2014-04-23.log

--- Log opened Wed Apr 23 00:00:05 2014
--- Day changed Wed Apr 23 2014
fennunit tests00:00
fenner, regression testing00:00
fennthat's all i got00:00
xmjcustomers yelling "Why does this not look the same across all my browsers / devices ???"00:01
xmj"My macbook air displays differntly than my Galaxy S999!!!"00:02
@kanzureoften just me yelling at myself about that00:02
fenn"because it's not an image?"00:02
@kanzurejust because it's not an image doesn't mean that i get to ignore rendering engines00:02
fennwhy not00:02
@kanzureweinre is pretty helpful00:02
fennhow many different engines are there anyway00:04
fennmore than 3?00:04
@kanzuregecko, webkit, presto, trident00:04
@kanzureblink00:04
@kanzureservo00:04
@kanzureeach have their own versions, bundled into applications that also have lots of versioning, and then those applications have different distributions for each device00:05
fennis it the goal of the engine developers to be standards compliant?00:07
fenni.e.  do what the spec says as best they can00:07
fenni can't think of any other field where massive amounts of effort is spent tailoring the input around the bugs of the software00:09
fennmaybe government work00:09
@kanzurehave you ever watched a web developer do his thing?00:09
fenni guess not00:10
@kanzurestalkerwatch someone next time you're in a coffee shop00:10
fennwhat's a web developer?00:10
@kanzureyou'll either laugh or cry00:10
@kanzureit's the person using 10 devices and 100 browsers00:10
fennis this where you take the photoshop drawing the client has given you and chop it into pieces?00:10
Lemminkainenand then you animate it with now.js, fenn00:10
@kanzurethat's sometimes one part of it, but at this point i just outsource that to psd2html.com00:10
Lemminkainencan't forget that part00:10
Lemminkainenpopcorn.js is also very important, it makes your web apps smell like butter00:11
fennso, i want to get rid of all that shit and just use LCARS for everything00:11
fennhow do i reverse all the shit into clean structured data?00:11
LemminkainenI have a flock of highly trained pigeons to sell you, then00:11
@kanzurewell, you can start by not writing for the web00:11
fenni'm thinking some kind of evolutionary classifier, similar to a spam filter00:12
fenn"this is the content, this is a nav menu header, this is a nav element, this is a caption" etc00:13
@kanzurei already don't like where this is going00:13
@kanzureLCARS was crap too00:13
fenni disagree, it was way ahead of its time00:14
fennthe 3d graphics were crap, but only because they didn't have the knowhow to make it fit with the rest of the interface00:15
@kanzurewhy is this interesting http://upload.wikimedia.org/wikipedia/commons/a/aa/Lcars_wallpaper.gif00:15
@kanzurewhat the fuck are the numbers on the left00:15
@kanzureand why are there curved edges?00:15
fennsorry i am neck deep in swap atm00:17
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@kanzureyou have like 2 MB of RAM00:17
@kanzureafter you account for 800 MB of nsa.img00:17
fennhah00:17
fenni always wondered why chrome needed 190MB to show a one paragraph wikipedia entry00:18
@kanzurelet me know when your baseband processor stops being a secret-sharing monster00:18
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fennless arbitrary crap http://www.oocities.org/tana100750/00:20
fennthe font is a little bit much, but other than that it's a very elegant design00:20
@kanzurelook at all those wasted pixels by curves00:20
fennit's a touchscreen interface00:20
fennfat fingers waste pixels00:20
fennso i am thinking you have something like ranger, where each window opens another bar, and the previous bar falls off the side of the screen (but you can go back to it if necessary)00:21
@kanzurei think i'll be keeping my keyboard interface for now00:22
fennlike a vertical tab bar in a browser00:22
@kanzurei carry that keyboard in my pocket00:22
fennin fact it would be a web browser too00:22
fennhave you tried the steno app for ipad?00:22
@kanzureno, also haven't seen it00:23
fennah. well, it exists00:23
fennthe developer sells a silicone thingy that goes over the screen so you hold your hands in the right place, or something00:23
fennbut you can use it without the thingy00:23
fennanyway my point was that onscreen keyboards suck00:24
@kanzurei wonder if ALS patients have control of that ear membrane muscle00:24
fenni also like the automatic callouts on diagrams. remember filelight? http://en.wikipedia.org/wiki/Filelight i'm going to re-do that with d3: http://bl.ocks.org/mbostock/406342300:27
fennthere's a pretty good android disk usage app (called "disk usage" believe it or not) that is similar to how filelight worked, but with rectangles00:28
fennthrash thrash thrash00:29
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fennhttps://code.google.com/p/diskusage/00:31
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fennoh yes there is also a tricorder app with no rounded corners https://f-droid.org/repository/browse/?fdid=org.hermit.tricorder http://www.appszoom.com/android_applications/tools/tricorder_bsf_screenshots.html00:52
fennprobably others like that00:52
fennit seems like most of the stuff on the internet is either a toy (completely not functional for anything but blinkenlights) or the developer hasn't put much thought into a coherent system that spans more than a single app00:57
fennthere was a java widget toolkit but i dunno what came out of that00:57
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fennthe nook looks so much like the star trek PADD because it reflects the ambient light off a flat surface instead of glowing and bouncing light around inside it http://fennetic.net/irc/nook_padd.jpg http://images.auctionworks.com/hi/3/3282/padd-29.jpg01:31
fennan lcd looks a lot different http://wiki.maemo.org/images/1/15/ThemeShot3.jpg01:33
ebowdenOh, is this functioning?01:33
ebowdenThe non-LCD one.01:34
ebowden(The non-LCD one.)01:34
fennnook_padd.jpg is how i'm chatting right now01:34
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fennpadd-29 is a prop made by laser printing onto a transparency sheet01:35
ebowdenAh, ok.01:36
ebowdenI wonder if it would be possible to make one look exactly like the printed one.01:36
fennyeah there are zillions of replicas, that might even be a replica01:37
fennthere is a reflective color display technology in perpetual vaporware stage from pixel qi01:38
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fenni've never actually seen one though01:39
ebowdenOk.01:39
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fennoops not pixel qi, i meant Mirasol: http://techcrunch.com/2010/02/15/color-e-reader-uses-butterfly-based-technology-to-save-power/01:41
ebowdenOk.01:43
fennsomething that doesn't come through so well in pictures is how light the nook is. it weighs less than my phone despite having 4 times the surface area01:46
fenni double checked and the phone actually weighs 40% less. but it FEELS heavier01:50
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delinquentmehttp://www.mensjournal.com/magazine/print-view/do-men-suck-at-friendship-2014042201:56
delinquentmetrue!01:56
delinquentmebrownies, kanzure , fenn ParahSailin  you guys are my fronds :D01:56
delinquentmeI hope you die a long time after everyone else <#01:56
fennwhat happened to that heart?01:58
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delinquentmeI stepped on the top half02:00
delinquentmeIts how the umbuttu tribesmen relay man-appreciation over instant messaging02:00
archelsyou want your friends to die? gee whiz02:00
Lemminkainenmutation before death, dammit02:02
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delinquentme^^^^02:16
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archelsdon't suppose anyone has a digital copy of Longevitize lying around?02:25
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mosasaurIs MIRI that bad? I know I share the feelings, but probably for completely different reasons. I mean I am against academia *and* billionaires.03:17
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archelspaperbot: http://www.sciencedirect.com/science/article/pii/S026240791262755903:19
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/9542a0ea6c79693d3c44a08fd6ebbf97.txt03:19
archelspaperbot: http://www.sciencedirect.com/science/article/pii/S0262407912627559/pdfft?md5=bad43cabdd6be43e92c389edbb61ae5f&pid=1-s2.0-S0262407912627559-main.pdf03:20
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/a3166d720c2d175befa4fc95ae51fd82.pdf03:20
archels<303:20
* archels wonders what that MD5 is for03:20
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* pasky scratches head at http://arxiv.org/abs/1401.121905:26
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mosasaurpasky: I think they're still trying to solve the problem that quantum measurements require an observer.06:36
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ebowden_paperbot: http://www.sciencedirect.com/science/article/pii/S027153170500104106:47
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/ad2643a7c38c723359b9773d838f7b59.txt06:47
ebowden_paperbot: http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf06:47
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/d010a7e0119e15952a7d1e1d2777a7c.txt06:47
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ebowden_Oh, hello FourFire.06:48
FourFireello06:48
ebowden_paperbot: http://www.journals.elsevierhealth.com/periodicals/ntr/article/PIIS0271531705001041/abstract06:49
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/65eed9b74197844031fb7fb611ba259f.txt06:49
ebowden_paperbot: http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf06:50
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/a61172a0bfd230e00134d62372fb488b.txt06:50
ebowden_Damnit.06:50
ebowden_I am not good at paperbot.06:51
ebowden_paperbot: http://download.journals.elsevierhealth.com/pdfs/journals/0271-5317/PIIS0271531705001041.pdf06:52
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/2db8ec5f4524416ddc08562c59b3b358.txt06:52
ebowden_:(06:52
ebowden_Does anyone here know how to properly use paperbot?06:54
mosasaurebowden_: is it supposed to extract the javascript generated content?06:55
ebowden_I have absolutely no idea how it works, but normally it gives you a nice pretty PDF.06:56
* mosasaur wonders what it does with a google groups page06:56
mosasaurpaperbot: https://groups.google.com/forum/#!forum/endgame-singularity06:58
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/3a73de0d7d8f7aaac21d63537a91056a.txt06:58
mosasaurnope :-(06:58
ebowden_Oh, no, it extracts a PDF text file.06:59
ebowden_Doesn't create one.06:59
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@kanzureebowden_: instructions are here, https://github.com/kanzure/paperbot07:14
ebowden_Ah, thanks.07:14
ebowden_Well, night.07:14
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@kanzurehttp://info.5amsolutions.com/blog/bid/157752/Venter-s-Human-Longevity-Academic-vs-Private-Genomics-Round-207:20
@kanzurehttp://www.humanlongevity.com/07:20
@kanzure"hey plan to sequence between 40,000 and 100,000 genomes a year. To do that, they’ve purchased two of Illumina’s new high-end DNA sequencing devices, the HiSeq X Ten, which is advertised as able to sequence a complete human genome for the long-sought-after price of $1,000."07:20
@kanzure"So far they’ve raised $70M for this venture. $20M will go for those two sequencers, and $40M will go to sequence those first 40,000 genomes, so no doubt they’ll be looking for other sources of funding soon. Given Venter’s success at Celera in building interest in the potential commercial value of the human genome, I’d say he’ll have little trouble raising more funds - Celera pulled in over $1B from their public offerings of stock."07:21
@kanzure"The company, according to their press release, is “focused on extending the healthy, high performance human life span” and is going to “tackle the diseases associated with aging-related human biological decline”."07:21
cluckjo_O07:22
@kanzurediamandis is on the board of directors haha07:22
cluckjdeCode part 2?07:22
@kanzure"HLI has entered into a collaboration with Metabolon Inc., the world’s leader in the field of metabolomics. Metabolon has developed proprietary technology to quickly identify and measure the body’s biochemicals and will provide such biochemical profiling services to HLI. In the initial term of the agreement Metabolon will carry out small molecule analysis of 10,000 subjects and collaborate with HLI to map changes in the small molecules to ...07:23
@kanzure... end points of disease and gene mutations."07:23
cluckjso craig venter wants to live forever, now? :)07:23
@kanzureoh cool they have a public phone number: 858-249-750007:24
@kanzuretotally going to prank call them07:24
cluckjask if their $10 million sequencer is running07:24
FourFirekanzure, I'm all for cheaper sequencing07:25
FourFiredo they have orders, or are they just doing it on random people?07:26
FourFire(first 40 000)07:26
@kanzuredunno, so far the pitch seems sort of fucked up07:26
@kanzuregive us $70M so we can buy some dna sequencers and do lots of sequencing?07:26
FourFirewho are they sequencing though?07:27
@kanzurewhy does that matter?07:27
cluckjthere's probably more going on there than their pitch suggests07:27
@kanzurecraig has cancer?07:27
@kanzurehrmm no he would have done something cancer-specific07:27
FourFirewell, if they could offer a, say 80% off sequencing, 250$ per genome after they are already funded, they'll be turning a profit07:27
cluckjhe's getting old; wants to live forever07:28
cluckjI dunno07:28
@kanzureFourFire: i don't think this is a generic sequencing company07:28
@kanzureFourFire: nothing about this says "we want to sell direct-to-consumer sequencing services"07:28
FourFire250$ is near where I would consider it worthwhile to get my genome sequenced07:29
@kanzurecluckj: i guess that $600 million from exxon is about empty07:29
cluckjlol07:29
FourFirekanzure, which 600 million?07:29
cluckjcraig's M.O. is to find things to patent07:29
cluckjso what is patentable there?07:29
@kanzureFourFire: craig venter got a $600 million deal with exxon for his company, synthetic genomics inc.07:30
FourFireoh, right07:30
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@kanzurefenn: the entire world is a strange loop that folds back into itself roughly every 10 years https://www.allegro.cc/forums/thread/34540307:35
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@kanzure"Hellman: I smile when you say Merkle, I mean Merkle is just someone who makes you smile. He’s a comic. He comes and plops down in your office—have you met Ralph?"07:55
@kanzure"Hellman: He plops down in your chair and says, ‘Hi!’ I remember, this was after the discovery of public key cryptography, maybe fifteen years ago, he comes into my office and plops down and says, ‘Hi, I’m building a human brain.’ He’s one of the stars in nanotechnology. Building human brains and repairing human brains on dead people so you can bring them back to life some time in the distant future is one of his passions."07:55
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@kanzurei think i need some soot goggles for interneting from now on http://www.entertainmentearth.com/images/AUTOIMAGES/EP828410lg.jpg08:00
@kanzurejgarzik bitcoin satellite groupies https://groups.google.com/forum/#!forum/bitsat-project08:02
@kanzurehttp://www.google.com/url?q=http%3A%2F%2Fwww.dunveganspace.com%2Fgoals%2Fbitsat%2FBitSatUpdate1.pdf&sa=D&sntz=1&usg=AFQjCNFzqytlkxLDkAz0J39nZCB-pbY9gA08:02
@kanzureoops i mean http://www.dunveganspace.com/goals/bitsat/BitSatUpdate1.pdf08:02
@kanzurehttp://www.dunveganspace.com/goals/bitsat/BitSatArchitecture-0.1.pdf08:03
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FourFirelol, Kanzure you saying "back in the day" what are you, early 30s ?08:07
@kanzure2408:07
FourFirelate 20s?08:07
FourFireso when you were 14, you were saying "back in the day"08:08
@kanzureinternet accelerates your aging by a factor of like 1000x08:08
FourFireI doubt it, I should be much more mature by now if that was the case08:08
@kanzureor your curve is different08:08
FourFireor perhaps "this here web 2.0 bullshit ain like it used to be... back in the days"08:08
@kanzureyep, first phase of web 2.0 was the real bullshit08:09
FourFire"I used to know 10% of the internet, by name! back in the day!"08:09
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@kanzure14 year olds can't have days to talk back about?08:10
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FourFirewell, sure they can. it just seems pretentious to me, but then I probably said similar things when I was 14.08:28
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@kanzure(not an actual recommendation) http://www.amazon.com/The-Knowledge-Rebuild-World-Scratch/dp/159420523X08:30
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@kanzurelong video about ants https://www.youtube.com/watch?v=Z-gIx7LXcQM08:40
@kanzureeudoxia: http://web.archive.org/web/19980109011052im_/http://extropians.mit.edu/extropy.gif08:44
eudoxiakanzure: it's rather sad that the MIT extropians were run by a bunch of racists and fell apart08:47
@kanzurehuh?08:48
eudoxiahttp://web.mit.edu/observer/www/1-1/articles/ad1.html08:49
eudoxiathere was some drama and they disbanded or something08:50
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@kanzureneat, chrome has been handling 326 tabs open for 15 days08:57
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paskyhmm it seems my 360-tab firefox is running for 11 days now09:30
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paskysooner or later it ends up eating 100% CPU for no easily discernable reason and I have to restart it though09:31
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dingoi recommend the tree style tab plugin for FF09:40
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@kanzuretree style tab wont solve his memory problems09:41
