anyway
15:41 < kanzure> you wouldn't want a dna synthesizer because most of the projects require research
15:41 < CaptHindsight> kanzure: plus hasn't nature done the brute force for the past several billion years
15:42 < fenn> .py 4**3080000000
15:42 < yoleaux> 404 Not FoundError: Not Found
The requested URL /py/4**3080000000 was not found on this server.
15:43 < kanzure> .py eval("4*" + "*3080000000")
15:43 < yoleaux> 404 Not FoundError: Not Found
The requested URL /py/eval(%224*%22%20%2B%20%22*3080000000%22) was not found on this server.
15:43 < kanzure> brutal
15:43 < fenn> the .py plugin just doesn't work
15:43 < poppingtonic> vimeo.com/63008845
15:45 < fenn> guess i will kill that python calculation before i run out of swap space
15:46 < fenn> it's a really big number
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15:48 < CaptHindsight> lets say we had the inkjet oligo maker.... what is the cost to QC each pool before assembling each know good section or the cost to QC the whole pool after assembly?
15:50 < fenn> yeah i asked steve to solve that math problem but he dodged
15:50 < fenn> the QC before/after question
15:52 < CaptHindsight> I want to see how the proteins do QC
15:52 < fenn> they look at base pair mismatch
15:53 < fenn> nature never synthesizes single stranded dna (except maybe TdT)
15:53 < fenn> it's always copy error correction
15:53 < CaptHindsight> I know I'm just looking at possibly using it for the QC
15:54 < fenn> there are some schemes that precipitate out mismatches by binding to them
15:54 < CaptHindsight> OC, cleaving and bonding
15:55 < fenn> OC?
15:55 < CaptHindsight> finding the mismatches
15:55 < CaptHindsight> quality control
15:57 < CaptHindsight> the inkjet printer doesn't do a perfect job
15:57 < CaptHindsight> of printing the oligos
15:59 < CaptHindsight> it's a patent minefield but it's not difficult to MEMS a femtoliter printhead with K's of nozzles
16:02 < Jawmare> If you cap it do you still end up with mismatch?
16:03 < poppingtonic> Open Invention Network for SynthBio
16:13 < maaku> you guys seem to be working on some sort of inkjet protein / DNA printer for molecular assembly. is there any writeup of this overall plan / strategy?
16:13 < maaku> (not asking for an explanation over IRC, I kinda get the IRC tl;dr. I'm wondering if there's a more detailed wiki page or something...)
16:14 < maaku> I ask because there's a lot that is non-intuitive to me, such as exactly how useful it would be outside of synthetic bio
16:20 < fenn> maaku http://diyhpl.us/wiki/dna/synthesis/notes/ and http://bioinformatics.org/pogo/ or if you mean "what do you do with DNA" see http://diyhpl.us/wiki/dna/projects/
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16:22 < kanzure> Jawmare: capping is necessary during each cycle
16:22 < fenn> jawmare you always have some amount of mismatches because the reactions don't 100% complete, because of side reactions, because of coincidentally similar sequences
16:22 < kanzure> Jawmare: for quality control, you can shoot light at it and figure out how many nucleotides are there, but also you usually have to perform dna sequencing to make sure the actual strands are good
16:22 < Jawmare> and how do commerical dna synth solve that problem?
16:22 < kanzure> however, personally i think dna synthesis is hard enough on its own, adding dna sequencing into the equation is ugh
16:23 < kanzure> commercial dyna synthesizers solve this problem by synthesizing very short strands, and lots of them. then the companies just sequence 'em and if it's bad they chunk it out.
16:23 < kanzure> s/chunk it out/throw it out.
16:25 < kanzure> when you synthesize a small amount (nanograms or less?) of dna, you have to use dna polymerase to make copies; if the wrong strands outcompete the correct strands then you have to start over.
16:26 < fenn> nothing's competing, you just amplify a mixture of sequences
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16:29 < kanzure> shorter strands take less time to replicate. it's competitive.
