| --- Log opened Sat Feb 02 00:00:48 2013 | ||
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| @fenn | no objection, but it would have been better a year ago | 00:35 |
|---|---|---|
| @fenn | huh seems like it was longer than that | 00:36 |
| @kanzure | not true, it's better now because nmz787 has a home and things | 00:37 |
| @kanzure | <--- unit tests passing, i'm a very happy person. | 00:37 |
| nmz787 | what? | 00:38 |
| nmz787 | ahh | 00:38 |
| nmz787 | if we built laser anything, i think it would still have micro XY, but that it would expose resist rather than ablate | 00:40 |
| nmz787 | well | 00:40 |
| nmz787 | i guess it would use the same optics actually | 00:40 |
| nmz787 | so we could just try both | 00:40 |
| nmz787 | fenn: what's your situation these days? | 00:41 |
| nmz787 | fenn: i drove past indiana in december and thought of you, i think you had been there back then maybe | 00:41 |
| nmz787 | fenn: i last remember you asking me to find 3D schematics for some part of that laser cutter | 00:42 |
| @fenn | i'm in DC doing nothing interesting | 00:42 |
| nmz787 | fenn this is what I'm looking at now | 00:42 |
| nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/ed800170t | 00:43 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Three-Dimensional%20Printing%20Using%20a%20Photoinitiated%20Polymer.pdf | 00:43 |
| brownies | well that doesn't sound very interesting. | 00:44 |
| @fenn | looks identical to lemoncurry | 00:44 |
| nmz787 | fenn https://nano-cemms.illinois.edu/materials/3d_printing_full | 00:44 |
| @fenn | except it goes down into a vat instead of being exposed on the bottom and drawing out | 00:45 |
| nmz787 | this way makes more sense than that | 00:45 |
| @fenn | why do they call it "nano" | 00:45 |
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| nmz787 | where? | 00:46 |
| @fenn | nevermind, that's just the institution they're at | 00:46 |
| @fenn | " incredibly thin polymer layers (on the order of 400 nm)" so by this definition reprap is "nanotechnology" | 00:47 |
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| nmz787 | so basically i was thinking I'd hook up a projector to my microscope, add a webcam for feedback, and make casting masters | 00:47 |
| @fenn | make it so, number one | 00:48 |
| nmz787 | but you could just as easily put a laser in place of the projector and scan the exposure | 00:49 |
| nmz787 | that's what azonenberg wants to do | 00:50 |
| @fenn | you could even do two photon for sooper dooper resolution | 00:50 |
| @fenn | but i imagine you want the negative of what a laser would scan | 00:51 |
| nmz787 | i don't know if this gel is compatible with the reactions I want to do though, so I might be limited to one layer anyway, just to stamp into PDMS | 00:51 |
| @fenn | probably better that way | 00:51 |
| nmz787 | but if it was able to be coerced into compatibility, that would be cool | 00:51 |
| @fenn | "embossed" | 00:51 |
| nmz787 | it's basically polyacrylamide | 00:51 |
| nmz787 | with some http://www.sigmaaldrich.com/catalog/product/aldrich/246816?lang=en®ion=US | 00:52 |
| @fenn | there are other chemistries available, see http://code.google.com/p/lemoncurry/wiki/main | 00:53 |
| @fenn | jeez they haven't made any progress on that at all | 00:53 |
| @fenn | see "customers also viewed" on that sigma page :) | 00:55 |
| @fenn | anyway, bucktownpolymers might do what you want without the hassle of sigma aldrich | 00:55 |
| @kanzure | there, i've added http response saving for unit tests | 00:56 |
| @kanzure | https://github.com/kanzure/python-requestions#readme | 00:56 |
| @fenn | now it's just a SMOP to get it to actually do something | 00:59 |
| @kanzure | ? | 00:59 |
| @fenn | httpickle or whatever you're calling it | 01:00 |
| @kanzure | httpretty is just some unit testing wrapper thing for mocking the requests library | 01:01 |
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| nmz787 | fenn: bucktown looks like it might be a lot more expensive than sigma | 01:01 |
| @kanzure | but why would i want to manually write HTTPretty.register_uri in each unit test.. why not just load the actual result i received from the real request, and just test against that. | 01:01 |
