| --- Log opened Thu Oct 08 00:00:51 2015 | ||
| -!- sandeepkr [~sandeepkr@111.235.64.135] has joined ##hplusroadmap | 00:01 | |
| kanzure | "a visual introduction to venture financing" http://dlopuch.github.io/venture-dealr/ | 00:01 |
|---|---|---|
| kanzure | and obligatory criticism https://news.ycombinator.com/item?id=10346585 | 00:05 |
| -!- sandeepkr [~sandeepkr@111.235.64.135] has quit [Ping timeout: 256 seconds] | 00:27 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 00:28 | |
| -!- sandeepkr [~sandeepkr@111.235.64.135] has joined ##hplusroadmap | 00:33 | |
| kanzure | maybe you could get octopus chromatophore skin display to show information about neural plasticity status in some high-resolution map | 00:34 |
| -!- Houshalter [~Houshalte@oh-71-50-57-55.dhcp.embarqhsd.net] has quit [Ping timeout: 265 seconds] | 00:38 | |
| -!- sandeepkr [~sandeepkr@111.235.64.135] has quit [Ping timeout: 260 seconds] | 00:50 | |
| -!- sandeepkr [~sandeepkr@111.235.64.135] has joined ##hplusroadmap | 00:58 | |
| -!- sandeepkr [~sandeepkr@111.235.64.135] has quit [Ping timeout: 265 seconds] | 01:19 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] | 01:57 | |
| -!- Viper168_ is now known as Viper168 | 02:04 | |
| -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 02:04 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 265 seconds] | 02:06 | |
| -!- poppingtonic1 is now known as poppingtonic | 02:06 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 02:18 | |
| -!- 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. | 02:49 |
| 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? | 02:50 |
| -!- Nadano [~Nadano@remote.diagnoptics.com] has joined ##hplusroadmap | 02:56 | |
| -!- delinquentme [~delinquen@74.61.157.78] has quit [Ping timeout: 244 seconds] | 02:57 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 240 seconds] | 03:00 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 03:00 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 03:44 | |
| -!- c0rw1n [~c0rw1n@91.176.79.56] has quit [] | 03:47 | |
| -!- c0rw1n [~c0rw1n@91.176.79.56] has joined ##hplusroadmap | 03:47 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 03:52 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Read error: Connection reset by peer] | 03:57 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 04:04 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 04:10 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 04:12 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 04:21 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 04:26 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] | 04:32 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 04:39 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 250 seconds] | 04:45 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 04:46 | |
| -!- Nadano [~Nadano@remote.diagnoptics.com] has quit [Quit: Leaving] | 04:49 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 05:02 | |
| -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 05:02 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 246 seconds] | 05:03 | |
| -!- poppingtonic1 is now known as poppingtonic | 05:03 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 05:04 | |
| -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 05:10 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 252 seconds] | 05:12 | |
| -!- poppingtonic1 is now known as poppingtonic | 05:12 | |
| -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-pajafuggyfawdtik] has quit [Quit: Connection closed for inactivity] | 05:13 | |
| -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-sdukozyibiffkjng] has quit [Quit: Connection closed for inactivity] | 05:32 | |
| -!- 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] | 05:38 | |
| -!- eudoxia [~eudoxia@r167-56-139-150.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap | 05:39 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 05:46 | |
| -!- cpopell`werk [~cpopell@209.48.69.2] has joined ##hplusroadmap | 05:55 | |
| -!- Burnin8 [~Burn@pool-74-96-98-64.washdc.fios.verizon.net] has quit [Ping timeout: 244 seconds] | 06:03 | |
| JayDugger1 | kanzure, do have a reference for those Freitas hierarchical ontologies you mentioned? | 06:04 |
| -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 06:33 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 250 seconds] | 06:34 | |
| -!- poppingtonic1 is now known as poppingtonic | 06:34 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap | 06:49 | |