16:30 < fenn> the wrong strands are only 1 bp shorter
16:31 < fenn> maybe that's enough of an advantage over many rounds of replication to completely swamp the signal
16:35 < fenn> maaku: cheap enough dna synthesis is still a roadblock even for institutional scientists working on good stuff like neuroscience, metabolism, aging, etc
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16:36 < fenn> even if you happen to be well funded there is not enough DNA to go around
16:36 < fenn> at least not enough to treat gene synthesis like any other lab tool
16:37 < fenn> the prices are falling but nowhere near as fast as sequencing
16:37 < fenn> imagine trying to program a computer without a keyboard and you had to copy and paste things by gnawing at the mouse buttons with your gums
16:38 < fenn> that's where biology is at without DNA synthesis
16:38 < fenn> but each cut/paste operation takes 4 hours
16:40 < kanzure> and also you can only use like 3 punch cards
16:41 < kanzure> i seem to be stuck in a time vortex today
16:41 < fenn> welcome to the time vortex
16:41 < fenn> find a cybernetic dolphin to be your guide
16:42 * fenn goes off in search of magnesium
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17:00 < kanzure> been working on lunch for the last 7 hours, i blame time vortex
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18:28 < CaptHindsight> and how do commerical dna synth solve that problem? like kanzure mentioned or they get quiet about it when asked directly
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19:17 < kanzure> http://2014.igem.org/Team:UChicago
19:17 < kanzure> "A novel directed evolution system, termed feedback-regulated evolution of phenotype (FREP), incorporates a dynamic mutation rate to overcome the existing problems of directed evolution by mimicking the plasticity of the mutation rate in natural evolution. This is achieved through dynamic control of a mutator element that is negatively regulated by the desired end product. In this feedback scheme, as more of the desired biomolecule is ...
19:17 < kanzure> ... produced, the rate of mutation decreases and eventually approaches zero, allowing evolution and maintenance of a high level of production while minimizing the accumulation of toxic, nonspecific mutations."
19:18 < kanzure> "We successfully created FREP-ready ARM constructs containing the mutagenizing proteins EmrR, Dam and mutH(E56A) and the reporter mCherry-LVA under the control of the tyrosine-sensitive promoter paroF und although we were not able to implement FREP due to time constraints."
19:18 < kanzure> bah
19:20 < kanzure> there was also this thing http://2014.igem.org/Team:SYSU-China/content.html#Project/Discussion
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19:54 < mgin> anyone going to the alcor conference??
19:56 < kanzure> nah, they didn't have room for my presentation
19:56 < kanzure> as of a week ago
19:58 < kanzure> aschwin de wolf's publication looked somewhat interesting as an update to his research work
20:02 < Jawmare> removing anhydrous acetoniltilre from sureseal bottles...
20:03 < kanzure> gravity-assist
20:03 < kanzure> or uh.. i think one of the designs pumped argon into the bottle
20:03 < Jawmare> with syringe.... :(
20:04 < JayDugger1> I didn't see anything about classification or ontologies in Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines. Just hierarchy.
20:05 < kanzure> most ontologies are hierarchies
20:05 < kanzure> aren't they?
20:05 < Jawmare> acetoniltrile - not that bad if you spill it in a fume hood, it evaporates quickly
20:05 < JayDugger1> Hierarchies of machine shops?
20:06 < kanzure> JayDugger1: his "table of contents" tend to be fairly thorough
20:06 < kanzure> Jawmare: substitutes welcomed
20:06 < Jawmare> the really only substitution that might work is dmso or dmf
20:06 < JayDugger1> I think mostly, yes. His work's a pleasure to read for its useful indexes and tables of contents. I started with those.
20:06 < kanzure> well the biologists sure do love them some dmso
20:06 < Jawmare> which if you ask most chemist they would rather use acetonitirle
20:07 < JayDugger1> I'll look at KSRM and his other work later todayl
20:07 < Jawmare> dmso have a high boiling point, removing the solvent is going to require a vaccum distillation
20:07 < JayDugger1> ONce I wake enough to accurately type.
20:07 < Jawmare> or distilling at 190 degree celsius
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20:08 < Jawmare> this funny named company is a pretty good source for DMSO http://www.gaylordchemical.com/index.php?page=replace-acetonitrile-with-dmso
20:09 < JayDugger1> And after I finished reading what suspiciously looks like Tolkien fanfic at first glance, by Freitas, at http://www.nanomedicine.com/Frodo.htm.