| @fenn | nmz787: really? i thought they were quoting something like $40/kg | 01:02 |
| @fenn | anyway the problem with sigma is getting them to sell anything at all | 01:02 |
| nmz787 | i've bought from sigma before | 01:03 |
| nmz787 | they just need a commercial shipping address | 01:03 |
| nmz787 | that's with most of these companies | 01:04 |
| @fenn | kanzure: so this whole thing is just unit tests for python-requests? doesn't it have its own unit tests? | 01:04 |
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| @kanzure | did langton count as commercial? | 01:04 |
| @kanzure | fenn: python-requests comes bundled with httpbin, and i think it runs an httpbin server | 01:04 |
| @kanzure | i mean it runs an instance of httpbin for the unit testing | 01:04 |
| nmz787 | fenn: gallon of vis curable $235, gallon of UV curable $1040 | 01:04 |
| @fenn | um, langton probably could have gotten away with commercial shipping | 01:04 |
| @kanzure | "fenn why are there 20 barrels marked 'alibaba, not illicit' in the garage?" | 01:05 |
| nmz787 | it literally depends on the property zoning record | 01:05 |
| @kanzure | nobody would have noticed | 01:05 |
| @fenn | is there no readily available UV cure resin for hobby stuff? | 01:06 |
| @kanzure | what does lemoncurry use? | 01:06 |
| nmz787 | I might be able to use the sigma stuff for electrophoresis gel too | 01:06 |
| @fenn | i mean this is basic chemistry, just need to add some uv absorbing dye to limit penetration | 01:06 |
| @kanzure | also if there is no curable polymer we can always get treadwell to make something up, he has been begging for a relevant project. | 01:07 |
| nmz787 | hmm well i guess sigma wants $150 for kg | 01:07 |
| nmz787 | so that's prob 1/4 gallon ish | 01:07 |
| @kanzure | . units 1 kg | 01:07 |
| @kanzure | .units | 01:07 |
| @kanzure | fuck the bots | 01:07 |
| nmz787 | and that's the 80% | 01:07 |
| @fenn | 80%? | 01:08 |
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| @fenn | i for one welcome our silent IRC overlords | 01:08 |
| nmz787 | yeah i dunno what the other 20% is! | 01:09 |
| @kanzure | fenn: no really why don't we have a unitbot | 01:09 |
| @fenn | so people dont use the channel as their personal command line | 01:10 |
| @fenn | .wa kg | 01:10 |
| yoleaux | kg (kilogram): Conversions to other units: 1 kg: 2.205 lb (pounds): 2 pounds 3.274 ounces: 1000 grams; Conversions from other units: 1 lb: 0.4536 kg; 1 oz: 0.02835 kg; 1 g: 0.001 kg; Physical quantity: mass; Unit type: SI base unit; Unit systems: Système International d'Unités (SI): decimeter-kilogram-second (DKS): meter-kilogram-second (MKS) | 01:10 |
| @kanzure | oh, wolfram. | 01:10 |
| @fenn | anyway we don't know the density or at least i'm too lazy to look it up | 01:11 |
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| nmz787 | yeah i'll just assume it's water | 01:13 |
| nmz787 | :p | 01:13 |
| @fenn | always a valid assumption when dealing with unfamiliar organics | 01:14 |
| @fenn | "hexanediol acrylamide? goes well with gin" | 01:14 |
| @fenn | well it's past my bedtime. i believe we've discussed most of this before | 01:16 |
| nmz787 | this is pretty similar http://www.sigmaaldrich.com/catalog/product/aldrich/411744?lang=en®ion=US | 01:17 |
| nmz787 | $1/mL | 01:17 |
| nmz787 | so add the activator and you're at the same price as bucktown | 01:17 |
| nmz787 | so i guess their visible stuff is OK priced | 01:18 |
| nmz787 | maybe they'll sell me less for a sample | 01:18 |
| nmz787 | hmm, but they seem to only take paypal | 01:18 |
| @fenn | try asking info@bucktownpolymers.com | 01:19 |
| @fenn | it's probably just one guy | 01:20 |
| nmz787 | cool | 01:22 |
| nmz787 | thanks | 01:22 |
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| AirmanEpic | hey guys! I'm stefan, curious about biohacking but with very little actual experience | 08:53 |
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| AirmanEpic | ohai | 09:03 |
| yashgaroth | I'll warn you, saturday mornings aren't usually our busiest, but welcome | 09:04 |
| AirmanEpic | thanks. I just recently found this, it was just what I was looking for so I figured I'd keep it open | 09:05 |