| kanzure | nah just ksrm and stuff | 06:56 |
| -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 07:04 | |
| 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 | 07:05 | |
| -!- 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 | 07:06 |
| kanzure | foresight institute video stuff https://vimeo.com/foresightinst/videos | 07:07 |
| kanzure | bah george church was at a foresight institute conference to pimp cadnano, what a bunch of traitors | 07:08 |
| 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.... | 07:09 |
| -!- Nadano [~Nadano@remote.diagnoptics.com] has joined ##hplusroadmap | 07:19 | |
| -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:f5d5:bf3d:8100:28fc] has joined ##hplusroadmap | 07:26 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] | 07:27 | |
| -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:f5d5:bf3d:8100:28fc] has quit [Read error: Connection reset by peer] | 07:32 | |
| kanzure | "nasa technology transfer initiative" http://www.technology.nasa.gov/startup | 07:38 |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 07:40 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 07:42 | |
| -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-ovjcayurkymvbzun] has joined ##hplusroadmap | 07:49 | |
| 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 | 07:55 |
| -!- seanph_ [~seanph@101.230.15.34] has quit [Remote host closed the connection] | 07:56 | |
| -!- seanph [~seanph@174.139.17.218] has joined ##hplusroadmap | 07:56 | |
| -!- Nadano [~Nadano@remote.diagnoptics.com] has left ##hplusroadmap ["Leaving"] | 07:58 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap | 08:06 | |
| -!- Houshalter is now known as Hous | 08:09 | |
| -!- c0rw1n is now known as c0 | 08:10 | |
| -!- seanph [~seanph@174.139.17.218] has quit [Remote host closed the connection] | 08:10 | |
| -!- seanph [~seanph@174.139.17.218] has joined ##hplusroadmap | 08:11 | |
| -!- c0 is now known as c0rw1n | 08:12 | |
| -!- seanph [~seanph@174.139.17.218] has quit [Ping timeout: 260 seconds] | 08:15 | |
| -!- poppingtonic1 [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 08:24 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 264 seconds] | 08:26 | |
| -!- poppingtonic1 is now known as poppingtonic | 08:26 | |
| -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-wedtqydjmtcxckcu] has joined ##hplusroadmap | 09:01 | |
| CaptHindsight | kanzure: I more interested in how the proteins bond strands | 09:02 |
| CaptHindsight | have to read over all the work by the three that won the recent Nobel for Chemistry | 09:03 |
| CaptHindsight | why reinvent the wheel http://www.hhmi.org/research/dna-mismatch-repair-and-genetic-stability | 09:06 |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] | 09:12 | |
| 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 | 09:13 |
| 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 | 09:14 |
| CaptHindsight | and the errors in synthesis are easily detected since the oligos are so short | 09:16 |
| -!- eudoxia_ [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap | 09:17 | |
| 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 | 09:19 |
| 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 | 09:20 |
| 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 | 09:21 |
| CaptHindsight | I have some catching up to do | 09:23 |
| CaptHindsight | but it already splices and bonds | 09:23 |
| CaptHindsight | what's a good way to make quick money in DNA synthesis? | 09:28 |
| CaptHindsight | combine that with the plans for the tech, hand it to several co's in China... | 09:29 |
| 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] | 09:30 | |
| maaku | love the AI Now guy | 10:18 |
| maaku | can't tell if it is satire or earnest naiveté | 10:18 |
| Hous | he's serious | 10:19 |
| Hous | just crazy | 10:19 |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 246 seconds] | 10:24 | |
| -!- c0rw1n is now known as c0rw|afk | 10:30 | |
| -!- cpopell`werk2 [~cpopell@209.48.69.2] has joined ##hplusroadmap | 10:38 | |
| -!- cpopell`werk [~cpopell@209.48.69.2] has quit [Ping timeout: 268 seconds] | 10:42 | |
| -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-tbqqavldgkbhzipn] has joined ##hplusroadmap | 10:49 | |
| -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-ovjcayurkymvbzun] has quit [Quit: Connection closed for inactivity] | 10:53 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 11:00 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 11:05 | |
