--- Log opened Wed Apr 23 00:00:05 2014
--- Day changed Wed Apr 23 2014
00:00 < fenn> unit tests
00:00 < fenn> er, regression testing
00:00 < fenn> that's all i got
00:01 < xmj> customers yelling "Why does this not look the same across all my browsers / devices ???"
00:02 < xmj> "My macbook air displays differntly than my Galaxy S999!!!"
00:02 <@kanzure> often just me yelling at myself about that
00:02 < fenn> "because it's not an image?"
00:02 <@kanzure> just because it's not an image doesn't mean that i get to ignore rendering engines
00:02 < fenn> why not
00:02 <@kanzure> weinre is pretty helpful
00:04 < fenn> how many different engines are there anyway
00:04 < fenn> more than 3?
00:04 <@kanzure> gecko, webkit, presto, trident
00:04 <@kanzure> blink
00:04 <@kanzure> servo
00:05 <@kanzure> each have their own versions, bundled into applications that also have lots of versioning, and then those applications have different distributions for each device
00:07 < fenn> is it the goal of the engine developers to be standards compliant?
00:07 < fenn> i.e.  do what the spec says as best they can
00:09 < fenn> i can't think of any other field where massive amounts of effort is spent tailoring the input around the bugs of the software
00:09 < fenn> maybe government work
00:09 <@kanzure> have you ever watched a web developer do his thing?
00:10 < fenn> i guess not
00:10 <@kanzure> stalkerwatch someone next time you're in a coffee shop
00:10 < fenn> what's a web developer?
00:10 <@kanzure> you'll either laugh or cry
00:10 <@kanzure> it's the person using 10 devices and 100 browsers
00:10 < fenn> is this where you take the photoshop drawing the client has given you and chop it into pieces?
00:10 < Lemminkainen> and then you animate it with now.js, fenn
00:10 <@kanzure> that's sometimes one part of it, but at this point i just outsource that to psd2html.com
00:10 < Lemminkainen> can't forget that part
00:11 < Lemminkainen> popcorn.js is also very important, it makes your web apps smell like butter
00:11 < fenn> so, i want to get rid of all that shit and just use LCARS for everything
00:11 < fenn> how do i reverse all the shit into clean structured data?
00:11 < Lemminkainen> I have a flock of highly trained pigeons to sell you, then
00:11 <@kanzure> well, you can start by not writing for the web
00:12 < fenn> i'm thinking some kind of evolutionary classifier, similar to a spam filter
00:13 < fenn> "this is the content, this is a nav menu header, this is a nav element, this is a caption" etc
00:13 <@kanzure> i already don't like where this is going
00:13 <@kanzure> LCARS was crap too
00:14 < fenn> i disagree, it was way ahead of its time
00:15 < fenn> the 3d graphics were crap, but only because they didn't have the knowhow to make it fit with the rest of the interface
00:15 <@kanzure> why is this interesting http://upload.wikimedia.org/wikipedia/commons/a/aa/Lcars_wallpaper.gif
00:15 <@kanzure> what the fuck are the numbers on the left
00:15 <@kanzure> and why are there curved edges?
00:17 < fenn> sorry i am neck deep in swap atm
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00:17 <@kanzure> you have like 2 MB of RAM
00:17 <@kanzure> after you account for 800 MB of nsa.img
00:17 < fenn> hah
00:18 < fenn> i always wondered why chrome needed 190MB to show a one paragraph wikipedia entry
00:18 <@kanzure> let me know when your baseband processor stops being a secret-sharing monster
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00:20 < fenn> less arbitrary crap http://www.oocities.org/tana100750/
00:20 < fenn> the font is a little bit much, but other than that it's a very elegant design
00:20 <@kanzure> look at all those wasted pixels by curves
00:20 < fenn> it's a touchscreen interface
00:20 < fenn> fat fingers waste pixels
00:21 < fenn> so 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)
00:22 <@kanzure> i think i'll be keeping my keyboard interface for now
00:22 < fenn> like a vertical tab bar in a browser
00:22 <@kanzure> i carry that keyboard in my pocket
00:22 < fenn> in fact it would be a web browser too
00:22 < fenn> have you tried the steno app for ipad?
00:23 <@kanzure> no, also haven't seen it
00:23 < fenn> ah. well, it exists
00:23 < fenn> the developer sells a silicone thingy that goes over the screen so you hold your hands in the right place, or something
00:23 < fenn> but you can use it without the thingy
00:24 < fenn> anyway my point was that onscreen keyboards suck
00:24 <@kanzure> i wonder if ALS patients have control of that ear membrane muscle
00:27 < fenn> i 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/4063423
00:28 < fenn> there's a pretty good android disk usage app (called "disk usage" believe it or not) that is similar to how filelight worked, but with rectangles
00:29 < fenn> thrash thrash thrash
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00:31 < fenn> https://code.google.com/p/diskusage/
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00:52 < fenn> oh 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.html
00:52 < fenn> probably others like that
00:57 < fenn> it 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 app
00:57 < fenn> there was a java widget toolkit but i dunno what came out of that
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01:31 < fenn> the 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.jpg
01:33 < fenn> an lcd looks a lot different http://wiki.maemo.org/images/1/15/ThemeShot3.jpg
01:33 < ebowden> Oh, is this functioning?
01:34 < ebowden> The non-LCD one.
01:34 < ebowden> (The non-LCD one.)
01:34 < fenn> nook_padd.jpg is how i'm chatting right now
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01:35 < fenn> padd-29 is a prop made by laser printing onto a transparency sheet
01:36 < ebowden> Ah, ok.
01:36 < ebowden> I wonder if it would be possible to make one look exactly like the printed one.
01:37 < fenn> yeah there are zillions of replicas, that might even be a replica
01:38 < fenn> there is a reflective color display technology in perpetual vaporware stage from pixel qi
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01:39 < fenn> i've never actually seen one though
01:39 < ebowden> Ok.
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01:41 < fenn> oops not pixel qi, i meant Mirasol: http://techcrunch.com/2010/02/15/color-e-reader-uses-butterfly-based-technology-to-save-power/
01:43 < ebowden> Ok.
01:46 < fenn> something 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 area
01:50 < fenn> i double checked and the phone actually weighs 40% less. but it FEELS heavier
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01:56 < delinquentme> http://www.mensjournal.com/magazine/print-view/do-men-suck-at-friendship-20140422
01:56 < delinquentme> true!
01:56 < delinquentme> brownies, kanzure , fenn ParahSailin  you guys are my fronds :D
01:56 < delinquentme> I hope you die a long time after everyone else <#
01:58 < fenn> what happened to that heart?
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02:00 < delinquentme> I stepped on the top half
02:00 < delinquentme> Its how the umbuttu tribesmen relay man-appreciation over instant messaging
02:00 < archels> you want your friends to die? gee whiz
02:02 < Lemminkainen> mutation before death, dammit
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02:16 < delinquentme> ^^^^
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02:25 < archels> don't suppose anyone has a digital copy of Longevitize lying around?
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03:17 < mosasaur> Is MIRI that bad? I know I share the feelings, but probably for completely different reasons. I mean I am against academia *and* billionaires.
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03:19 < archels> paperbot: http://www.sciencedirect.com/science/article/pii/S0262407912627559
03:19 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/9542a0ea6c79693d3c44a08fd6ebbf97.txt
03:20 < archels> paperbot: http://www.sciencedirect.com/science/article/pii/S0262407912627559/pdfft?md5=bad43cabdd6be43e92c389edbb61ae5f&pid=1-s2.0-S0262407912627559-main.pdf
03:20 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/a3166d720c2d175befa4fc95ae51fd82.pdf
03:20 < archels> <3
03:20  * archels wonders what that MD5 is for
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05:26  * pasky scratches head at http://arxiv.org/abs/1401.1219
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06:36 < mosasaur> pasky: I think they're still trying to solve the problem that quantum measurements require an observer.
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06:47 < ebowden_> paperbot: http://www.sciencedirect.com/science/article/pii/S0271531705001041
06:47 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/ad2643a7c38c723359b9773d838f7b59.txt
06:47 < ebowden_> paperbot: http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf
06:47 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/d010a7e0119e15952a7d1e1d2777a7c.txt
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06:48 < ebowden_> Oh, hello FourFire.
06:48 < FourFire> ello
06:49 < ebowden_> paperbot: http://www.journals.elsevierhealth.com/periodicals/ntr/article/PIIS0271531705001041/abstract
06:49 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/65eed9b74197844031fb7fb611ba259f.txt
06:50 < ebowden_> paperbot: http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf
06:50 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/a61172a0bfd230e00134d62372fb488b.txt
06:50 < ebowden_> Damnit.
06:51 < ebowden_> I am not good at paperbot.
06:52 < ebowden_> paperbot: http://download.journals.elsevierhealth.com/pdfs/journals/0271-5317/PIIS0271531705001041.pdf
06:52 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/2db8ec5f4524416ddc08562c59b3b358.txt
06:52 < ebowden_> :(
06:54 < ebowden_> Does anyone here know how to properly use paperbot?
06:55 < mosasaur> ebowden_: is it supposed to extract the javascript generated content?
06:56 < 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 page
06:58 < mosasaur> paperbot: https://groups.google.com/forum/#!forum/endgame-singularity
06:58 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/3a73de0d7d8f7aaac21d63537a91056a.txt
06:58 < mosasaur> nope :-(
06:59 < ebowden_> Oh, no, it extracts a PDF text file.
06:59 < ebowden_> Doesn't create one.
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07:14 <@kanzure> ebowden_: instructions are here, https://github.com/kanzure/paperbot
07:14 < ebowden_> Ah, thanks.
07:14 < ebowden_> Well, night.
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07:20 <@kanzure> http://info.5amsolutions.com/blog/bid/157752/Venter-s-Human-Longevity-Academic-vs-Private-Genomics-Round-2
07:20 <@kanzure> http://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."
07:21 <@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”."
07:22 < cluckj> o_O
07:22 <@kanzure> diamandis is on the board of directors haha
07:22 < cluckj> deCode part 2?
07:23 <@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 < cluckj> so craig venter wants to live forever, now? :)
07:24 <@kanzure> oh cool they have a public phone number: 858-249-7500
07:24 <@kanzure> totally going to prank call them
07:24 < cluckj> ask if their $10 million sequencer is running
07:25 < FourFire> kanzure, I'm all for cheaper sequencing
07:26 < FourFire> do they have orders, or are they just doing it on random people?
07:26 < FourFire> (first 40 000)
07:26 <@kanzure> dunno, so far the pitch seems sort of fucked up
07:26 <@kanzure> give us $70M so we can buy some dna sequencers and do lots of sequencing?
07:27 < FourFire> who are they sequencing though?
07:27 <@kanzure> why does that matter?
07:27 < cluckj> there's probably more going on there than their pitch suggests
07:27 <@kanzure> craig has cancer?
07:27 <@kanzure> hrmm no he would have done something cancer-specific
07:27 < FourFire> well, if they could offer a, say 80% off sequencing, 250$ per genome after they are already funded, they'll be turning a profit
07:28 < cluckj> he's getting old; wants to live forever
07:28 < cluckj> I dunno
07:28 <@kanzure> FourFire: i don't think this is a generic sequencing company
07:28 <@kanzure> FourFire: nothing about this says "we want to sell direct-to-consumer sequencing services"
07:29 < FourFire> 250$ is near where I would consider it worthwhile to get my genome sequenced
07:29 <@kanzure> cluckj: i guess that $600 million from exxon is about empty
07:29 < cluckj> lol
07:29 < FourFire> kanzure, which 600 million?
07:29 < cluckj> craig's M.O. is to find things to patent
07:29 < cluckj> so what is patentable there?
07:30 <@kanzure> FourFire: craig venter got a $600 million deal with exxon for his company, synthetic genomics inc.
07:30 < FourFire> oh, right
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07:35 <@kanzure> fenn: the entire world is a strange loop that folds back into itself roughly every 10 years https://www.allegro.cc/forums/thread/345403
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07:55 <@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."
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08:00 <@kanzure> i think i need some soot goggles for interneting from now on http://www.entertainmentearth.com/images/AUTOIMAGES/EP828410lg.jpg
08:02 <@kanzure> jgarzik bitcoin satellite groupies https://groups.google.com/forum/#!forum/bitsat-project
08:02 <@kanzure> http://www.google.com/url?q=http%3A%2F%2Fwww.dunveganspace.com%2Fgoals%2Fbitsat%2FBitSatUpdate1.pdf&sa=D&sntz=1&usg=AFQjCNFzqytlkxLDkAz0J39nZCB-pbY9gA
08:02 <@kanzure> oops i mean http://www.dunveganspace.com/goals/bitsat/BitSatUpdate1.pdf
08:03 <@kanzure> http://www.dunveganspace.com/goals/bitsat/BitSatArchitecture-0.1.pdf
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08:07 < FourFire> lol, Kanzure you saying "back in the day" what are you, early 30s ?
08:07 <@kanzure> 24
08:07 < FourFire> late 20s?
08:08 < FourFire> so when you were 14, you were saying "back in the day"
08:08 <@kanzure> internet accelerates your aging by a factor of like 1000x
08:08 < FourFire> I doubt it, I should be much more mature by now if that was the case
08:08 <@kanzure> or your curve is different
08:08 < FourFire> or perhaps "this here web 2.0 bullshit ain like it used to be... back in the days"
08:09 <@kanzure> yep, first phase of web 2.0 was the real bullshit
08:09 < FourFire> "I used to know 10% of the internet, by name! back in the day!"
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08:10 <@kanzure> 14 year olds can't have days to talk back about?
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08:28 < FourFire> well, sure they can. it just seems pretentious to me, but then I probably said similar things when I was 14.
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08:30 <@kanzure> (not an actual recommendation) http://www.amazon.com/The-Knowledge-Rebuild-World-Scratch/dp/159420523X
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08:40 <@kanzure> long video about ants https://www.youtube.com/watch?v=Z-gIx7LXcQM
08:44 <@kanzure> eudoxia: http://web.archive.org/web/19980109011052im_/http://extropians.mit.edu/extropy.gif
08:47 < eudoxia> kanzure: it's rather sad that the MIT extropians were run by a bunch of racists and fell apart
08:48 <@kanzure> huh?