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| AirmanEpic | hey, I just remembered what a plasmid is! | 09:30 |
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| yashgaroth | well, good | 09:30 |
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| AirmanEpic | xD this stuff is ridiculously beyond my league. | 09:33 |
| yashgaroth | I recommend a copy of Molecular Biology of the Gene, to be paired with Molecular Biology of the Cell | 09:34 |
| chris_99 | yeah i got the latter one, seems really good | 09:36 |
| AirmanEpic | I'm getting the former as we speak | 09:37 |
| AirmanEpic | never really read a textbook before, meh | 09:37 |
| yashgaroth | well you're gonna need to if you want to do anything beyond making a glowing bacterium | 09:37 |
| yashgaroth | and you'll need to read it anyway if you want to understand how you're making said bacterium | 09:38 |
| yashgaroth | don't worry it's easy there's no math | 09:38 |
| AirmanEpic | Which I do, eventually xD. Thanks for the help. What's the craziest thing you've done, yash? | 09:39 |
| yashgaroth | craziest? I try to do everything in a coherent state of mind | 09:40 |
| AirmanEpic | oh. ... well good point | 09:40 |
| AirmanEpic | How about "most impressive" | 09:40 |
| yashgaroth | idk I purified like 15 grams of plasmid last week, that was impressive to me | 09:41 |
| AirmanEpic | what was the plasmid for? | 09:41 |
| yashgaroth | I'm afraid I can't disclose that information since it was for work, but it was part of a DNA vaccine | 09:41 |
| yashgaroth | in my free time, I'm working on a plasmid that expresses follistatin, which I will then inject into my muscles | 09:42 |
| yashgaroth | I hope to have that done within 6 months, depending on a lot of factors | 09:43 |
| AirmanEpic | damn, sorry, I didn't want to pry. I googled follistatin but couldn't get any answers. What is it? | 09:44 |
| yashgaroth | it's one of several inhibitors of myostatin, and myostatin is a muscle regulating factor, i.e. if you reduce the action of myostatin, muscles will grow | 09:45 |
| AirmanEpic | ah so it's a bit of a steriod | 09:45 |
| AirmanEpic | steroid? | 09:45 |
| yashgaroth | yes, in a way, but without most of the side-effects hopefully | 09:45 |
| yashgaroth | not that steroids have many side effects if used correctly, but still | 09:45 |
| AirmanEpic | sweet. That is impressive indeed, good luck, can't wait to see the results | 09:46 |
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| AirmanEpic | this may be a stupid question, but why is it that your body won't reject the plasmids? | 09:49 |
| yashgaroth | the immune system doesn't have any problem with DNA in itself, and follistatin is a normal human protein, I just want to make more of it | 09:50 |
| yashgaroth | most gene therapy work involves viruses and/or foreign proteins, which is when you might get rejection | 09:50 |
| yashgaroth | err, 'foreign' in the sense that you're lacking a normal protein, which would be immunogenic since you don't have it | 09:51 |
| AirmanEpic | I see. That makes sense. Hmmm. Is there a way to make a protein not immunogenic? | 09:52 |
| yashgaroth | you can mess around with the sequence, but not reliably - that's one of the holy grails of biomedicine | 09:53 |
| AirmanEpic | of course xD. | 09:53 |
| AirmanEpic | I was getting all excited | 09:53 |
| yashgaroth | so while those with big research dollaz investigate that, I'm sticking with non-immunogenic proteins that I already have, and having my body make more of them | 09:54 |
| yashgaroth | that's also why I spend a lot of time telling people that getting a glowing GFP tattoo isn't useful for anything at the moment, except as a vaccine against GFP | 09:55 |
| AirmanEpic | exactly. I came to the same conclusion. Or messing with bacteria and keeping them outside the dermis | 09:55 |
| yashgaroth | yes, modifying gut bacteria to make useful things is another interest, and applicable to DIYbio | 09:56 |
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| AirmanEpic | It would be incredibly handy to allow a diet expansion | 09:58 |
| yashgaroth | or contraction - eat whatever you want, and your gut flora will make sure you have enough vitamins, essential amino acids etc | 10:00 |