20:09 < kanzure> i think you mean http://www.nanomedicine.com/Frodo.htm
20:10 < kanzure> .title
20:10 < yoleaux> The Last Transmission of Frodo Baggins
20:10 < kanzure> maybe this is cleverly disguised ralph merkle tolkien fanfic
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20:12 < JayDugger1> Very clever, indeed.
20:12 < kanzure> Jawmare: how much debugging would a synthesis project like this take? how many things can go wrong.
20:13 < Jawmare> depending on how much synthesis experience he have
20:13 < Jawmare> you can't learn synthesis from books, only trial and error
20:13 < Jawmare> my prof mentioned that making a 9 chained peptide takes his group ~ a year and a half to make
20:13 < kanzure> because the books suck?
20:14 < Jawmare> thats a postdoc + 1-2 grad student
20:14 < Jawmare> because bench skill is something you learn from experience
20:14 < Jawmare> btw that a year and a half figure is without any previous literature
20:15 < kanzure> purpose of machine is to compress all that into something that has tight engineering requirements
20:15 < kanzure> ah that's good news then
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20:16 < Jawmare> in my opinion, functionalizing glass slide and do solid state synth is going to be much more robust
20:17 < kanzure> more robust than?
20:17 < Jawmare> without solid support
20:17 < kanzure> btw we could also print functionalized microbeads first
20:17 < kanzure> magnetic microbeads that we can lock to the surface
20:18 < fenn> the acetonitrile seemed relatively safe, but people had warned about the toxicity of 3-methoxypropionitrile
20:18 < kanzure> either has to be functionalized to surface or to beads or something, otherwise the wash step on each cycle will blow everything away
20:18 < fenn> only a small amount of 3-methoxypropionitrile is used but it does get mixed in with large quantities of acetonitrile
20:20 < Jawmare> where do you use 3-methoxypropioniltrile?
20:22 < fenn> inkjet fluid solvent, for dispensing the phosphoramidites i think
20:24 < Jawmare> just because it have a nitrile group, doesn't mean it is as poisonous as cyanide
20:25 < Jawmare> Look, in a lab we expect you have at least a fume hood
20:25 < Jawmare> spill kits, fire extingusher, eyewash etc
20:25 < Jawmare> and it is expected that you wear (and replace gloves) regularly, and wearing lab coats
20:26 < Jawmare> I'd say 3-methoxypropioniltrile is safe if you take reasonable protective measure
20:27 < fenn> ok
20:28 < Jawmare> I just did Steglich esterification in a undergrad lab, yes we were constantly reminded that DMAP is highly toxic and absorb through skin, but it wasn't really that bad
20:28 < Jawmare> and 3-methoxypropionitrile is not as bad as DMAP
20:30 < Jawmare> Yes it is toxic, and yes you will die if you drink it / get it on your skin / get it on your eyes
20:32 < fenn> it would be good to eventually figure out how to recycle the solvent because it and the dry nitrogen is the majority of the cost of a synthesis run
20:32 < fenn> nitrogen can be replaced with a small pump
20:33 < fenn> or maybe just using a better sprayer will reduce solvent use enough that it is no longer a major expense
20:34 < Jawmare> anhydrous acetoniltrile is expensive
20:34 < Jawmare> do we really have to use anhydrous?
20:34 < Jawmare> (and also, hard to get)
20:34 < fenn> yes it's important that it is anhydrous because water terminates the reaction
20:34 < Jawmare> right
20:39 < Jawmare> it is like what.. less than $100 per litre?
20:39 < Jawmare> https://www.fishersci.com/shop/products/acetonitrile-anhydrous-dna-synthesis-fisher-bioreagents-3/p-23824
20:40 < Jawmare> https://www.alfa.com/en/catalog/42311
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20:47 < fenn> much less than $100/litre
20:47 < fenn> the posam people were buying it in drums
20:48 < Jawmare> yes, if you buy it in drums
20:48 < Jawmare> now how do you keep it anhydrous
20:49 < Jawmare> tips: CaCl2 or molecular sieves
20:51 < Jawmare> if you collect the waste in a waste bucket
20:51 < Jawmare> I think you can recover it but it is going to be nasty
20:52 < fenn> for the past 20 minutes i have been derping on why the posam user manual is 29 pages instead of 31... there should be a cost breakdown on page 30
20:55 < fenn> i could just shrug and say they must not have written that part, but i've actually read the cost breakdown in the past somewhere
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20:55 * fenn greps the logs
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20:56 < Jawmare> anyways, good night... another 4+- 2 hours of lab tomorrow
20:56 < Jawmare> probably more like 7 :(
20:58 < fenn> (for posterity) posam cost breakdown: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC507883/table/T1/
20:58 < Jawmare> halogenation, recrystalize. hplc, 2d nmr
20:58 < Jawmare> fml
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21:36 < kanzure> http://newsoffice.mit.edu/2014/algorithm-recovers-speech-from-vibrations-0804
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21:36 < kanzure> "MIT reports recovering voices from high-frame-rate video of a potato-chip bag, extracting information from vibrational displacements as small as 1/100 of a pixel. This reminds me of an idea floated decades ago by the fictional character Daedelus in a now-defunct column in Nature: Recover ancient voices from pots by reading the tiny ripples left by vibration of the potters’ fingers."