08:49 < eudoxia> http://web.mit.edu/observer/www/1-1/articles/ad1.html
08:50 < eudoxia> there was some drama and they disbanded or something
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08:57 <@kanzure> neat, chrome has been handling 326 tabs open for 15 days
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09:30 < pasky> hmm it seems my 360-tab firefox is running for 11 days now
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09:31 < pasky> sooner or later it ends up eating 100% CPU for no easily discernable reason and I have to restart it though
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09:40 < dingo> i recommend the tree style tab plugin for FF
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09:41 <@kanzure> tree style tab wont solve his memory problems
09:43 < nmz787_i> paperbot: http://ar.iiarjournals.org/content/33/11/4757.full.pdf
09:43 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/b7cc5d5fdf484e246df172676a9922e9.txt
09:44 < dingo> i recommend a strict diet of lynx
09:45 < xmj> xombrero is nice for that
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09:45 <@kanzure> i would be okay with not using tabs if page caching actually worked
09:46 < dingo> if 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 <@kanzure> braille interfaces are obscenely expensive
09:47 < dingo> karl dahlke rather, he does a good math site i think
09:47 < dingo> http://eklhad.net/
09:49 <@ParahSailin> yeah i think blind people generally use modern browsers with screen readers
09:53 < nmz787_i> kanzure: 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 <@kanzure> i would use webkit/blink before cefpython
09:54 <@kanzure> webkit has a .haf format but i don't know if it stores all in-memory objects correctly
09:54 <@kanzure> another option is to use mitmproxy to capture all resources and just replay it in the future
09:54 <@kanzure> so you don't have to keep the tab loaded in memory, and later can reload it without actually hitting the real interwebs
10:01 <@kanzure> if the web page is non-deterministic then it might cause other requests to be made when the page is reloaded in the future
10:04 < nmz787_i> isn't blink what chromium uses already?
10:04 <@kanzure> chromium has a bunch of other stuff on top of blink
10:04 < nmz787_i> aren't those desirable things?
10:04 < nmz787_i> 'features'
10:05 <@kanzure> dunno, the answer is most likely no, because all those 'features' are why you can't have 10000 tabs in firefox
10:05 < nmz787_i> firefox doesn't use chromium though
10:05 <@kanzure> whatever :)
10:10 <@kanzure> "Functional electrical stimulation-facilitated
10:11 <@kanzure> "Functional electrical stimulation-facilitated proliferation and regeneration of neural precursor"
10:11 <@kanzure> paperbot: http://www.sjzsyj.org/CN/article/openArticlePDF.jsp?id=862
10:11 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/7ba419edd532526e0b5359e818fcc72b.pdf
10:12 <@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."
10:15 <@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"
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10:19 < nmz787_i> so how do i contact langton labs to see about sleeping there?
10:19 <@kanzure> take blood oath at burning man?
10:20 < nmz787_i> that is after makerfaire
10:20 < nmz787_i> so won't work
10:21 <@kanzure> .tell fenn nmz787_i would like information about contacting or staying at langton labs
10:21 < yoleaux> kanzure: I'll pass your message to fenn.
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10:27 < pasky> hmm seems like switching from vertical tabs to tree-style tabs is not so trivial
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10:31 < nmz787_i> this is pretty cool https://www.sparkfun.com/products/12042
10:31 <@kanzure> .title
10:31 < nmz787_i> Z-axis conductive tape
10:31 < yoleaux> Z-Axis Conductive Tape
10:31 < nmz787_i> gtfo yoleaux, this is my link!
10:31 <@kanzure> i was impatient
10:31 < nmz787_i> psh
10:31 < nmz787_i> stupid latent bot
10:32 < nmz787_i> all 3 seconds slower than me
10:36 < nmz787_i> is yoleaux a play on YOLO?
10:36 <@kanzure> yes, ask the #swhack people
10:39 <@kanzure> huh, opencascade "community edition" still has activity https://github.com/tpaviot/oce
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10:58 <@kanzure> that guy with the ABI 310 w/o software is going to have problems
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10:58 <@kanzure> i think i'm going to recommend he sets up linux in front of the machine
10:58 <@kanzure> and then sets up an ssh server for me to login to
10:59 <@kanzure> and then i'll poke around the machine
10:59 <@kanzure> but i think i need to get a ROM dump of whatever microcontroller is inside the machine
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11:04 < nmz787_i> Whoo! http://www.nature.com/news/start-up-investor-bets-on-biotech-1.15096
11:04 < nmz787_i> Y combinator application here I come!
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11:06 < chris_99> cool, good luck nmz787
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11:16 <@kanzure> heh i should have expected substack to have a thing for technical debt https://github.com/substack/codebux
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12:07 <@kanzure> this is very cool https://github.com/twolfson/phantomjsify
12:08 <@kanzure> oh, not much is shimmed. hrm.
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12:25 <@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."
12:26 <@kanzure> http://openpowerfoundation.org/
12:26 < dingo> they did that with opensparc, nobody did anything with it unfortunately
12:26 <@kanzure> hmm no files.
12:27 <@kanzure> what's up with a separate foundation for each idea?
12:27 <@kanzure> surely ibm owns a non-profit about something
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14:59 < 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 < kanzure> https://news.ycombinator.com/item?id=7633515
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15:02 < kanzure> 15-20% margins on reselling modafinil http://www.gwern.net/Modafinil#margin-estimation
15:03 < kanzure> also there's a simple assay mentioned down the page
15:03 < kanzure> http://www.pharmacyreviewer.com/forum/discussion-online-pharmacies-featured-general-reviews-section/16335-edandmore-feedbacks-10.html#post139862
15:03 < 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 ...
15:04 < 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 < QuantumG> ha, I didn't know it was a sulfa drug.. good I never got my hands on it, eh? (apparently I'm allergic.)
15:04 < kanzure> how apparent is apparently
15:05 < QuantumG> like, it's written on my birth certificate, but I've never experienced the symptoms
15:05 < kanzure> allergies are written on birth certs?
15:05 < QuantumG> weird eh
15:06 < nmz787_i> apparently 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_i> just what i heard recently
15:07 < kanzure> so does that mean i can mail them a book of the jedi order?
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15:08 < nmz787_i> i dont think os
15:08 < nmz787_i> so
15:10 < QuantumG> mailing the three volumes of Knuth would be expensive.
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15:17 < 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 < kanzure> http://en.wikipedia.org/wiki/Lathe
15:18 < kanzure> http://historicgames.com/lathes/Egyptstone.jpg
15:19 < kanzure> http://argenteriedesbauges.free.fr/1egyptien.JPG
15:19 < kanzure> pfft obviously they should have invented the four-person lathe
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15:24 < fenn> pixtronix 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.pdf
15:24 < yoleaux> 17:21Z <kanzure> fenn: nmz787_i would like information about contacting or staying at langton labs
15:27 < fenn> the 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 backlight
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15:28 < fenn> this is why we need intellectual property taxes
15:28 < nmz787_i> do you still have contacts at langton fenn?\
15:29 < fenn> i don't know; i haven't checked my email for about a year
15:29 < fenn> i suspect you'd be welcome
15:30 < fenn> you just want to stay for a weekend ish?
15:30 < nmz787_i> yeah, 4 folks total, we'll have tents so yard/slab is fine also... 2 of us will share  abed
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15:30 < nmz787_i> so 3 'beds'
15:31 < nmz787_i> fenn: do you know Cadence Allegro (PCB software) and want a job in Oregon for a bit?
15:32 < nmz787_i> the job also involves Python, and would be a contract with Intel through a temp agency
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15:32 < kanzure> don't you think he has better things to be doing than bothering with a temp agency?
15:32 < QuantumG> I know someone who might
15:32 < nmz787_i> some kind of PCB routing thin, i think
15:33 < nmz787_i> kanzure: no idea, seems like his kind of thing though, and it would be a reason to live here during the summer
15:33 < nmz787_i> QuantumG: get them to send me a resume nmz787 at gmail
15:34 < kanzure> once you accumulate any non-negligble amount of skill, you want to avoid temp agencies like the plague
15:34 < nmz787_i> have you been to Oregon during the summer?
15:34 < nmz787_i> having any reason to come here is worth it
15:34 < nmz787_i> especially since its a contract
15:35 < nmz787_i> come visit, see the sights, GTFO if you want
15:36 < cpopell>  /query nmz787_i
15:36 < cpopell> whoops!
15:36 < cpopell> Anyway, nmz787_i, are you involved with a staffing agency up there, or did you just hear about it?
15:36 < nmz787_i> no, my manager is reviewing resumes now
15:37 < cpopell> oh, k.
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15:40 < fenn> nmz787_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 faire
15:41 < fenn> i've never used Cadence
15:42 < fenn> what kind of temp agency hires EDA professionals?
15:42 < fenn> that's like, a real job
15:43 < kanzure> i assume there's a split in the industry
15:43 < kanzure> where there's some who are doing vsli stuff
15:43 < kanzure> and then others who are like blender/maya monkeys
15:43 < kanzure> and 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"
15:44 < kanzure> *vlsi
15:44 < fenn> that's what blender is for though
15:44 < kanzure> with programming you can take advantage of efficiencies that you introduce, with point and click this is less true
15:45 < kanzure> when you need a bunch of labor to click, you go pick a temp agency to supply you with labor
15:45 < kanzure> just theorizing here, re: your observation about a "real" job
15:46 < kanzure> +.
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15:48 < fenn> I respect 3d artists like http://www.mikeanash.com/p/hard-surface-bust.html who do nothing but click on buttons all day
15:48 < dingo> i'm not seeing it in the buffer, which specific industry?
15:48 < dingo> just 3d modelling?
15:48 < fenn> he's just ranting about point and click interfaces, pay no attention
15:49 < fenn> kanzure: okay but the clicking is to _DO_ something, and it's the thought that goes into where you click that is important
15:49 < kanzure> i don't think i've claimed that thinking is unimportant
15:49 < dingo> well 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 such
15:49 < QuantumG> how about some division of labor? Hire the artist to do artistic shit and the programmer to automate his crappy workflow.
15:49 < fenn> it takes skill, experience, and education to design and "capture" an electronic circuit/layout
15:50 -!- augur [~augur@129-2-129-33.wireless.umd.edu] has quit [Remote host closed the connection]
15:50 < kanzure> also, i'd point out that nate specifically mentioned a python requirement, so there's obv. some programming expectations
15:50 < dingo> many gaming and movie studios have tirtuary tooling -- mostly the junior programmers
15:50 < kanzure> the junior programmers build their tools?
15:50 < fenn> tirtuary?
15:50 < kanzure> tertiary?
15:50 < QuantumG> then the artist can get more arty stuff done, resulting in more product
15:50 < dingo> like i know a guy at uhh whats it called, rockstar for gta, right?
15:51 < dingo> all he does is make gui interfaces for backend processing tools, none of it is in the game, just used to build the game
15:51 < fenn> we call that development tools
15:51 < nmz787_i> it is a real job, but they might not want to keep you around to maintain the software after its written
15:51 < fenn> heh that's fine with me :P
15:52 < fenn> wait is this software or electronics
15:52 < nmz787_i> software
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15:52 < kanzure> fenn: why would you be more interested in that instead of doing your robocompany
15:52 < fenn> what does cadence have to do with it then
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15:52 < nmz787_i> it needs scripted with Python
15:52 < fenn> define "it"
15:52 < nmz787_i> cadence :P
15:52 < nmz787_i> i really don't know
15:53 < QuantumG> the other guy says he'll do it remote, but nuts to Oregon.
15:53 < nmz787_i> i can ask for more info, but its some automagic generation via scripting thing
15:54 < nmz787_i> but I know they want Cadence Allegro and Python experience
15:54 < fenn> i wonder if wiping fabric softener on my screen will keep dust off
15:56 < nmz787_i> kanzure: 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 work
15:57 < juri_> cadence. ick.
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15:59 < fenn> juri_: please elaborate
16:00 < 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.
16:01 < nmz787_i> juri_: do you use an intel processor?
16:01 < fenn> oh, i agree completely
16:01 < 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.
16:02 < fenn> "i designed the block diagram, layout is left as an exercise for the student" (literally)
16:02 < fenn> my microwave runs an intel Z80
16:02 < kanzure> why does intel have a z80?
16:03 < fenn> uh, nevermind
16:03 < kanzure> "The Z80 came about when Federico Faggin, after working on the 8080, left Intel at the end of 1974 to found Zilog"
16:04 < fenn> i guess the z80 was compatible in many ways with the intel 8080
16:04 < kanzure> http://en.wikipedia.org/wiki/Zilog_Z80
16:05 < dingo> they used to have Z80 add-on cards for the intel
16:05 < dingo> so you could boot cp/m
16:06 < kanzure> http://upload.wikimedia.org/wikipedia/commons/d/d1/Z80A-HD.jpg
16:08 < fenn> so has anyone made a microchip CPU in their garage yet
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16:08 < kanzure> i believe azonenberg has in #homecmos http://code.google.com/p/homecmos/
16:08 < fenn> wow really?
16:08 < kanzure> but he may have been cheating because he definitely stil has access to university lab stuff
16:08 < kanzure> *still
16:09 < nmz787_i> i don't think so
16:09 < nmz787_i> he's probably made a proc on a  fpga for sure
16:09 < kanzure> i would be extremely surprised if he hasn't done a transistor
16:09 < nmz787_i> but that's more design than fab
16:09 < fenn> anyone can download an fpga core
16:09 < kanzure> nah, fpgas are standard curriculum these days, not interesting
16:09 < kanzure> i mean, no points
16:10 < nmz787_i> its a common course excercise to design the proc yourself, so I think he's probably done more than just download some existing one
16:10 < kanzure> i'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 < kanzure> he was asking about manufacturing/etching
16:10 < kanzure> and i assume operating
16:11 < fenn> i wonder if it's possible to turn off prerendering in chrome so things dont use so much ram
16:12 < kanzure> fenn: have fun http://code.google.com/p/chromium/wiki/AndroidBuildInstructions
16:12 < fenn> i meant my laptop
16:12 < nmz787_i> he did some fpga circuit editing recently
16:12 < nmz787_i> but that was with a FIB in school
16:14 < fenn> at least i guess it's due to prerendering, i can't imagine why else a wikipedia page would need 100MB of ram
16:14 < kanzure> closing the last chrome tab may not kill the original chrome process
16:15 < juri_> fenn: we're working on diamond like carbon deposition here at hacDC.
16:15 < fenn> juri_: why?
16:15 < fenn> kanzure: i'm killing tabs in the chrome task manager
16:15 < juri_> potential integrated circuit applications, plus 3d printer hotend applications.
16:16 < fenn> what are those applications
16:16 < 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)
16:17 < fenn> okay so why diamond and not, i dunno, steel
16:17 < juri_> steel is conductive, so won't work on my heater core.
16:17 < fenn> stainless steel lasts quite a while in oxidizing environments at 500C
16:17 < fenn> diamond is also conductive
16:17 < juri_> we're going to use steel underneath the diamond, to handle molten aluminium.
16:18 < juri_> DLC is not conductive of electricity, is conductive of heat. exactly what we need.
16:18 < fenn> investigating
16:19 < juri_> this makes good sense, since its used under some chips nowadays. if it was electricly conductive, they would have problems. ;)
16:22 < fenn> hm. 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 < fenn> best of both worlds
16:22 < juri_> selectively conductive.
16:22 < juri_> ;D
16:22 < fenn> apparently they can be semiconductors too
16:23 < 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 < fenn> cool
16:24 < fenn> how 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.
16:25 < 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.