| AirmanEpic | gut flora xD that's a pretty freakin awesome thought. Could you make something that, say, detects your BMI and adjusts it? | 10:02 |
| yashgaroth | that would be far more complex, but your brain does an okay job of it already | 10:04 |
| AirmanEpic | ah ok. | 10:05 |
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| cpopell | I'll be around here a lot more from now on | 10:49 |
| AirmanEpic | sweet | 10:50 |
| cpopell | fucking budget cuts. | 10:50 |
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| AirmanEpic | budget cuts? | 10:57 |
| cpopell | yeah. | 10:57 |
| cpopell | I worked for the navy | 10:57 |
| AirmanEpic | oh yes. | 10:58 |
| AirmanEpic | Haven't really effected the AF yet | 10:58 |
| cpopell | are you active duty? | 10:59 |
| AirmanEpic | yeah. | 10:59 |
| cpopell | I was two steps away from safety | 10:59 |
| cpopell | I was a civilian contractor | 10:59 |
| cpopell | not even technically a fed employee | 10:59 |
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| AirmanEpic | sorry man | 11:00 |
| cpopell | Shrug. | 11:00 |
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| cpopell | Time to spread my wings. | 11:00 |
| AirmanEpic | metaphorical pr physical? | 11:02 |
| cpopell | metaphorical. | 11:02 |
| AirmanEpic | damn. dreams crushed. | 11:02 |
| cpopell | I already spread them physically :P http://www.exrx.net/WeightExercises/PectoralSternal/DBFly.html | 11:03 |
| AirmanEpic | wasn't exactly what I had in mind ;P | 11:03 |
| cpopell | brb with a real client | 11:08 |
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| ThomasEgi | AirmanEpic, physical wings on humans wouldn't be enough for flying anyway. | 11:13 |
| ThomasEgi | gliding wolud work. | 11:13 |
| chris_99 | some cats have wings ;) | 11:13 |
| chris_99 | alas they don't fly | 11:13 |
| ThomasEgi | so you could jump down a skyscraper or a mountain wihout breaking your bones | 11:13 |
| ThomasEgi | would still be fun to se a foldable wing for gliding in action. | 11:14 |
| AirmanEpic | I was kidding ThomasEgi, I'm well aware of the lack of muscle structure/bone density | 11:14 |
| chris_99 | http://upload.wikimedia.org/wikipedia/commons/thumb/d/df/Wingsuit-01.jpg/300px-Wingsuit-01.jpg ThomasEgi | 11:15 |
| ThomasEgi | chris_99, not exactly what i had in mind with foldable. those are more.. über-cool-falling-suits | 11:15 |
| chris_99 | mm, they look amazing fun | 11:16 |
| ThomasEgi | i was more thinking about something that slows your fall down enough to be used to land yourself without breaking everybone in your body | 11:16 |
| ThomasEgi | so maybe somewhere along the 5m wingspan or so | 11:16 |
| chris_99 | heh, supposedly iirc some people where going to try and land using one of those wingsuits | 11:16 |
| chris_99 | not sure how though | 11:16 |
| ThomasEgi | hm.. you'd have to gain speed first. | 11:17 |
| AirmanEpic | retro rockets, just sayin | 11:17 |
| AirmanEpic | or a huge pile of boxes | 11:17 |
| ThomasEgi | and once you have top speed. you pull horizontal short above the ground. using your momentum and the wings to create vertical lift. | 11:17 |
| ThomasEgi | it': still be a very fast landing | 11:17 |
| ThomasEgi | might work well if you land on wet grass or ice | 11:18 |
| ThomasEgi | where friction is rather low so you don't immedially stumble and roll all over the place | 11:18 |
| ThomasEgi | would be a bit like.. jumping off a speeding car | 11:18 |
| AirmanEpic | why not just use a parachute during the last bit? | 11:19 |
| ThomasEgi | that's standard^ | 11:19 |
| AirmanEpic | exactly. | 11:19 |
| ThomasEgi | everyone does that. almost no risk, no thrill, no chance to die or ripp of half your skin on the ground | 11:19 |
| chris_99 | haha | 11:19 |
| AirmanEpic | sounds good to me ;D | 11:20 |
| AirmanEpic | http://en.wikipedia.org/wiki/Flying_squirrel | 11:20 |
| ThomasEgi | one idea that i totaly liked.. taking a parachute and be slingshot in the air | 11:20 |
| ThomasEgi | that name is missleading. it's actually gliding | 11:20 |
