--- Log opened Thu Oct 08 00:00:51 2015 00:01 -!- sandeepkr [~sandeepkr@111.235.64.135] has joined ##hplusroadmap 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 00:27 -!- sandeepkr [~sandeepkr@111.235.64.135] has quit [Ping timeout: 256 seconds] 00:28 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 00:33 -!- sandeepkr [~sandeepkr@111.235.64.135] has joined ##hplusroadmap 00:34 < kanzure> maybe you could get octopus chromatophore skin display to show information about neural plasticity status in some high-resolution map 00:38 -!- Houshalter [~Houshalte@oh-71-50-57-55.dhcp.embarqhsd.net] has quit [Ping timeout: 265 seconds] 00:50 -!- sandeepkr [~sandeepkr@111.235.64.135] has quit [Ping timeout: 260 seconds] 00:58 -!- sandeepkr [~sandeepkr@111.235.64.135] has joined ##hplusroadmap 01:19 -!- sandeepkr [~sandeepkr@111.235.64.135] has quit [Ping timeout: 265 seconds] 01:57 -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] 02:04 -!- Viper168_ is now known as Viper168 02:04 -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 02:06 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 265 seconds] 02:06 -!- poppingtonic1 is now known as poppingtonic 02:18 -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap 02:49 -!- delinquentme [~delinquen@74.61.157.78] has joined ##hplusroadmap 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? 02:56 -!- Nadano [~Nadano@remote.diagnoptics.com] has joined 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has quit [Quit: Connection closed for inactivity] 05:32 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-sdukozyibiffkjng] has quit [Quit: Connection closed for inactivity] 05:38 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] 05:38 -!- Quashie [~boingredd@ool-18bccfe5.dyn.optonline.net] has quit [Ping timeout: 250 seconds] 05:39 -!- eudoxia [~eudoxia@r167-56-139-150.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 05:46 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 05:55 -!- cpopell`werk [~cpopell@209.48.69.2] has joined ##hplusroadmap 06:03 -!- Burnin8 [~Burn@pool-74-96-98-64.washdc.fios.verizon.net] has quit [Ping timeout: 244 seconds] 06:04 < JayDugger1> kanzure, do have a reference for those Freitas hierarchical ontologies you mentioned? 06:33 -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 06:34 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 250 seconds] 06:34 -!- poppingtonic1 is now known as poppingtonic 06:49 -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap 06:56 < kanzure> nah just ksrm and stuff 07:04 -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 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 07:05 -!- Houshalter [~Houshalte@oh-71-50-56-224.dhcp.embarqhsd.net] has joined ##hplusroadmap 07:06 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 255 seconds] 07:06 -!- poppingtonic1 is now known as poppingtonic 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.... 07:19 -!- Nadano [~Nadano@remote.diagnoptics.com] has joined ##hplusroadmap 07:26 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:f5d5:bf3d:8100:28fc] has joined ##hplusroadmap 07:27 -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] 07:32 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:f5d5:bf3d:8100:28fc] has quit [Read error: Connection reset by peer] 07:38 < kanzure> "nasa technology transfer initiative" http://www.technology.nasa.gov/startup 07:40 -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] 07:42 -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap 07:49 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-ovjcayurkymvbzun] has joined ##hplusroadmap 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 07:56 -!- seanph_ [~seanph@101.230.15.34] has quit [Remote host closed the connection] 07:56 -!- seanph [~seanph@174.139.17.218] has joined ##hplusroadmap 07:58 -!- Nadano [~Nadano@remote.diagnoptics.com] has left ##hplusroadmap ["Leaving"] 08:06 -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap 08:09 -!- Houshalter is now known as Hous 08:10 -!- c0rw1n is now known as c0 08:10 -!- seanph [~seanph@174.139.17.218] has quit [Remote host closed the connection] 08:11 -!- seanph [~seanph@174.139.17.218] has joined ##hplusroadmap 08:12 -!- c0 is now known as c0rw1n 08:15 -!- seanph [~seanph@174.139.17.218] has quit [Ping timeout: 260 seconds] 08:24 -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 08:26 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 264 seconds] 08:26 -!- poppingtonic1 is now known as poppingtonic 09:01 -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-wedtqydjmtcxckcu] has joined ##hplusroadmap 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 09:12 -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] 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 09:17 -!- eudoxia_ [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 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 09:20 -!- eudoxia [~eudoxia@r167-56-139-150.dialup.adsl.anteldata.net.uy] has quit [Ping timeout: 256 seconds] 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 09:30 -!