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16:31 < nmz787_i> kanzure: what was the bitcoin donation thing?
16:31 < nmz787_i> the easy one, to start a donation campaign thing
16:32 < kanzure> uh, might have been anything, coinbas.come? blockchain.info?
16:32 < kanzure> *coinbase.com?
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16:34 < nmz787_i> is there one with a counter though, like "# bitcoin raised"
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16:34 < kanzure> nmz787_i: http://bitcoinchipin.com/
16:35 < fenn> juri_: have you considered something like the wax inkjet but for aluminum? spraying microdroplets that fuse on contact with the workpiece
16:35 < nmz787_i> kanzure: thanks
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16:36 < fenn> i'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 resistance
16:38 < nmz787_i> alumina?
16:39 < nmz787_i> i guess that's already oxidized
16:39 < fenn> i wasn't sure if alumina would stand up to molten aluminum for extended periods
16:39 < fenn> aluminum is highly reactive
16:40 < fenn> this means alumina is very stable, but in a fight with aluminum, they come out even
16:40 < QuantumG> do it in a noble gas?
16:41  * fenn looks at a periodic table
16:41 < fenn> QuantumG: also a good option, but it complicates logistics
16:41 < QuantumG> or semi-noble.. aka nitrogen
16:41 < QuantumG> heck, even co2 would probably do, if you're just trying to avoid oxidization
16:42 < fenn> yes you could use getters and molecular sieve pumps
16:42 < nmz787_i> none of those damn peasant gasses
16:42 < QuantumG> for sho
16:42 < fenn> pressure swing oxygen concentrators i mean
16:46 < fenn> http://en.wikipedia.org/wiki/Reactivity_series  MgO, CaO ceramics are probably good options (why is Si not on this chart?)
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16:52 < juri_> fenn: honestly, i haven't. i figgure go for the brass ring.
16:53 < 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.
16:54 < juri_> two birds. one (admitedly heavy) stone.
16:54 < nmz787_i> kanzure: I can't tell if its working https://bitcoinchipin.com/widgets/u/takeitapartdan/send-takeitapart-to-maker-fair
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17:11 < fenn> i meant for aluminum printing, not diamond
17:11 < QuantumG> so did I
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17:12 < fenn> i just saw 10 minutes of "silicon valley" - probably the most depressing piece of distilled reality i've seen in a while
17:13 < QuantumG> I've seen ever episode.. people complaining that it isn't realistic are missing the purpose of FICTION
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17:14 < fenn> what's not realistic about it?
17:14 < QuantumG> they 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 ...
17:15 < jrayhawk> ... points is sort of like redesigning a horse so that it's a motorcycle."
17:15 < fenn> maybe they are confusing "silicon valley" with "san francisco"
17:15 < jrayhawk> huh, a comment from 2007 actually sells me on
17:15 < jrayhawk> Urbit
17:15 < kanzure> i was staying in downtown sf a few weeks ago
17:15 < kanzure> and i forgot about the screams of the undead during the night
17:15 < dingo> SJ claims to be *the* silicon valley, which is pretty silly
17:15 < fenn> jrayhawk: they web has a global namespace though
17:15 < kanzure> very weird place.
17:16 < kanzure> san jose is boring
17:16 < QuantumG> ya
17:16 < dingo> san francisco smells like garbage
17:16 < QuantumG> Palo Alto baby
17:16 < dingo> i don't like either, i'm a country boy myself
17:16 < kanzure> that's because of the garbage
17:16 < jrayhawk> No, DNS is not a part of the web.
17:16 < dingo> vim
17:16 < fenn> google hq is literally built next to a landfill.. go figure
17:17 < fenn> jrayhawk: what?
17:17 < jrayhawk> And neither is IP.
17:17 < fenn> what?
17:17 < jrayhawk> HTTP is a socket.
17:17 < fenn> define "the web" plz
17:18 < jrayhawk> http://en.wikipedia.org/wiki/World_Wide_Web
17:18 < QuantumG> I 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 < kanzure> when was your stay at vmware?
17:18 < dingo> i don't know where this conversation is headed but i'm pulling out :-)
17:18 < fenn> hm. 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 < kanzure> was that before or after vmware started making crap like vcloudsphere
17:19 < kanzure> or vcow
17:19 < QuantumG> before.. but the writing was on the wall
17:19 < kanzure> what went wrong?
17:20 < fenn> they became a large organization
17:20 < QuantumG> I don't know how they ever made money.
17:20 < QuantumG> lots of sales dudes hitting the phones at the end of financial year, it seemed
17:20 < kanzure> weren't they venture backed and going for the "long haul" of no sales?
17:20 < QuantumG> nope
17:21 < QuantumG> they were desperately trying to find a market beyond "I wanna run Windows in a VM on my linux box" from day one.
17:22 < QuantumG> including selling hardware at one point..
17:22 < kanzure> how about, "lots of big enterprises have terrible software running on terrible old hardware that could instead be virtualized because ???"
17:23 < kanzure> i forget the rest
17:23 < 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.
17:24 < QuantumG> yeah, 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 something
17:25 < 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 < QuantumG> plus, they didn't want to confuse people by explaining that virtualization is essentially dynamic recompilation
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17:32 < fenn> why is it recompilation if it's compiled for the same instruction set as your host hardware?
17:33 < fenn> am i missing something
17:34 < kanzure> maybe it's using the virtualization extensions on chip
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17:34 < kanzure> or it's not using the same instruction set
17:34 < fenn> but windows and linux use the same instruction set, no?
17:34 < QuantumG> this was pre-chip
17:35 < QuantumG> most instructions you can just copy, some have to be "virtualized"
17:35 < fenn> i want a chrome extension that colors my tabs by CPU usage
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17:37 < fenn> juri_: how about titanium boride instead of diamond: http://en.wikipedia.org/wiki/Aluminium_carbide#Occurrence
17:38 < QuantumG> those x86/x64 virtualization instructions did basically prove how stupid it was for VMware to focus on those architectures because they're hard to virtualize.
17:39 < fenn> TiB2 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 acid
17:40 < fenn> the 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,
17:41 < fenn> electroplating 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]
17:42 < fenn> so you'd want to make the bulk of your nozzle out of graphite and electroplate TiB2 onto that
17:42 < fenn> or maybe even silicon would work
17:43 < fenn> then you could just use a pre-made inkjet nozzle
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17:43 < juri_> i like the way you're thinking; now to source the materials.
17:46 < fenn> "Solution phase reaction of NaBH4 and TiCl4" <- gnarly chemicals
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17:47 < fenn> paperbot: http://www.sciencedirect.com/science/article/pii/S0167577X06008081
17:47 < fenn> .title
17:47 < yoleaux> Preparation of the TiB2 coatings by electroplating in molten salts
17:47 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/700d72474d9db8c0016026c3e8e922a1.txt
17:48 < kanzure> paperbot: http://www.sciencedirect.com/science/article/pii/S0167577X06008081/pdfft?md5=29ca21048e348f649287e28ea51b2d0d&pid=1-s2.0-S0167577X06008081-main.pdf
17:48 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/4bd972db526fcaca0c537123e04ffb78.pdf
17:48 < fenn> .title
17:48 < yoleaux> fenn: Sorry, that command (.title) crashed.
17:48 < kanzure> doesn't work on pdfs
17:49 < fenn> if it were a pdf you wouldn't have to use paperbot
17:49 < fenn> .title http://www.sciencedirect.com/science/article/pii/S0167577X06008081/pdfft?md5=29ca21048e348f649287e28ea51b2d0d&pid=1-s2.0-S0167577X06008081-main.pdf
17:49 < yoleaux> Preparation of the TiB2 coatings by electroplating in molten salts
17:49 < fenn> huh
17:49 < kanzure> the reason .title works there is because yoleaux doesn't have access
17:49 < kanzure> so sciencedirect.com redirects the bot to an html page
17:51 < fenn> i 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 force
17:51 < QuantumG> yeah, automated mig wire art
17:52 < kanzure> i want a wire keyboard.
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17:56 < fenn> the 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 mm
17:56 < fenn> if only to prevent oxide buildup around the electrode and eventual inclusion in the part
17:56 < fenn> er, s/electrode/nozzle/
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17:58 < fenn> may need some kind of oxide skimmer because your feed material will have an oxide coating before it gets melted
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18:02 < fenn> there'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 though
18:02 < fenn> thrash thrash thrash
18:04 < fenn> inexpensive heatsinks with built in heat pipes would lead to some interesting possibilities
18:05 < kanzure> machinewiki should be dumped into diyhpluswiki.git
18:05 < fenn> what is machinewiki
18:05 < fenn> the gingery things?
18:05 < kanzure> oops machines
18:05 < kanzure> http://fennetic.net/machines/
18:05 < kanzure> i have been on a wiki merging spree lately
18:05 < fenn> ya i was hoping to come up with something better than wikis
18:05 < fenn> but that was a long time ago and it hasn't happened
18:05 < kanzure> los angeles biohackers lost their mediawiki install
18:06 < kanzure> cory emailed me an sql dump today
18:06 < kanzure> most of these wikis are going to evaporate
18:06 < kanzure> isn't tmp2 a wiki?
18:06 < fenn> every wiki should have a "dump database" button imho
18:06 < kanzure> mediawiki has a kinda-dump button, but you have to stare at it sternly
18:06 < QuantumG> reminds me of what I asked you the other day kanzure..
18:06 < fenn> an end-user-accessible button
18:07 < QuantumG> got a list of biotechnology machines?
18:07 < fenn> of course you also need a merge button, thus ikiwiki
18:07 < kanzure> i gave you one
18:07 < kanzure> http://diyhpl.us/cgit/skdb/tree/doc/BOMs/diybio-equipment.yaml
18:07 < fenn> QuantumG: cows, pigs, sheep, corn, e. coli
18:07 < kanzure> hah i forgot about this http://diyhpl.us/cgit/skdb/tree/doc/tech-tree
18:07 < fenn> like the list? i made it myself
18:08 < kanzure> "I spent over a day writing a silly Python program to read in a Civilization 2 Technology Tree."
18:08 < kanzure> uggghhh
18:08 < QuantumG> have 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 < kanzure> why is it ridiculous?
18:09 < kanzure> http://www.charlesmerriam.com/blog/2008/04/fun-with-programming-a-technology-tree/
18:09 < QuantumG> I'm after a list of commercial lab machinery
18:09 < kanzure> oh you mean the equipment they wont sell you?
18:09 < QuantumG> ya
18:09 < QuantumG> what they do, what they're for, etc
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18:09 < kanzure> ABI {100..900}{A..Z}
18:09 <@ParahSailin> you can build an ironclad before iron working
18:09 <@ParahSailin> and gunpowder
18:09 < fenn> iirc openwetware had a list of their preferred commercial bio lab equipment
18:10 <@ParahSailin> there are two destroyers?
18:10 < kanzure> drew endy approved equipment?
18:10 < kanzure> oh yeah, a backup of openwetware too.. god damn wikis.
18:10 < fenn> one wiki to rule them all, one wiki to bind them
18:10 < kanzure> i dunno if i want to dump openwetware straight into diyhpluswiki.git
18:10 < kanzure> it's not like anyone other than me edits diyhpluswiki.git
18:11 <@ParahSailin> oh, the second destroyer "steel" is supposed to be cruiser
18:11 <@ParahSailin> electricity is destroyer
18:14 < fenn> pierre 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/
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18:15 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=9ea01bce Bryan Bishop: list of wikis to merge into this wiki
18:16 < kanzure> http://diyhpl.us/wiki/wikis/
18:17 < fenn> isn't openwetware still an active wiki (it's like their primary public-facing website)
18:18 < kanzure> i believe the only reason it's active is because igem teams are coerced into posting their projects
18:18 < fenn> i mean why would you even consider copying it
18:18 < kanzure> i merged their diybio pages into diyhpluswiki.git a while back
18:18 < kanzure> so maybe some of the other content is wort htaking
18:18 < kanzure> *worth taking
18:18 < fenn> signal to noise ratio is important
18:18 < kanzure> i said some :)
18:20 < fenn> there are so many bio people i've never heard of
18:20 < kanzure> that's why i started writing them down. who the hell are these people?
18:21 < fenn> maybe it's just so hard to get anything done with biology that nobody makes a lasting impression
18:21 < fenn> the gap between brilliant idea and practice is too large
18:21 < kanzure> the parts of biology that require secret incantations should be thrown out in favor of anything that works well with the words "solid state"
18:22 < fenn> are microfluidics solid state?
18:22 < fenn> yes i know you also said "works well"
18:22 < kanzure> what's wrong with regular fluidics
18:23 < kanzure> do you really always need laminar flow?
18:23 < fenn> regular fluidics is big
18:23 < fenn> there is certainly a case to be made for mesofluidics
18:23 < kanzure> bigness hasn't been one of the constraints as far as i know?
18:23 < kanzure> erm, size
18:24 < kanzure> "you know, all this biology stuff is great, but what i really need is a place to put my shoes"
18:24 < fenn> someone was coming up with a chemistry reactor compiler (3d print a silicone thing to synthesize a batch of chemicals)
18:24 < fenn> kanzure: size of lab equipment determines where you can and can't put a lab
18:25 < fenn> for 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 workspace
18:25 < fenn> this has obvious implications for who can and can't do lab work
18:26 < fenn> if anyone with a backpack can contribute to your research then your pool of potential contributors goes up by orders of magnitude
18:26 < kanzure> those implications don't seem to be a limiting factor at the moment
18:26 < kanzure> there seem to be other limiting factors that are extering more influence
18:26 < fenn> like what
18:26 < fenn> (i honestly dont know)
18:26 < fenn> why are people contributing to wikipedia but not diybio
18:27 < kanzure> i was going to complain about everyone who built the original equipment being dead after swallowed up by big bio in ancient history
18:27 < kanzure> but, the thesis that there are limiting factors that are preventing biology things, might also be flawed
18:28 < QuantumG> biometh labs
18:28 < kanzure> what about them
18:29 < fenn> also 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 done
18:29 < QuantumG> just a visual
18:29 < QuantumG> if your lab is (smoothly) automated you don't have to get up from your desk
18:29 < kanzure> fenn: the reason i decided that microfluidics was too much work was because the number of variables increases so dramatically compared to non-microfluidics
18:29 < fenn> QuantumG: also if you pay someone else to do it
18:30 < kanzure> fenn: engineering is about working on known constraints and within known tolerances, not adding arbitrary parts to your project until you hope it works
18:30 < QuantumG> that too
18:30 < kanzure> the 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 intractable
18:31 < kanzure> if possible i prefer to focus on tractable things
18:31 < QuantumG> people are pretty buggy too
18:31 < kanzure> i wasn't using that as an argument against lab automation, sigh
18:32 < fenn> its the same amount of debugging, it's just harder to inspect
18:32 < kanzure> i was using that as an argument for why the microfluidic dna synthesizer is a huge project
18:32 < QuantumG> total quality management is like inevitable, man
18:32 < fenn> microfluidics _enables_ massive combinatorial explosions, but they're not required
18:32 < kanzure> why is adding arbitrary amounts of unknowns into a project good?