| AirmanEpic | "This changes the tautness of the patagium, a furry parachute-like membrane that stretches from wrist to ankle.[4] It has a fluffy tail that stabilizes in flight. The tail acts as an adjunct airfoil, working as an air brake before landing on a tree trunk.[5] | 11:20 |
| chris_99 | http://www.youtube.com/watch?v=dRB-woVjlFY | 11:21 |
| chris_99 | it's been done | 11:21 |
| AirmanEpic | fluffy tails, people, why didn't I think of that | 11:21 |
| ThomasEgi | AirmanEpic, cause if you stuck a fluffy tail to your behind you'd no longer do anything else but be obsessed with your own fluffyness | 11:22 |
| AirmanEpic | I didn't think of that bit. | 11:22 |
| AirmanEpic | you can make it selectively fluffy, only made fluffy instinctively | 11:23 |
| ThomasEgi | those cardboard boxes.. | 11:23 |
| ThomasEgi | that'd make the most awesome cardboardboxfortress ever!! | 11:23 |
| ThomasEgi | ok how bout wingsuits and rocketboots? | 11:25 |
| AirmanEpic | been done | 11:25 |
| chris_99 | haha | 11:25 |
| AirmanEpic | the trick is coming up with a rocket boot that doesn't kill you with fumes or require huge ammounts of reaction mass | 11:25 |
| AirmanEpic | the only thing they've really come up with is a hydrogen peroxide engine | 11:26 |
| ThomasEgi | hm.. how bout good ol RC turbines? | 11:27 |
| AirmanEpic | highly explosive fuel, fumes, heat, etc. | 11:28 |
| AirmanEpic | http://en.wikipedia.org/wiki/Wingsuit_flying#Jet-powered_wingsuits | 11:29 |
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| cpopell_ | hey look a real client | 11:31 |
| cpopell_ | lol | 11:31 |
| AirmanEpic | I'm just using the plain old web client xD | 11:32 |
| ThomasEgi | still better than flipping microswitches like madness | 11:33 |
| AirmanEpic | how so? | 11:34 |
| ThomasEgi | ever typed with microswitches as input? | 11:34 |
| AirmanEpic | ......... no | 11:34 |
| ThomasEgi | aint too much fun | 11:35 |
| AirmanEpic | I beleive you | 11:35 |
| AirmanEpic | I'm making a doorbell for my room. | 11:36 |
| AirmanEpic | dorm* room | 11:37 |
| AirmanEpic | I love how closely related biohacking is to normal hacking | 11:39 |
| AirmanEpic | need a micro xy control for your camera? No worries, plug your arduino board in. | 11:40 |
| AirmanEpic | need a quick centerfuge? 3D print one! | 11:40 |
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| AirmanEpic | I'll be back eventually | 12:42 |
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| @kanzure | "Regaring parseInt(), the story is even more complex though :) You should never use it without the radix because that behavior is not reliable when it comes to implying octal representation. Calling parseInt("016") yields 16 in Chrome (ES5 compliant [1]), while 14 in Firefox, Opera and IE8." | 13:05 |
| @kanzure | https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/parseInt | 13:05 |
| @kanzure | argh javascript | 13:05 |
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| @kanzure | bwahahaha dub of the north star http://www.youtube.com/watch?v=twH93a4JYgI | 13:55 |
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| nmz787 | interesting use of microfluidics http://www.tactustechnology.com/documents/Tactus_Technology_White_Paper.pdf | 15:20 |
| nmz787 | i want one already | 15:20 |
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| @fenn | tactus technology: bringing new dimensions to sexting | 15:42 |
| @fenn | it's not very many buttons | 15:43 |
| @fenn | it seems like they're not addressable, just inanimate plastic blobs that you can push | 15:46 |
| @fenn | "A class-action lawsuit | 15:46 |
| @fenn | was filed by LightHouse for the Blind and Visually Impaired against videodisc rental service | 15:46 |
| @fenn | Redbox | 15:46 |
| @fenn | why do blind people need access to video disc rental? | 15:47 |
| @kanzure | because maybe they watch movies | 15:47 |
| @kanzure | legally blind is not no visual input whatsoever | 15:47 |
| @kanzure | s/no visual input/no audio-visual input whatsoever | 15:47 |
| @kanzure | blergh broken regex. | 15:48 |
| juri_ | i support a blind user, who enjoys all kinds of series'. he just listens to them. | 15:48 |
| @kanzure | but, realistically, they should use torrents and not be subjected to the horrors of redbox | 15:48 |