nmz787_ipaperbot: http://ar.iiarjournals.org/content/33/11/4757.full.pdf09:43
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/b7cc5d5fdf484e246df172676a9922e9.txt09:43
dingoi recommend a strict diet of lynx09:44
xmjxombrero is nice for that09:45
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@kanzurei would be okay with not using tabs if page caching actually worked09:45
dingoif you really want to get hardcore, try a web browser written by a blind guy (Dave Khale, cool dude) http://the-brannons.com/edbrowse/09:46
@kanzurebraille interfaces are obscenely expensive09:46
dingokarl dahlke rather, he does a good math site i think09:47
dingohttp://eklhad.net/09:47
@ParahSailinyeah i think blind people generally use modern browsers with screen readers09:49
nmz787_ikanzure: with that cefpython module... do you think we could actually write a chrome-based tab caching browser? Or would that work as a chrome extension?09:53
@kanzurei would use webkit/blink before cefpython09:53
@kanzurewebkit has a .haf format but i don't know if it stores all in-memory objects correctly09:54
@kanzureanother option is to use mitmproxy to capture all resources and just replay it in the future09:54
@kanzureso you don't have to keep the tab loaded in memory, and later can reload it without actually hitting the real interwebs09:54
@kanzureif the web page is non-deterministic then it might cause other requests to be made when the page is reloaded in the future10:01
nmz787_iisn't blink what chromium uses already?10:04
@kanzurechromium has a bunch of other stuff on top of blink10:04
nmz787_iaren't those desirable things?10:04
nmz787_i'features'10:04
@kanzuredunno, the answer is most likely no, because all those 'features' are why you can't have 10000 tabs in firefox10:05
nmz787_ifirefox doesn't use chromium though10:05
@kanzurewhatever :)10:05
@kanzure"Functional electrical stimulation-facilitated10:10
@kanzure"Functional electrical stimulation-facilitated proliferation and regeneration of neural precursor"10:11
@kanzurepaperbot: http://www.sjzsyj.org/CN/article/openArticlePDF.jsp?id=86210:11
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/7ba419edd532526e0b5359e818fcc72b.pdf10:11
@kanzure"Prehensile traction test results showed that, at 14 days, prehension function of rats in the functional electrical stimulation group was significantly better than in the placebo group. These results suggest that functional electrical stimulation can promote endogenous neural precursor cell proliferation in the brains of acute cerebral infarction rats, enhance expression of basic fibroblast growth factor and epidermal growth factor, and ...10:12
@kanzure... improve the motor function of rats."10:12
@kanzure"yo dawg we got 100 rats and we cut their brain blood flow for a bit, then we shocked them with electricity for a few weeks because science, it's all good"10:15
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nmz787_iso how do i contact langton labs to see about sleeping there?10:19
@kanzuretake blood oath at burning man?10:19
nmz787_ithat is after makerfaire10:20
nmz787_iso won't work10:20
@kanzure.tell fenn nmz787_i would like information about contacting or staying at langton labs10:21
yoleauxkanzure: I'll pass your message to fenn.10:21
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paskyhmm seems like switching from vertical tabs to tree-style tabs is not so trivial10:27
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nmz787_ithis is pretty cool https://www.sparkfun.com/products/1204210:31
@kanzure.title10:31
nmz787_iZ-axis conductive tape10:31
yoleauxZ-Axis Conductive Tape10:31
nmz787_igtfo yoleaux, this is my link!10:31
@kanzurei was impatient10:31
nmz787_ipsh10:31
nmz787_istupid latent bot10:31
nmz787_iall 3 seconds slower than me10:32
nmz787_iis yoleaux a play on YOLO?10:36
@kanzureyes, ask the #swhack people10:36
@kanzurehuh, opencascade "community edition" still has activity https://github.com/tpaviot/oce10:39
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@kanzurethat guy with the ABI 310 w/o software is going to have problems10:58
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@kanzurei think i'm going to recommend he sets up linux in front of the machine10:58
@kanzureand then sets up an ssh server for me to login to10:58
@kanzureand then i'll poke around the machine10:59
@kanzurebut i think i need to get a ROM dump of whatever microcontroller is inside the machine10:59
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nmz787_iWhoo! http://www.nature.com/news/start-up-investor-bets-on-biotech-1.1509611:04
nmz787_iY combinator application here I come!11:04
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chris_99cool, good luck nmz78711:06
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@kanzureheh i should have expected substack to have a thing for technical debt https://github.com/substack/codebux11:16
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@kanzurethis is very cool https://github.com/twolfson/phantomjsify12:07
@kanzureoh, not much is shimmed. hrm.12:08
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@kanzure"IBM’s chip business needs help. So the company has opened up the technology of its Power microprocessors, inviting others to modify and manufacture Power-based designs pretty much as they see fit. This open, liberal licensing initiative is conducted under the auspices of the OpenPower Foundation, which was incorporated in December."12:25
@kanzurehttp://openpowerfoundation.org/12:26
dingothey did that with opensparc, nobody did anything with it unfortunately12:26
@kanzurehmm no files.12:26
@kanzurewhat's up with a separate foundation for each idea?12:27
@kanzuresurely ibm owns a non-profit about something12:27
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kanzure"Back in the 60s NASA considered a plan for a manned flyby of Venus using Apollo-derived hardware. I've wondered if a modern day manned flyby mission might make sense. A rover could be landed on Venus more easily than on Mars, but it would, by necessity, have a very short lifetime on the surface. Once it's out of coolant, the mission is over. So if you were going to land a rover (or rovers) on the surface of Venus, you'd need to maximize ...14:59
kanzure... their effectiveness. One way to do this would be to teleoperate them in near real-time, which could be done if rover landing were coordinated with a manned flyby."14:59
kanzure"A manned flyby of Venus would be substantially cheaper and less risky than a manned mission to Mars. There's no manned landing component, and the flyby mission itself would take a little over a year, which is pushing the limit for human exposure to micogravity, but within the range that we have actual experience. This kind of mission will, of course, only make sense if you are an advocate of manned space exploration in the first place."14:59
kanzurehttps://news.ycombinator.com/item?id=763351514:59
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kanzure15-20% margins on reselling modafinil http://www.gwern.net/Modafinil#margin-estimation15:02
kanzurealso there's a simple assay mentioned down the page15:03
kanzurehttp://www.pharmacyreviewer.com/forum/discussion-online-pharmacies-featured-general-reviews-section/16335-edandmore-feedbacks-10.html#post13986215:03
kanzure"Modafinil is a sulfa drug, containing a certain chemical group called a sulfonamide group66. And lo and behold I stumbled across a simple pair of chemical tests for sulfonamides."15:03
kanzure"I took about a third of a pill and placed it in a test tube, adding a few ml of dilute NaOH. I then mixed it up and heated it over an alcohol burner. This should produce ammonia, which has a really characteristic odor. I got a whiff of my tube and, indeed, it was ammonia! I also tested the fumes with a piece of litmus paper - it turned blue, as expected [litmus turns red for acids & blue for bases; ammonia is a base]. Then I put another ...15:03
kanzure... third of a pill in another test tube and added dilute HCl. Upon heating it, sulfur dioxide should be produced - another gas with a characteristic, pungent odor. So I sniffed my tube - it smelled awful! Further, my litmus paper turned red, which is what I’d expect because SO2 is acidic."15:04
kanzure"Finally, one other test - I wanted to make sure this isn’t a characteristic of pill binder substances or anything. So I took half a caffeine pill and did the NaOH -> NH3 test on it. No ammonia whatsoever."15:04
kanzure"This test is crude and likely produces many false positives and negatives67, but may still be worth using. Checking, 50+ strips of pH/litmus paper is ~$5; hydrochloric acid is harder to find, but seems to be obtainable at $10-20 online; and sodium hydroxide similarly (and no doubt purchasable cheaper locally), for a worst-case cost of $45. This is roughly a third of EcstasyData.org’s price, and enough to test 50+ samples at a worst-case ...15:04
kanzure... cost of ~$1 per sample."15:04
QuantumGha, I didn't know it was a sulfa drug.. good I never got my hands on it, eh? (apparently I'm allergic.)15:04
kanzurehow apparent is apparently15:04
QuantumGlike, it's written on my birth certificate, but I've never experienced the symptoms15:05
kanzureallergies are written on birth certs?15:05
QuantumGweird eh15:05
nmz787_iapparently you can get a passport if you don't have a birth certificate, but have your name and birthdate written in a 'family bible' (you send the passport office your bible, potentially more evidence)15:06
nmz787_ijust what i heard recently15:06
kanzureso does that mean i can mail them a book of the jedi order?15:07
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nmz787_ii dont think os15:08
nmz787_iso15:08
QuantumGmailing the three volumes of Knuth would be expensive.15:10
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kanzure"The origin of turning dates to around 1300 BCE when the Ancient Egyptians first developed a two-person lathe. One person would turn the wood work piece with a rope while the other used a sharp tool to cut shapes in the wood. Ancient Rome improved the Egyptian design with the addition of a turning bow. In the Middle Ages a pedal replaced hand-operated turning, freeing both the craftsman's hands to hold the woodturning tools. The pedal was ...15:17
kanzure... usually connected to a pole, often a straight-grained sapling. The system today is called the "spring pole" lathe. Spring pole lathes were in common use into the early 20th century."15:17
kanzurehttp://en.wikipedia.org/wiki/Lathe15:17
kanzurehttp://historicgames.com/lathes/Egyptstone.jpg15:18
kanzurehttp://argenteriedesbauges.free.fr/1egyptien.JPG15:19
kanzurepfft obviously they should have invented the four-person lathe15:19
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fennpixtronix optical MEMS shutter transflective color low power display, another neat technology buried in the depths of qualcomm's dungeons: http://www.the-digital-reader.com/2011/12/08/qualcomm-bought-pixtronix-a-mirasol-competitor/  http://ko.com.ua/files/Pixtronix_Direct_View_MEMS_%20Display_Whitepaper.pdf15:24
yoleaux17:21Z <kanzure> fenn: nmz787_i would like information about contacting or staying at langton labs15:24
fennthe video is too long; summary: looks like a plasma tv, sizes as big or small as you want, about 25% of backlit lcd power consumption, and works in full sunlight with reduced color gamut, or black and white with no backlight15:27
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fennthis is why we need intellectual property taxes15:28
nmz787_ido you still have contacts at langton fenn?\15:28
fenni don't know; i haven't checked my email for about a year15:29
fenni suspect you'd be welcome15:29
fennyou just want to stay for a weekend ish?15:30
nmz787_iyeah, 4 folks total, we'll have tents so yard/slab is fine also... 2 of us will share  abed15:30
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nmz787_iso 3 'beds'15:30
nmz787_ifenn: do you know Cadence Allegro (PCB software) and want a job in Oregon for a bit?15:31
nmz787_ithe job also involves Python, and would be a contract with Intel through a temp agency15:32
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kanzuredon't you think he has better things to be doing than bothering with a temp agency?15:32
QuantumGI know someone who might15:32
nmz787_isome kind of PCB routing thin, i think15:32
nmz787_ikanzure: no idea, seems like his kind of thing though, and it would be a reason to live here during the summer15:33
nmz787_iQuantumG: get them to send me a resume nmz787 at gmail15:33
kanzureonce you accumulate any non-negligble amount of skill, you want to avoid temp agencies like the plague15:34
nmz787_ihave you been to Oregon during the summer?15:34
nmz787_ihaving any reason to come here is worth it15:34
nmz787_iespecially since its a contract15:34
nmz787_icome visit, see the sights, GTFO if you want15:35
cpopell /query nmz787_i15:36
cpopellwhoops!15:36
cpopellAnyway, nmz787_i, are you involved with a staffing agency up there, or did you just hear about it?15:36
nmz787_ino, my manager is reviewing resumes now15:36
cpopelloh, k.15:37
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fennnmz787_i: there is no yard/slab at langton. 4 people is the full capacity of the guest room so that may not be possible, especially with other people in town for maker faire15:40
fenni've never used Cadence15:41
fennwhat kind of temp agency hires EDA professionals?15:42
fennthat's like, a real job15:42
kanzurei assume there's a split in the industry15:43
kanzurewhere there's some who are doing vsli stuff15:43
kanzureand then others who are like blender/maya monkeys15:43
kanzureand i don't mean the "write beautiful code for dreamworks inc to automate 3d production pipelines", i mean "clicking buttons in blender all day for weeks"15:43
kanzure*vlsi15:44
fennthat's what blender is for though15:44
kanzurewith programming you can take advantage of efficiencies that you introduce, with point and click this is less true15:44
kanzurewhen you need a bunch of labor to click, you go pick a temp agency to supply you with labor15:45
kanzurejust theorizing here, re: your observation about a "real" job15:45
kanzure+.15:46
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fennI respect 3d artists like http://www.mikeanash.com/p/hard-surface-bust.html who do nothing but click on buttons all day15:48
dingoi'm not seeing it in the buffer, which specific industry?15:48
dingojust 3d modelling?15:48
fennhe's just ranting about point and click interfaces, pay no attention15:48
fennkanzure: okay but the clicking is to _DO_ something, and it's the thought that goes into where you click that is important15:49
kanzurei don't think i've claimed that thinking is unimportant15:49
dingowell i dunno, i used to make a lot of quake 1 levels, its a lot of point and clicking, but its also "programming", not my cup of tea really... no opinion ... i did write plug-ins and know ppl who do plug-ins for 3d modelling software -- now thats great fun, working with vectors and nodes and such15:49
QuantumGhow about some division of labor? Hire the artist to do artistic shit and the programmer to automate his crappy workflow.15:49
fennit takes skill, experience, and education to design and "capture" an electronic circuit/layout15:49
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kanzurealso, i'd point out that nate specifically mentioned a python requirement, so there's obv. some programming expectations15:50
dingomany gaming and movie studios have tirtuary tooling -- mostly the junior programmers15:50
kanzurethe junior programmers build their tools?15:50
fenntirtuary?15:50
kanzuretertiary?15:50
QuantumGthen the artist can get more arty stuff done, resulting in more product15:50
dingolike i know a guy at uhh whats it called, rockstar for gta, right?15:50
dingoall he does is make gui interfaces for backend processing tools, none of it is in the game, just used to build the game15:51
fennwe call that development tools15:51
nmz787_iit is a real job, but they might not want to keep you around to maintain the software after its written15:51
fennheh that's fine with me :P15:51
fennwait is this software or electronics15:52
nmz787_isoftware15:52
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kanzurefenn: why would you be more interested in that instead of doing your robocompany15:52
fennwhat does cadence have to do with it then15:52
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nmz787_iit needs scripted with Python15:52
fenndefine "it"15:52
nmz787_icadence :P15:52
nmz787_ii really don't know15:52
QuantumGthe other guy says he'll do it remote, but nuts to Oregon.15:53
nmz787_ii can ask for more info, but its some automagic generation via scripting thing15:53
nmz787_ibut I know they want Cadence Allegro and Python experience15:54
fenni wonder if wiping fabric softener on my screen will keep dust off15:54
nmz787_ikanzure: the job market is weird around here for tech, as the economy crash thing cut a lot of highly skilled workers from salaried positions, and temp agencies are their way of getting something done and evaluating you for potential salaried position if they like you and have money for maintenance or other longer term work15:56
juri_cadence. ick.15:57
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fennjuri_: please elaborate15:59
juri_fenn: whats to say? non-free software is non-free, and there is an intire industry in users that do not know how to perform jobs, using the non-free tools to perform said jobs.16:00
nmz787_ijuri_: do you use an intel processor?16:01
fennoh, i agree completely16:01
juri_i maintained cadence for a college of engineering for 3 years. during that time, i learned enough EE to need to route my own boards. i soon discovered the combined might of the professors of the entire college could not route a PCB to save their lives.16:01