18:33 < QuantumG> usually it's the benefits you can't get from avoiding them.. like using C++
18:33 < kanzure> QuantumG: context is http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf
18:33 < fenn> ok 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 literature
18:33 < kanzure> 1) those don't reaaaally exist
18:33 < QuantumG> whenever 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.
18:34 < fenn> right because those people are all long dead
18:34 < fenn> and they didn't write down their secrets
18:34 < kanzure> no, they aren't dead
18:34 < kanzure> ParahSailin spent a bunch of time on microfluidics stuff
18:34 < fenn> so we're actually stuck with option 2 either way
18:34 < fenn> what does microfluidics have to do with anything
18:34 < kanzure> you were trying to convince me to focus on small devices
18:34 < kanzure> so i skipped ahead in the conversation
18:34 < fenn> i thought you wanted to make a 1980s DNA synthesizer with the big glass bottles hanging off the front
18:34 <@ParahSailin> i think cambrian folks are going to have the most sort of success doing dna synth
18:35 < kanzure> that doesn't really help anyone but their customers
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18:35 < kanzure> i mean, they are explicitly mail order only iirc
18:36 < fenn> QuantumG: C++ wasn't anti-hacker enough so they invented java?
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18:37 < fenn> question, is cambrian "solid state"?
18:37 < kanzure> well they are certainly using a laser somewhere in their pipeline
18:37 < fenn> there's also lots of shit literally flying around
18:38 < fenn> how many other machines have literally millions of moving parts
18:38 < fenn> yet still somehow it's more reliable than microfluidics?
18:38 < fenn> what am i missing here
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18:40 < fenn> maybe it's the difference between uncorrected error and feedback
18:40 < QuantumG> so, stupid question, ya never got anywhere on this project?
18:40 < kanzure> it's interesting that you and i have a different perspective on picking (in)tractable projects
18:41 < kanzure> QuantumG: nmz787 is still going at it, but i backed out when i realized the existential horror of it all
18:41 < fenn> i think you are over-exaggerating
18:41 < kanzure> well, then let's re-calibrate me (in general)
18:41 < fenn> and i think nmz787_i likes to fiddle with things
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18:42 < QuantumG> any interest left in the "enzymatic synthesis by direct control of DNA polymerase" version?
18:42 < kanzure> as you can increase the number of parts in a system you increase (at minimum) the number of possible failures
18:42 < kanzure> QuantumG: sure, http://diyhpl.us/~bryan/papers2/polymerase/ has some research notes
18:42 < fenn> QuantumG: it's interesting but theoretically stalled
18:42 < kanzure> yes
18:43 < kanzure> or, theoretically waiting on more theory stuff
18:43 < kanzure> "Protein conformational dynamics probed by single-molecule electron transfer.pdf"
18:43 < fenn> something like the inverse of the pacific bio synthesizer should be possible
18:43 < kanzure> "review - Making contact - Connecting molecules electrically to the macroscopic world.pdf"
18:44 < fenn> i mean nano volumes saturated by various frequencies of light that turn on a specific reaction
18:44 < kanzure> i 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 device
18:45 <@ParahSailin> protein engineering is awful
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18:45 < kanzure> the 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 < fenn> the difference is that the microfluidic device problem can be decomposed into different working parts
18:45 < kanzure> same with proteins actually
18:46 < kanzure> ... to some extent. not always in the way that you need.
18:46 < fenn> i disagree
18:46 < kanzure> there are literally specific domains in the enzyme itself
18:46 < fenn> it's true you can combine functional subunits with linkers
18:46 < kanzure> not even subunits
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18:46 < fenn> but when all your functional subunits work on the same active site, they have to be at least designed with an awareness of each other
18:46 <@ParahSailin> you might be able to get a polymerase that would halt if you changed its conformation by tugging on it with a magnetic bead
18:46 < kanzure> subunits as in other proteins (like from other genes) that form together to build the overall thing, right?
18:46 <@ParahSailin> but that would be a hell of a protein engineering project
18:46 < QuantumG> I completely agree that it's a different problem
18:46 < kanzure> dna polymerase often doesn't have subunits, but it does have functionally-specific components
18:47 < fenn> by subunit i was thinking "here's the part that adds 'A', here's the part that adds 'G' etc"
18:47 < kanzure> quick model of a polymerase is a hand with the thumb feeding into the inner chamber
18:47 < QuantumG> the 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 problem
18:48 < kanzure> and then some weirdo chute where nucleotides get matched up
18:48 < QuantumG> the payoffs are also different though.
18:48 <@ParahSailin> most dna polymerases except for phage ones have subunits
18:48 < fenn> if separate polymerases have to fall off and reconnect to the strand for each base, the kinetics are too slow
18:48 < kanzure> ParahSailin: clearly i have to go kill myself now..
18:48 <@ParahSailin> there are a lot of viral polymerases though
18:48 < kanzure> QuantumG: i'm curious about how you would characterize the straightforwardness in those last two..
18:49 < kanzure> the good thing about polymerase is that it's one of the really good molecules for directed evolution
18:49 < kanzure> but then you need to figure out if your problem is evolutionarily-solvable
18:49 < QuantumG> well, no-one would argue that the last project is doable.. whereas the microfluidics project has unknowns
18:49 < fenn> microfluidics you're inventing both the process and the device; with the bulk fluidic synthesizer you're just inventing the device (process is known)
18:50 < kanzure> disagree, but yes obviously microfluidics has more work
18:50 < fenn> somehow making it smaller changes the process (don't ask me)
18:50 < kanzure> my original statement was that the amount of debugging and iterations for the microfluidic version would be way higher
18:50 < kanzure> it's not just making it smaller
18:51 < QuantumG> maybe I'm not understanding the last project though.. automate-a-manual-process is how I saw it, no?
18:51 < kanzure> it's different materials, chemistries, flow, valves, etc.
18:51 < fenn> why does it have to be different materials and chemistries
18:51 < QuantumG> I wonder if you're not taking that literally enough
18:51 < kanzure> QuantumG: 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 < fenn> we can make glass chips; the chemistry scales down (no?)
18:52 < QuantumG> I mean, you *can* make reasonably long DNA sequences with glassware, right?
18:52 < fenn> QuantumG: yes
18:52 < kanzure> manual dna synthesis definitely works, if you have iron patience
18:52 < QuantumG> a Baxter is only $22k ;)
18:52 < kanzure> although the yields might be less than you'd hope
18:52 < kanzure> and this will ultimately constrain the maximum length
18:52 < QuantumG> sounds expensive, until you automate a few different processes with the same robot.
18:53 < kanzure> besides the usual types of errors: http://diyhpl.us/~bryan/papers2/DNA/Origin%20of%20impurities%20in%20oligonucleotides.pdf
18:54 < fenn> QuantumG: a Boxter is only $9k http://www.ebay.com/itm/Porsche-Boxster-Roadster-Convertible-2-Door-2000-porsche-boxter-/121322965246
18:55 < QuantumG> yeah, synthesize your own DNA, I'm going cruisin'
18:57 < fenn> ok so what is the major difference between automating it with pumps and valves and stirrers, and automating it with micropumps and microvalves and micromixers
18:58 <@ParahSailin> its 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 bird
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18:58 <@ParahSailin> and that the optimal way to synthesize long dna will not resemble nature at all
18:58 < kanzure> ligation?
18:58 -!- marciogm [~marciogm@179.126.69.68] has quit [Quit: Computer has gone to sleep.]
18:58 < kanzure> oh wait, that's from nature
18:58 < fenn> ParahSailin: surely you mean flapping wings, not "beak"
18:59 < kanzure> yeah, i haven't seen much hypothesizing about extremely long dna synthesis
18:59 < kanzure> screw 1 gigabase genomes, what about 1 terabase etc
18:59 <@ParahSailin> fenn: im sure some people tried beaks when wings didnt work
18:59 < fenn> the truth is big birds fly more by catching thermals than by flapping their wings; we just didn't pay attention
19:00 < fenn> it's possible that da vinci built a hang glider and was able to catch thermals
19:00 < fenn> nobody really knows
19:00 < kanzure> obviously the correct way to synthesize extremely long dna molecules is through particle acceleration
19:00 < fenn> anyway, de novo DNA synthesis doesn't really happen in nature
19:01 < kanzure> GNA and other variants of DNA are an interesting concept too
19:01 < fenn> what's GNA
19:01 < kanzure> because you could possibly find something that is easier to do chemistry on, and then convert it to DNA
19:01 < kanzure> it's just a modified backbone, "simpler" chemistry or something
19:01 < fenn> eh who cares
19:01 < kanzure> and apparently it was polymerase-compatible
19:01 < kanzure> well, because if you get to pick your chemistry, then you have more options
19:01 <@ParahSailin> glycerol phosphate or something?
19:02 < kanzure> http://en.wikipedia.org/wiki/Glycol_nucleic_acid
19:02 -!- marciogm [~marciogm@179.126.69.68] has joined ##hplusroadmap
19:02 < 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 < fenn> how 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."
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19:02 < fenn> different charge patterns in the wells attract different bases
19:03 < kanzure> why?
19:03 < kanzure> what if instead you just have different nucleotides available in separate containers
19:03 < fenn> because it's parallel instead of serial
19:03 < kanzure> oh, well, single-nucleotide ligation doesn't happen
19:03 < fenn> why not
19:03 < kanzure> grabs longer sequences only iirc
19:03 < fenn> how long does it have to be
19:04 <@ParahSailin> i think cambrian is promising because phosphothioate is pretty effective chemistry that we have a good handle on
19:04 <@ParahSailin> and you can build fancy error checking and ligation on top of that
19:04 < fenn> "Oligonucleotides as short as 8 nucleotides can be efficiently assembled using T4 DNA Ligase"
19:05 < fenn> note that's in free solution, not bound to a plate
19:05 < fenn> i'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 3D
19:06 < kanzure> i've seen lots of stuff about enzymes being bound to ATP n' stuff
19:06 < kanzure> and sometimes surfaces, like biotinylated
19:06 < fenn> if you can get it down to ~4 bp oligos, then it's cominatorially feasible to just dump in oligos instead of bases
19:06 < kanzure> "Generation of biotin/avidin/enzyme nanostructures with maskless photolithography" stuff like that
19:06 < QuantumG> damn wget, walking up your directory tree
19:06 < kanzure> wget -m -np
19:06 < kanzure> plz
19:07 <@ParahSailin> oh dang, i didnt know that one existed, i always was using -I
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19:08 < fenn> 4^8 = 65536, 4^7 = 16384, 4^6 = 4096, 4^5 = 1024, 4^4 = 256   so maybe 6 bp sequences is reasonably
19:08 < kanzure> oligomer libraries are a thing, you know
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19:08 < kanzure> but it doesn't require surface binding
19:09 < kanzure> paperbot: http://pubs.acs.org/doi/abs/10.1021/ac970957t
19:09 < kanzure> .title
19:09 < yoleaux> Microelectrode Control of Surface-Bound Enzymatic Activity
19:09 < kanzure> oh, hrm.
19:09 < kanzure> yeah these are all going to be electrode chemistry
19:10 < fenn> patent 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 < paperbot> XMLSyntaxError: None (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 51, in _go)
19:11 < fenn> yeah this patent is basically what I was trying to describe
19:11 < kanzure> the problem with in-solution oligomer libraries is that you need to either have enough wings to avoid wrong additions,
19:11 < kanzure> or if you do it once per cycle then you need a bazillion wash reactions
19:11 < kanzure> and that's an imperial bazillion
19:12 < fenn> i guess they were doing random sequences though
19:12 < fenn> what's a "cycle" in this context
19:13 < kanzure> phosphoramidite/oligonucleotide synthesis involves a few steps that get repeated a bunch: wash, insert chemicals, wait for reaction, cap, wash, repeat
19:14 <@ParahSailin> why dont find efficient ways to error check and ligate phosophoramidite microarrays
19:14 < fenn> this method would be reduced to: insert oligos, wash, insert ligase, wash, repeat
19:14 < kanzure> so robotic pipetting of microarray? ala what george is doing?
19:15 < fenn> even better if your oligo solution has anti-ligase properties
19:15 < fenn> gotta keep the hot side hot and the cool side cool
19:15 <@ParahSailin> isnt he using beads instead of pipettes?
19:17 < QuantumG> phrasing
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19:17 < fenn> oh, so the moving bead is coated with the complementary oligo, and the stationary reaction site holds the strand you're working on?
19:17 < fenn> this seems slow
19:17 < fenn> moving beads around takes time
19:18 < kanzure> i think it was this one
19:18 < kanzure> http://diyhpl.us/~bryan/papers2/DNA/High-fidelity%20gene%20synthesis%20by%20retrieval%20of%20sequence-verified%20DNA%20identified%20using%20high-throughput%20pyrosequencing%20-%20supplementary.pdf
19:18 < fenn> are you talking about what i'm talking about? or is this unrelated?
19:18 < kanzure> i'm talking about ParahSailin's suggestion of micropipetting
19:18 <@ParahSailin> yeah thats it
19:19 <@ParahSailin> you could probably come up with faster ways to move beads around
19:19 < fenn> that's what cambrian's laser thingy is for
19:19 < kanzure> they laser at a microarray?
19:19 < fenn> basically
19:19 <@ParahSailin> they use two lasers
19:19 < kanzure> but where does the bead go?
19:20 <@ParahSailin> one for microarray, one for beads
19:20 < kanzure> so bead goes up into the air, another laser pushes it?
19:20 < kanzure> by... acoustic vibration?
19:21 < heath> hmm.
19:21 < heath> i think i'm going to switch back to python
19:21 < fenn> they 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 well
19:22 <@ParahSailin> beads are in water
19:22 <@ParahSailin> theres no sequencer well, its sequencing illumina style
19:22 < kanzure> i still don't know where the laser part is
19:23 < fenn> ok they have like 96 sequencers running in parallel then
19:23 < fenn> the laser is directly above the sequencer input
19:23 < fenn> the plate with the beads is upside down over the input, being moved around by an XY table
19:24 < fenn> i think both the laser and the plate are moving, so they can get the desired bead into the desired sequencer input
19:24 < fenn> either that or the sequencer moves, i haven't actually seen it
19:25 <@ParahSailin> theres no 96 sequencers, in illumina sequencing you have one synchronized reaction and one or multiple microscope cameras scanning a plate in a raster pattern
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19:29 < 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 then
19:29 < fenn> uses 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 improvising
19:30 < kanzure> "uses a laser printer to retrieve the DNA"
19:31 < fenn> there used to be a better explanation of this online, it's probably in the logs somewhere
19:32 < fenn> okay 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 assembly
19:32 < kanzure> the better explanation is anselm's second email over here https://groups.google.com/forum/#!searchin/diybio/cambrian$20genomics/diybio/YqGUf3A9AKo/NCFQ12T_8SwJ
19:33 < fenn> just pretend i said "reaction well" instead of "sequencer well"
19:33 < kanzure> well, nevermind, i don't think he points out the full process
19:33 <@ParahSailin> i wonder if you'd even have more luck using the poxvirus dna pol instead of gibson
19:33 < fenn> kanzure: hey why isnt this on the hplus wiki
19:33 <@ParahSailin> poxvirus pol only needs overlap of 15nt or so, and it doesnt chew things up willy nilly
19:34 <@ParahSailin> only problem is that you have to sacrifice a child infected with chickenpox to isolate this enzyme
19:34 <@ParahSailin> so its not commonly used
19:34 < fenn> i really doubt that's the reason
19:35 <@ParahSailin> heh
19:35 < fenn> fuck you too google *grump*
19:35 <@ParahSailin> it is pretty expensive, but only because it requires mammal cell culture
19:36 < kanzure> why does anselm call micropipetting "very high throughput"?