| -!- c0rw|afk [~c0rw1n@91.176.79.56] has quit [Ping timeout: 264 seconds] | 11:12 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 264 seconds] | 11:18 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 11:21 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 264 seconds] | 11:33 | |
| -!- Hous [~Houshalte@oh-71-50-56-224.dhcp.embarqhsd.net] has quit [Read error: Connection reset by peer] | 11:43 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has quit [Ping timeout: 246 seconds] | 11:49 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap | 11:57 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 11:57 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 11:59 | |
| -!- XaTuring [~XaTuring@195.214.190.188] has joined ##hplusroadmap | 12:00 | |
| -!- c0rw|afk [~c0rw1n@91.176.79.56] has joined ##hplusroadmap | 12:04 | |
| -!- c0rw|afk is now known as c0rw1n | 12:06 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 12:11 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 12:21 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has joined ##hplusroadmap | 12:22 | |
| kanzure | XaTuring: greetings | 12:26 |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 12:27 | |
| -!- eudoxia [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap | 12:31 | |
| -!- nsh [~lol@wikipedia/nsh] has quit [Excess Flood] | 12:49 | |
| -!- nsh [~lol@wikipedia/nsh] has joined ##hplusroadmap | 12:51 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 12:53 | |
| -!- FourFire [~FourFire@43-229-11.connect.netcom.no] has joined ##hplusroadmap | 12:59 | |
| -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] | 13:00 | |
| 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. | 13:13 |
| xrr | What determines n? | 13:16 |
| kanzure | physics, limits of the universe and all time and space | 13:17 |
| -!- 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. | 13:18 |
| 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... | 13:21 |
| 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 | 13:25 |
| kanzure | "Reconstruction and Simulation of Neocortical Microcircuitry" | 13:26 |
| yoleaux | kanzure: Sorry, that doesn't appear to be an HTML page. | 13:26 |
| 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 | 13:28 | |
| kanzure | 13:32 <+dpk> "Soviet nuclear submarine. Sailor for scale" http://i.imgur.com/XSUt1wu.jpg | 13:33 |
| CaptHindsight | the inkjet method already makes full custom oligos ~100bp long | 13:34 |
| kanzure | solid state can be way better than chemical synthesis | 13:34 |
| 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 | 13:35 |
| CaptHindsight | the latest nobel winners in Chemistry have figured out how proteins scan, cleave and bind on the nanoscale | 13:37 |
| 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? | 13:38 |
| CaptHindsight | with something you can control on demand | 13:39 |
| kanzure | that's novel research territory | 13:39 |
| CaptHindsight | well you've pretty much proven that there's nobody to copy :) | 13:40 |
| 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 | 13:41 |
| CaptHindsight | have to keep looking for them | 13:42 |
| 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 | 13:43 |
| 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. | 13:44 |
| 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? | 13:45 |
| 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. | 13:46 |
| kanzure | drug trials are $100M minimum these days, sorta dumb but that's how the FDA rolls. and how the costs work out, apparently... | 13:47 |
| 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/ | 13:48 |
| 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? | 13:49 |
| CaptHindsight | is there an anti-synthetic DNA group or lobby? | 13:50 |
| kanzure | ETC group | 13:50 |
| -!- 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/ | 13:52 |
| CaptHindsight | yeah, industrial uses | 13:53 |
| kanzure | stuff like "gastrointestinal microbe to treat lactose intolerance" would be interesting | 13:53 |
| CaptHindsight | lots of em | 13:53 |
| 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. | 13:54 |
| 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 | 13:56 |
| 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. | 13:57 |
| kanzure | (or blood is another popular one there, w/e) | 13:58 |
| CaptHindsight | print synthetic spider silk on demand as you repel down the mountain | 13:59 |