juri_nmz787_i: depends on the task.16:01
fenn"i designed the block diagram, layout is left as an exercise for the student" (literally)16:02
fennmy microwave runs an intel Z8016:02
kanzurewhy does intel have a z80?16:02
fennuh, nevermind16:03
kanzure"The Z80 came about when Federico Faggin, after working on the 8080, left Intel at the end of 1974 to found Zilog"16:03
fenni guess the z80 was compatible in many ways with the intel 808016:04
kanzurehttp://en.wikipedia.org/wiki/Zilog_Z8016:04
dingothey used to have Z80 add-on cards for the intel16:05
dingoso you could boot cp/m16:05
kanzurehttp://upload.wikimedia.org/wikipedia/commons/d/d1/Z80A-HD.jpg16:06
fennso has anyone made a microchip CPU in their garage yet16:08
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kanzurei believe azonenberg has in #homecmos http://code.google.com/p/homecmos/16:08
fennwow really?16:08
kanzurebut he may have been cheating because he definitely stil has access to university lab stuff16:08
kanzure*still16:08
nmz787_ii don't think so16:09
nmz787_ihe's probably made a proc on a  fpga for sure16:09
kanzurei would be extremely surprised if he hasn't done a transistor16:09
nmz787_ibut that's more design than fab16:09
fennanyone can download an fpga core16:09
kanzurenah, fpgas are standard curriculum these days, not interesting16:09
kanzurei mean, no points16:09
nmz787_iits a common course excercise to design the proc yourself, so I think he's probably done more than just download some existing one16:10
kanzurei'm sure. but the ability to design a 4-bit chip is irrelevant (high school students can do that bored in math classes).16:10
kanzurehe was asking about manufacturing/etching16:10
kanzureand i assume operating16:10
fenni wonder if it's possible to turn off prerendering in chrome so things dont use so much ram16:11
kanzurefenn: have fun http://code.google.com/p/chromium/wiki/AndroidBuildInstructions16:12
fenni meant my laptop16:12
nmz787_ihe did some fpga circuit editing recently16:12
nmz787_ibut that was with a FIB in school16:12
fennat least i guess it's due to prerendering, i can't imagine why else a wikipedia page would need 100MB of ram16:14
kanzureclosing the last chrome tab may not kill the original chrome process16:14
juri_fenn: we're working on diamond like carbon deposition here at hacDC.16:15
fennjuri_: why?16:15
fennkanzure: i'm killing tabs in the chrome task manager16:15
juri_potential integrated circuit applications, plus 3d printer hotend applications.16:15
fennwhat are those applications16:16
juri_(i'm crazy. i'm trying to print aluminium. mirage is a different type of crazy, and wants to print chips.16:16
fenn(i've only ever seen CVD used as a wear resistant coating on machine tool cutters)16:16
fennokay so why diamond and not, i dunno, steel16:17
juri_steel is conductive, so won't work on my heater core.16:17
fennstainless steel lasts quite a while in oxidizing environments at 500C16:17
fenndiamond is also conductive16:17
juri_we're going to use steel underneath the diamond, to handle molten aluminium.16:17
juri_DLC is not conductive of electricity, is conductive of heat. exactly what we need.16:18
fenninvestigating16:18
juri_this makes good sense, since its used under some chips nowadays. if it was electricly conductive, they would have problems. ;)16:19
fennhm. from http://en.wikipedia.org/wiki/Diamond#Electrical_conductivity "Substantial conductivity is commonly observed in nominally undoped diamond grown by chemical vapor deposition. This conductivity is associated with hydrogen-related species adsorbed at the surface, and it can be removed by annealing or other surface treatments."16:22
fennbest of both worlds16:22
juri_selectively conductive.16:22
juri_;D16:22
fennapparently they can be semiconductors too16:22
juri_we're refurbishing a SEM at the space, as well.16:23
juri_me and mirage are excited, as this will let us verify our work.16:23
fenncool16:23
fennhow often is the space open these days? is it likely it would be open if i dropped by randomly?16:24
juri_its not quite that often, but its getting to about 50% chance.16:24
juri_that said, if you want to drop by, i'm willing to open it up for a tour, or to get some work done. just give me the word.16:25
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nmz787_ikanzure: what was the bitcoin donation thing?16:31
nmz787_ithe easy one, to start a donation campaign thing16:31
kanzureuh, might have been anything, coinbas.come? blockchain.info?16:32
kanzure*coinbase.com?16:32
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nmz787_iis there one with a counter though, like "# bitcoin raised"16:34
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kanzurenmz787_i: http://bitcoinchipin.com/16:34
fennjuri_: have you considered something like the wax inkjet but for aluminum? spraying microdroplets that fuse on contact with the workpiece16:35
nmz787_ikanzure: thanks16:35
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fenni'm still not convinced diamond is necessary for this application. surely there are other things that don't dissolve in aluminum, have high temperature stability and oxidation resistance16:36
nmz787_ialumina?16:38
nmz787_ii guess that's already oxidized16:39
fenni wasn't sure if alumina would stand up to molten aluminum for extended periods16:39
fennaluminum is highly reactive16:39
fennthis means alumina is very stable, but in a fight with aluminum, they come out even16:40
QuantumGdo it in a noble gas?16:40
* fenn looks at a periodic table16:41
fennQuantumG: also a good option, but it complicates logistics16:41
QuantumGor semi-noble.. aka nitrogen16:41
QuantumGheck, even co2 would probably do, if you're just trying to avoid oxidization16:41
fennyes you could use getters and molecular sieve pumps16:42
nmz787_inone of those damn peasant gasses16:42
QuantumGfor sho16:42
fennpressure swing oxygen concentrators i mean16:42
fennhttp://en.wikipedia.org/wiki/Reactivity_series  MgO, CaO ceramics are probably good options (why is Si not on this chart?)16:46
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juri_fenn: honestly, i haven't. i figgure go for the brass ring.16:52
juri_microwave induced carbon vapour deposition looks like a 'simple enough' procedure.16:53
juri_plus, it gets us on our way to using the same procedure for integrated circuit applications.16:53
juri_two birds. one (admitedly heavy) stone.16:54
nmz787_ikanzure: I can't tell if its working https://bitcoinchipin.com/widgets/u/takeitapartdan/send-takeitapart-to-maker-fair16:54
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fenni meant for aluminum printing, not diamond17:11
QuantumGso did I17:11
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fenni just saw 10 minutes of "silicon valley" - probably the most depressing piece of distilled reality i've seen in a while17:12
QuantumGI've seen ever episode.. people complaining that it isn't realistic are missing the purpose of FICTION17:13
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fennwhat's not realistic about it?17:14
QuantumGthey seem to think Silicon Valley is "weirder than that"17:14
jrayhawk"Perhaps the idea you mean is that the Web should be a distributed programming environment rather than just a way to deliver documents. True, but it's sort of too late to fix that. It's like expecting MS-DOS to magically morph into Unix. If you built a global namespace from scratch you would not reuse names (no mutable resources), and the namespace would be rooted in a secure identity model. Refactoring the Web to include these ...17:14
jrayhawk... points is sort of like redesigning a horse so that it's a motorcycle."17:15
fennmaybe they are confusing "silicon valley" with "san francisco"17:15
jrayhawkhuh, a comment from 2007 actually sells me on17:15
jrayhawkUrbit17:15
kanzurei was staying in downtown sf a few weeks ago17:15
kanzureand i forgot about the screams of the undead during the night17:15
dingoSJ claims to be *the* silicon valley, which is pretty silly17:15
fennjrayhawk: they web has a global namespace though17:15
kanzurevery weird place.17:15
kanzuresan jose is boring17:16
QuantumGya17:16
dingosan francisco smells like garbage17:16
QuantumGPalo Alto baby17:16
dingoi don't like either, i'm a country boy myself17:16
kanzurethat's because of the garbage17:16
jrayhawkNo, DNS is not a part of the web.17:16
dingovim17:16
fenngoogle hq is literally built next to a landfill.. go figure17:16
fennjrayhawk: what?17:17
jrayhawkAnd neither is IP.17:17
fennwhat?17:17
jrayhawkHTTP is a socket.17:17
fenndefine "the web" plz17:17
jrayhawkhttp://en.wikipedia.org/wiki/World_Wide_Web17:18
QuantumGI enjoyed the 8 months I spent at VMware, but I don't nitpick every little thing in a tv show that's different to my experience.17:18
kanzurewhen was your stay at vmware?17:18
dingoi don't know where this conversation is headed but i'm pulling out :-)17:18
fennhm. define:www and the first result is amazon.com - long live the web!17:18
QuantumG'specially seeing as it was 13 years ago.17:18
kanzurewas that before or after vmware started making crap like vcloudsphere17:18
kanzureor vcow17:19
QuantumGbefore.. but the writing was on the wall17:19
kanzurewhat went wrong?17:19
fennthey became a large organization17:20
QuantumGI don't know how they ever made money.17:20
QuantumGlots of sales dudes hitting the phones at the end of financial year, it seemed17:20
kanzureweren't they venture backed and going for the "long haul" of no sales?17:20
QuantumGnope17:20
QuantumGthey were desperately trying to find a market beyond "I wanna run Windows in a VM on my linux box" from day one.17:21
QuantumGincluding selling hardware at one point..17:22
kanzurehow about, "lots of big enterprises have terrible software running on terrible old hardware that could instead be virtualized because ???"17:22
kanzurei forget the rest17:23
juri_quantumg: i have found there is a class of people that is bought into the "free means its cheap" mindset. maybe that's how they make money.17:23
QuantumGyeah, I think they thought x86 (and later x64) was the hardest thing to virtualize so they had to focus on that to keep competitors out.. or something17:24
juri_i'm slowly converting one of those who spends WAYTOOMUCH to run free software fast, simply by setting up light debian instances, and trouncing his huge boxes with machines thrown away by others.17:25
QuantumGplus, they didn't want to confuse people by explaining that virtualization is essentially dynamic recompilation17:25
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fennwhy is it recompilation if it's compiled for the same instruction set as your host hardware?17:32
fennam i missing something17:33
kanzuremaybe it's using the virtualization extensions on chip17:34
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kanzureor it's not using the same instruction set17:34
fennbut windows and linux use the same instruction set, no?17:34
QuantumGthis was pre-chip17:34
QuantumGmost instructions you can just copy, some have to be "virtualized"17:35
fenni want a chrome extension that colors my tabs by CPU usage17:35
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fennjuri_: how about titanium boride instead of diamond: http://en.wikipedia.org/wiki/Aluminium_carbide#Occurrence17:37
QuantumGthose x86/x64 virtualization instructions did basically prove how stupid it was for VMware to focus on those architectures because they're hard to virtualize.17:38
fennTiB2 is resistant to oxidation in air at temperatures up to 1100 °C,[2] and to hydrochloric and hydrofluoric acids, but reacts with alkalis, nitric acid and sulfuric acid17:39
fennthe melting point is about 2970 °C, and, thanks to a layer of titanium dioxide that forms on the surface of the particles of a powder, it is very resistant to sintering. Admixture of about 10% silicon nitride facilitates the sintering,17:40
fennelectroplating of TiB2 layers possess two main advantages compared with physical vapor deposition or chemical vapor deposition: the growing rate of the layer is 200 times higher (up to 5 μm/s) and [you can plate inside small holes, important for your application]17:41
fennso you'd want to make the bulk of your nozzle out of graphite and electroplate TiB2 onto that17:42
fennor maybe even silicon would work17:42
fennthen you could just use a pre-made inkjet nozzle17:43
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juri_i like the way you're thinking; now to source the materials.17:43
fenn"Solution phase reaction of NaBH4 and TiCl4" <- gnarly chemicals17:46
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fennpaperbot: http://www.sciencedirect.com/science/article/pii/S0167577X0600808117:47
fenn.title17:47
yoleauxPreparation of the TiB2 coatings by electroplating in molten salts17:47
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/700d72474d9db8c0016026c3e8e922a1.txt17:47
kanzurepaperbot: http://www.sciencedirect.com/science/article/pii/S0167577X06008081/pdfft?md5=29ca21048e348f649287e28ea51b2d0d&pid=1-s2.0-S0167577X06008081-main.pdf17:48
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/4bd972db526fcaca0c537123e04ffb78.pdf17:48
fenn.title17:48
yoleauxfenn: Sorry, that command (.title) crashed.17:48
kanzuredoesn't work on pdfs17:48
fennif it were a pdf you wouldn't have to use paperbot17:49
fenn.title http://www.sciencedirect.com/science/article/pii/S0167577X06008081/pdfft?md5=29ca21048e348f649287e28ea51b2d0d&pid=1-s2.0-S0167577X06008081-main.pdf17:49
yoleauxPreparation of the TiB2 coatings by electroplating in molten salts17:49
fennhuh17:49
kanzurethe reason .title works there is because yoleaux doesn't have access17:49
kanzureso sciencedirect.com redirects the bot to an html page17:49
fenni saw a robot that used a mig welder to 3d print stuff. you can get amazingly high aspect ratio shapes because of the stiffness and lack of mechanical force17:51
QuantumGyeah, automated mig wire art17:51
kanzurei want a wire keyboard.17:52
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fennthe mig process uses a thin stream of "shield gas" that surrounds the electrode; this should probably be used around the stream of aluminum, even though it is only going a few mm17:56
fennif only to prevent oxide buildup around the electrode and eventual inclusion in the part17:56
fenner, s/electrode/nozzle/17:56
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fennmay need some kind of oxide skimmer because your feed material will have an oxide coating before it gets melted17:58
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fennthere's been a lot of noise in the past about syntactic(?) metal foams but no way to make them; a high resolution 3d metal printer could actually do it though18:02
fennthrash thrash thrash18:02
fenninexpensive heatsinks with built in heat pipes would lead to some interesting possibilities18:04
kanzuremachinewiki should be dumped into diyhpluswiki.git18:05
fennwhat is machinewiki18:05
fennthe gingery things?18:05
kanzureoops machines18:05
kanzurehttp://fennetic.net/machines/18:05
kanzurei have been on a wiki merging spree lately18:05
fennya i was hoping to come up with something better than wikis18:05
fennbut that was a long time ago and it hasn't happened18:05
kanzurelos angeles biohackers lost their mediawiki install18:05
kanzurecory emailed me an sql dump today18:06
kanzuremost of these wikis are going to evaporate18:06
kanzureisn't tmp2 a wiki?18:06
fennevery wiki should have a "dump database" button imho18:06
kanzuremediawiki has a kinda-dump button, but you have to stare at it sternly18:06
QuantumGreminds me of what I asked you the other day kanzure..18:06
fennan end-user-accessible button18:06
QuantumGgot a list of biotechnology machines?18:07
fennof course you also need a merge button, thus ikiwiki18:07
kanzurei gave you one18:07
kanzurehttp://diyhpl.us/cgit/skdb/tree/doc/BOMs/diybio-equipment.yaml18:07
fennQuantumG: cows, pigs, sheep, corn, e. coli18:07
kanzurehah i forgot about this http://diyhpl.us/cgit/skdb/tree/doc/tech-tree18:07
fennlike the list? i made it myself18:07
kanzure"I spent over a day writing a silly Python program to read in a Civilization 2 Technology Tree."18:08
kanzureuggghhh18:08
QuantumGhave you got one that isn't ridiculous?18:08
kanzure"The Civilization 2 Technology Tree has five errors, including two “Destroyer” units and a bunch of redundant dependencies, such as Fusion Power doesn’t need to depend on Nuclear Power."18:08
kanzurewhy is it ridiculous?18:08
kanzurehttp://www.charlesmerriam.com/blog/2008/04/fun-with-programming-a-technology-tree/18:09
QuantumGI'm after a list of commercial lab machinery18:09
kanzureoh you mean the equipment they wont sell you?18:09
QuantumGya18:09
QuantumGwhat they do, what they're for, etc18:09
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kanzureABI {100..900}{A..Z}18:09
@ParahSailinyou can build an ironclad before iron working18:09
@ParahSailinand gunpowder18:09
fenniirc openwetware had a list of their preferred commercial bio lab equipment18:09
@ParahSailinthere are two destroyers?18:10
kanzuredrew endy approved equipment?18:10
kanzureoh yeah, a backup of openwetware too.. god damn wikis.18:10
fennone wiki to rule them all, one wiki to bind them18:10
kanzurei dunno if i want to dump openwetware straight into diyhpluswiki.git18:10
kanzureit's not like anyone other than me edits diyhpluswiki.git18:10
@ParahSailinoh, the second destroyer "steel" is supposed to be cruiser18:11
@ParahSailinelectricity is destroyer18:11
fennpierre baldi ChemDB, about 5 million chemical isomers in the database are available for download, including all of their primary chemical annotations. They are available for download as a collection of gzipped SDF molecular format files, each about 100 MB large. http://cdb.ics.uci.edu/18:14
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gnushahttps://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=9ea01bce Bryan Bishop: list of wikis to merge into this wiki18:15
kanzurehttp://diyhpl.us/wiki/wikis/18:16