19:36 <@ParahSailin> clontech sells it for like $20/rxn which is not that expensive in the whole scheme of things
19:36 < kanzure> if you have a 1024x1024 microarray, the only way you're going to have high throughput is with a 1024x1024 micropipetting device
19:36 < fenn> ParahSailin: just use recombinant e. coli to make your enzyme. what's the problem
19:36 <@ParahSailin> fenn: nope they tried that
19:37 <@ParahSailin> viruses are evil, they never do what you want them to do
19:37 < kanzure> terrorize children?
19:37 <@ParahSailin> free north korea?
19:37 < fenn> ya gotta believe me
19:38 < kanzure> how fast can you drive a micropipette over a million wells
19:38 < fenn> kanzure: that's what the laser is for
19:38 < kanzure> stoping at each well to do the necessary
19:38 < fenn> how many times do i have to say it
19:38 < kanzure> *stopping
19:38 < kanzure> apparently you need to say it again
19:38 <@ParahSailin> paperbot: https://www.sciencedirect.com/science/article/pii/S0042682299997052
19:39 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/335a64ef75c98c46d28e301479744549.txt
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19:39 < fenn> since apparently i need google chrome to look at a google groups page, i'm still waiting to read the diybio post
19:39 < kanzure> fenn: how does the laser speed up the pipetting?
19:40 < kanzure> oh wait, is it a game of 2048?
19:41 -!- Adifex is now known as Adifex|pub
19:41 < ebowden> paperbot: http://diyhpl.us/~bryan/papers2/paperbot/3a73de0d7d8f7aaac21d63537a91056a.txt
19:41 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/99cb84d56d5df36e73c5ced10d36d30e.txt
19:42 < kanzure> what
19:42 <@ParahSailin> paperbot: http://diyhpl.us/~bryan/papers2/paperbot/99cb84d56d5df36e73c5ced10d36d30e.txt
19:42 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/bbdc9be894f39be6b87612761b47809c.txt
19:43 < kanzure> paperbot: file://
19:43 < kanzure> oh right, i anticipated thta one
19:43 < fenn> paperbot hacks into your system and liberates the paper
19:44 < kanzure> paperbot is the source of all knowledge (and some anti-knowledge)
19:44 < kanzure> anyhow: how does the laser speed up pipetting a million wells?
19:44 < QuantumG> Light controlled synthesis of nucleic acids - Pinheiro - 2010 .. looks like a winner to me
19:45 < kanzure> yeah they use photolithography and DMDs for the synthesis of oligos
19:45 <@ParahSailin> you dont have to move that many beads around to be orders of magnitude better than contemporary techniques
19:46 < fenn> kanzure: i just re-read all that and i'm honestly not understanding what you're missing
19:46 <@ParahSailin> a million beads to make all the yeast chromosomes, but most people would be happy with 100 beads
19:46 < kanzure> okay, so the pipette visits each of the 100 wells each step?
19:47 < fenn> 10^5 oligos -> 10^6 beads, sequence the beads (in place apparently), pop off the beads you want into the desired well for assembly
19:47 < fenn> there is no pipette anywhere
19:47 <@ParahSailin> there exists at least one pipette somewhere
19:48 < fenn> maybe there are pipettes once you get into the assembly stuff
19:48 < yashgaroth> when you find the good bead you pipette it out
19:48 < kanzure> "pop off" okay.. but it's still in the same well.
19:48 < fenn> yashgaroth: NO
19:48 < yashgaroth> argh
19:48 <@ParahSailin> might not even be wells, it could be emulsion bubbles
19:48 < kanzure> the point is, it's still separated from all the other molecules
19:48 < kanzure> (including sequencing reactants)
19:49 < fenn> kanzure: pop off means it literally goes flying through the air
19:49 < kanzure> to land where?
19:49 < fenn> in the assembly reaction well
19:49 < QuantumG> in the punter's drink, obviously
19:50 < fenn> which is conveniently placed directly underneath the bead
19:50 < fenn> pew pew
19:50 < fenn> plop plop
19:51 < ebowden> paperbot: file:http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf
19:51 < kanzure> underneath the bead was the bottom of the well
19:52 < QuantumG> I expect ya need to drop the file:
19:52 < fenn> the bead is hanging from the bottom side of a glass plate
19:52 < fenn> the laser shoots at it, dislodging it, and it falls straight down
19:53 < kanzure> so there are two entrances to each well?
19:53 < kanzure> you know, wells usually have at least one side
19:53 < kanzure> call 'em holes pls
19:53 < fenn> i dont know what the well looks like. i assumed it was a 4096 well plastic plate
19:54 < ebowden> paperbot: http://www.nrjournal.com/article/S0271-5317(05)00104-1/pdf
19:54 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/5b9aea9f64767417d97210f5f97bf8a2.txt
19:54 < ebowden> paperbot: file:http://diyhpl.us/~bryan/papers2/paperbot/5b9aea9f64767417d97210f5f97bf8a2.txt
19:54 < kanzure> uh..
19:55 < fenn> er, apparently 4096 well plates dont exist
19:55 < fenn> anyway, some relatively large yet still manageable number
19:55 < fenn> 4096 seems to be where i'm at today
19:56 < kanzure> so they are straight-through holes
19:56 < fenn> no
19:56 < fenn> let's say it's a 96 well plate
19:57 < kanzure> a 96 well plate usually has a bottom
19:57 < kanzure> such that you can only access each well through the top
19:57 < fenn> correct
19:57 < kanzure> now, if it's upside down, gravity takes your stuff
19:57 < fenn> no, the bead is hanging off a glass microscope slide. it's adhered by (unknown, irrelevant)
19:58 < kanzure> yes, but you wanted your bead to react to chemicals etc
19:58 < fenn> right
19:58 < fenn> it has dna growing on it
19:58 < yashgaroth> at like 1536 wells you can probably rely on capillary action
19:59 < ebowden> kanzure, paperbot does not appear to work with that site, does it work with sciencedirect?
19:59 < yashgaroth> against gravity that is
19:59 < kanzure> paperbot does not have 100% access to sciencedirect
19:59 < ebowden> Ok.
19:59 < kanzure> yashgaroth: so how do you insert the new reactants?
19:59 < fenn> yashgaroth: 4096 is only 64 by 64; for a 100mm plate that's like a 1mm diameter well
20:00 < fenn> maintaining +- 0.5mm is not that hard
20:00 < yashgaroth> fuck knows how you insert stuff into that, unless you're okay with using a pipette *cough*
20:00 < fenn> hell, even reprap can do it
20:00 < kanzure> yashgaroth: are you as confused as i am
20:00 < ebowden> what about elsevierhealth?
20:00 < yashgaroth> mhm
20:00 < fenn> i am confused about why you guys are confused
20:00 < kanzure> ebowden: try it, who cares?
20:00 < kanzure> fenn: have you ever used a microarray
20:01 < yashgaroth> how did you get to pew-pewing beads off of a plate
20:01 < kanzure> fenn: or, seen it enough to have a good understanding of how it works
20:01 < fenn> yashgaroth: we are talking about how the cambrian genomics "dna laser printer" works
20:01 < kanzure> here's a big plate: http://arrayit.com/Products/Microarray_Slides/Microarray_ProPlate_Glass/microarray_proplate_assemble.jpg
20:01 < fenn> why, i dont know
20:01 < yashgaroth> well it mostly runs on bullshit and VC money but that's just my opinion
20:02 < fenn> kanzure: what the hell is that
20:02 < kanzure> so is it capillary action?
20:02 < yashgaroth> that's a 96 well
20:02 < kanzure> plate gets inverted, capillary action to hold chemical solution in each well ?
20:02 < kanzure> so molecular feedstock is added prior to flipping plate?
20:02 < fenn> how does it even seal the liquid gap between wells
20:03 < fenn> or is contamination not important
20:03 < yashgaroth> if they're not filled up all the way you're fine
20:03 < yashgaroth> presumably if you've got beads attached to the bottom somehow, contamination isn't an issue anyway
20:04  * kanzure nods
20:04 < fenn> so each of those 96 wells has its own pattern with a zillion different dna strands?
20:04 < fenn> like a silicon wafer before it's cut into chips
20:05 < yashgaroth> per cambrian, each has one bead with 100k copies of an identical clone
20:05 < fenn> i'm confused what this picture is
20:05 < fenn> microarray_proplate_assemble.jpg
20:06 < yashgaroth> that's a plate with 96 wells in it
20:06 < fenn> no, it's a clear smooth piece of glass and a black plastic thing with 96 holes in it
20:06 < yashgaroth> glass optional, but yes
20:06 < kanzure> the holes only go through less than 100% of the material
20:07 < fenn> okay the glass being there is the confusing part
20:07 < fenn> god i should just stop
20:08 < QuantumG> DNA (or RNA) typewriter is a nice term
20:08 < yashgaroth> I remember us having the same discussion about how the hell cambrian's technology worked, some months ago
20:09 < 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 < 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 < fenn> er, The adhesive provides a water-tight seal between microplate wells.
20:10 < yashgaroth> okay microarrays is more apt for this discussion, same deal where they're not separated but each reaction has a specific spot on the array
20:10 < yashgaroth> since 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 place
20:11 < kanzure> "Synthesis,1249034,NSF,NSF,SBIR,2013,1,150000.00,Cambrian Genomics Inc"
20:11 < fenn> okay i dont really care about this proplate thing
20:13 < kanzure> 665 Third St	Suite 425	San Francisco
20:13 < kanzure> phone: 6075920123
20:13 < fenn> you can just watch the tv show, bloomberg brink on netflix
20:13 < 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 ...
20:14 < 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."
20:16 < QuantumG> so, I guess we need light activated phosphoribosyltransferases that respond to four distinct spectra.
20:16 < fenn> this 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 it
20:16 < yashgaroth> so the principle is that you could pull single molecules out, isolate them, and then amplify each one enough to determine its sequence
20:17 < fenn> yashgaroth: correct
20:17 < fenn> and do that a million times in parallel
20:17 < yashgaroth> and do it on a small enough scale that it's more cost effective than traditional synthesis
20:18 < yashgaroth> but, good luck with that shit
20:18 < yashgaroth> which is why I'm hopeful but not optimistic on their approach
20:18 < heath> omg, python, how i've missed you
20:18 < kanzure> heath: except its packaging sucks :(
20:18 < heath> so much productivicheese
20:19 < fenn> programming languages shouldn't have package managers IMHO
20:19 < heath> fenn would like component
20:19 < fenn> eh?
20:19 < kanzure> a web thing? hell no
20:20 < fenn> "component" is a software framework or something (why do people keep using these un-googlable names)
20:20 < kanzure> it's like bower except not
20:20 < fenn> it's like <thing you've never heard of> but not
20:20 < fenn> oh?
20:20 < heath> whoops, for some reason, i though holowaychuk inc.  were creating a language agnostic package manager
20:21 < xentrac> like dpkg?
20:21 < kanzure> like dpkg except not
20:21 < xentrac> well, like dpkg and apt?
20:21 < fenn> yeah it's called {dpkg, gentoo}
20:21 < kanzure> the problem is that python's ability to load a module sucks too
20:21 < kanzure> so it's not just packages that blow
20:21 < fenn> what's wrong with modules
20:21 < kanzure> you can't even unload a module
20:21 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has quit [Remote host closed the connection]
20:21 < fenn> why would you do that
20:22 <@ParahSailin> sounds like a challenge
20:22 <@ParahSailin> matplotlib's module loading side effects are totally evil
20:22 < kanzure> maybe you no longer need the module loaded
20:22 < fenn> can't you do "import foo as bar ; del bar"
20:22 < kanzure> that doesn't unload the module
20:22 < kanzure> nice try though
20:23 < cpopell> don'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 today
20:23 -!- nmz787_i [~nmccorkx@192.55.54.42] has joined ##hplusroadmap
20:23 < fenn> kanzure: i dont know what you're talking about
20:23 < kanzure> reload() is also broken
20:23 < xentrac> cpopell: no, they go into the global module namespace in sys.modules, and also ld.so's symbol table
20:23 < xentrac> I tried to fix reload() more than ten years ago
20:24 < xentrac> I realized I don't know how
20:24 < cpopell> xentrac: hmmm
20:24 < cpopell> this was the result of our discussion earlier
20:24 < xentrac> the local name for the module is indeed limited to the function that imports it
20:24 < cpopell> mmm.
20:24 < cpopell> I see what you mean
20:24 < xentrac> but if another function or module imports the same module later, it won't get loaded a second time
20:24 < kanzure> cpopell: this is wizard magic unrelated to your immediate issue of scope
20:25 < fenn> okay so i load foo as bar1, delete bar1, change foo, load foo as bar2, now bar2 == bar1?
20:25 < xentrac> yes, except tht bar1 is a NameError
20:25 < cpopell> is there a module to simplify the action of deleting modules?
20:25 < cpopell> ...
20:25 < fenn> is there any reason you would ever do that?
20:25 < xentrac> you can del things from sys.modules; that works for the Python part
20:25 < kanzure> reload() is very very nifty... if it would actually work.
20:26 < xentrac> it doesn't work for the ld.so part
20:26 <@ParahSailin> why though
20:26 < QuantumG> paperbot http://pubs.acs.org/doi/abs/10.1021/bi00633a029
20:26 -!- Viper168_ [~Viper@unaffiliated/viper168] has quit [Ping timeout: 255 seconds]
20:26 <@ParahSailin> side effects in module loading should just not be done
20:27 < kanzure> "Please accept that Python indeed does not support unloading modules for severe, fundamental, insurmountable, technical problems, in 2.x."
20:27 < kanzure> oh is it fixed in 3.x?