| @kanzure | braille computer interfaces are terrible and evil, people think that crippling a device for a cripple is a good idea | 15:49 |
| @kanzure | "let's put windows ce on it! yeah!" | 15:50 |
| juri_ | my blind user uses windows XP. | 15:50 |
| @fenn | i'm really wondering why there aren't any good or popular audio operating systems in common use | 15:51 |
| @fenn | at least some kind of standard interface that could be implemented anywhere | 15:51 |
| @kanzure | 口笛が聴こえるiu ios has good tty support i hearos | 15:51 |
| @kanzure | wtf happened in that message | 15:51 |
| juri_ | something something something speaking? | 15:52 |
| @fenn | "whistle can be heard" | 15:52 |
| juri_ | i still have basically no kanji. | 15:53 |
| @fenn | i cheated :) | 15:53 |
| juri_ | :P | 15:53 |
| @kanzure | ah i blame hiei http://www.youtube.com/watch?v=0XHa2HMBxiU | 15:53 |
| juri_ | me and my partner are both teaching ourselves japanese. | 15:53 |
| juri_ | we're to the point where we watch as much anime without subs, as with subs. | 15:54 |
| @fenn | ... and you can understand anything? | 15:54 |
| juri_ | oh yes. | 15:54 |
| @fenn | kanzure: you listen to jpop? | 15:55 |
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| @kanzure | juri_: then you can join us for the hplusroadmap re-enactment of 北斗の拳 | 15:55 |
| @kanzure | fenn: sorta.. http://www.youtube.com/playlist?list=PL85F050BEFA28E044 | 15:56 |
| juri_ | kanzure: again, i don't do much kanji. ;) | 15:56 |
| @fenn | fist of the north star | 15:57 |
| @kanzure | dub of the north star was hilarious. "last time on mad max..." | 15:57 |
| juri_ | mm. not one of my series. | 15:57 |
| @fenn | it's what will happen when yashgaroth's myostatin inhibitors interact with the ultrasonic transcranial stimulation | 15:57 |
| @kanzure | or when we revive bruce lee through skeleton dna sampling | 15:58 |
| @fenn | how does he expect plasmids injected into the muscle to be expressed anyway? | 15:58 |
| yashgaroth | by strong viral promoters | 15:59 |
| @fenn | but mammalian cells aren't competent | 15:59 |
| @kanzure | he has spoken | 15:59 |
| @kanzure | electroporation | 15:59 |
| yashgaroth | you make them competent with elec yeah | 15:59 |
| @fenn | in vivo electroporation? | 15:59 |
| @kanzure | ex vivo | 15:59 |
| yashgaroth | fuck yeah bro | 15:59 |
| yashgaroth | it's in vivo | 15:59 |
| @fenn | ex vivo, so, red blood cells? | 15:59 |
| yashgaroth | all up in those vivos | 15:59 |
| @kanzure | erm, i mean, stabbing yourself | 15:59 |
| @fenn | okay so, uh, how do you keep from burning the shit out of yourself with the electricity | 16:00 |
| yashgaroth | it's only a millisecond pulse | 16:00 |
| @fenn | but it's a lot of energy | 16:00 |
| yashgaroth | not necessarily | 16:00 |
| @fenn | i mean it works by ripping holes in the membrane | 16:00 |
| yashgaroth | small, transient holes | 16:00 |
| yashgaroth | also there's theoretically an electrophoresis effect | 16:01 |
| @kanzure | what's wrong with steroids again? | 16:01 |
| yashgaroth | nothing, really | 16:01 |
| yashgaroth | ironically, experimental genetic augmentation is easier for me | 16:02 |
| @fenn | steroids don't do quite the same thing | 16:02 |
| @fenn | you still have to lift weights to gain muscle with steroids | 16:02 |
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| yashgaroth | you still gain some muscle just sitting around with 'roids | 16:03 |
| @kanzure | no you gain just by sitting around | 16:03 |
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| @kanzure | not as much | 16:03 |
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| @fenn | huh so this is basically the same technology as the DNA vaccine you're doing | 16:04 |
| yashgaroth | which DNA vaccine, the one I mentioned to that diybio fellow? | 16:05 |
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| yashgaroth | pretty much all DNA vaccines and non-viral gene therapy trials these days use electroporation, and many of them use Ichor Medical's electroporator | 16:06 |
| @fenn | man that's some star trek shit | 16:07 |
| yashgaroth | yeah I don't know why they designed it like that | 16:08 |