fennisn't openwetware still an active wiki (it's like their primary public-facing website)18:17
kanzurei believe the only reason it's active is because igem teams are coerced into posting their projects18:18
fenni mean why would you even consider copying it18:18
kanzurei merged their diybio pages into diyhpluswiki.git a while back18:18
kanzureso maybe some of the other content is wort htaking18:18
kanzure*worth taking18:18
fennsignal to noise ratio is important18:18
kanzurei said some :)18:18
fennthere are so many bio people i've never heard of18:20
kanzurethat's why i started writing them down. who the hell are these people?18:20
fennmaybe it's just so hard to get anything done with biology that nobody makes a lasting impression18:21
fennthe gap between brilliant idea and practice is too large18:21
kanzurethe parts of biology that require secret incantations should be thrown out in favor of anything that works well with the words "solid state"18:21
fennare microfluidics solid state?18:22
fennyes i know you also said "works well"18:22
kanzurewhat's wrong with regular fluidics18:22
kanzuredo you really always need laminar flow?18:23
fennregular fluidics is big18:23
fennthere is certainly a case to be made for mesofluidics18:23
kanzurebigness hasn't been one of the constraints as far as i know?18:23
kanzureerm, size18:23
kanzure"you know, all this biology stuff is great, but what i really need is a place to put my shoes"18:24
fennsomeone was coming up with a chemistry reactor compiler (3d print a silicone thing to synthesize a batch of chemicals)18:24
fennkanzure: size of lab equipment determines where you can and can't put a lab18:24
fennfor example, can you have a lab in your backpack? in your closet? in your guest room? or do you need to rent a storage unit or workspace18:25
fennthis has obvious implications for who can and can't do lab work18:25
fennif anyone with a backpack can contribute to your research then your pool of potential contributors goes up by orders of magnitude18:26
kanzurethose implications don't seem to be a limiting factor at the moment18:26
kanzurethere seem to be other limiting factors that are extering more influence18:26
fennlike what18:26
fenn(i honestly dont know)18:26
fennwhy are people contributing to wikipedia but not diybio18:26
kanzurei was going to complain about everyone who built the original equipment being dead after swallowed up by big bio in ancient history18:27
kanzurebut, the thesis that there are limiting factors that are preventing biology things, might also be flawed18:27
QuantumGbiometh labs18:28
kanzurewhat about them18:28
fennalso consider workflow, if your stuff is all on one desk then you dont have to run laps around a huge lab just to get anything done18:29
QuantumGjust a visual18:29
QuantumGif your lab is (smoothly) automated you don't have to get up from your desk18:29
kanzurefenn: the reason i decided that microfluidics was too much work was because the number of variables increases so dramatically compared to non-microfluidics18:29
fennQuantumG: also if you pay someone else to do it18:29
kanzurefenn: engineering is about working on known constraints and within known tolerances, not adding arbitrary parts to your project until you hope it works18:30
QuantumGthat too18:30
kanzurethe amount of debugging necessary per additional buggy component that you add into your system makes "make a 1000-gate microfluidic device for a 12 step chemical reaction" almost intractable18:30
kanzureif possible i prefer to focus on tractable things18:31
QuantumGpeople are pretty buggy too18:31
kanzurei wasn't using that as an argument against lab automation, sigh18:31
fennits the same amount of debugging, it's just harder to inspect18:32
kanzurei was using that as an argument for why the microfluidic dna synthesizer is a huge project18:32
QuantumGtotal quality management is like inevitable, man18:32
fennmicrofluidics _enables_ massive combinatorial explosions, but they're not required18:32
kanzurewhy is adding arbitrary amounts of unknowns into a project good?18:32
QuantumGusually it's the benefits you can't get from avoiding them.. like using C++18:33
kanzureQuantumG: context is http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf18:33
fennok i see what this argument is about. option 1) replicate known working devices from the literature. option 2) build new devices based on principles learned from the literature18:33
kanzure1) those don't reaaaally exist18:33
QuantumGwhenever someone asks me why we use C++ I just cut to the chase and say "because we're idiots", it's what they want to hear.18:33
fennright because those people are all long dead18:34
fennand they didn't write down their secrets18:34
kanzureno, they aren't dead18:34
kanzureParahSailin spent a bunch of time on microfluidics stuff18:34
fennso we're actually stuck with option 2 either way18:34
fennwhat does microfluidics have to do with anything18:34
kanzureyou were trying to convince me to focus on small devices18:34
kanzureso i skipped ahead in the conversation18:34
fenni thought you wanted to make a 1980s DNA synthesizer with the big glass bottles hanging off the front18:34
@ParahSailini think cambrian folks are going to have the most sort of success doing dna synth18:34
kanzurethat doesn't really help anyone but their customers18:35
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kanzurei mean, they are explicitly mail order only iirc18:35
fennQuantumG: C++ wasn't anti-hacker enough so they invented java?18:36
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fennquestion, is cambrian "solid state"?18:37
kanzurewell they are certainly using a laser somewhere in their pipeline18:37
fennthere's also lots of shit literally flying around18:37
fennhow many other machines have literally millions of moving parts18:38
fennyet still somehow it's more reliable than microfluidics?18:38
fennwhat am i missing here18:38
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fennmaybe it's the difference between uncorrected error and feedback18:40
QuantumGso, stupid question, ya never got anywhere on this project?18:40
kanzureit's interesting that you and i have a different perspective on picking (in)tractable projects18:40
kanzureQuantumG: nmz787 is still going at it, but i backed out when i realized the existential horror of it all18:41
fenni think you are over-exaggerating18:41
kanzurewell, then let's re-calibrate me (in general)18:41
fennand i think nmz787_i likes to fiddle with things18:41
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QuantumGany interest left in the "enzymatic synthesis by direct control of DNA polymerase" version?18:42
kanzureas you can increase the number of parts in a system you increase (at minimum) the number of possible failures18:42
kanzureQuantumG: sure, http://diyhpl.us/~bryan/papers2/polymerase/ has some research notes18:42
fennQuantumG: it's interesting but theoretically stalled18:42
kanzureyes18:42
kanzureor, theoretically waiting on more theory stuff18:43
kanzure"Protein conformational dynamics probed by single-molecule electron transfer.pdf"18:43
fennsomething like the inverse of the pacific bio synthesizer should be possible18:43
kanzure"review - Making contact - Connecting molecules electrically to the macroscopic world.pdf"18:43
fenni mean nano volumes saturated by various frequencies of light that turn on a specific reaction18:44
kanzurei wonder if i should estimate the engineering difficulty of that polymerase enzyme as either more or less than the potential bug/iteration count of a large microfluidic device18:44
@ParahSailinprotein engineering is awful18:45
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kanzurethe fake polymerase enzyme is much more fantasy so probably can't be estimated at all (the solution will probably end up being "directed evolution, and then magic happens, and oh look you got it on the 3rd month")18:45
fennthe difference is that the microfluidic device problem can be decomposed into different working parts18:45
kanzuresame with proteins actually18:45
kanzure... to some extent. not always in the way that you need.18:46
fenni disagree18:46
kanzurethere are literally specific domains in the enzyme itself18:46
fennit's true you can combine functional subunits with linkers18:46
kanzurenot even subunits18:46
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fennbut when all your functional subunits work on the same active site, they have to be at least designed with an awareness of each other18:46
@ParahSailinyou might be able to get a polymerase that would halt if you changed its conformation by tugging on it with a magnetic bead18:46
kanzuresubunits as in other proteins (like from other genes) that form together to build the overall thing, right?18:46
@ParahSailinbut that would be a hell of a protein engineering project18:46
QuantumGI completely agree that it's a different problem18:46
kanzuredna polymerase often doesn't have subunits, but it does have functionally-specific components18:46
fennby subunit i was thinking "here's the part that adds 'A', here's the part that adds 'G' etc"18:47
kanzurequick model of a polymerase is a hand with the thumb feeding into the inner chamber18:47
QuantumGthe enzyme-version is a science project.. the microfluidics-version is an engineering problem (but a pretty science project-y one), and the traditional-chemistry-with-some-modern-automation is a straight engineering problem18:47
kanzureand then some weirdo chute where nucleotides get matched up18:48
QuantumGthe payoffs are also different though.18:48
@ParahSailinmost dna polymerases except for phage ones have subunits18:48
fennif separate polymerases have to fall off and reconnect to the strand for each base, the kinetics are too slow18:48
kanzureParahSailin: clearly i have to go kill myself now..18:48
@ParahSailinthere are a lot of viral polymerases though18:48
kanzureQuantumG: i'm curious about how you would characterize the straightforwardness in those last two..18:48
kanzurethe good thing about polymerase is that it's one of the really good molecules for directed evolution18:49
kanzurebut then you need to figure out if your problem is evolutionarily-solvable18:49
QuantumGwell, no-one would argue that the last project is doable.. whereas the microfluidics project has unknowns18:49
fennmicrofluidics you're inventing both the process and the device; with the bulk fluidic synthesizer you're just inventing the device (process is known)18:49
kanzuredisagree, but yes obviously microfluidics has more work18:50
fennsomehow making it smaller changes the process (don't ask me)18:50
kanzuremy original statement was that the amount of debugging and iterations for the microfluidic version would be way higher18:50
kanzureit's not just making it smaller18:50
QuantumGmaybe I'm not understanding the last project though.. automate-a-manual-process is how I saw it, no?18:51
kanzureit's different materials, chemistries, flow, valves, etc.18:51
fennwhy does it have to be different materials and chemistries18:51
QuantumGI wonder if you're not taking that literally enough18:51
kanzureQuantumG: yes, lots of that equipment exists. basically think stereotypical 1970s chemistry process, "hey let's sell a machine", "okay let's make something that looks like our glassware setup"..18:51
fennwe can make glass chips; the chemistry scales down (no?)18:51
QuantumGI mean, you *can* make reasonably long DNA sequences with glassware, right?18:52
fennQuantumG: yes18:52
kanzuremanual dna synthesis definitely works, if you have iron patience18:52
QuantumGa Baxter is only $22k ;)18:52
kanzurealthough the yields might be less than you'd hope18:52
kanzureand this will ultimately constrain the maximum length18:52
QuantumGsounds expensive, until you automate a few different processes with the same robot.18:52
kanzurebesides the usual types of errors: http://diyhpl.us/~bryan/papers2/DNA/Origin%20of%20impurities%20in%20oligonucleotides.pdf18:53
fennQuantumG: a Boxter is only $9k http://www.ebay.com/itm/Porsche-Boxster-Roadster-Convertible-2-Door-2000-porsche-boxter-/12132296524618:54
QuantumGyeah, synthesize your own DNA, I'm going cruisin'18:55
fennok so what is the major difference between automating it with pumps and valves and stirrers, and automating it with micropumps and microvalves and micromixers18:57
@ParahSailinits possible that the idea of trying to make a dna polymerase that you can control from the macro scale is like putting a beak on an aircraft so that it will fly like a bird18:58
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@ParahSailinand that the optimal way to synthesize long dna will not resemble nature at all18:58
kanzureligation?18:58
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kanzureoh wait, that's from nature18:58
fennParahSailin: surely you mean flapping wings, not "beak"18:58
kanzureyeah, i haven't seen much hypothesizing about extremely long dna synthesis18:59
kanzurescrew 1 gigabase genomes, what about 1 terabase etc18:59
@ParahSailinfenn: im sure some people tried beaks when wings didnt work18:59
fennthe truth is big birds fly more by catching thermals than by flapping their wings; we just didn't pay attention18:59
fennit's possible that da vinci built a hang glider and was able to catch thermals19:00
fennnobody really knows19:00
kanzureobviously the correct way to synthesize extremely long dna molecules is through particle acceleration19:00
fennanyway, de novo DNA synthesis doesn't really happen in nature19:00
kanzureGNA and other variants of DNA are an interesting concept too19:01
fennwhat's GNA19:01
kanzurebecause you could possibly find something that is easier to do chemistry on, and then convert it to DNA19:01
kanzureit's just a modified backbone, "simpler" chemistry or something19:01
fenneh who cares19:01
kanzureand apparently it was polymerase-compatible19:01
kanzurewell, because if you get to pick your chemistry, then you have more options19:01
@ParahSailinglycerol phosphate or something?19:01
kanzurehttp://en.wikipedia.org/wiki/Glycol_nucleic_acid19:02
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kanzure"The 2,3-dihydroxypropylnucleoside analogues were first prepared by Ueda et al. (1971). Soon thereafter it was shown that phosphate-linked oligomers of the analogues do in fact exhibit hypochromicity in the presence of RNA and DNA in solution (Seita et al. 1972). The preparation of the polymers was later described by Cook et al. (1995, 1999) and Acevedo and Andrews (1996). The GNA-GNA self-pairing described by Zhang and Meggers is however ...19:02
kanzure... novel, and the specificity of interaction well-demonstrated."19:02
kanzure"DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas GNA's backbone is composed of repeating glycol units linked by phosphodiester bonds. The glycol unit has just three carbon atoms and still shows Watson-Crick base pairing. The Watson-Crick base pairing is much more stable in GNA than its natural counterparts DNA and RNA as it requires a high temperature to melt a duplex of GNA. It is possibly the simplest of the ...19:02
fennhow about changing the surface chemistry of an array of microwells to accept various bases (conveniently lined up and waiting for ligation)19:02
kanzure... nucleic acids, so making it a hypothetical precursor to RNA."19:02
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fenndifferent charge patterns in the wells attract different bases19:02
kanzurewhy?19:03
kanzurewhat if instead you just have different nucleotides available in separate containers19:03
fennbecause it's parallel instead of serial19:03
kanzureoh, well, single-nucleotide ligation doesn't happen19:03
fennwhy not19:03
kanzuregrabs longer sequences only iirc19:03
fennhow long does it have to be19:03
@ParahSailini think cambrian is promising because phosphothioate is pretty effective chemistry that we have a good handle on19:04
@ParahSailinand you can build fancy error checking and ligation on top of that19:04
fenn"Oligonucleotides as short as 8 nucleotides can be efficiently assembled using T4 DNA Ligase"19:04
fennnote that's in free solution, not bound to a plate19:05
fenni'd expect activity to be higher when bound to a plate (for enzymes that like the plate) because it's 2D reaction kinetics instead of 3D19:05
kanzurei've seen lots of stuff about enzymes being bound to ATP n' stuff19:06
kanzureand sometimes surfaces, like biotinylated19:06
fennif you can get it down to ~4 bp oligos, then it's cominatorially feasible to just dump in oligos instead of bases19:06
kanzure"Generation of biotin/avidin/enzyme nanostructures with maskless photolithography" stuff like that19:06
QuantumGdamn wget, walking up your directory tree19:06
kanzurewget -m -np19:06
kanzureplz19:06
@ParahSailinoh dang, i didnt know that one existed, i always was using -I19:07
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fenn4^8 = 65536, 4^7 = 16384, 4^6 = 4096, 4^5 = 1024, 4^4 = 256   so maybe 6 bp sequences is reasonably19:08
kanzureoligomer libraries are a thing, you know19:08
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kanzurebut it doesn't require surface binding19:08
kanzurepaperbot: http://pubs.acs.org/doi/abs/10.1021/ac970957t19:09
kanzure.title19:09
yoleauxMicroelectrode Control of Surface-Bound Enzymatic Activity19:09
kanzureoh, hrm.19:09
kanzureyeah these are all going to be electrode chemistry19:09
fennpatent 5,650,489 june 1991  library of bio-oligomers of defined size and known composition, in which the library contains all of the possible sequences of the bio-oligomers, and a method of synthesis thereof.19:10
paperbotXMLSyntaxError: None (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 51, in _go)19:10
fennyeah this patent is basically what I was trying to describe19:11
kanzurethe problem with in-solution oligomer libraries is that you need to either have enough wings to avoid wrong additions,19:11
kanzureor if you do it once per cycle then you need a bazillion wash reactions19:11