- eudoxia_ [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 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 10:24 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 246 seconds] 10:30 -!- c0rw1n is now known as c0rw|afk 10:38 -!- cpopell`werk2 [~cpopell@209.48.69.2] has joined 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[~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 11:57 -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap 11:59 -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] 12:00 -!- XaTuring [~XaTuring@195.214.190.188] has joined ##hplusroadmap 12:04 -!- c0rw|afk [~c0rw1n@91.176.79.56] has joined ##hplusroadmap 12:06 -!- c0rw|afk is now known as c0rw1n 12:11 -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap 12:21 -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] 12:22 -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap 12:26 < kanzure> XaTuring: greetings 12:27 -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap 12:31 -!- eudoxia [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 12:49 -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] 12:51 -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap 12:53 -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap 12:59 -!- FourFire [~FourFire@43-229-11.connect.netcom.no] has joined ##hplusroadmap 13:00 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 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 13:18 -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has joined ##hplusroadmap 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 13:28 -!- math3 [uid54897@gateway/web/irccloud.com/x-xeyqsiseyejyssge] has joined ##hplusroadmap 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 13:52 -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 265 seconds] 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 14:02 -!- delinquentme [~delinquen@74.61.157.78] has joined ##hplusroadmap 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 14:08 -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has quit [Quit: Textual IRC Client: www.textualapp.com] 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 14:09 -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has joined ##hplusroadmap 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 14:22 -!- eudoxia [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 14:23 -!- yorick [~yorick@oftn/member/yorick] has quit [Read error: Connection reset by peer] 14:23 -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap 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 14:27 -!- yashgaroth [~yashgarot@2602:306:35fa:d500:7021:4657:d3ac:e424] has joined ##hplusroadmap 14:28 < maaku> kanzure: ? 14:28 < kanzure> well, it's not like it's a diamond or anything 14:29 < maaku> oh ok 14:29 -!- delinquentme [~delinquen@74.61.157.78] has quit [Ping timeout: 268 seconds] 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 14:30 -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has quit [Quit: Textual IRC Client: www.textualapp.com] 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 14:30 -!- Burninate [~Burn@pool-74-96-98-64.washdc.fios.verizon.net] has joined ##hplusroadmap 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 14:37 -!- delinquentme [~delinquen@74.61.157.78] has joined ##hplusroadmap 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 14:46 -!- FourFire [~FourFire@43-229-11.connect.netcom.no] has quit [Quit: Leaving] 14:46 < kanzure> can't you already do shape-specific chemical vapor deposition growth of diamonds? 14:46 -!- hehelleshin [~talinck@66-161-138-110.ubr1.dyn.lebanon-oh.fuse.net] has quit [Ping timeout: 264 seconds] 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 14:52 -!- augur [~augur@c-73-46-94-9.hsd1.fl.comcast.net] has quit [Quit: Leaving...] 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 15:01 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 244 seconds] 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 15:06 -!- augur [~augur@c-73-46-94-9.hsd1.fl.comcast.net] has joined ##hplusroadmap 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) 15:11 -!- XaTuring [~XaTuring@195.214.190.188] has quit [Quit: XaTuring] 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 15:13 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 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) 15:19 -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has joined ##hplusroadmap 15:19 < Jawmare> kanzure, find out what kind of tubes commerical dna machine uses 15:19 < Jawmare> I bet its tygon 15:19 -!- delinquentme [~delinquen@74.61.157.78] has quit [Ping timeout: 240 seconds] 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 15:22 -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] 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>
/py/4**3080000000
was not found on this server./py/eval(%224*%22%20%2B%20%22*3080000000%22)
was not found on this server.