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| yashgaroth | anyway point is you get a solid 100-1000x increase in plasmid uptake, which is better/cheaper/less toxic than all the various chemicals that people otherwise use for transfection | 16:09 |
| cpopell | yash, I got my 23andme results. | 16:11 |
| @fenn | i guess it's easier than viral packaging? | 16:11 |
| yashgaroth | cpopell: yeah you mentioned, and also my condolences - about the work stuff that is, not your genes | 16:12 |
| cpopell | Shrug. Going to spread wings a bit. | 16:12 |
| cpopell | anyway, I'm 47.6% ashkenazi :V | 16:12 |
| cpopell | my dad was way, way more pure blood than he thought he was. | 16:12 |
| yashgaroth | it's quite a lot easier than viruses, though mostly I dislike viruses because you need to be on severe immunosuppressants before/during/after | 16:12 |
| yashgaroth | congrats | 16:12 |
| @fenn | oh i didn't know that | 16:12 |
| @fenn | people aren't exposed to milligrams of intravenous viral material in the wild | 16:13 |
| yashgaroth | and most wild-type humans have pre-existing immunities to AAV, the current darling viral vector | 16:13 |
| yashgaroth | unlike the lab monkeys and mice that they test it on | 16:14 |
| yashgaroth | so you have an initial response that kills all cells that took up the viral particles, and then you develop a neutralizing response the next time you need said virus | 16:14 |
| yashgaroth | I mean, you can try doing immunosuppressants for a month, but I'm sure as fuck not doing that outside of a bubble-boy bubble | 16:15 |
| @fenn | yeah that sounds sub optimal | 16:15 |
| yashgaroth | so if you've got [serious medical condition] viruses are fine, since you'd die otherwise | 16:16 |
| @fenn | did my idea of ex vivo electroporation with blood cells make sense? does follistatin need to be expressed in muscle tissue? | 16:17 |
| yashgaroth | it makes sense; it doesn't necessarily need to be in muscle cells, but it's a semi-localized effect so you'd need a lot of it circulating, which can cause off-target effects | 16:17 |
| yashgaroth | also muscle cells persist for a long time so you get excellent duration, unlike skin/liver/immune cells | 16:17 |
| @fenn | well that's not necessarily a good thing if you discover unexpected side effects | 16:18 |
| yashgaroth | there's been a few studies, they haven't noticed anything weird; primary concern is effects on your nads | 16:19 |
| AirmanEpic | hope you like your brand new fur xD | 16:19 |
| yashgaroth | here's one in primates that's now in clinical trials http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852878/ | 16:19 |
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| AirmanEpic | well there ya go, no need to worry | 16:21 |
| @fenn | cool. i didn't think it would be so easy to do this | 16:21 |
| yashgaroth | oh it won't be easy, plasmids are still far less efficient than viruses | 16:21 |
| yashgaroth | there's some optimization you can do, but still | 16:21 |
| @fenn | how are you cloning plasmids? | 16:22 |
| yashgaroth | the traditional way | 16:22 |
| yashgaroth | btw our diybio lab in san diego got approved | 16:22 |
| AirmanEpic | nice. 'gratz. | 16:23 |
| @fenn | what's "approved" mean? | 16:23 |
| AirmanEpic | by the way, can you get off of immunosupressants once the virus is through it's course? | 16:24 |
| yashgaroth | the city agreed to lease us the space for $1/year and pay all utilities | 16:24 |
| yashgaroth | you can go off immunosuppressants once all the viral particles have been digested by your cells, so maybe like a week after or something idk | 16:24 |
| @fenn | the reason i ask about cloning is if people start injecting themselves with lysate they might not know about endotoxin and so on | 16:24 |
| yashgaroth | well I am going to purify it | 16:24 |
| yashgaroth | endotoxin is fairly easy to separate from plasmid with the right protocols, as it turns out | 16:25 |
| @fenn | how do you get just plasmid dna and not genomic dna? (don't you need large quantities of DNA too?) | 16:25 |
| yashgaroth | genomic is harder to separate but it's usually only a tiny fraction, same with RNA | 16:26 |
| yashgaroth | current FDA regs are like 1% genomic, which is high, but the method I have access to is very good at separating that out too | 16:26 |