kanzureand that's an imperial bazillion19:11
fenni guess they were doing random sequences though19:12
fennwhat's a "cycle" in this context19:12
kanzurephosphoramidite/oligonucleotide synthesis involves a few steps that get repeated a bunch: wash, insert chemicals, wait for reaction, cap, wash, repeat19:13
@ParahSailinwhy dont find efficient ways to error check and ligate phosophoramidite microarrays19:14
fennthis method would be reduced to: insert oligos, wash, insert ligase, wash, repeat19:14
kanzureso robotic pipetting of microarray? ala what george is doing?19:14
fenneven better if your oligo solution has anti-ligase properties19:15
fenngotta keep the hot side hot and the cool side cool19:15
@ParahSailinisnt he using beads instead of pipettes?19:15
QuantumGphrasing19:17
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fennoh, so the moving bead is coated with the complementary oligo, and the stationary reaction site holds the strand you're working on?19:17
fennthis seems slow19:17
fennmoving beads around takes time19:17
kanzurei think it was this one19:18
kanzurehttp://diyhpl.us/~bryan/papers2/DNA/High-fidelity%20gene%20synthesis%20by%20retrieval%20of%20sequence-verified%20DNA%20identified%20using%20high-throughput%20pyrosequencing%20-%20supplementary.pdf19:18
fennare you talking about what i'm talking about? or is this unrelated?19:18
kanzurei'm talking about ParahSailin's suggestion of micropipetting19:18
@ParahSailinyeah thats it19:18
@ParahSailinyou could probably come up with faster ways to move beads around19:19
fennthat's what cambrian's laser thingy is for19:19
kanzurethey laser at a microarray?19:19
fennbasically19:19
@ParahSailinthey use two lasers19:19
kanzurebut where does the bead go?19:19
@ParahSailinone for microarray, one for beads19:20
kanzureso bead goes up into the air, another laser pushes it?19:20
kanzureby... acoustic vibration?19:20
heathhmm.19:21
heathi think i'm going to switch back to python19:21
fennthey grow oligos on a plate with DLP and photosynthesis, release the oligos into dilute solution, bind to beads such that statistically only one sequence per bead, do surface-bound PCR to amplify the oligos on the beads, then pop the beads off into a sequencer well19:21
@ParahSailinbeads are in water19:22
@ParahSailintheres no sequencer well, its sequencing illumina style19:22
kanzurei still don't know where the laser part is19:22
fennok they have like 96 sequencers running in parallel then19:23
fennthe laser is directly above the sequencer input19:23
fennthe plate with the beads is upside down over the input, being moved around by an XY table19:23
fenni think both the laser and the plate are moving, so they can get the desired bead into the desired sequencer input19:24
fenneither that or the sequencer moves, i haven't actually seen it19:24
@ParahSailintheres no 96 sequencers, in illumina sequencing you have one synchronized reaction and one or multiple microscope cameras scanning a plate in a raster pattern19:25
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fenn" separate DNA strands from the microarray (biochips). They attach each strand to its very own bead, where they replicate it 100,000 times. Next, they attach the beads to a glass surface, and optically sequence them—one color for each of the four letters in a DNA sequence. In this way, they are able to read out the sequence, and pick those with the highest quality score. Cambrian Genomics then19:29
fennuses a laser printer to retrieve the DNA sequences. Using laser light, Heinz is able to quickly read one billion strands; find and print the correct ones;" i dont really understand that last sentence, maybe the journalist was improvising19:29
kanzure"uses a laser printer to retrieve the DNA"19:30
fennthere used to be a better explanation of this online, it's probably in the logs somewhere19:31
fennokay so the point of this is to do gene synthesis; eventually you need to get a few oligos in a reaction well to start doing your gibson assembly19:32
kanzurethe better explanation is anselm's second email over here https://groups.google.com/forum/#!searchin/diybio/cambrian$20genomics/diybio/YqGUf3A9AKo/NCFQ12T_8SwJ19:32
fennjust pretend i said "reaction well" instead of "sequencer well"19:33
kanzurewell, nevermind, i don't think he points out the full process19:33
@ParahSailini wonder if you'd even have more luck using the poxvirus dna pol instead of gibson19:33
fennkanzure: hey why isnt this on the hplus wiki19:33
@ParahSailinpoxvirus pol only needs overlap of 15nt or so, and it doesnt chew things up willy nilly19:33
@ParahSailinonly problem is that you have to sacrifice a child infected with chickenpox to isolate this enzyme19:34
@ParahSailinso its not commonly used19:34
fenni really doubt that's the reason19:34
@ParahSailinheh19:35
fennfuck you too google *grump*19:35
@ParahSailinit is pretty expensive, but only because it requires mammal cell culture19:35
kanzurewhy does anselm call micropipetting "very high throughput"?19:36
@ParahSailinclontech sells it for like $20/rxn which is not that expensive in the whole scheme of things19:36
kanzureif you have a 1024x1024 microarray, the only way you're going to have high throughput is with a 1024x1024 micropipetting device19:36
fennParahSailin: just use recombinant e. coli to make your enzyme. what's the problem19:36
@ParahSailinfenn: nope they tried that19:36
@ParahSailinviruses are evil, they never do what you want them to do19:37
kanzureterrorize children?19:37
@ParahSailinfree north korea?19:37
fennya gotta believe me19:37
kanzurehow fast can you drive a micropipette over a million wells19:38
fennkanzure: that's what the laser is for19:38
kanzurestoping at each well to do the necessary19:38
fennhow many times do i have to say it19:38
kanzure*stopping19:38
kanzureapparently you need to say it again19:38
@ParahSailinpaperbot: https://www.sciencedirect.com/science/article/pii/S004268229999705219:38
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/335a64ef75c98c46d28e301479744549.txt19:39
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fennsince apparently i need google chrome to look at a google groups page, i'm still waiting to read the diybio post19:39
kanzurefenn: how does the laser speed up the pipetting?19:39
kanzureoh wait, is it a game of 2048?19:40
-!- Adifex is now known as Adifex|pub19:41
ebowdenpaperbot: http://diyhpl.us/~bryan/papers2/paperbot/3a73de0d7d8f7aaac21d63537a91056a.txt19:41
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/99cb84d56d5df36e73c5ced10d36d30e.txt19:41
kanzurewhat19:42
@ParahSailinpaperbot: http://diyhpl.us/~bryan/papers2/paperbot/99cb84d56d5df36e73c5ced10d36d30e.txt19:42
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/bbdc9be894f39be6b87612761b47809c.txt19:42
kanzurepaperbot: file://19:43
kanzureoh right, i anticipated thta one19:43
fennpaperbot hacks into your system and liberates the paper19:43
kanzurepaperbot is the source of all knowledge (and some anti-knowledge)19:44
kanzureanyhow: how does the laser speed up pipetting a million wells?19:44
QuantumGLight controlled synthesis of nucleic acids - Pinheiro - 2010 .. looks like a winner to me19:44
kanzureyeah they use photolithography and DMDs for the synthesis of oligos19:45
@ParahSailinyou dont have to move that many beads around to be orders of magnitude better than contemporary techniques19:45
fennkanzure: i just re-read all that and i'm honestly not understanding what you're missing19:46
@ParahSailina million beads to make all the yeast chromosomes, but most people would be happy with 100 beads19:46
kanzureokay, so the pipette visits each of the 100 wells each step?19:46
fenn10^5 oligos -> 10^6 beads, sequence the beads (in place apparently), pop off the beads you want into the desired well for assembly19:47
fennthere is no pipette anywhere19:47
@ParahSailinthere exists at least one pipette somewhere19:47
fennmaybe there are pipettes once you get into the assembly stuff19:48
yashgarothwhen you find the good bead you pipette it out19:48
kanzure"pop off" okay.. but it's still in the same well.19:48
fennyashgaroth: NO19:48
yashgarothargh19:48
@ParahSailinmight not even be wells, it could be emulsion bubbles19:48
kanzurethe point is, it's still separated from all the other molecules19:48
kanzure(including sequencing reactants)19:48
fennkanzure: pop off means it literally goes flying through the air19:49
kanzureto land where?19:49
fennin the assembly reaction well19:49
QuantumGin the punter's drink, obviously19:49
fennwhich is conveniently placed directly underneath the bead19:50
fennpew pew19:50
fennplop plop19:50
ebowdenpaperbot: file:http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf19:51
kanzureunderneath the bead was the bottom of the well19:51
QuantumGI expect ya need to drop the file:19:52
fennthe bead is hanging from the bottom side of a glass plate19:52
fennthe laser shoots at it, dislodging it, and it falls straight down19:52
kanzureso there are two entrances to each well?19:53
kanzureyou know, wells usually have at least one side19:53
kanzurecall 'em holes pls19:53
fenni dont know what the well looks like. i assumed it was a 4096 well plastic plate19:53
ebowdenpaperbot: http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf19:54
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/5b9aea9f64767417d97210f5f97bf8a2.txt19:54
ebowdenpaperbot: file:http://diyhpl.us/~bryan/papers2/paperbot/5b9aea9f64767417d97210f5f97bf8a2.txt19:54
kanzureuh..19:54
fenner, apparently 4096 well plates dont exist19:55
fennanyway, some relatively large yet still manageable number19:55
fenn4096 seems to be where i'm at today19:55
kanzureso they are straight-through holes19:56
fennno19:56
fennlet's say it's a 96 well plate19:56
kanzurea 96 well plate usually has a bottom19:57
kanzuresuch that you can only access each well through the top19:57
fenncorrect19:57
kanzurenow, if it's upside down, gravity takes your stuff19:57
fennno, the bead is hanging off a glass microscope slide. it's adhered by (unknown, irrelevant)19:57
kanzureyes, but you wanted your bead to react to chemicals etc19:58
fennright19:58
fennit has dna growing on it19:58
yashgarothat like 1536 wells you can probably rely on capillary action19:58
ebowdenkanzure, paperbot does not appear to work with that site, does it work with sciencedirect?19:59
yashgarothagainst gravity that is19:59
kanzurepaperbot does not have 100% access to sciencedirect19:59
ebowdenOk.19:59
kanzureyashgaroth: so how do you insert the new reactants?19:59
fennyashgaroth: 4096 is only 64 by 64; for a 100mm plate that's like a 1mm diameter well19:59
fennmaintaining +- 0.5mm is not that hard20:00
yashgarothfuck knows how you insert stuff into that, unless you're okay with using a pipette *cough*20:00
fennhell, even reprap can do it20:00
kanzureyashgaroth: are you as confused as i am20:00
ebowdenwhat about elsevierhealth?20:00
yashgarothmhm20:00
fenni am confused about why you guys are confused20:00
kanzureebowden: try it, who cares?20:00
kanzurefenn: have you ever used a microarray20:00
yashgarothhow did you get to pew-pewing beads off of a plate20:01
kanzurefenn: or, seen it enough to have a good understanding of how it works20:01
fennyashgaroth: we are talking about how the cambrian genomics "dna laser printer" works20:01
kanzurehere's a big plate: http://arrayit.com/Products/Microarray_Slides/Microarray_ProPlate_Glass/microarray_proplate_assemble.jpg20:01
fennwhy, i dont know20:01
yashgarothwell it mostly runs on bullshit and VC money but that's just my opinion20:01
fennkanzure: what the hell is that20:02
kanzureso is it capillary action?20:02
yashgaroththat's a 96 well20:02
kanzureplate gets inverted, capillary action to hold chemical solution in each well ?20:02
kanzureso molecular feedstock is added prior to flipping plate?20:02
fennhow does it even seal the liquid gap between wells20:02
fennor is contamination not important20:03
yashgarothif they're not filled up all the way you're fine20:03
yashgarothpresumably if you've got beads attached to the bottom somehow, contamination isn't an issue anyway20:03
* kanzure nods20:04
fennso each of those 96 wells has its own pattern with a zillion different dna strands?20:04
fennlike a silicon wafer before it's cut into chips20:04
yashgarothper cambrian, each has one bead with 100k copies of an identical clone20:05
fenni'm confused what this picture is20:05
fennmicroarray_proplate_assemble.jpg20:05
yashgaroththat's a plate with 96 wells in it20:06
fennno, it's a clear smooth piece of glass and a black plastic thing with 96 holes in it20:06
yashgarothglass optional, but yes20:06
kanzurethe holes only go through less than 100% of the material20:06
fennokay the glass being there is the confusing part20:07
fenngod i should just stop20:07
QuantumGDNA (or RNA) typewriter is a nice term20:08
yashgarothI remember us having the same discussion about how the hell cambrian's technology worked, some months ago20:08
fenn"Arrayit offers ProPlate Microarray technology for users wishing to print microarrays on glass plates and subsequently attach the printed plates to adhesive microplates for 96-well and 384-well sample processing."20:09
fennArrayit offers ProPlate Microarray technology for users wishing to print microarrays on glass plates and subsequently attach the printed plates to adhesive microplates for 96-well and 384-well sample processing.20:09
fenner, The adhesive provides a water-tight seal between microplate wells.20:09
yashgarothokay microarrays is more apt for this discussion, same deal where they're not separated but each reaction has a specific spot on the array20:10
yashgarothsince they're bound to that spot you can isolate them with lasers or whatever, and contamination isn't an issue since the interesting stuff is stuck to a particular place20:10
kanzure"Synthesis,1249034,NSF,NSF,SBIR,2013,1,150000.00,Cambrian Genomics Inc"20:11
fennokay i dont really care about this proplate thing20:11
kanzure665 Third StSuite 425San Francisco20:13
kanzurephone: 607592012320:13
fennyou can just watch the tv show, bloomberg brink on netflix20:13
kanzure"This Small Business Innovation Research (SBIR) Phase I project attempts to radically reduce the cost of error-free oligonucleotides for use with gene synthesis. DNA Synthesis of large molecules is done by the assembly of many short oligonucleotide fragments of DNA 60-100bp in length. Currently, each DNA fragment is synthesized in relatively small numbers at an excessive macroscopic scale that incurs a large manufacturing overhead in its ...20:13
kanzure... production costs. This sets a high cost floor for the entire DNA synthesis process. One route to making cheaper oligonucleotides is to synthesize them in large sets on microarrays. However, array-synthesized DNA is both extremely error-prone and produced as dilute, complex mixtures. This proposed project will use massively parallel sequencers to sequence clonally amplified copies of DNA species sampled from the microarray in order to sort ...20:13
kanzure... every species apart from one another as well as to identify correctly synthesized oligonucleotides from incorrect ones. Further, it is proposed to use focused laser pulses in a custom laser ejection device to eject and recover desired subsets of perfect oligos from micron-scale sequenced colonies into multiwell plates for assembly into genes. The goal is to be able to recover tens of thousands of sequence-verified oligonucleotides in ...20:13
kanzure... several hours from sequencer flowcells. The broader impact/commercial potential of this project is to achieve truly disruptive cost decreases in the DNA synthesis of arbitrary genetic information. With the abundance of sequencing data, it is possible to imagine entering a new era of "constructive" biology, where in addition to classical reductive experiments on components, it will be possible to test our understanding of genetic- and ...20:13
kanzure... protein-based circuits by synthesizing new designs and measuring their discrepancy from predicted behaviors. The low-cost industrial production of arbitrary synthetic DNA has the potential to change the practice of biology such that it becomes cost effective to engineer whole genetic pathways and even genomes, accelerating the development of bioengineering, synthetic biomaterials production, as well as medical and research applications."20:14
QuantumGso, I guess we need light activated phosphoribosyltransferases that respond to four distinct spectra.20:16
fennthis could be an interesting method for wild DNA sampling; load up a plate of beads each with a single wild bacterium (unculturable) and see what's in it20:16
yashgarothso the principle is that you could pull single molecules out, isolate them, and then amplify each one enough to determine its sequence20:16
fennyashgaroth: correct20:17
fennand do that a million times in parallel20:17
yashgarothand do it on a small enough scale that it's more cost effective than traditional synthesis20:17
yashgarothbut, good luck with that shit20:18
yashgarothwhich is why I'm hopeful but not optimistic on their approach20:18
heathomg, python, how i've missed you20:18
kanzureheath: except its packaging sucks :(20:18
heathso much productivicheese20:18
fennprogramming languages shouldn't have package managers IMHO20:19
heathfenn would like component20:19
fenneh?20:19
kanzurea web thing? hell no20:19
fenn"component" is a software framework or something (why do people keep using these un-googlable names)20:20
kanzureit's like bower except not20:20
fennit's like <thing you've never heard of> but not20:20
fennoh?20:20
heathwhoops, for some reason, i though holowaychuk inc.  were creating a language agnostic package manager20:20
xentraclike dpkg?20:21
kanzurelike dpkg except not20:21
xentracwell, like dpkg and apt?20:21
fennyeah it's called {dpkg, gentoo}20:21
kanzurethe problem is that python's ability to load a module sucks too20:21
kanzureso it's not just packages that blow20:21