20:28 < nmz787_i> kanzure: 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_i> so that sounds like some engineering to build on top of
20:28 < kanzure> great, feel free to pay for $500/prototype yourself
20:28 < kanzure> ugh
20:29 < nmz787_i> i only have to make 114 bp/second to make 300k gross/year
20:29 <@ParahSailin> thats a lot of glass
20:29 < nmz787_i> reaction will def be less than 60s, scaling # of reactors still takes up less than 10 sq cm real estate
20:30 < nmz787_i> and prob not more than a meter or two sq otherwise
20:30 < nmz787_i> likewise, 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 transformation
20:31 < kanzure> neither does your chip
20:31 < nmz787_i> ( reaction on macro scale needs 2 mins)
20:31 < fenn> you'll have overhead beyond 10 sq cm of microfluidic plate
20:31 < nmz787_i> fenn: yeah that's what the extra ~2 sq meters was for
20:31 < paperbot> XMLSyntaxError: None (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 51, in _go)
20:31 < nmz787_i> kanzure: yes it does
20:31 < kanzure> your chip doesn't exist
20:31 < nmz787_i> kanzure: that has been my plan for 4-5 years
20:31 <@ParahSailin> poor paperbot
20:32 < nmz787_i> my CAD has a v 0.1
20:32 < QuantumG> I just used the library anyway
20:32 < kanzure> you can't just handwave a lot of engineering effort into existence and claim it will magically work
20:32 < nmz787_i> you have to set requirements before you start a project, generally
20:32 < fenn> oligos or GTFO
20:32 < fenn> lol
20:32 < nmz787_i> fuck oligo
20:32 < nmz787_i> :p
20:33 <@ParahSailin> if you are doing novel chemistry, dont do novel apparatus at the same time
20:33 < kanzure> i need a mathematical model that corresponds to your estimate of amount of work per added component on a project
20:33 < nmz787_i> nope
20:33 < kanzure> same goes with you fenn
20:33 < nmz787_i> not novel chem
20:33 < fenn> work is force times distance
20:33 < kanzure> just because it's not novel chemistry doesn't mean your layout works the first time or the first 100 times
20:33 <@ParahSailin> phosphoramidite?
20:33 < nmz787_i> though i just put out a call for a chemist/polymerchemist/materialsscientist today
20:34 < nmz787_i> yeah some PDMS compatible version
20:34 < kanzure> fenn: you know what i meant
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20:34 <@ParahSailin> by pdms you mean this is going to be a disposable device?
20:34 < fenn> you know what i meant. "work" is undefined otherwise
20:34 < kanzure> engineering time
20:34 < kanzure> number of iterations, prototypes, critical bugs
20:35 < fenn> number of bugs is proportional to number of interacting systems squared
20:35 < kanzure> is the material of each wall considered an "interacting system"
20:35 < fenn> probably not
20:35 < kanzure> is the yield rate of a chemical reaction considered an "interacting system"
20:36 < fenn> yield rate is a parameter, not a system
20:36 < kanzure> yield can be impacted by all sorts of interesting factors, like ambient environment, temperature, light, ph, etc
20:36 < fenn> great
20:37 < xentrac> speaking of chemistry, it occurred to me today why buses smell kind of like matches
20:37 < fenn> also parameters
20:37 < xentrac> a substantial part of match smoke is phosphorus oxide
20:37 < kanzure> what is your maximum amount of debugging then
20:37 < xentrac> the bus smell is from burning sulfur
20:37 < fenn> the rubber in the floor tiles contains sulfur vulcanizing residue?
20:37 < kanzure> because apparently you think this idea is below some threshold amount
20:37 < xentrac> no, from sulfur in the fuel
20:37 < kanzure> and i'm really confused what your personal estimates are here
20:38 < xentrac> here in Argentina, not in the US
20:38 <@ParahSailin> paperbot: http://nar.oxfordjournals.org/content/40/3/e23.full
20:39 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Error%20correction%20of%20microchip%20synthesized%20genes%20using%20Surveyor%20nuclease.pdf
20:39 < nmz787_i> ParahSailin: 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 < fenn> kanzure: 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 ability
20:39 <@ParahSailin> abandon all hope of regenerating, reconditioning, etc the pdms, but im sure its good for prototyping
20:40 < nmz787_i> nah, not really regenerating, just more like, use it until it dies
20:40 < nmz787_i> flushing is part of the synthesis, so its there already
20:40 < nmz787_i> cleaning is sort of built in I guess you could say
20:41 < kanzure> QuantumG: do you know of any nasa reports regarding failure estimation?
20:41 < nmz787_i> unless the PDMS is slowly swelling, or if some corner is too sharp and causes crystallization to start and clog up
20:41 < fenn> kanzure: 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 before
20:41 <@ParahSailin> wow ^paper made a 723nt construct
20:41 < QuantumG> NASA does the world's worst statistics
20:42 < QuantumG> and no
20:42 < xentrac> I thought PDMS was pretty dimensionally stable
20:42 < nmz787_i> xentrac: depends on solvent absorbtivity
20:42 <@ParahSailin> pdms swells
20:42 < kanzure> the slide with "weighted technology impact rating" is weird (the ones before it are worthless) http://start1.jpl.nasa.gov/pubPro/Alan_Wilhite.pdf
20:43 <@ParahSailin> http://www.biotechniques.com/multimedia/archive/00036/BTN_A_04364PF01_O_36417a.pdf
20:43 < kanzure> QuantumG: how is that possible, don't they do the famous "1 failure in a billion" numbers
20:43 < xentrac> nmz787_i: thanks
20:44 < QuantumG> yeah, how do you think they come up with those numbers?
20:44 < kanzure> oh :(
20:45 < kanzure> this seems like something that large-scale engineering projects need to have had addressed though
20:45 < kanzure> like the LHC.. you don't just go put that sucker in the ground without knowing the constraints, tolerances, and expected failure rate.
20:45 < QuantumG> heheh.. ya do know they did exactly that right?
20:45 < kanzure> huh?
20:46 < QuantumG> hooked 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 design
20:46 < kanzure> that's pathetic
20:46 < nmz787_i> all 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 that
20:47 < nmz787_i> block co-polymer synthesis is all around
20:47 < nmz787_i> ABS
20:47 -!- QuadIngi [~fourfire@245-201-15.connect.netcom.no] has quit [Ping timeout: 264 seconds]
20:47 < 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_i> that's only 1 monomer type less than DNA code
20:48 < fenn> QuantumG: why didn't the LHC work as designed?
20:48 < QuantumG> I love the way history on Wikipedia for the LHC starts in 2008.
20:48  * fenn is too lazy to read up on it
20:48 < QuantumG> 10 Sep 2008 	CERN successfully fired the first protons around the entire tunnel circuit in stages.
20:48 < QuantumG> yeah, cause the LHC just magically popped into existence.
20:49 < QuantumG> The construction of LHC was approved in 1995
20:49 < xentrac> kanzure: they did run into a lot of unexpected failures actually
20:49 < fenn> the LHC was warped in via microsingularity transport
20:49 < xentrac> which is what usually happens when you do things nobody has done before
20:50 < kanzure> there are lots of ways to estimate likely types of failures
20:50 < kanzure> did they even have a failure estimation model
20:50 < QuantumG> http://en.wikipedia.org/wiki/Large_Hadron_Collider#Construction_accidents_and_delays
20:50 < kanzure> in 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 etc
20:50 < QuantumG> it's the second last section before "Popular culture" and "See also".
20:51 < fenn> kanzure: and the actual measured catastrophic failure rate was 2 in 135
20:52 < QuantumG> .. and doesn't even include the stuff I vaguely remember reading.
20:52 < fenn> plus or minus some hand waving
20:52 < kanzure> insert stereotypical "haha they used english feet and we used meters" story
20:52 < QuantumG> http://web.archive.org/web/20080616063402/http://www.photonics.com/content/news/2007/April/4/87089.aspx
20:52 < xentrac> kanzure: I'm sure they did, or they wouldn't have been able to ever get it to work
20:52 < QuantumG> .title
20:52 < yoleaux> Fermilab 'Dumbfounded' by Fiasco That Broke Magnet
20:53 < fenn> the mars orbiter screwup was actually much more complicated and hard to explain than the newtons/foot-poundals mixup that we've been told
20:53 < kanzure> "Fermilab designed and built nine of the magnet assemblies for CERN and conducted four engineering reviews between 1998 and 2002"
20:53 < kanzure> aka "someone looked at this only four times" :)
20:53 < xentrac> journalists always love it when "boffins" are "baffled"
20:54 < xentrac> they can safely be ignored
20:54 < QuantumG> in a project that large, the reviews are nothing more than rubber stamps anyway
20:54 < kanzure> i feel like freitas/merkle might have written about estimation in their book on kinematic self-replicating machines
20:55 < kanzure> oh wait, maybe AASM instead
20:55 < QuantumG> there's plenty of it in Nanosystems
20:55 < kanzure> AASM seems like the place they would do it
20:55  * ParahSailin is disappointed that nobody looked at the awesome paper i linked
20:55 < kanzure> http://www.islandone.org/MMSG/aasm/
20:56 < xentrac> QuantumG: why do you think that projects being large requires that reviews be ineffective?
20:56 < kanzure> haha "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."
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20:56 < fenn> ParahSailin: i thought you were being sarcastic
20:56 < kanzure> that' sthe only mention of failure
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20:57 < QuantumG> ParahSalin: looks neat
20:57 <@ParahSailin> i think it has potential to be scaled
20:58 < fenn> in 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 yield
20:58 < kanzure> also, a lot of this is part failure, like mechanical failure under load
20:58 < kanzure> rather than system design problems
20:58 < kanzure> i dunno what to call the system design type of problem
20:59 <@ParahSailin> fenn: apparently not all
20:59 < fenn> systemantics?
20:59 -!- nmz787_i [~nmccorkx@192.55.54.42] has quit [Quit: Leaving.]
20:59 < fenn> ParahSailin: if you have very low yield you need to amplify (probably with PCR) which has some finite error rate of its own
21:00  * fenn shrugs
21:00 < fenn> i guess there are fancy low error PCR enzymes now
21:00 < QuantumG> kanzure: 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 < fenn> the shuttle mentality
21:01 <@ParahSailin> fenn: expectations are really low right now for dna synthesis
21:01 < kanzure> i am a shuttle voom
21:01 < fenn> nyoom
21:01 < QuantumG> Ares I is what I had in mind, but the examples abound
21:01 <@ParahSailin> even with a couple pcr errors, a multi kb construct is sploosh
21:01 < fenn> the average nasa engineer during apollo was 26
21:02 < QuantumG> everything is either a success or cancelled by those stupid policy makers at NASA.
21:02 < QuantumG> (sarcasm)
21:02 < fenn> average nasa age is now 47
21:02 < QuantumG> if your spacecraft crashes, that's not a failure, that's.. like.. space is hard man
21:03 < QuantumG> if 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 < fenn> i'm more worried about not sending anything up at all
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21:03 < justanotheruser> That's science! Their theory that their mission would be successful was wrong
21:03 < fenn> who cares if it crashes
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21:04 < fenn> we still dont have an equatorial LEO laboratory
21:05 < fenn> stuff costs too much
21:05 < QuantumG> yeah, it costs too much because of that attitude
21:06 < fenn> soon we'll have unpiloted aerostats and the satellite industry will die, taking the rest of commercial space with it, unless something big changes
21:06 < QuantumG> "soon" has been soon for a long time when it comes to aerosats
21:06 < xmj> moin
21:06 < fenn> the FAA is dragging its knuckles
21:07 < QuantumG> I don't think that's the problem
21:07 < fenn> i think it is
21:07 < QuantumG> how do you figure?
21:07 < fenn> well, why don't we have aerostats flying around?
21:08 < fenn> they exist
21:08 < kanzure> 1) make a correct failure estimation model 2) proceed to building dyson sphere
21:08 < kanzure> *engineering design failure
21:08 < fenn> expected chance of success building dyson sphere: 1e-1337
21:08 < kanzure> you have already failed
21:08 < fenn> you are already dead
21:09 < xentrac> we do have aerostats flying around for weather monitoring
21:09 < cpopell> muda muda muda
21:09 < QuantumG> I'm pretty sure you mean aerosats.. aerostats already exist and fly around the US all the time
21:09 < xmj> fenn: "still bigger than the last web startup i funded. here, have some VC money"
21:09 < kanzure> do you think the death punch is possible? you could inject some chemicals that cause a body to explode, right?
21:09 < fenn> xentrac: a balloon is not an aerostat because it moves randomly
21:09 < xmj> can aerostats be geostationary?
21:10 < cpopell> kanzure: what about the high pressure knives?
21:10 < xentrac> fenn: I think it is: https://en.wikipedia.org/wiki/Aerostat#Free_balloons
21:11 < fenn> whatever
21:12 < fenn> let's abuse language and make everything mean nothing and nothing everything
21:12 < xentrac> .ety aerostat
21:12 < yoleaux> Sorry, I couldn't find the etymology of that.
21:12 < xentrac> what's the FAA doing?
21:12 < QuantumG> in any case, there's plenty of FAA support for balloon delivered comms services.. I don't think that's the problem.
21:12 < QuantumG> I think the problem is that flying a permanent balloon platform is really hard.
21:13 < fenn> xentrac: the "stat" part means "static" as in "not moving"
21:13 < fenn> "aero" means it's in the air
21:13 < xentrac> there is a discussion of this at https://en.wikipedia.org/wiki/Talk%3AAerostat#Meaning
21:14 < fenn> a balloon without motive power. Contrasted with {aerodyne}. [1913 Webster
21:14 < xentrac> it turns out that "stat" means that its lift is not derived from moving, as opposed to aerodynes
21:14 < 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."
21:16 < fenn> so a kite is not an aerostat?
21:16 < fenn> what's the point of even having the word
21:16 < xentrac> no, it's lifted by aerodynamic lift
21:17 < fenn> why not just say "balloon"
21:17 < xentrac> is a zeppelin a balloon?
21:17 < fenn> yes
21:17 <@ParahSailin> greek roots sound more professional
21:17 < xentrac> not normally
21:17 < xmj> ParahSailin: moin
21:18 < xentrac> the point of having the word is probably to distinguish the two major types of aircraft: heavier-than-air and lighter-than-air
21:18 < fenn> stationkeeping flying thingy is too much
21:18 < QuantumG> anyway, I dunno how commsats are still around.. people like their soccer delivered that way I guess
21:18 <@ParahSailin> møin møin møin
21:19 < QuantumG> and people keep building LEO constellations despite the fact that none have ever turned a profit.
21:19 < fenn> and "statite" already has a meaning related to solar sails
21:19 < xentrac> there are probably classified funding source for LEO constellations
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21:20 < QuantumG> nah VCs just like the idea.
21:20 < QuantumG> this time it'll be different because SpaceX
21:20 -!- Qfwfq [~Qfwfq@unaffiliated/washirving] has quit [Ping timeout: 252 seconds]
21:20 < fenn> what does SpaceX do that radically changes things?