| 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 | 14:00 |
| 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 | 14:02 | |
| CaptHindsight | custom organism vs current method | 14:03 |
| CaptHindsight | polymer production could be a big one | 14:03 |
| CaptHindsight | chemical sensors | 14:04 |
| kanzure | lots of sensors, yes | 14:04 |
| CaptHindsight | thats where the hybridization can come in | 14:04 |
| 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 ... | 14:05 |
| 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) | 14:06 |
| 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") | 14:08 |
| 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 | 14:09 |
| CaptHindsight | but just works | 14:10 |
| CaptHindsight | easy to connect | 14:10 |
| CaptHindsight | and standardized | 14:10 |
| CaptHindsight | or it connects itself | 14:11 |
| 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 | 14:12 |
| 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 | 14:13 |
| CaptHindsight | I'm just looking further | 14:14 |
| kanzure | probably lots of gene trade over the interwebs | 14:15 |
| CaptHindsight | I'm picturing remote controlled or monitored cells | 14:16 |
| 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 | 14:17 |
| kanzure | speculation goal is "really cool things to do with biology that wouldn't be impossible, and would actually be useful"? | 14:18 |
| CaptHindsight | most of the list looks like things that are just bulk production or materials or sensing | 14:19 |
| CaptHindsight | say 10K cells tweaked to sense some odor | 14:20 |
| CaptHindsight | when you get enough consensus you found it | 14:20 |
| -!- eudoxia [~eudoxia@r167-56-161-182.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] | 14:22 | |
| -!- yorick [~yorick@oftn/member/yorick] has quit [Read error: Connection reset by peer] | 14:23 | |
| -!- yorick [~yorick@oftn/member/yorick] has joined ##hplusroadmap | 14:23 | |
| 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) | 14:24 |
| kanzure | well, i mean, cheap dna synthesis.... | 14:25 |
| 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 | 14:27 | |
| maaku | kanzure: ? | 14:28 |
| kanzure | well, it's not like it's a diamond or anything | 14:28 |
| 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 | 14:29 |
| -!- 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 | 14:30 |
| 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 | 14:31 |
| 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? | 14:32 |
| 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/ | 14:33 |
| 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/ | 14:34 |
| 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/ | 14:35 |
| 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 | 14:36 |
| 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 | 14:37 |
| 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/ | 14:40 |
| 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 | 14:44 |
| CaptHindsight | oh no they have cured a few patients already | 14:45 |
| CaptHindsight | let me find a link | 14:45 |
| kanzure | clinicaltrials.gov | 14:45 |
| 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 | 14:46 |
| 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 | 14:47 |
| maaku | using just 1st generation dumb diamandoid materials | 14:48 |
| CaptHindsight | rocket boots | 14:48 |
| kanzure | "Poliovirus Vaccine for Recurrent Glioblastoma Multiforme (GBM) (PVS-RIPO)" https://clinicaltrials.gov/ct2/show/NCT01491893 | 14:49 |
| 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? | 14:50 |
| 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 | 14:51 |
| 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...] | 14:52 | |
| 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 | 14:53 |
| 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 | 14:55 |
| fenn | https://en.wikipedia.org/wiki/Bacterial_nanowires | 14:56 |
| CaptHindsight | neat | 14:57 |
| CaptHindsight | maaku: also nanoscale cutting tools | 14:59 |
| 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 | 15:00 |
| -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 244 seconds] | 15:01 | |
| kanzure | .wik protein design | 15:01 |
| 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.... | 15:02 |
| 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. | 15:04 |
| 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 | 15:06 | |
| kanzure | yep sure | 15:07 |
| kanzure | thing i just proposed is minor abstraction on top of proteins, to hide the unpredictable useless parts | 15:07 |