fennwhat's wrong with modules20:21
kanzureyou can't even unload a module20:21
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fennwhy would you do that20:21
@ParahSailinsounds like a challenge20:22
@ParahSailinmatplotlib's module loading side effects are totally evil20:22
kanzuremaybe you no longer need the module loaded20:22
fenncan't you do "import foo as bar ; del bar"20:22
kanzurethat doesn't unload the module20:22
kanzurenice try though20:22
cpopelldon't modules have scope limited to the function they're called in if you call them in a function? I was chatting about this with a friend just earlier today20:23
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fennkanzure: i dont know what you're talking about20:23
kanzurereload() is also broken20:23
xentraccpopell: no, they go into the global module namespace in sys.modules, and also ld.so's symbol table20:23
xentracI tried to fix reload() more than ten years ago20:23
xentracI realized I don't know how20:24
cpopellxentrac: hmmm20:24
cpopellthis was the result of our discussion earlier20:24
xentracthe local name for the module is indeed limited to the function that imports it20:24
cpopellmmm.20:24
cpopellI see what you mean20:24
xentracbut if another function or module imports the same module later, it won't get loaded a second time20:24
kanzurecpopell: this is wizard magic unrelated to your immediate issue of scope20:24
fennokay so i load foo as bar1, delete bar1, change foo, load foo as bar2, now bar2 == bar1?20:25
xentracyes, except tht bar1 is a NameError20:25
cpopellis there a module to simplify the action of deleting modules?20:25
cpopell...20:25
fennis there any reason you would ever do that?20:25
xentracyou can del things from sys.modules; that works for the Python part20:25
kanzurereload() is very very nifty... if it would actually work.20:25
xentracit doesn't work for the ld.so part20:26
@ParahSailinwhy though20:26
QuantumGpaperbot http://pubs.acs.org/doi/abs/10.1021/bi00633a02920:26
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@ParahSailinside effects in module loading should just not be done20:26
kanzure"Please accept that Python indeed does not support unloading modules for severe, fundamental, insurmountable, technical problems, in 2.x."20:27
kanzureoh is it fixed in 3.x?20:27
nmz787_ikanzure: a fab service recently told me "We process about 5 metric tons of glass per year into micro fluidic devices, micro-valves and pumps, micro reactors and MEM's devices."20:28
nmz787_iso that sounds like some engineering to build on top of20:28
kanzuregreat, feel free to pay for $500/prototype yourself20:28
kanzureugh20:28
nmz787_ii only have to make 114 bp/second to make 300k gross/year20:29
@ParahSailinthats a lot of glass20:29
nmz787_ireaction will def be less than 60s, scaling # of reactors still takes up less than 10 sq cm real estate20:29
nmz787_iand prob not more than a meter or two sq otherwise20:30
nmz787_ilikewise, if you consider desktop synthesizers, you'd need about 57 sq meter real estate, and that doesn't include other stuff, doesn't include purification, doesn't include transformation20:30
kanzureneither does your chip20:31
nmz787_i( reaction on macro scale needs 2 mins)20:31
fennyou'll have overhead beyond 10 sq cm of microfluidic plate20:31
nmz787_ifenn: yeah that's what the extra ~2 sq meters was for20:31
paperbotXMLSyntaxError: None (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 51, in _go)20:31
nmz787_ikanzure: yes it does20:31
kanzureyour chip doesn't exist20:31
nmz787_ikanzure: that has been my plan for 4-5 years20:31
@ParahSailinpoor paperbot20:31
nmz787_imy CAD has a v 0.120:32
QuantumGI just used the library anyway20:32
kanzureyou can't just handwave a lot of engineering effort into existence and claim it will magically work20:32
nmz787_iyou have to set requirements before you start a project, generally20:32
fennoligos or GTFO20:32
fennlol20:32
nmz787_ifuck oligo20:32
nmz787_i:p20:32
@ParahSailinif you are doing novel chemistry, dont do novel apparatus at the same time20:33
kanzurei need a mathematical model that corresponds to your estimate of amount of work per added component on a project20:33
nmz787_inope20:33
kanzuresame goes with you fenn20:33
nmz787_inot novel chem20:33
fennwork is force times distance20:33
kanzurejust because it's not novel chemistry doesn't mean your layout works the first time or the first 100 times20:33
@ParahSailinphosphoramidite?20:33
nmz787_ithough i just put out a call for a chemist/polymerchemist/materialsscientist today20:33
nmz787_iyeah some PDMS compatible version20:34
kanzurefenn: you know what i meant20:34
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@ParahSailinby pdms you mean this is going to be a disposable device?20:34
fennyou know what i meant. "work" is undefined otherwise20:34
kanzureengineering time20:34
kanzurenumber of iterations, prototypes, critical bugs20:34
fennnumber of bugs is proportional to number of interacting systems squared20:35
kanzureis the material of each wall considered an "interacting system"20:35
fennprobably not20:35
kanzureis the yield rate of a chemical reaction considered an "interacting system"20:35
fennyield rate is a parameter, not a system20:36
kanzureyield can be impacted by all sorts of interesting factors, like ambient environment, temperature, light, ph, etc20:36
fenngreat20:36
xentracspeaking of chemistry, it occurred to me today why buses smell kind of like matches20:37
fennalso parameters20:37
xentraca substantial part of match smoke is phosphorus oxide20:37
kanzurewhat is your maximum amount of debugging then20:37
xentracthe bus smell is from burning sulfur20:37
fennthe rubber in the floor tiles contains sulfur vulcanizing residue?20:37
kanzurebecause apparently you think this idea is below some threshold amount20:37
xentracno, from sulfur in the fuel20:37
kanzureand i'm really confused what your personal estimates are here20:37
xentrachere in Argentina, not in the US20:38
@ParahSailinpaperbot: http://nar.oxfordjournals.org/content/40/3/e23.full20:38
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/Error%20correction%20of%20microchip%20synthesized%20genes%20using%20Surveyor%20nuclease.pdf20:39
nmz787_iParahSailin: yeah, i don't want to think about cleaning it... but I've got flush lines abounding, so I think it probably will until it gets clogged or something.20:39
nmz787_i*probably will keep working*20:39
fennkanzure: reading various essays about programming management (ie. the mythical man month) has led me to believe that estimating these kinds of things is beyond my ability20:39
@ParahSailinabandon all hope of regenerating, reconditioning, etc the pdms, but im sure its good for prototyping20:39
nmz787_inah, not really regenerating, just more like, use it until it dies20:40
nmz787_iflushing is part of the synthesis, so its there already20:40
nmz787_icleaning is sort of built in I guess you could say20:40
kanzureQuantumG: do you know of any nasa reports regarding failure estimation?20:41
nmz787_iunless the PDMS is slowly swelling, or if some corner is too sharp and causes crystallization to start and clog up20:41
fennkanzure: it's one thing to estimate something you've done before (known unknowns) and another thing completely to estimate something you've never done before (unknown unknowns) and then yet another thing completely for something that has never been done before20:41
@ParahSailinwow ^paper made a 723nt construct20:41
QuantumGNASA does the world's worst statistics20:41
QuantumGand no20:42
xentracI thought PDMS was pretty dimensionally stable20:42
nmz787_ixentrac: depends on solvent absorbtivity20:42
@ParahSailinpdms swells20:42
kanzurethe slide with "weighted technology impact rating" is weird (the ones before it are worthless) http://start1.jpl.nasa.gov/pubPro/Alan_Wilhite.pdf20:42
@ParahSailinhttp://www.biotechniques.com/multimedia/archive/00036/BTN_A_04364PF01_O_36417a.pdf20:43
kanzureQuantumG: how is that possible, don't they do the famous "1 failure in a billion" numbers20:43
xentracnmz787_i: thanks20:43
QuantumGyeah, how do you think they come up with those numbers?20:44
kanzureoh :(20:44
kanzurethis seems like something that large-scale engineering projects need to have had addressed though20:45
kanzurelike the LHC.. you don't just go put that sucker in the ground without knowing the constraints, tolerances, and expected failure rate.20:45
QuantumGheheh.. ya do know they did exactly that right?20:45
kanzurehuh?20:45
QuantumGhooked up all the superconducting doo-dahs and discovered that not only didn't it work but that it wasn't even close to a functioning design20:46
kanzurethat's pathetic20:46
nmz787_iall those enzyme things seem silly though, DNA synthesis isn't really super crazy complex of a reaction... there are like 8 or 10 reagents involved, keep it dry of water, get your metering right and your purification in-line and that's that20:46
nmz787_iblock co-polymer synthesis is all around20:47
nmz787_iABS20:47
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kanzure"Early estimates by managers at NASA put the risk of catastrophic failure during a mission at 1 in 100,000; engineers, on the other hand, put the estimate at 1 in 100. A study recently released using all the data available from 30 years of flights reveals that the danger was in fact much higher. "20:47
nmz787_ithat's only 1 monomer type less than DNA code20:47
fennQuantumG: why didn't the LHC work as designed?20:48
QuantumGI love the way history on Wikipedia for the LHC starts in 2008.20:48
* fenn is too lazy to read up on it20:48
QuantumG10 Sep 2008 CERN successfully fired the first protons around the entire tunnel circuit in stages.20:48
QuantumGyeah, cause the LHC just magically popped into existence.20:48
QuantumGThe construction of LHC was approved in 199520:49
xentrackanzure: they did run into a lot of unexpected failures actually20:49
fennthe LHC was warped in via microsingularity transport20:49
xentracwhich is what usually happens when you do things nobody has done before20:49
kanzurethere are lots of ways to estimate likely types of failures20:50
kanzuredid they even have a failure estimation model20:50
QuantumGhttp://en.wikipedia.org/wiki/Large_Hadron_Collider#Construction_accidents_and_delays20:50
kanzurein a system with 1 million parts, it's probably a good idea to have at least a rough estimate of failure, or even make up fake lower bounds which tell you how much manpower you will need for maintenance or replacement etc20:50
QuantumGit's the second last section before "Popular culture" and "See also".20:50
fennkanzure: and the actual measured catastrophic failure rate was 2 in 13520:51
QuantumG.. and doesn't even include the stuff I vaguely remember reading.20:52
fennplus or minus some hand waving20:52
kanzureinsert stereotypical "haha they used english feet and we used meters" story20:52
QuantumGhttp://web.archive.org/web/20080616063402/http://www.photonics.com/content/news/2007/April/4/87089.aspx20:52
xentrackanzure: I'm sure they did, or they wouldn't have been able to ever get it to work20:52
QuantumG.title20:52
yoleauxFermilab 'Dumbfounded' by Fiasco That Broke Magnet20:52
fennthe mars orbiter screwup was actually much more complicated and hard to explain than the newtons/foot-poundals mixup that we've been told20:53
kanzure"Fermilab designed and built nine of the magnet assemblies for CERN and conducted four engineering reviews between 1998 and 2002"20:53
kanzureaka "someone looked at this only four times" :)20:53
xentracjournalists always love it when "boffins" are "baffled"20:53
xentracthey can safely be ignored20:54
QuantumGin a project that large, the reviews are nothing more than rubber stamps anyway20:54
kanzurei feel like freitas/merkle might have written about estimation in their book on kinematic self-replicating machines20:54
kanzureoh wait, maybe AASM instead20:55
QuantumGthere's plenty of it in Nanosystems20:55
kanzureAASM seems like the place they would do it20:55
* ParahSailin is disappointed that nobody looked at the awesome paper i linked20:55
kanzurehttp://www.islandone.org/MMSG/aasm/20:55
xentracQuantumG: why do you think that projects being large requires that reviews be ineffective?20:56
kanzurehaha "Because of the already challenging design problem, it is highly desirable to keep all seed systems as simple as possible in both structure and function. This should help reduce the risk of partial or total system failure and make closure less difficult to achieve at all levels."20:56
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fennParahSailin: i thought you were being sarcastic20:56
kanzurethat' sthe only mention of failure20:56
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QuantumGParahSalin: looks neat20:57
@ParahSailini think it has potential to be scaled20:57
fennin the diybio post made by anselm (linked here a couple hours ago) he says that mismatch endonucleases chew up all your DNA, leaving very little yield20:58
kanzurealso, a lot of this is part failure, like mechanical failure under load20:58
kanzurerather than system design problems20:58
kanzurei dunno what to call the system design type of problem20:58
@ParahSailinfenn: apparently not all20:59
fennsystemantics?20:59
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fennParahSailin: if you have very low yield you need to amplify (probably with PCR) which has some finite error rate of its own20:59
* fenn shrugs21:00
fenni guess there are fancy low error PCR enzymes now21:00
QuantumGkanzure: NASA is a great place to propose a barely working concept, get billions spent on trying to figure out how it could possibly work (because failure isn't an option!) and then move onto the next thing (after not failing).21:00
fennthe shuttle mentality21:00
@ParahSailinfenn: expectations are really low right now for dna synthesis21:01
kanzurei am a shuttle voom21:01
fennnyoom21:01
QuantumGAres I is what I had in mind, but the examples abound21:01
@ParahSailineven with a couple pcr errors, a multi kb construct is sploosh21:01
fennthe average nasa engineer during apollo was 2621:01
QuantumGeverything is either a success or cancelled by those stupid policy makers at NASA.21:02
QuantumG(sarcasm)21:02
fennaverage nasa age is now 4721:02
QuantumGif your spacecraft crashes, that's not a failure, that's.. like.. space is hard man21:02
QuantumGif you put a rover on Mars that costs 10x more than you said it would at the start of the program.. that's a success.21:03
fenni'm more worried about not sending anything up at all21:03
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justanotheruserThat's science! Their theory that their mission would be successful was wrong21:03
fennwho cares if it crashes21:03
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fennwe still dont have an equatorial LEO laboratory21:04
fennstuff costs too much21:05
QuantumGyeah, it costs too much because of that attitude21:05
fennsoon we'll have unpiloted aerostats and the satellite industry will die, taking the rest of commercial space with it, unless something big changes21:06
QuantumG"soon" has been soon for a long time when it comes to aerosats21:06
xmjmoin21:06
fennthe FAA is dragging its knuckles21:06
QuantumGI don't think that's the problem21:07
fenni think it is21:07
QuantumGhow do you figure?21:07
fennwell, why don't we have aerostats flying around?21:07
fennthey exist21:08
kanzure1) make a correct failure estimation model 2) proceed to building dyson sphere21:08
kanzure*engineering design failure21:08
fennexpected chance of success building dyson sphere: 1e-133721:08
kanzureyou have already failed21:08
fennyou are already dead21:08
xentracwe do have aerostats flying around for weather monitoring21:09
cpopellmuda muda muda21:09
QuantumGI'm pretty sure you mean aerosats.. aerostats already exist and fly around the US all the time21:09
xmjfenn: "still bigger than the last web startup i funded. here, have some VC money"21:09
kanzuredo you think the death punch is possible? you could inject some chemicals that cause a body to explode, right?21:09
fennxentrac: a balloon is not an aerostat because it moves randomly21:09
xmjcan aerostats be geostationary?21:09
cpopellkanzure: what about the high pressure knives?21:10
xentracfenn: I think it is: https://en.wikipedia.org/wiki/Aerostat#Free_balloons21:10
fennwhatever21:11
fennlet's abuse language and make everything mean nothing and nothing everything21:12
xentrac.ety aerostat21:12
yoleauxSorry, I couldn't find the etymology of that.21:12
xentracwhat's the FAA doing?21:12
QuantumGin any case, there's plenty of FAA support for balloon delivered comms services.. I don't think that's the problem.21:12
QuantumGI think the problem is that flying a permanent balloon platform is really hard.21:12
fennxentrac: the "stat" part means "static" as in "not moving"21:13
fenn"aero" means it's in the air21:13
xentracthere is a discussion of this at https://en.wikipedia.org/wiki/Talk%3AAerostat#Meaning21:13
fenna balloon without motive power. Contrasted with {aerodyne}. [1913 Webster21:14
xentracit turns out that "stat" means that its lift is not derived from moving, as opposed to aerodynes21:14
xentrac"All three of those bulleted definitions mean exactly the same thing, which has been the conventional meaning for well over a century. The second meaning referred to is the recent narrow use of the "stat" bit to indicate static mooring in contrast to a free-flying airship, e.g. as used by the US General Accounting Office, but it is very much a minority usage by those who are not technically knowledgeable."21:14
fennso a kite is not an aerostat?21:16
fennwhat's the point of even having the word21:16
xentracno, it's lifted by aerodynamic lift21:16
fennwhy not just say "balloon"21:17
xentracis a zeppelin a balloon?21:17
fennyes21:17
@ParahSailingreek roots sound more professional21:17
xentracnot normally21:17
xmjParahSailin: moin21:17
xentracthe point of having the word is probably to distinguish the two major types of aircraft: heavier-than-air and lighter-than-air21:18