21:36 < kanzure> from http://metamodern.com/2014/08/08/recovering-ancient-voices-from-clay-pots/
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21:41 < kanzure> didn't know the "molecular manufacturing shortcut group" was headed by a dude from raytheon http://www.islandone.org/MMSG/
21:54 < fenn> was at nasa too https://en.wikipedia.org/wiki/McKendree_cylinder
21:58 < kanzure> hmm foresight institute does not have "an index of really really cool atomically precise molecular manufacturing machine stuff". huge oversight.
21:58 < kanzure> and nanoengineer's partlib is kinda empty. has a few gears and bearings i guess.
21:59 < kanzure> i thought there would be a list on old sci.nanotech posts but nope
22:00 < kanzure> actually i didn't even see utility fog mentioned on alt.sci.nanotech either; are people just braindead or what.
22:03 < CaptHindsight> if the tools to fabricate are low enough cost to get enough out there then that's the way around all the obvious patents for the next 10-20 years
22:03 < kanzure> yep, kits and stuff
22:03 < kanzure> or kits about kits
22:04 < CaptHindsight> sub micro tools are expensive and even if you have them what can you make that doesn't violate some obvious patent
22:04 < kanzure> need to flip things around; patents need to stop violating my ability to get shit done.
22:04 < CaptHindsight> cheap tools and lots of people tinkering will work
22:07 < CaptHindsight> we need more shops around like the ones in Blade Runner "I make your eyes, just eyes"
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22:19 < fenn> "i've personally made 70 billion copies of my book" - george church
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22:28 < fenn> "robot concentration (nM)"
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22:52 <@nmz787> kanzure: your spooling idea is interesting, one problem I see is you'd have to cut out the primers (at least on one side of each oligo to be joined)... or figure out some sort of primerless primers :/
22:55 < kanzure> what about chemically attaching the primers permanently
22:55 < kanzure> the primers that aren't "in range" are irrelevant anyway
22:56 < kanzure> .title https://news.ycombinator.com/item?id=10357791
22:56 < yoleaux> MakerBot lays off 20% of its staff for the second time this year | Hacker News
22:57 < kanzure> re: in range; imagine droplet that covers only 1% of the superlong spooled dna molecule. the chemically-attached primers at other locations don't matter because the polymerase can't physically get to them.
22:58 < kanzure> you could also use fluorophores to delineate the transition areas for sections of the molecule
22:58 < fenn> i liked the george church @ foresight talk, it had a good mix of recent biotech developments and a good bit of stuff i didn't know about http://vimeo.com/63008845
22:59 < kanzure> .title http://vimeo.com/63008845
22:59 < yoleaux> George Church: "Regenesis: Bionano" at Foresight Technical Conference 2013 on Vimeo
22:59 < fenn> for some value of recent :P
22:59 < kanzure> well since he sleeps so little he's technically from the future, so his recent is more relatively recent than otherwise
22:59 < fenn> oh? how much does he sleep?
23:00 < kanzure> like zero?