| 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? | 15:08 |
| 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 | 15:09 |
| fenn | you can link them with glycine chains that don't do anything | 15:10 |
| kanzure | doesn't that lose out on structural precision? | 15:10 |
| 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 | 15:11 |
| fenn | you just have to make sure that the individual pieces fold fast enough that it never mis-folds | 15:12 |
| 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 | 15:13 | |
| 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 | 15:14 |
| 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 | 15:15 |
| 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 | 15:16 |
| 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 | 15:17 |
| kanzure | poppingtonic: nanoengineer was abandoned, cadnano seems to still be developed (haven't looked) | 15:18 |
| -!- 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] | 15:19 | |
| 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 | 15:20 |
| 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 | 15:22 |
| 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) | 15:23 |
| 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 | 15:24 |
| poppingtonic | hmmm kanzure, I thought it was you | 15:25 |
| kanzure | nah i only rescued nanoengineer from oblivion | 15:25 |
| 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 | 15:26 |
| fenn | it used to be spelled caDNAno | 15:27 |
| 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 | 15:28 |
| kanzure | "mostly lousy sensors" :D | 15:29 |
| poppingtonic | well, he mentions it... | 15:30 |
| fenn | i would hope so | 15:30 |
| 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 | 15:32 |
| 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 | 15:33 |
| 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 | 15:34 |
| 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 | 15:35 |
| fenn | or even regular vaccines | 15:36 |
| fenn | or serum or whatever | 15:36 |
| CaptHindsight | kanzure: sounds similar to a windoze machine | 15:36 |
| 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. | 15:37 |
| 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 | 15:38 |
| 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 | 15:39 |
| 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! | 15:40 |
| 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 | 15:41 |
| fenn | .py 4**3080000000 | 15:42 |
| yoleaux | <html><head><meta http-equiv="content-type" content="text/html;charset=utf-8"><title>404 Not Found</title></head><body text=#000000 bgcolor=#ffffff><h1>Error: Not Found</h1><h2>The requested URL <code>/py/4**3080000000</code> was not found on this server.</h2><h2></h2></body></html> | 15:42 |
| kanzure | .py eval("4*" + "*3080000000") | 15:43 |
| yoleaux | <html><head><meta http-equiv="content-type" content="text/html;charset=utf-8"><title>404 Not Found</title></head><body text=#000000 bgcolor=#ffffff><h1>Error: Not Found</h1><h2>The requested URL <code>/py/eval(%224*%22%20%2B%20%22*3080000000%22)</code> was not found on this server.</h2><h2></h2></body></html> | 15:43 |
| kanzure | brutal | 15:43 |
| fenn | the .py plugin just doesn't work | 15:43 |
| poppingtonic | vimeo.com/63008845 | 15:43 |
| fenn | guess i will kill that python calculation before i run out of swap space | 15:45 |
| fenn | it's a really big number | 15:46 |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap | 15:47 | |
| 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? | 15:48 |
| fenn | yeah i asked steve to solve that math problem but he dodged | 15:50 |
| fenn | the QC before/after question | 15:50 |
| CaptHindsight | I want to see how the proteins do QC | 15:52 |
| fenn | they look at base pair mismatch | 15:52 |
| 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 | 15:53 |
| fenn | there are some schemes that precipitate out mismatches by binding to them | 15:54 |
| CaptHindsight | OC, cleaving and bonding | 15:54 |
| fenn | OC? | 15:55 |
| CaptHindsight | finding the mismatches | 15:55 |
| CaptHindsight | quality control | 15:55 |
| CaptHindsight | the inkjet printer doesn't do a perfect job | 15:57 |
| CaptHindsight | of printing the oligos | 15:57 |
| CaptHindsight | it's a patent minefield but it's not difficult to MEMS a femtoliter printhead with K's of nozzles | 15:59 |
| Jawmare | If you cap it do you still end up with mismatch? | 16:02 |