fennstationkeeping flying thingy is too much21:18
QuantumGanyway, I dunno how commsats are still around.. people like their soccer delivered that way I guess21:18
@ParahSailinmøin møin møin21:18
QuantumGand people keep building LEO constellations despite the fact that none have ever turned a profit.21:19
fennand "statite" already has a meaning related to solar sails21:19
xentracthere are probably classified funding source for LEO constellations21:19
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QuantumGnah VCs just like the idea.21:20
QuantumGthis time it'll be different because SpaceX21:20
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fennwhat does SpaceX do that radically changes things?21:20
QuantumGcheaper launch, is the argument21:21
xentraccontrol costs21:21
QuantumGmostly cheaper because you don't have to take your payloads to Russia, but yeah21:21
fennwasnt this the point of sealaunch21:21
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QuantumGyeah, and they got sued21:22
xentracdidn't know that21:22
xentrac.g sealaunch lawsuit21:22
yoleauxhttp://www.reuters.com/article/2013/02/04/boeing-sealaunch-idUSL1N0B31GP2013020421:22
fennsued for what21:22
QuantumGitar21:22
fennhuh?21:22
fennbecause sailing is "export"?21:23
xentracoddly enough, that article says:21:23
QuantumGno, Boeing failed to keep their tech out of Russian/Ukranian hands21:23
xentrac"Sea Launch sent its first satellite into space in 1999, but filed for bankruptcy in 2009 because of weaker demand, mounting debt and a failed launch that led to a $53.2 million arbitration award against the company"21:23
fennso, not itar?21:24
xentrac.g "sea launch" itar21:24
yoleauxhttp://www.alston.com/files/docs/3-23-11-Items-Insert.pdf21:24
QuantumGyeah, part of that weaker demand was the supposed benefits of using them over Russian launch - not going through the ITAR process - was proven false.. graphically21:24
xentrac"The assets owned by Sea Launch created other21:25
xentracregulatory and defense-related issues, including the fact that the equipment (the vessel and the platform21:25
xentracutilized to launch rockets) is subject to the International Trafficking in Arms Regulations (ITAR). The21:25
xentracITAR regulations created issues in connection with obtaining DIP financing as lenders were concerned21:25
xentracabout the ability to liquidate and monetize those assets. Today Sea Launch is now reorganized and21:25
xentracoperating in Luxemburg and Switzerland (with the physical assets still in Long Beach, California, the21:25
xentracreorganization was successful and created significant value for the stakeholders and customers.21:25
xentrac"21:25
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fenni think sealaunch was a great idea and SpaceX should take advantage of it21:26
fennit's practically in their back yard21:26
xentracSea Launch was largely Russian-owned21:26
QuantumGdear god why?21:26
xentracand Ukrainian-owned21:26
xmjxentrac: that means essentially the same thing, doesn't it.21:27
QuantumGthe launching from the equator stuff was never the purpose of the partnership.. that was just some nonsense to avoid export regulations and it didn't work21:27
xmjjust use Soviet-owned.21:27
xmj:]21:27
fenni never knew anything about the russian partnership21:27
QuantumGThe US now has "export free zones" like the Mid-Atlantic Regional Spaceport to do something similar.21:28
dingo21:28
fennum except Virginia is nowhere near the equator21:28
QuantumGall of this stuff stems from the time when it was considered crazy talk to say you were going to make your own rockets.21:29
QuantumGlaunching from the equator gives you a tiny performance improvement which doesn't make up for the all the butt-hurt you get from having to go outside the US.. ya know, assuming you're a US company21:29
xmjlol21:30
xentraccos(latitude(virginia)) is pretty close to 121:30
QuantumGOrbital Sciences launches from MARS because 90% of their rocket is made in other countries.21:30
xmjyes, because local subsidiaries to circumvent export regulation is... hard to do, really21:30
fennit also provides transportation to your launch site, a wide open launch range, a launch pad21:31
QuantumGxmj: local subsidiaries full of non-US citizens?21:31
fenni thought orbital sciences used "MARS" (what a terrible name, it's WALLOPS FLIGHT FACILITY) because of a treaty that forbids launches of ICBMs except from vandenberg and virginia21:32
QuantumGthat could be why WALLOPS exists, but it's not why Orbital cares21:33
fennorbital was using a minotaur V (when i was paying attention)21:34
fennthe LADEE launch21:34
fennOrbital's Minotaur V launches LADEE mission to the Moon ...21:34
fenn Launch to Occur from NASA's Wallops Flight Facility in Virginia on Friday --(Wallops Island, VA 5 September 2013)21:34
@ParahSailinalso is pretty cool that railroads go to virginia, and not french guyana21:34
xentracwell, LADEE DA21:34
QuantumGyeah? and?21:35
xmjParahSailin: boats go21:35
fennsorry for the spam21:35
fenni watched that launch through binoculars, it was pretty cool21:35
fennvery orange21:35
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xentrac.g latitude of virginia21:36
yoleauxhttp://www.worldatlas.com/webimage/countrys/namerica/usstates/valatlog.htm21:36
fenn.wa latitude of virginia21:36
xentrac.g cos(37.5 degrees)21:36
yoleauxhttps://answers.yahoo.com/question/index?qid=20100515221911AA8dWT521:36
yoleauxVirginia: center coordinates: 37° 31' 7"N, 78° 53' 28"W21:36
fenncome on wolfram, you don't know what latitude means?21:36
xentrac.c cos(37.5 degrees)21:36
yoleauxcos(37.50°) = 0.793353...21:36
@ParahSailin.wa circumference of earth21:37
yoleauxEarth: equatorial circumference: 40075.017 km (kilometers); Unit conversions: 24901.461 miles; 4.0075017×10⁷ meters; 21638.778 nmi (nautical miles); 0.13367587 light seconds; Comparison as length: ~1.9 × length of the Great Wall of China (~21196 km); Corresponding quantities: Light travel time t in vacuum from t = x/c:: 134 ms (milliseconds); Light travel time t in an optical fiber t = 1.48x/c:: 198 ms (milliseconds)21:37
xentrac.wa circumference of earth / 1 day21:37
yoleauxEarth: equatorial circumference/(1 day): 40075.017 km/day (kilometers per day); Unit conversions: 463.83121 m/s (meters per second); 0.46383121 km/s (kilometers per second); 0.28821135 mi/s (miles per second); 17.292681 mi/min (miles per minute); 1037.5609 mph (miles per hour)21:37
fenn.wa latitude of vandenberg california21:37
yoleauxfenn: Sorry, no result!21:37
xentrac463 m/s21:37
fenn.wa latitude of vandenberg air force base21:37
yoleauxVandenberg AFB: latitude: 34° 44' 14"N; Unit conversions: 606.3 mrad (milliradians); 0.6063 radians; 34 degrees 44 arc minutes 14.4 arc seconds; 2^h 18^m 56.96^s (right ascension); 38.6 grads (unit officially deprecated)21:38
xentrac.wa leo speed21:38
yoleauxLeo (male given name): Speed (male given name): Information for births: | Leo: Speed; rank: 134th: beyond 1000th; fraction: 1 in 704 people (0.14%): less than 1 in 12500 people (0.008%); number: 2855 people per year: < 200 people per year (US data based on 2012 births and other SSA registrations in the US)21:38
xentrac.g leo speed21:38
yoleauxhttp://en.wikipedia.org/wiki/Low_Earth_orbit21:38
fennoh but vandenberg can't do equatorial launches because it would kill those honest god fearing people in nebraska21:38
@ParahSailindelta v starts at about 10km/s21:38
xentracyeah, I was trying to figure out whether I want to deduct the 21% of 463 m/s from delta v or orbital velocity:21:39
xentrac"orbital velocity needed to maintain a stable low earth orbit is about 7.8 km/s, but reduces with increased orbital altitude."21:39
xentrac.c 21% * 463 m/s21:39
yoleaux21%×463 m/s (meters per second) = 97.23 m/s (meters per second)21:40
xentrac.c 21% * 463 m/s / (7.8 km/s)21:40
yoleaux21%×(463 m/s (meters per second))/(7.80 km/s (kilometers per second)) = 0.012521:40
fennfrom delta V; orbit is around the center of earth, not any arbitrary latitude line21:40
xentrac.c 21% * 463 m/s / (7.8 km/s - 463 m/s)21:41
yoleaux21%×(463 m/s (meters per second))/(7.80 km/s (kilometers per second)-463 m/s (meters per second)) = 0.013321:41
xentracso launching from the equator instead of Virginia saves you 1⅓% of the orbital velocity you need21:41
xentracor more like 1% if the delta-v is actually the relevant number, as ParahSailin says it is21:42
QuantumG.. and most launches are underperforming anyway.21:42
fennwhen 95% of your mass is fuel, 1% is a lot21:43
xentrachow much, fenn?21:43
fennhow much what?21:43
xentrachow much is 1%?21:43
@ParahSailinfuel requirement is geometric wrt delta v21:43
fenn0.01?21:43
xentracor is the answer to that question really "come back after you've played Kerbal Space Program for a couple of weeks"?21:44
@ParahSailin.g tsiolkovsky equation21:44
yoleauxhttp://en.wikipedia.org/wiki/Tsiolkovsky_rocket_equation21:44
Dariuswhat does .c use?21:45
kanzurechinese children21:45
Dariusthey're very quick21:45
kanzurewell there's a lot21:45
fenni hate wikipedia's equations, they are light colored staticky pixels around black letters on a gray background, pretty much ensuring i can't read them21:45
kanzureswitch the css theme, there's a dropdown box somewhere21:46
kanzurethe css theme might determine their latex generator image thing21:46
fennwikipedia has themes?21:47
kanzurehttp://en.wikipedia.org/wiki/Wikipedia:Skin#How_to_change_the_skin21:47
xentracDarius: on #swhack, where yoleaux comes from, it's currently using Wolfram Alpha21:47
kanzure"Once you have an account, go to your preferences and go to the "Skin" section of the Appearance tab. With the default skin, this page can be accessed at any time from the "my preferences" link placed on the top right corner. Choose your skin and then click Save. Then, all pages will be loaded with the new selected skin."21:47
@ParahSailinIsp of kerosene/lox is 353s21:48
xentracbut I don't know if yoleaux has been updated yet21:48
kanzure"However, any user may change the skin of a page for them only, but only one each time, by typing ?useskin=skinname to the end of the URL (i.e.: ?useskin=vector)"21:48
fennxentrac: the simple answer is, weigh your rocket fully fueled, multiply its mass by 1% and that's the amount of extra payload you get by launching at the equator21:49
xentracfenn: ah, so 20%?21:50
xentrac(in that 100%-95%-1% is 120% of 100%-95%)21:51
fennoh also " the minimum orbital inclination without a plane-change maneuver is the latitude of the launch site"21:51
xentracbut ParahSailin says "fuel requirement is geometric wrt delta v" so perhaps not21:52
@ParahSailinif you can get 6.4% in orbit with the balance as fuel, going for delta v of 9.5 km/s, you can get 6.2% launch mass in orbit at 9.5 * 1.01 delta v21:52
xentracthat's a substantial improvement but not nearly as much as my other number21:55
fennkanzure: thanks i was guessing randomly ?skin=dark ?skin=black21:55
fennthey are all black text on white background though?21:56
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xmjfenn: did you see http://opensslrampage.com/ ?21:59
xmjer22:00
xmjfenn: did you see http://www.libressl.org/ ?22:00
xmjThis page scientifically designed to annoy web hipsters. Donate now to stop the Comic Sans and Blink Tags22:00
fennno, why should i care?22:01
fennSSL sucks anyway22:01
xentracfenn: where does your gray background come from?22:01
xentracmy Wikipedia background is always white (so I can't see the staticky pixels)22:02
fenncat ~/.dillo/style.css22:02
fenn* { background-color: #272727 !important; ...22:02
@ParahSailini've done some patches to hs-tls22:02
xentracah22:03
xentracI didn't know Dillo even supported CSS22:04
fennit doesn't really22:04
fennit will do borders and text and colors, but not float or various box model things22:05
fennas for why i'm using dillo, see previous complaints about thrashing and ram and tabs22:06
fennkanzure: i thought you had a watermark removal script22:09
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fenni mean, i thought it was running on paperbot's output22:09
xentracno, I totally understand wanting to use dillo22:09
fennbut i clearly see a watermark from a paper downloaded today at <location redacted>22:09
fennxentrac: i recently discovered "netsurf" which, despite its odd origins and intended audience, is actually a damn fine first draft of a browser22:10
fennit just needs javascript and some minor bugfixes22:10
fennnetsurf is as fast as dillo, but it properly renders CSS22:11
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xentracI think I tried using netsurf once but couldn't get it to stop crashing22:13
xentracbut I might have confused it with something else22:13
kanzurefenn: pdfparanoia does not have 100% coverage22:13
kanzurefenn: https://github.com/kanzure/pdfparanoia/issues report a bug22:13
xentracpresumably if it doesn't have JS it doesn't have the DOM either22:13
xentracwhich means that getting it to run modern JS would presumably involve implementing the DOM and restructuring its rendering around the DOM, which I presume would make it no longer as fast as dillo or in the same ballpark22:14
kanzureservo is the only modern practical option at this point22:14
kanzurewebkit and blink are both massive22:14
xentracservo is still a proof of concept22:15
xmjit's too bad opera stamped their engine and settled for webkit22:15
xmjopera's was by far the fastest22:16
xentracI didn't realie that22:16
xentracrealize22:16
fennoh, oxford journals is already listed as a bug22:16
xentracI stopped using opera in 200022:16
fenn90% of the time i don't care about javascript, i just want to see the page22:17
fennso maybe have a browser that loads webkit for the other 10%22:17
fennor i could just switch browsers i guess22:17
xentracI'm wondering at this point if it makes sense to write a browser that recognizes bootstrap and has a fast path for it22:18
fennactually midori worked fine before i "upgraded" to 13.1022:18
xentracmidori's still webkit, no?22:18
fennyes, but it was pretty fast still22:18
xentracI guess I figure that 95% of the stuff on current web sites is trying to accomplish pretty simple things22:18
fennand it didn't explode on more than 10 tabs, like all mainstream browsers do22:18
fennwhat do you mean "has a fast path for it"?22:19
xentracif you could stick in optimizations to recognize which things people are trying to accomplish, and then accomplish them in more efficient ways, you could probably save a lot of memory and CPU22:19
fennoh like a self optimizing JIT for javascript22:19
xentracno22:20
fenn(i thought chrome did that with v8)22:20
xentraclike a large library of extremely specific optimizations for not just JS but also CSS and HTML22:20
xentracmostly CSS and HTML in fact22:20
kanzure"oh look, the billionth webpage that's using float:left"22:20
kanzure"and jquery"22:20
xmjxentrac: did you see the stackoverflow page telling you to use jquery for simple things like adding two numbers?22:21
fenni understand having a local cache of jquery, but how do you fix float:left?22:21
xentracI don't know specifically what the things are that make e.g. Twitter take multiple seconds to scroll down22:21
xentracon my netbook22:21
xentracbut the end result is a pretty mundane change to what's on the screen22:22
kanzurewhy are all the google scholar results for "design flaws" all about software? :(22:22
fennusually my problem is: i open a new tab, paste in a url, and nothing happens for 5-50 seconds22:22
xentracyou would think that whatever particular chunk of DOM that Bootstrap is constructing and then twiddling, I could stick a Bootstrap-DOM-recognizing hack into the browser engine that recognizes this particular case as "oh yeah, that's Bootstrap DOM for a pulldown menu"22:23
fennsomehow chrome is using 4GB of (virtual) RAM22:23
fennits like it doesn't understand the difference between ram and swap22:24
xentracor "this is going to scroll the page down"22:24
fennhow is this different from memoizing function calls22:25
kanzure"design errors" is also all software and vlsi stuff. so, what, design errors don't happen in buildings or supercolliders?22:25
fenni guess the DOM varies because the colors are different or something?22:25
fennso the function call is not exactly the same and you get a cache miss22:26
Lemminkainenpaperbot http://www.sciencedirect.com/science/article/pii/S016372581100165322:26
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/fd72b379e6676e13c477f45520c6534a.txt22:26
xentracI guess I'd have to dig into some DOM to find out22:26
fennxentrac: what do you think about throwing away all the webmaster-provided styling information and using LCARS instead?22:28
xentrac<sadtrombone />22:28
xentracI think I'd rather read Wikipedia with any of the Wikipedia skins than with LCARS22:29
fennbut styling is just reinventing the UI wheel for every website in existence22:29
fennfine, s/LCARS/vector/22:29
xentracit would be okay for some pages22:29
xentracand not others22:29
fennthe way i see it, there's a page with some data (content) and some affordances (menus, buttons, etc) and i really dont give a shit about anything else22:30
fennall that stuff can just fuck off and leave me alone22:31
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fenncustom mouse cursor that sprinkles fairy dust -> /dev/null22:31
xentraceven if you just remove the inline style tag from e.g. http://canonical.org/~kragen/sw/aspmisc/my-very-first-raytracer.html it becomes substantially less readable22:32
fennaside from the large renderings breaking up the text flow, i dunno what i'm missing22:33
* fenn waits for chrome to do anything at all22:34
fennprocessing request...22:34
fennprocessing...22:34
fenn[Pages Unresponsive]22:35
xentracpasting the style tags from https://en.wikipedia.org/wiki/Wikipedia:Vital_articles into it improves the situation somewhat22:35
fennoh there it is. oh look, it has a logo in the upper left corner22:35