21:21 < QuantumG> cheaper launch, is the argument
21:21 < xentrac> control costs
21:21 < QuantumG> mostly cheaper because you don't have to take your payloads to Russia, but yeah
21:21 < fenn> wasnt this the point of sealaunch
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21:22 < QuantumG> yeah, and they got sued
21:22 < xentrac> didn't know that
21:22 < xentrac> .g sealaunch lawsuit
21:22 < yoleaux> http://www.reuters.com/article/2013/02/04/boeing-sealaunch-idUSL1N0B31GP20130204
21:22 < fenn> sued for what
21:22 < QuantumG> itar
21:22 < fenn> huh?
21:23 < fenn> because sailing is "export"?
21:23 < xentrac> oddly enough, that article says:
21:23 < QuantumG> no, Boeing failed to keep their tech out of Russian/Ukranian hands
21:23 < 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"
21:24 < fenn> so, not itar?
21:24 < xentrac> .g "sea launch" itar
21:24 < yoleaux> http://www.alston.com/files/docs/3-23-11-Items-Insert.pdf
21:24 < QuantumG> yeah, part of that weaker demand was the supposed benefits of using them over Russian launch - not going through the ITAR process - was proven false.. graphically
21:25 < xentrac> "The assets owned by Sea Launch created other
21:25 < xentrac> regulatory and defense-related issues, including the fact that the equipment (the vessel and the platform
21:25 < xentrac> utilized to launch rockets) is subject to the International Trafficking in Arms Regulations (ITAR). The
21:25 < xentrac> ITAR regulations created issues in connection with obtaining DIP financing as lenders were concerned
21:25 < xentrac> about the ability to liquidate and monetize those assets. Today Sea Launch is now reorganized and
21:25 < xentrac> operating in Luxemburg and Switzerland (with the physical assets still in Long Beach, California, the
21:25 < xentrac> reorganization was successful and created significant value for the stakeholders and customers.
21:25 < xentrac> "
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21:26 < fenn> i think sealaunch was a great idea and SpaceX should take advantage of it
21:26 < fenn> it's practically in their back yard
21:26 < xentrac> Sea Launch was largely Russian-owned
21:26 < QuantumG> dear god why?
21:26 < xentrac> and Ukrainian-owned
21:27 < xmj> xentrac: that means essentially the same thing, doesn't it.
21:27 < QuantumG> the 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 work
21:27 < xmj> just use Soviet-owned.
21:27 < xmj> :]
21:27 < fenn> i never knew anything about the russian partnership
21:28 < QuantumG> The US now has "export free zones" like the Mid-Atlantic Regional Spaceport to do something similar.
21:28 < dingo> ☭
21:28 < fenn> um except Virginia is nowhere near the equator
21:29 < QuantumG> all 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 < QuantumG> launching 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 company
21:30 < xmj> lol
21:30 < xentrac> cos(latitude(virginia)) is pretty close to 1
21:30 < QuantumG> Orbital Sciences launches from MARS because 90% of their rocket is made in other countries.
21:30 < xmj> yes, because local subsidiaries to circumvent export regulation is... hard to do, really
21:31 < fenn> it also provides transportation to your launch site, a wide open launch range, a launch pad
21:31 < QuantumG> xmj: local subsidiaries full of non-US citizens?
21:32 < fenn> i 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 virginia
21:33 < QuantumG> that could be why WALLOPS exists, but it's not why Orbital cares
21:34 < fenn> orbital was using a minotaur V (when i was paying attention)
21:34 < fenn> the LADEE launch
21:34 < fenn> Orbital'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 <@ParahSailin> also is pretty cool that railroads go to virginia, and not french guyana
21:34 < xentrac> well, LADEE DA
21:35 < QuantumG> yeah? and?
21:35 < xmj> ParahSailin: boats go
21:35 < fenn> sorry for the spam
21:35 < fenn> i watched that launch through binoculars, it was pretty cool
21:35 < fenn> very orange
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21:36 < xentrac> .g latitude of virginia
21:36 < yoleaux> http://www.worldatlas.com/webimage/countrys/namerica/usstates/valatlog.htm
21:36 < fenn> .wa latitude of virginia
21:36 < xentrac> .g cos(37.5 degrees)
21:36 < yoleaux> https://answers.yahoo.com/question/index?qid=20100515221911AA8dWT5
21:36 < yoleaux> Virginia: center coordinates: 37° 31' 7"N, 78° 53' 28"W
21:36 < fenn> come on wolfram, you don't know what latitude means?
21:36 < xentrac> .c cos(37.5 degrees)
21:36 < yoleaux> cos(37.50°) = 0.793353...
21:37 <@ParahSailin> .wa circumference of earth
21:37 < yoleaux> Earth: 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 day
21:37 < yoleaux> Earth: 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 california
21:37 < yoleaux> fenn: Sorry, no result!
21:37 < xentrac> 463 m/s
21:37 < fenn> .wa latitude of vandenberg air force base
21:38 < yoleaux> Vandenberg 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 speed
21:38 < yoleaux> Leo (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 speed
21:38 < yoleaux> http://en.wikipedia.org/wiki/Low_Earth_orbit
21:38 < fenn> oh but vandenberg can't do equatorial launches because it would kill those honest god fearing people in nebraska
21:38 <@ParahSailin> delta v starts at about 10km/s
21:39 < xentrac> yeah, 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/s
21:40 < yoleaux> 21%×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 < yoleaux> 21%×(463 m/s (meters per second))/(7.80 km/s (kilometers per second)) = 0.0125
21:40 < fenn> from delta V; orbit is around the center of earth, not any arbitrary latitude line
21:41 < xentrac> .c 21% * 463 m/s / (7.8 km/s - 463 m/s)
21:41 < yoleaux> 21%×(463 m/s (meters per second))/(7.80 km/s (kilometers per second)-463 m/s (meters per second)) = 0.0133
21:41 < xentrac> so launching from the equator instead of Virginia saves you 1⅓% of the orbital velocity you need
21:42 < xentrac> or more like 1% if the delta-v is actually the relevant number, as ParahSailin says it is
21:42 < QuantumG> .. and most launches are underperforming anyway.
21:43 < fenn> when 95% of your mass is fuel, 1% is a lot
21:43 < xentrac> how much, fenn?
21:43 < fenn> how much what?
21:43 < xentrac> how much is 1%?
21:43 <@ParahSailin> fuel requirement is geometric wrt delta v
21:43 < fenn> 0.01?
21:44 < xentrac> or 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 equation
21:44 < yoleaux> http://en.wikipedia.org/wiki/Tsiolkovsky_rocket_equation
21:45 < Darius> what does .c use?
21:45 < kanzure> chinese children
21:45 < Darius> they're very quick
21:45 < kanzure> well there's a lot
21:45 < fenn> i hate wikipedia's equations, they are light colored staticky pixels around black letters on a gray background, pretty much ensuring i can't read them
21:46 < kanzure> switch the css theme, there's a dropdown box somewhere
21:46 < kanzure> the css theme might determine their latex generator image thing
21:47 < fenn> wikipedia has themes?
21:47 < kanzure> http://en.wikipedia.org/wiki/Wikipedia:Skin#How_to_change_the_skin
21:47 < xentrac> Darius: on #swhack, where yoleaux comes from, it's currently using Wolfram Alpha
21:47 < 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."
21:48 <@ParahSailin> Isp of kerosene/lox is 353s
21:48 < xentrac> but I don't know if yoleaux has been updated yet
21:48 < 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)"
21:49 < fenn> xentrac: 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 equator
21:50 < xentrac> fenn: ah, so 20%?
21:51 < xentrac> (in that 100%-95%-1% is 120% of 100%-95%)
21:51 < fenn> oh also " the minimum orbital inclination without a plane-change maneuver is the latitude of the launch site"
21:52 < xentrac> but ParahSailin says "fuel requirement is geometric wrt delta v" so perhaps not
21:52 <@ParahSailin> if 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 v
21:55 < xentrac> that's a substantial improvement but not nearly as much as my other number
21:55 < fenn> kanzure: thanks i was guessing randomly ?skin=dark ?skin=black
21:56 < fenn> they are all black text on white background though?
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21:59 < xmj> fenn: did you see http://opensslrampage.com/ ?
22:00 < xmj> er
22:00 < xmj> fenn: did you see http://www.libressl.org/ ?
22:00 < xmj> This page scientifically designed to annoy web hipsters. Donate now to stop the Comic Sans and Blink Tags
22:01 < fenn> no, why should i care?
22:01 < fenn> SSL sucks anyway
22:01 < xentrac> fenn: where does your gray background come from?
22:02 < xentrac> my Wikipedia background is always white (so I can't see the staticky pixels)
22:02 < fenn> cat ~/.dillo/style.css
22:02 < fenn> * { background-color: #272727 !important; ...
22:02 <@ParahSailin> i've done some patches to hs-tls
22:03 < xentrac> ah
22:04 < xentrac> I didn't know Dillo even supported CSS
22:04 < fenn> it doesn't really
22:05 < fenn> it will do borders and text and colors, but not float or various box model things
22:06 < fenn> as for why i'm using dillo, see previous complaints about thrashing and ram and tabs
22:09 < fenn> kanzure: i thought you had a watermark removal script
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22:09 < fenn> i mean, i thought it was running on paperbot's output
22:09 < xentrac> no, I totally understand wanting to use dillo
22:09 < fenn> but i clearly see a watermark from a paper downloaded today at <location redacted>
22:10 < fenn> xentrac: i recently discovered "netsurf" which, despite its odd origins and intended audience, is actually a damn fine first draft of a browser
22:10 < fenn> it just needs javascript and some minor bugfixes
22:11 < fenn> netsurf is as fast as dillo, but it properly renders CSS
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22:13 < xentrac> I think I tried using netsurf once but couldn't get it to stop crashing
22:13 < xentrac> but I might have confused it with something else
22:13 < kanzure> fenn: pdfparanoia does not have 100% coverage
22:13 < kanzure> fenn: https://github.com/kanzure/pdfparanoia/issues report a bug
22:13 < xentrac> presumably if it doesn't have JS it doesn't have the DOM either
22:14 < xentrac> which 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 ballpark
22:14 < kanzure> servo is the only modern practical option at this point
22:14 < kanzure> webkit and blink are both massive
22:15 < xentrac> servo is still a proof of concept
22:15 < xmj> it's too bad opera stamped their engine and settled for webkit
22:16 < xmj> opera's was by far the fastest
22:16 < xentrac> I didn't realie that
22:16 < xentrac> realize
22:16 < fenn> oh, oxford journals is already listed as a bug
22:16 < xentrac> I stopped using opera in 2000
22:17 < fenn> 90% of the time i don't care about javascript, i just want to see the page
22:17 < fenn> so maybe have a browser that loads webkit for the other 10%
22:17 < fenn> or i could just switch browsers i guess
22:18 < xentrac> I'm wondering at this point if it makes sense to write a browser that recognizes bootstrap and has a fast path for it
22:18 < fenn> actually midori worked fine before i "upgraded" to 13.10
22:18 < xentrac> midori's still webkit, no?
22:18 < fenn> yes, but it was pretty fast still
22:18 < xentrac> I guess I figure that 95% of the stuff on current web sites is trying to accomplish pretty simple things
22:18 < fenn> and it didn't explode on more than 10 tabs, like all mainstream browsers do
22:19 < fenn> what do you mean "has a fast path for it"?
22:19 < xentrac> if 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 CPU
22:19 < fenn> oh like a self optimizing JIT for javascript
22:20 < xentrac> no
22:20 < fenn> (i thought chrome did that with v8)
22:20 < xentrac> like a large library of extremely specific optimizations for not just JS but also CSS and HTML
22:20 < xentrac> mostly CSS and HTML in fact
22:20 < kanzure> "oh look, the billionth webpage that's using float:left"
22:20 < kanzure> "and jquery"
22:21 < xmj> xentrac: did you see the stackoverflow page telling you to use jquery for simple things like adding two numbers?
22:21 < fenn> i understand having a local cache of jquery, but how do you fix float:left?
22:21 < xentrac> I don't know specifically what the things are that make e.g. Twitter take multiple seconds to scroll down
22:21 < xentrac> on my netbook
22:22 < xentrac> but the end result is a pretty mundane change to what's on the screen
22:22 < kanzure> why are all the google scholar results for "design flaws" all about software? :(
22:22 < fenn> usually my problem is: i open a new tab, paste in a url, and nothing happens for 5-50 seconds
22:23 < xentrac> you 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 < fenn> somehow chrome is using 4GB of (virtual) RAM
22:24 < fenn> its like it doesn't understand the difference between ram and swap
22:24 < xentrac> or "this is going to scroll the page down"
22:25 < fenn> how is this different from memoizing function calls
22:25 < kanzure> "design errors" is also all software and vlsi stuff. so, what, design errors don't happen in buildings or supercolliders?
22:25 < fenn> i guess the DOM varies because the colors are different or something?
22:26 < fenn> so the function call is not exactly the same and you get a cache miss
22:26 < Lemminkainen> paperbot http://www.sciencedirect.com/science/article/pii/S0163725811001653
22:26 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/fd72b379e6676e13c477f45520c6534a.txt
22:26 < xentrac> I guess I'd have to dig into some DOM to find out
22:28 < fenn> xentrac: what do you think about throwing away all the webmaster-provided styling information and using LCARS instead?
22:28 < xentrac> <sadtrombone />
22:29 < xentrac> I think I'd rather read Wikipedia with any of the Wikipedia skins than with LCARS
22:29 < fenn> but styling is just reinventing the UI wheel for every website in existence
22:29 < fenn> fine, s/LCARS/vector/
22:29 < xentrac> it would be okay for some pages
22:29 < xentrac> and not others
22:30 < fenn> the 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 else
22:31 < fenn> all that stuff can just fuck off and leave me alone
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22:31 < fenn> custom mouse cursor that sprinkles fairy dust -> /dev/null
22:32 < xentrac> even 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 readable
22:33 < fenn> aside from the large renderings breaking up the text flow, i dunno what i'm missing
22:34  * fenn waits for chrome to do anything at all
22:34 < fenn> processing request...
22:34 < fenn> processing...
22:35 < fenn> [Pages Unresponsive]
22:35 < xentrac> pasting the style tags from https://en.wikipedia.org/wiki/Wikipedia:Vital_articles into it improves the situation somewhat
22:35 < fenn> oh there it is. oh look, it has a logo in the upper left corner
22:36 < xentrac> at least the <pre> tags have a different background
22:36 < fenn> and the code text flows into the rendering making it hard to read
22:36 -!- Darius [~quassel@adsl-69-231-35-194.dsl.irvnca.pacbell.net] has quit [Read error: Connection reset by peer]
22:36 < xentrac> but all the text is run up against the left edge of the page with a single pixel of whitespace, which makes it hard to read
22:36 < xentrac> and the width of the text is way too wide
22:37 < kanzure> conceptual design flaws exist, right?
22:37 < kanzure> it's not all just "your load bearing loadbearer wasn't able to bear enough bears"?