23:00 < fenn> are you just making that up or is it based on some anecdote
23:00 < kanzure> wikipedia says george church has narcolepsy
23:00 <@nmz787> kanzure: hmm, then you'd need a restriction enzyme to cut out the amplified segments
23:01 <@nmz787> those things conflict... narcolepsy and sleeping-like-zero
23:01 < kanzure> narcolepsy can have similar symptoms as insomnia
23:02 <@nmz787> I can only remember the deuce bigalow narcolepsy scene at the bowling alley
23:02 * nmz787 reality overwritten
23:02 < kanzure> apparently you can view images of george church's colon and ass online https://my.pgp-hms.org/profile/hu43860C
23:02 <@nmz787> gross
23:03 <@nmz787> why am i copying that link
23:03 < kanzure> here is his sleep data https://my.pgp-hms.org/user_file/download/531
23:03 < kanzure> (csv)
23:04 < kanzure> JUST KIDDING IT'S HIS BUTTHOLE
23:05 < fenn> definitely not butthole data
23:05 <@nmz787> well this is his... umm... bank account number: https://my.pgp-hms.org/user_file/download/539
23:05 <@nmz787> polyp in the old rectum, eh
23:06 <@nmz787> isn't that some sort of sea creature's life cycle?
23:06 <@nmz787> why is that in there???
23:07 < fenn> if i made fun of other people's health data i'd be unable to pretend outrage when others made fun of my health data...
23:07 < kanzure> yes because pretend outrage is pretty high on your priority list
23:07 <@nmz787> yup, basdically what I'm thinking
23:07 <@nmz787> I'll have to chuckle away my squamous basal layer deteriorating to shit or whatever
23:07 <@nmz787> hahah
23:08 * nmz787 oh yeah, at least my face is falling off just in time for halloween
23:08 < kanzure> tried chemo for that?
23:09 <@nmz787> idk, looks like he gets between 5 and 7 hours a night on avg
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23:09 < fenn> if i'm reading this data right george church only sleeps 5-6 hours a night
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23:09 <@nmz787> see, we have good correlation
23:09 < fenn> high five to six
23:09 < fenn> go team
23:11 <@nmz787> where should I upload 4 log files for #brlcad to look into... is there a pastebin that can group uploads like imgur?
23:11 < fenn> when you figure in meals and puttering that's like an extra day every day vs my sleep
23:11 < kanzure> plus he has goons
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23:12 < fenn> goons upon goons
23:12 < fenn> are we his goons?
23:12 < fenn> i forget
23:12 <@nmz787> no, those are grad students
23:12 < kanzure> not in any real sense
23:12 < kanzure> perhaps indirectly
23:12 <@nmz787> he probably reads the logs once in a while, or greps them?
23:13 <@nmz787> or has a goon do that
23:13 < kanzure> i doubt it
23:13 < fenn> hi george! and goon!
23:13 < kanzure> nobody knows about hplusroadmap
23:13 < fenn> what, it comes up in my google searches constantly
23:13 <@nmz787> haha
23:13 < kanzure> that's google's search bubble thing
23:13 <@nmz787> filetype:pdf
23:14 < fenn> rule 34
23:15 < kanzure> i don't think there's that much traffic on the wiki
23:15 < kanzure> or the logs for that matter
23:15 < kanzure> although i haven't checked in like... five years?
23:15 <@nmz787> i use the logs at work
23:16 < kanzure> v. sneaky
23:16 <@nmz787> lately pidgin doesn't even work there, and the webchat kind sucks as it disconnects often
23:16 < kanzure> wiki could link to logs more prominently
23:16 < kanzure> but the good stuff is just burried in the logs, nobody knows where to look
23:16 < kanzure> any random click is gonna show you a bunch of disconnects and joins. what good is that?
23:19 < fenn> random disconnects are IRC's way of letting you know that time has passed
23:22 < kanzure> at one point i got the faint sense that ellington was reading diybio email traffic but i didn't have enough evidence to catch him
23:27 < kanzure> why don't the hplusroadmap irc logs trigger any of the google alerts i setup?
23:27 < kanzure> and yet some of the logs show up in search results
23:29 <@nmz787> hmm, so i want to design an adjustable current controlled power source for the laser etcher, as it is only on/off
23:30 <@nmz787> idk if anyone in here has experience with opamps and such... i'm thinking a lm317, a voltage follower around the current resistor, and adding in some bias to the follower via RC smoothed PWM
23:30 <@nmz787> since the lm317 current out follows: 1.25V/feedback_resistor
23:32 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20and%20simulation%20of%20neocortical%20microcircuitry.pdf
23:32 < kanzure> and http://www.nytimes.com/2015/10/09/science/rat-brain-digital-reconstruction-human-brain-project.html?_r=0
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