| poppingtonic | Open Invention Network for SynthBio | 16:03 |
| 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...) | 16:13 |
| 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 | 16:14 |
| 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/ | 16:20 |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] | 16:20 | |
| 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 | 16:22 |
| 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. | 16:23 |
| 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. | 16:25 |
| fenn | nothing's competing, you just amplify a mixture of sequences | 16:26 |
| -!- helleshin [~talinck@66-161-138-110.ubr1.dyn.lebanon-oh.fuse.net] has joined ##hplusroadmap | 16:28 | |
| kanzure | shorter strands take less time to replicate. it's competitive. | 16:29 |
| fenn | the wrong strands are only 1 bp shorter | 16:30 |
| fenn | maybe that's enough of an advantage over many rounds of replication to completely swamp the signal | 16:31 |
| fenn | maaku: cheap enough dna synthesis is still a roadblock even for institutional scientists working on good stuff like neuroscience, metabolism, aging, etc | 16:35 |
| -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-easwljrhxghwaezx] has joined ##hplusroadmap | 16:35 | |
| 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 | 16:36 |
| 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 | 16:37 |
| fenn | that's where biology is at without DNA synthesis | 16:38 |
| fenn | but each cut/paste operation takes 4 hours | 16:38 |
| kanzure | and also you can only use like 3 punch cards | 16:40 |
| 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 | 16:41 |
| * fenn goes off in search of magnesium | 16:42 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap | 16:46 | |
| kanzure | been working on lunch for the last 7 hours, i blame time vortex | 17:00 |
| -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Ping timeout: 255 seconds] | 17:05 | |
| -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap | 17:17 | |
| CaptHindsight | <Jawmare> and how do commerical dna synth solve that problem? like kanzure mentioned or they get quiet about it when asked directly | 18:28 |
| -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:559d:3823:53cb:4ce6] has joined ##hplusroadmap | 18:42 | |
| -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-easwljrhxghwaezx] has quit [Quit: Connection closed for inactivity] | 19:03 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] | 19:06 | |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has joined ##hplusroadmap | 19:15 | |
| 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." | 19:17 |
| 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 | 19:18 |
| kanzure | there was also this thing http://2014.igem.org/Team:SYSU-China/content.html#Project/Discussion | 19:20 |
| -!- wrldpc1 [~ben@bai859b91ac.bai.ne.jp] has quit [Quit: wrldpc1] | 19:25 | |
| -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has joined ##hplusroadmap | 19:32 | |
| -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has quit [Quit: My Mac has gone to sleep. ZZZzzz…] | 19:42 | |
| -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has joined ##hplusroadmap | 19:44 | |
| mgin | anyone going to the alcor conference?? | 19:54 |
| kanzure | nah, they didn't have room for my presentation | 19:56 |
| kanzure | as of a week ago | 19:56 |
| kanzure | aschwin de wolf's publication looked somewhat interesting as an update to his research work | 19:58 |
| Jawmare | removing anhydrous acetoniltilre from sureseal bottles... | 20:02 |
| kanzure | gravity-assist | 20:03 |
| kanzure | or uh.. i think one of the designs pumped argon into the bottle | 20:03 |
| Jawmare | with syringe.... :( | 20:03 |
| JayDugger1 | I didn't see anything about classification or ontologies in Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines. Just hierarchy. | 20:04 |
| 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? | 20:05 |
| 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 | 20:06 |
| 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 | 20:07 |
| -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-hgcklrdygvwjotir] has joined ##hplusroadmap | 20:07 | |
| Jawmare | this funny named company is a pretty good source for DMSO http://www.gaylordchemical.com/index.php?page=replace-acetonitrile-with-dmso | 20:08 |
| 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 | 20:09 |
| kanzure | .title | 20:10 |