22:37 < fenn> in 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 code
22:37 < xentrac> that's good
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22:37 < xentrac> I put CSS in there for that
22:37 < fenn> kanzure: doing the wrong thing faster is a moral hazard
22:37 < xentrac> what I meant was that even if I replace it with Wikipedia's CSS that's still there
22:37 -!- Darius [~quassel@adsl-69-231-35-194.dsl.irvnca.pacbell.net] has quit [Remote host closed the connection]
22:38 < xentrac> but I don't think Wikipedia's vector skin CSS is really an improvement
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22:38 < xentrac> the <pre> text overlapping the image is indeed a problem but I think it may actually be the least bad solution on a small screen
22:39 < fenn> xentrac: 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 browsers
22:40 < xentrac> oh, sure
22:40 < fenn> like an rss reader i guess
22:40 < xentrac> represent your data at a higher conceptual level so that you can automatically reformat it as desired
22:41 < xentrac> the thing is that people have been trying that since Scribe with limited success
22:41 < fenn> Scribe the book typography tool?
22:41 < fenn> (what is scribe?)
22:42 < xentrac> yeah, that one.  1979: https://en.wikipedia.org/wiki/Scribe_%28markup_language%29
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22:42 < fenn> i know this is confusing because a lot of people think SGML is just HTML
22:43 < fenn> HTML was sort of worse-is-better
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22:44 < xentrac> I know
22:44 < fenn> anyway 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 solution
22:45 < Lemminkainen> paperbot http://www.nature.com/nri/journal/v13/n3/pdf/nri3399.pdf
22:45 < paperbot> http://libgen.org/scimag/get.php?doi=10.1038%2Fnri3399
22:45 < Lemminkainen> hellllllllyuss
22:46 -!- marciogm [~marciogm@179.126.69.68] has quit [Quit: Computer has gone to sleep.]
22:46 < fenn> then 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 configurable
22:46 < xentrac> http://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 < xentrac> after 28 years of work, success is still limited
22:47 < fenn> the 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 mode
22:47 < xentrac> so I think the problem may be harder than you think
22:48 < kanzure> "it's only the sum of the number of parts"
22:48 < kanzure> :grumpy:
22:48 < fenn> in this case i'm processing relatively unstructured data (arbitrary webpages) and attempting to transform it to the ideal structured data
22:49 < fenn> so it's a different problem than "trying to get everyone to use your nerdball view of the world"
22:50 < fenn> ontological assimilation
22:51 < fenn> i just know this is an irc log i am going to find during some future web search
22:51 < kanzure> hello future me, fuck you
22:52 < xentrac> well, 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 display
22:52 < xentrac> than the current mishmash of skilled and unskilled webmasters tweaking CSS
22:52 < kanzure> fenn's idea is to just use a default minimum terrible level of "two-dimensional display"
22:52 < fenn> bullshit, the webmasters have no idea what my requirements are and even if they did, they wouldn't care
22:52 < kanzure> then you don't have to be disappointed anymore
22:53 < fenn> for example the black text on white background sucks when you are in a dark room
22:53 < xentrac> like the readability bookmarklet, plus some classifiers to apply more specialized presentations?
22:53 < kanzure> not that i agree, i just want software and package managers
22:53 < xentrac> yeah, it does, fenn
22:53 < fenn> white text on a black background sucks when you're using an e-ink reader
22:53 < xentrac> I prefer red text on a black background most of the time
22:53 < fenn> this is what CSS was supposed to solve, but instead we've gone and turned it into a do-anything rendering API
22:54 < xentrac> yeah.  and above I explained why I think that is
22:55 < fenn> i 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 there
22:55 < xentrac> and in the case of Wikipedia you need to rerender the equations
22:55 < xentrac> which btw you can do because the TeX source is present as alt text
22:55 < fenn> nah you can just do simple processing like "this has a white border and is transparent, invert the image"
22:56 < 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 < xentrac> do you mean a white background? (in the original page CSS?)
22:57 < fenn> nevermind, re-rendering the equation is probably the best general solution
22:57 < fenn> there will be cases when the TeX is not available, such as scanned images or "we converted this svg to a jpg for you"
22:58 < xentrac> it's not very general; it only applies to MediaWiki with TeX
22:58 < fenn> but consider what the equation represents, a mathematical function with symbols representing constants or parameters
22:59 < xentrac> hmm, it would be interesting if you could automatically do something interesting with that
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22:59 < fenn> it's not too far-fetched
23:00 < fenn> really any text should be OCR'ed
23:00 < xentrac> like Project Naphtha
23:00 < fenn> even text in images that aren't clearly computer generated
23:01 < kanzure> ugh now my queries are returning me stuff written by matt campbell
23:01 < kanzure> well i have clearly looped back on myself
23:02 < kanzure> maybe i should ask him
23:02 < kanzure> conceptual design flaws seems like a thing he might think about
23:02 < xentrac> fenn: maybe you could build a search engine that returns you equations scraped from Wikipedia pages
23:02 < fenn> most of campbell's stuff was about "conceptual design" anyway
23:02 < xentrac> and integrate it into a computer algebra system
23:03 < kanzure> are you trolling him? i can't tell
23:03 < fenn> xentrac: actually i hate equations
23:03 < fenn> they're supposed to look pretty and be compact or something
23:03 < xentrac> no, not at all; I think this might actually be useful
23:04 < fenn> but there's a reason japanese computer programmers don't use kanji in their code...
23:04 < xentrac> case in point, yesterday my ex-girlfriend and I were 3-D printing a Helmholtz resonator for a music box
23:04 < xentrac> https://en.wikipedia.org/wiki/Helmholtz_resonator has some relevant equations and variable definitions
23:05 < fenn> what is "project naphtha" all i see is petrochemical stuff
23:05 < xentrac> sorry, they misspelled the name
23:05 < xentrac> .g project naptha
23:05 < yoleaux> http://projectnaptha.com/
23:05 < xentrac> .t
23:05 < yoleaux> Thu, 24 Apr 2014 06:05:47 UTC
23:06 < xentrac> ...¿en serioooo?
23:06 < kanzure> weren't they in the news yesterday
23:06 < kanzure> their name screams "hey vegeta" to me
23:06 < fenn> napa = cabbage
23:06 < xentrac> anyway it turns out all the equations on that page use compatible naming of variables
23:06 < kanzure> .title https://www.youtube.com/watch?v=qslAuezumIA
23:06 < yoleaux> DBZ Abridged: The Best of Nappa
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23:07 < xentrac> and 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 other
23:08 < xentrac> turns out that a really crucial missing piece there is the Q factor of the resonator, which ought to be on that page but isn't
23:08 < fenn> oh 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)
23:09 < xentrac> fenn: sorry to hear that
23:10 < xentrac> could 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 spacing
23:11 < fenn> oh right i remember dillo introduced all this fancy text hyphenation stuff
23:12 < fenn> and netsurf just left-justifies it
23:13 < fenn> man wikipedia's equations really look like crap even with a white background
23:13 < fenn> must be optimized for speed instead of quality
23:14 < kanzure> it's all cached anyway so i doubt they are bothered by an extra 10-100ms during rendering
23:15 < fenn> what's with all the visible pixels then
23:15 < fenn> (aliasing)
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23:19 < fenn> xentrac: as you've no doubt deduced the same system could be applied to PDFs
23:19 < kanzure> figure/diagram extraction is a pain in the butt, much less OCR..
23:20 < fenn> you don't have to OCR the pdf because it's already text for the most part
23:20 < kanzure> i wish
23:20 < fenn> i've resorted to OCR'ing pdf files though
23:21 < fenn> this is the kind of problem that really shouldn't exist
23:21 < kanzure> it's not like i want to read a million pages of longform text to get effective at anything anyway
23:21 < kanzure> that's just not sustainable
23:21 < fenn> huh
23:22 < kanzure> i'm being grumpy about reading, this week
23:22 < fenn> you should be able to sort a table in a pdf by its headings
23:22 < xentrac> fenn: I don't see aliasing on Wikipedia equations on a white background
23:22 < kanzure> figshare does some of that but they are a company and i don't think they're giving away source/software
23:22 < fenn> and summarize columns, or whatever
23:22 < xentrac> I do see big pixels but that's because they're images and my zoom is >100%
23:23 < fenn> you dont see the huge pixels on the radical sign? https://upload.wikimedia.org/math/1/5/8/158e4d2f3b3610849e24263720118db6.png
23:23 < xentrac> fenn: I posted a bookmarklet for doing that on HTML to kragen-hacks a few years back
23:23 < xentrac> have you tried it?
23:24 < xentrac> oh, yeah, that's a little jaggy.  wonder why!
23:24 < fenn> a bookmarklet will let me sort pdf tables?
23:24 < kanzure> /topic mathematical aliasing criticism group
23:24 < xentrac> no, "on HTML"
23:25 < fenn> i'm of the school of thought that equations are about as dumb as cursive or astrological diagrams
23:25 < xentrac> looking at the equation in the GIMP, it seems to be antialiased wrongly
23:25 < xentrac> I think all the pixels should be black, with varying levels of opacity
23:26 < fenn> is it a png8 or a png24?
23:26 < fenn> png8 has boolean transparency i think
23:27 < xentrac> instead they are many different shades of gray, with only boolean transparency
23:27 < xmj> 2^8 shades of gray
23:27 < xentrac> "4-bit colormap"
23:27 < xmj> :o
23:27 < fenn> you'd think there would be a boolean luminance channel png8 with 2^8 shades of transparency
23:28 < fenn> i mean this is a pretty common scenario isn't it?
23:28 < fenn> take a black and white image, scale it down, share it on the net
23:29 < fenn> the tyranny of diurnalists reaches into the furthest corners of our lives!
23:30 < xentrac> it seems like the cleanest solution to that is to colormap the rendered image of the web page
23:31 < xentrac> black to red, white to black, presumably red to white, and other corners of the color cube to themselves?
23:31 < xentrac> anyway, I find equations useful because they describe relationships between things
23:32 < xentrac> have you considered trying to describe e.g. population standard deviation without a formula?
23:32 < fenn> i think we should use either code or pseudocode
23:32 < xentrac> it's the square root of the sum of the squared differences between each data value and the average of all the data values
23:32 < xentrac> code is a lot less expressive than equations
23:33 < fenn> people say that but i don't believe it
23:33 < fenn> equations just leave out all the important details and that fucks you up if you aren't already a domain expert
23:33 < xentrac> maybe that's not exactly right
23:33 < xentrac> it's not that code is less expressive, per se
23:33 < fenn> and if you're a domain expert you don't need to be reminded of the equation
23:34 < xentrac> it's that it is too powerful
23:34 < xentrac> according to the principle of least power, when a language loses power, it gains manipulability
23:34 < xentrac> and that is certainly true of equations
23:34 < fenn> does not compute. power = expressiveness (from my reading of paul graham at least)
23:35 < xmj> ln(f(x)) makes it certainly lose power :(
23:35 < xentrac> haha
23:35 < xentrac> are you familiar with the principle of least power?
23:35 < fenn> no
23:35 < xentrac> .g principle of least power
23:35 < yoleaux> http://www.w3.org/DesignIssues/Principles.html
23:36 < fenn> i'm guessing it's the difference between source code and data format
23:36 < xentrac> yes, and that's a continuum
23:36 < xentrac> something that's "data" from one perspective is "code" from another
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23:39 < xentrac> the 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 < xentrac> it also tells us how to compute the necessary neck length if instead the volume and neck diameter and gas are fixed
23:39 < xentrac> or how to compute the resonant frequency if all those things are fixed
23:40 < fenn> i'll just note that omega is never defined as frequency anywhere on the page
23:40 < xentrac> no, it's angular frequency, not frequency
23:41 < xentrac> and it is in fact defined right up at the top:
23:41 < xentrac> It 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 < fenn> how do you know that omega_H is angular frequency?
23:42 < xentrac> because it says right there
23:42 < fenn> no it doesn't
23:42 < xentrac> "the resonant angular frequency is given by: \omega_{H} ="
23:42 < fenn> it says "angular frequency is given by: (equation)"
23:42 < xentrac> it also allows us to compute the ambient pressure given a fixed resonator and gas, if we can measure the frequency
23:43 < xentrac> so that single equation gives us four different useful computations, which would need four different pieces of code to compute them
23:43 < fenn> now i know you've heard of prolog
23:43 < xentrac> yes.
23:44 < fenn> "prolog does that"
23:44 < xentrac> you would think you could do that kind of manipulation with prolog but in practice you cannot.
23:44 < xentrac> because prolog gave up that level of manipulability in order to be turing-complete.
23:44 < xentrac> very early arithmetic prolog programs from the 1970s can in fact be manipulated in this way.
23:44 < fenn> okay but does this mean we have to use funky hieroglyphics i can't even type with a keyboard or even a stream of characters?
23:45 < xentrac> no, of course not
23:45 < xentrac> you might, in a Turing-complete language, write a piece of code that can easily be manipulated in the same way
23:46 < xentrac> but as soon as you start sticking cuts or while-loops into your code, that kind of manipulation becomes very difficult
23:46 < fenn> it just seems like a case of lazy evaluation to me
23:46 < xentrac> ("cuts" are a Prolog thing)
23:46 < jrayhawk> hv3 does some javascript stuff
23:46 < xentrac> it seems like it, but it's actually a different phenomenon.
23:46 < fenn> don't invert the matrix until you need to, etc.
23:48 < xentrac> if you combine this equation with the equation of Q from https://en.wikibooks.org/wiki/Acoustics/Flow-induced_Oscillations_of_a_Helmholtz_Resonator
23:48 < xentrac> which is
23:48 < xentrac> Q = 2 \pi \sqrt{V (\frac{L'} {S})^3}
23:48 < fenn> jrayhawk: 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 < jrayhawk> No, I don't use hv3.
23:48 < jrayhawk> Automatic execution of unsigned code is a bug, not a feature.
23:49 < fenn> oh this was the tk thing. yeah, no.
23:50 < xentrac> then 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 vessel
23:50 < fenn> xentrac: obviously non-functional (as in functional programming) code can't be treated the same as functional code
23:51 < xentrac> even Turing-complete functional code is not generally manipulable in this way
23:51 < xentrac> Turner is exploring the limits of non-Turing-complete functional code, which might be promising in this way
23:52 < fenn> what's the problem with a while loop exactly?
23:54 < xentrac> the biggest difficulty is that it's uncomputable whether it terminates or not, and if so, when
23:55 < fenn> how is this different from equations with no solution?
23:55 < xentrac> consider the Ackermann function
23:55 < fenn> (possibly) no solution
23:57 < xentrac> which is actually just a nested for loop
23:57 < fenn> the 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 :P
23:57 < xentrac> not even a while loop; it's provably terminating
23:58 < fenn> it looks like the factorial function
23:59 < xentrac> it does addition, multiplication, exponentiation, and so on
--- Log closed Thu Apr 24 00:00:10 2014