xentracat least the <pre> tags have a different background22:36
fennand the code text flows into the rendering making it hard to read22:36
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xentracbut all the text is run up against the left edge of the page with a single pixel of whitespace, which makes it hard to read22:36
xentracand the width of the text is way too wide22:36
kanzureconceptual design flaws exist, right?22:37
kanzureit's not all just "your load bearing loadbearer wasn't able to bear enough bears"?22:37
fennin dillo the <pre> text has a different font and font size and it has a box around it, quite clear it's a block of code22:37
xentracthat's good22:37
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xentracI put CSS in there for that22:37
fennkanzure: doing the wrong thing faster is a moral hazard22:37
xentracwhat I meant was that even if I replace it with Wikipedia's CSS that's still there22:37
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xentracbut I don't think Wikipedia's vector skin CSS is really an improvement22:38
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xentracthe <pre> text overlapping the image is indeed a problem but I think it may actually be the least bad solution on a small screen22:38
fennxentrac: you're missing the point. i'm not talking about just swapping CSS themes, i mean wholly reorganizing the presentation of the underlying data structure and user interface so as to be consistent across websites and even programs that are not web browsers22:39
xentracoh, sure22:40
fennlike an rss reader i guess22:40
xentracrepresent your data at a higher conceptual level so that you can automatically reformat it as desired22:40
xentracthe thing is that people have been trying that since Scribe with limited success22:41
fennScribe the book typography tool?22:41
fenn(what is scribe?)22:41
xentracyeah, that one.  1979: https://en.wikipedia.org/wiki/Scribe_%28markup_language%2922:42
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fenni know this is confusing because a lot of people think SGML is just HTML22:42
fennHTML was sort of worse-is-better22:43
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xentracI know22:44
fennanyway the difference is that now we have an entire internet's worth of data and hacky webpage-as-UI that needs to get steamrollered into shape. i figure a bayesian classifier is a reasonable solution22:44
Lemminkainenpaperbot http://www.nature.com/nri/journal/v13/n3/pdf/nri3399.pdf22:45
paperbothttp://libgen.org/scimag/get.php?doi=10.1038%2Fnri339922:45
Lemminkainenhellllllllyuss22:45
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fennthen you have different pre-compiled presentation modules like "image gallery" or "long form text" or "comment thread" or "drop down menu" that all are end-user configurable22:46
xentrachttp://cr.yp.to/writing/visual.html describes how far we've come (as of 2007) with "The author should be concerned with the structure, not any particular visual representation."22:46
xentracafter 28 years of work, success is still limited22:46
fennthe user agent in this case can fetch pages that it thinks are relevant to the display, like say someone links you to a flickr photo in a set, it would fetch the thumbnails from the rest of the set and show you image gallery mode22:47
xentracso I think the problem may be harder than you think22:47
kanzure"it's only the sum of the number of parts"22:48
kanzure:grumpy:22:48
fennin this case i'm processing relatively unstructured data (arbitrary webpages) and attempting to transform it to the ideal structured data22:48
fennso it's a different problem than "trying to get everyone to use your nerdball view of the world"22:49
fennontological assimilation22:50
fenni just know this is an irc log i am going to find during some future web search22:51
kanzurehello future me, fuck you22:51
xentracwell, I'm just saying that even if web page authors had taken the time to provide you the structured data in the first place, current software will still do a much worse job of presenting it as a two-dimensional interactive display22:52
xentracthan the current mishmash of skilled and unskilled webmasters tweaking CSS22:52
kanzurefenn's idea is to just use a default minimum terrible level of "two-dimensional display"22:52
fennbullshit, the webmasters have no idea what my requirements are and even if they did, they wouldn't care22:52
kanzurethen you don't have to be disappointed anymore22:52
fennfor example the black text on white background sucks when you are in a dark room22:53
xentraclike the readability bookmarklet, plus some classifiers to apply more specialized presentations?22:53
kanzurenot that i agree, i just want software and package managers22:53
xentracyeah, it does, fenn22:53
fennwhite text on a black background sucks when you're using an e-ink reader22:53
xentracI prefer red text on a black background most of the time22:53
fennthis is what CSS was supposed to solve, but instead we've gone and turned it into a do-anything rendering API22:53
xentracyeah.  and above I explained why I think that is22:54
fenni spent several days tweaking tumblr to get it all as light text on dark background; absolutely boggling how many things needed to be fiddled with to get there22:55
xentracand in the case of Wikipedia you need to rerender the equations22:55
xentracwhich btw you can do because the TeX source is present as alt text22:55
fennnah you can just do simple processing like "this has a white border and is transparent, invert the image"22:55
xentrac<img src="//upload.wikimedia.org/math/9/4/5/945a66bb8ac5a46fd959ab6c12eebb00.png" alt="\Delta v = v_\text{e} \ln \frac {m_0} {m_1}" class="mwe-math-fallback-png-inline tex">22:56
xentracdo you mean a white background? (in the original page CSS?)22:56
fennnevermind, re-rendering the equation is probably the best general solution22:57
fennthere will be cases when the TeX is not available, such as scanned images or "we converted this svg to a jpg for you"22:57
xentracit's not very general; it only applies to MediaWiki with TeX22:58
fennbut consider what the equation represents, a mathematical function with symbols representing constants or parameters22:58
xentrachmm, it would be interesting if you could automatically do something interesting with that22:59
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fennit's not too far-fetched22:59
fennreally any text should be OCR'ed23:00
xentraclike Project Naphtha23:00
fenneven text in images that aren't clearly computer generated23:00
kanzureugh now my queries are returning me stuff written by matt campbell23:01
kanzurewell i have clearly looped back on myself23:01
kanzuremaybe i should ask him23:02
kanzureconceptual design flaws seems like a thing he might think about23:02
xentracfenn: maybe you could build a search engine that returns you equations scraped from Wikipedia pages23:02
fennmost of campbell's stuff was about "conceptual design" anyway23:02
xentracand integrate it into a computer algebra system23:02
kanzureare you trolling him? i can't tell23:03
fennxentrac: actually i hate equations23:03
fennthey're supposed to look pretty and be compact or something23:03
xentracno, not at all; I think this might actually be useful23:03
fennbut there's a reason japanese computer programmers don't use kanji in their code...23:04
xentraccase in point, yesterday my ex-girlfriend and I were 3-D printing a Helmholtz resonator for a music box23:04
xentrachttps://en.wikipedia.org/wiki/Helmholtz_resonator has some relevant equations and variable definitions23:04
fennwhat is "project naphtha" all i see is petrochemical stuff23:05
xentracsorry, they misspelled the name23:05
xentrac.g project naptha23:05
yoleauxhttp://projectnaptha.com/23:05
xentrac.t23:05
yoleauxThu, 24 Apr 2014 06:05:47 UTC23:05
xentrac...¿en serioooo?23:06
kanzureweren't they in the news yesterday23:06
kanzuretheir name screams "hey vegeta" to me23:06
fennnapa = cabbage23:06
xentracanyway it turns out all the equations on that page use compatible naming of variables23:06
kanzure.title https://www.youtube.com/watch?v=qslAuezumIA23:06
yoleauxDBZ Abridged: The Best of Nappa23:06
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xentracand so if you pulled that into a computer algebra system and set some of the variables to known values, you could get a thing that let you graph how the others are functions of each other23:07
xentracturns out that a really crucial missing piece there is the Q factor of the resonator, which ought to be on that page but isn't23:08
fennoh btw xentrac in my-very-first-raytracer.html the font kerning is all off in the google chrome version (maybe because it's trying to substitute some low quality font i have installed)23:08
xentracfenn: sorry to hear that23:09
xentraccould also be because I'm specifying that the text be justified, but browsers still don't hyphenate, which puts a lot of heavy demand on adjusting letter and word spacing23:10
fennoh right i remember dillo introduced all this fancy text hyphenation stuff23:11
fennand netsurf just left-justifies it23:12
fennman wikipedia's equations really look like crap even with a white background23:13
fennmust be optimized for speed instead of quality23:13
kanzureit's all cached anyway so i doubt they are bothered by an extra 10-100ms during rendering23:14
fennwhat's with all the visible pixels then23:15
fenn(aliasing)23:15
-!- Vutral_ [~ss@vutral.net] has joined ##hplusroadmap23:17
fennxentrac: as you've no doubt deduced the same system could be applied to PDFs23:19
kanzurefigure/diagram extraction is a pain in the butt, much less OCR..23:19
fennyou don't have to OCR the pdf because it's already text for the most part23:20
kanzurei wish23:20
fenni've resorted to OCR'ing pdf files though23:20
fennthis is the kind of problem that really shouldn't exist23:21
kanzureit's not like i want to read a million pages of longform text to get effective at anything anyway23:21
kanzurethat's just not sustainable23:21
fennhuh23:21
kanzurei'm being grumpy about reading, this week23:22
fennyou should be able to sort a table in a pdf by its headings23:22
xentracfenn: I don't see aliasing on Wikipedia equations on a white background23:22
kanzurefigshare does some of that but they are a company and i don't think they're giving away source/software23:22
fennand summarize columns, or whatever23:22
xentracI do see big pixels but that's because they're images and my zoom is >100%23:22
fennyou dont see the huge pixels on the radical sign? https://upload.wikimedia.org/math/1/5/8/158e4d2f3b3610849e24263720118db6.png23:23
xentracfenn: I posted a bookmarklet for doing that on HTML to kragen-hacks a few years back23:23
xentrachave you tried it?23:23
xentracoh, yeah, that's a little jaggy.  wonder why!23:24
fenna bookmarklet will let me sort pdf tables?23:24
kanzure/topic mathematical aliasing criticism group23:24
xentracno, "on HTML"23:24
fenni'm of the school of thought that equations are about as dumb as cursive or astrological diagrams23:25
xentraclooking at the equation in the GIMP, it seems to be antialiased wrongly23:25
xentracI think all the pixels should be black, with varying levels of opacity23:25
fennis it a png8 or a png24?23:26
fennpng8 has boolean transparency i think23:26
xentracinstead they are many different shades of gray, with only boolean transparency23:27
xmj2^8 shades of gray23:27
xentrac"4-bit colormap"23:27
xmj:o23:27
fennyou'd think there would be a boolean luminance channel png8 with 2^8 shades of transparency23:27
fenni mean this is a pretty common scenario isn't it?23:28
fenntake a black and white image, scale it down, share it on the net23:28
fennthe tyranny of diurnalists reaches into the furthest corners of our lives!23:29
xentracit seems like the cleanest solution to that is to colormap the rendered image of the web page23:30
xentracblack to red, white to black, presumably red to white, and other corners of the color cube to themselves?23:31
xentracanyway, I find equations useful because they describe relationships between things23:31
xentrachave you considered trying to describe e.g. population standard deviation without a formula?23:32
fenni think we should use either code or pseudocode23:32
xentracit's the square root of the sum of the squared differences between each data value and the average of all the data values23:32
xentraccode is a lot less expressive than equations23:32
fennpeople say that but i don't believe it23:33
fennequations just leave out all the important details and that fucks you up if you aren't already a domain expert23:33
xentracmaybe that's not exactly right23:33
xentracit's not that code is less expressive, per se23:33
fennand if you're a domain expert you don't need to be reminded of the equation23:33
xentracit's that it is too powerful23:34
xentracaccording to the principle of least power, when a language loses power, it gains manipulability23:34
xentracand that is certainly true of equations23:34
fenndoes not compute. power = expressiveness (from my reading of paul graham at least)23:34
xmjln(f(x)) makes it certainly lose power :(23:35
xentrachaha23:35
xentracare you familiar with the principle of least power?23:35
fennno23:35
xentrac.g principle of least power23:35
yoleauxhttp://www.w3.org/DesignIssues/Principles.html23:35
fenni'm guessing it's the difference between source code and data format23:36
xentracyes, and that's a continuum23:36
xentracsomething that's "data" from one perspective is "code" from another23:36
-!- Adifex is now known as Adifex|zzz23:36
xentracthe equation whose rendering we are criticizing here tells us how to compute the necessary volume of the resonator to achieve a given frequency, given a fixed static pressure, neck size and shape (A and Vₙ), and gas (which determines γ and m)23:39
xentracit also tells us how to compute the necessary neck length if instead the volume and neck diameter and gas are fixed23:39
xentracor how to compute the resonant frequency if all those things are fixed23:39
fenni'll just note that omega is never defined as frequency anywhere on the page23:40
xentracno, it's angular frequency, not frequency23:40
xentracand it is in fact defined right up at the top:23:41
xentracIt can be shown[2] that the resonant angular frequency is given by:23:41
xentrac\omega_{H} = \sqrt{\gamma\frac{A^2}{m} \frac{P_0}{V_0}} (rad/s),23:41
fennhow do you know that omega_H is angular frequency?23:41
xentracbecause it says right there23:42
fennno it doesn't23:42
xentrac"the resonant angular frequency is given by: \omega_{H} ="23:42
fennit says "angular frequency is given by: (equation)"23:42
xentracit also allows us to compute the ambient pressure given a fixed resonator and gas, if we can measure the frequency23:42
xentracso that single equation gives us four different useful computations, which would need four different pieces of code to compute them23:43
fennnow i know you've heard of prolog23:43
xentracyes.23:43
fenn"prolog does that"23:44
xentracyou would think you could do that kind of manipulation with prolog but in practice you cannot.23:44
xentracbecause prolog gave up that level of manipulability in order to be turing-complete.23:44
xentracvery early arithmetic prolog programs from the 1970s can in fact be manipulated in this way.23:44
fennokay but does this mean we have to use funky hieroglyphics i can't even type with a keyboard or even a stream of characters?23:44
xentracno, of course not23:45
xentracyou might, in a Turing-complete language, write a piece of code that can easily be manipulated in the same way23:45
xentracbut as soon as you start sticking cuts or while-loops into your code, that kind of manipulation becomes very difficult23:46
fennit just seems like a case of lazy evaluation to me23:46
xentrac("cuts" are a Prolog thing)23:46
jrayhawkhv3 does some javascript stuff23:46
xentracit seems like it, but it's actually a different phenomenon.23:46
fenndon't invert the matrix until you need to, etc.23:46
xentracif you combine this equation with the equation of Q from https://en.wikibooks.org/wiki/Acoustics/Flow-induced_Oscillations_of_a_Helmholtz_Resonator23:48
xentracwhich is23:48
xentracQ = 2 \pi \sqrt{V (\frac{L'} {S})^3}23:48
fennjrayhawk: do you compile your own hv3? "ECMAScript (a.k.a. javascript) is not supported since the corresponding library (SEE) is [not?] installed (not available in Debian yet).23:48
xentrac(which requires some variable renaming unfortunately)23:48
jrayhawkNo, I don't use hv3.23:48
jrayhawkAutomatic execution of unsigned code is a bug, not a feature.23:48
fennoh this was the tk thing. yeah, no.23:49
xentracthen you can specify that you want a given Q and resonant frequency and gas and ambient pressure, and solve the system of two equations to give you a relationship with one degree of freedom between the length of the neck, the diameter of the neck, and the volume of the vessel23:50
fennxentrac: obviously non-functional (as in functional programming) code can't be treated the same as functional code23:50
xentraceven Turing-complete functional code is not generally manipulable in this way23:51
xentracTurner is exploring the limits of non-Turing-complete functional code, which might be promising in this way23:51
fennwhat's the problem with a while loop exactly?23:52
xentracthe biggest difficulty is that it's uncomputable whether it terminates or not, and if so, when23:54
fennhow is this different from equations with no solution?23:55
xentracconsider the Ackermann function23:55
fenn(possibly) no solution23:55
xentracwhich is actually just a nested for loop23:57
fennthe article on ackermann function starts out with a lot of phrases that mean nothing to me, so i'm going to call it a night :P23:57
xentracnot even a while loop; it's provably terminating23:57
fennit looks like the factorial function23:58
xentracit does addition, multiplication, exponentiation, and so on23:59
--- Log closed Thu Apr 24 00:00:10 2014

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