| yoleaux | The Last Transmission of Frodo Baggins | 20:10 |
| kanzure | maybe this is cleverly disguised ralph merkle tolkien fanfic | 20:10 |
| -!- justanotheruser is now known as justanotherus1r | 20:10 | |
| JayDugger1 | Very clever, indeed. | 20:12 |
| kanzure | Jawmare: how much debugging would a synthesis project like this take? how many things can go wrong. | 20:12 |
| 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? | 20:13 |
| 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 | 20:14 |
| 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 | 20:15 |
| -!- justanotherus1r is now known as justanotheruser | 20:15 | |
| Jawmare | in my opinion, functionalizing glass slide and do solid state synth is going to be much more robust | 20:16 |
| 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 | 20:17 |
| 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 | 20:18 |
| Jawmare | where do you use 3-methoxypropioniltrile? | 20:20 |
| fenn | inkjet fluid solvent, for dispensing the phosphoramidites i think | 20:22 |
| Jawmare | just because it have a nitrile group, doesn't mean it is as poisonous as cyanide | 20:24 |
| 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 | 20:25 |
| Jawmare | I'd say 3-methoxypropioniltrile is safe if you take reasonable protective measure | 20:26 |
| fenn | ok | 20:27 |
| 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 | 20:28 |
| Jawmare | Yes it is toxic, and yes you will die if you drink it / get it on your skin / get it on your eyes | 20:30 |
| 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 | 20:32 |
| fenn | or maybe just using a better sprayer will reduce solvent use enough that it is no longer a major expense | 20:33 |
| 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 | 20:34 |
| 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 | 20:39 |
| Jawmare | https://www.alfa.com/en/catalog/42311 | 20:40 |
| -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-tbqqavldgkbhzipn] has quit [Quit: Connection closed for inactivity] | 20:43 | |
| fenn | much less than $100/litre | 20:47 |
| fenn | the posam people were buying it in drums | 20:47 |
| Jawmare | yes, if you buy it in drums | 20:48 |
| Jawmare | now how do you keep it anhydrous | 20:48 |
| Jawmare | tips: CaCl2 or molecular sieves | 20:49 |
| 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 | 20:51 |
| 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 | 20:52 |
| 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 | 20:55 |
| -!- drewbot [~cinch@ec2-54-162-98-210.compute-1.amazonaws.com] has quit [Remote host closed the connection] | 20:55 | |
| * fenn greps the logs | 20:55 | |
| -!- drewbot [~cinch@ec2-54-157-31-179.compute-1.amazonaws.com] has joined ##hplusroadmap | 20:55 | |
| Jawmare | anyways, good night... another 4+- 2 hours of lab tomorrow | 20:56 |
| Jawmare | probably more like 7 :( | 20:56 |
| 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 | 20:58 |
| -!- Houshalter [~Houshalte@oh-71-50-56-224.dhcp.embarqhsd.net] has joined ##hplusroadmap | 21:04 | |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 21:04 | |
| -!- salamandyr [~salamandy@cpe-104-172-250-37.socal.res.rr.com] has joined ##hplusroadmap | 21:16 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has joined ##hplusroadmap | 21:17 | |
| -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has quit [Quit: My Mac has gone to sleep. ZZZzzz…] | 21:18 | |
| -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has joined ##hplusroadmap | 21:19 | |
| -!- salamandyr [~salamandy@cpe-104-172-250-37.socal.res.rr.com] has left ##hplusroadmap ["Leaving"] | 21:21 | |
| -!- seanph [~seanph@101.230.15.34] has joined ##hplusroadmap | 21:22 | |
| -!- Ythogtha [~Ythogtha@unaffiliated/ythogtha] has quit [Quit: Textual IRC Client: www.textualapp.com] | 21:24 | |
| -!- poppingtonic [~Thunderbi@unaffiliated/poppingtonic] has quit [Ping timeout: 240 seconds] | 21:25 | |
| -!- sandeepkr [~sandeepkr@111.235.64.4] has quit [Ping timeout: 240 seconds] | 21:34 | |
| -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] | 21:35 | |
| kanzure | http://newsoffice.mit.edu/2014/algorithm-recovers-speech-from-vibrations-0804 | 21:36 |
| -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap | 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/ | 21:36 |
| -!- seanph [~seanph@101.230.15.34] has quit [Remote host closed the connection] | 21:40 | |
| -!- seanph [~seanph@174.139.17.218] has joined ##hplusroadmap | 21:41 | |
| kanzure | didn't know the "molecular manufacturing shortcut group" was headed by a dude from raytheon http://www.islandone.org/MMSG/ | 21:41 |
| fenn | was at nasa too https://en.wikipedia.org/wiki/McKendree_cylinder | 21:54 |
| 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. | 21:58 |
| kanzure | i thought there would be a list on old sci.nanotech posts but nope | 21:59 |
| kanzure | actually i didn't even see utility fog mentioned on alt.sci.nanotech either; are people just braindead or what. | 22:00 |
| 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 | 22:03 |
| 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 | 22:04 |
| CaptHindsight | we need more shops around like the ones in Blade Runner "I make your eyes, just eyes" | 22:07 |
| -!- Houshalter [~Houshalte@oh-71-50-56-224.dhcp.embarqhsd.net] has quit [Quit: Quit] | 22:09 | |
| -!- AmbulatoryCortex [~Ambulator@173-31-155-69.client.mchsi.com] has quit [Read error: Connection reset by peer] | 22:09 | |
| -!- math3 [uid54897@gateway/web/irccloud.com/x-xeyqsiseyejyssge] has quit [Quit: Connection closed for inactivity] | 22:10 | |
| fenn | "i've personally made 70 billion copies of my book" - george church | 22:19 |
| -!- yashgaroth [~yashgarot@2602:306:35fa:d500:7021:4657:d3ac:e424] has quit [Quit: Leaving] | 22:20 | |
| fenn | "robot concentration (nM)" | 22:28 |
| -!- seanph_ [~seanph@101.230.15.34] has joined ##hplusroadmap | 22:34 | |
| -!- seanph [~seanph@174.139.17.218] has quit [Ping timeout: 255 seconds] | 22:37 | |
| @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 :/ | 22:52 |
| kanzure | what about chemically attaching the primers permanently | 22:55 |
| kanzure | the primers that aren't "in range" are irrelevant anyway | 22:55 |
| 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 | 22:56 |
| 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. | 22:57 |
| 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 | 22:58 |
| 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? | 22:59 |
| 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 | 23:00 |
| @nmz787 | those things conflict... narcolepsy and sleeping-like-zero | 23:01 |
| kanzure | narcolepsy can have similar symptoms as insomnia | 23:01 |
| @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 | 23:02 |
| @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) | 23:03 |
| kanzure | JUST KIDDING IT'S HIS BUTTHOLE | 23:04 |
| 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 | 23:05 |
| @nmz787 | isn't that some sort of sea creature's life cycle? | 23:06 |
| @nmz787 | why is that in there??? | 23:06 |
| 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 | 23:07 |
| * nmz787 oh yeah, at least my face is falling off just in time for halloween | 23:08 | |
| kanzure | tried chemo for that? | 23:08 |
| @nmz787 | idk, looks like he gets between 5 and 7 hours a night on avg | 23:09 |
| -!- seanph_ [~seanph@101.230.15.34] has quit [Remote host closed the connection] | 23:09 | |
| fenn | if i'm reading this data right george church only sleeps 5-6 hours a night | 23:09 |
| -!- seanph [~seanph@67.198.144.130] has joined ##hplusroadmap | 23:09 | |
| @nmz787 | see, we have good correlation | 23:09 |
| fenn | high five to six | 23:09 |
| fenn | go team | 23:09 |
| @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 | 23:11 |
| -!- Madplatypus [uid19957@gateway/web/irccloud.com/x-wedtqydjmtcxckcu] has quit [Quit: Connection closed for inactivity] | 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? | 23:12 |
| @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 | 23:13 |
| fenn | rule 34 | 23:14 |
| 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 | 23:15 |
| 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? | 23:16 |
| fenn | random disconnects are IRC's way of letting you know that time has passed | 23:19 |
| 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 | 23:22 |
| 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 | 23:27 |
| @nmz787 | hmm, so i want to design an adjustable current controlled power source for the laser etcher, as it is only on/off | 23:29 |
| @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 | 23:30 |
| 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 | 23:32 |
| -!- heath [~heath@unaffiliated/ybit] has quit [Ping timeout: 250 seconds] | 23:51 | |
| -!- heath [~heath@unaffiliated/ybit] has joined ##hplusroadmap | 23:52 | |
| --- Log closed Fri Oct 09 00:00:51 2015 | ||
Generated by irclog2html.py 2.15.0.dev0 by Marius Gedminas - find it at mg.pov.lt!