| AirmanEpic | might i ask what endotoxin is? | 16:26 |
| @fenn | AirmanEpic: bacterial cell wall material; it's inherently irritating to your immune system and can cause side effects | 16:27 |
| yashgaroth | damn your fast fingers, yes | 16:27 |
| AirmanEpic | how bad, and what can you do to prevent it? | 16:27 |
| AirmanEpic | bow shicka xD | 16:27 |
| yashgaroth | anything up to and including septic shock | 16:27 |
| AirmanEpic | oh shyt. | 16:27 |
| yashgaroth | I always wonder how heroin addicts get away with it since heroin ain't exactly endo-free | 16:28 |
| @fenn | honestly i dont know that much about it | 16:28 |
| @fenn | well heroin is a semi purified product | 16:28 |
| yashgaroth | sure, but they're handling it with their grubby fingers and filth-infested spoons and whatnot | 16:29 |
| @fenn | i mean it's not a bacterial culture lysate | 16:29 |
| yashgaroth | true, but anyway my previously mentioned method is capable of <1EU/mg easy | 16:29 |
| yashgaroth | nonetheless I'll need to hunt down some horseshoe crab blood to make sure | 16:30 |
| @fenn | how does EU compare to CFU or ng or whatever | 16:30 |
| yashgaroth | 1 EU is like 1ng or something, I'll check | 16:31 |
| yashgaroth | ah 5 EU/ng | 16:31 |
| yashgaroth | CFU is harder to compare | 16:31 |
| @fenn | 1 EU = "about 10^5 bacteria" | 16:31 |
| AirmanEpic | horseshoe crab blood... you put foreign cells in it and it clumps up, right? | 16:32 |
| yashgaroth | yes, it's the classic assay for endotoxin | 16:32 |
| yashgaroth | CFUs will be approximately 0 since the final DNA process uses ethanol, and I've purified plasmid hundreds of times from culture and not had any issue with contamination | 16:33 |
| yashgaroth | assuming a working tissue culture hood, which I'm buying for the diybio lab | 16:33 |
| @fenn | well sure, because most molecular protocols kill bacteria through sheer chemical harshness | 16:33 |
| @fenn | but the dead cells are still there | 16:34 |
| yashgaroth | sure, but you can reliably bind DNA to a resin and not endotoxins, then wash | 16:34 |
| @fenn | so do you think this method would work for any peptide hormone? | 16:35 |
| yashgaroth | depends on the peptide, but "probably" | 16:35 |
| @fenn | i'm personally more interested by HGH than myostatin | 16:36 |
| @fenn | of course you can just get HGH on the grey market | 16:36 |
| yashgaroth | still expensive as fuck | 16:36 |
| @fenn | yeah, so if you're taking it daily as anti-aging therapy it's not feasible with the current system | 16:36 |
| yashgaroth | problem is, I doubt many labs will sell you either the HGH gene or the primers to get it | 16:36 |
| yashgaroth | and even if you get the primers you still need a fresh human pituitary gland | 16:37 |
| AirmanEpic | is there something I can use to restrict hair growth for a long time, like 2-4 years, but not permanently? | 16:37 |
| yashgaroth | wax and lasers | 16:37 |
| @fenn | i thought those blacklists were only for bio weapons and smallpox etc | 16:37 |
| yashgaroth | HGH is anti-aging now? what the hell | 16:37 |
| @fenn | has been for some time | 16:37 |
| yashgaroth | sure but I'm not risking the DEA coming down on my ass | 16:37 |
| AirmanEpic | thanks yash xD | 16:37 |
| yashgaroth | the synthesis companies don't *have* to report it, but they might just for kicks | 16:38 |
| @fenn | well anyway the genome is known and gene synthesis is coming down in price | 16:38 |
| yashgaroth | coming down excruciatingly slowly | 16:38 |
| @fenn | but purified HGH is going UP in price | 16:38 |
| @fenn | same old prohibition story | 16:38 |
| yashgaroth | because they can (tm) | 16:39 |
| @fenn | who would they report it to anyway | 16:40 |
| yashgaroth | DEA handles HGH | 16:40 |
| yashgaroth | and they have a lot more guns than the FDA | 16:40 |
| @fenn | bizarre | 16:40 |
| @fenn | "co-sponsored by the Death Enforcement Administration" | 16:41 |
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| AirmanEpic | just head to nebraska and do it in an underground lab. They'd never find you. | 16:41 |
| @fenn | AirmanEpic: that's part of why we're working on a DIY DNA synthesizer | 16:42 |
| yashgaroth | once you have the gene it's no problem, the main concern is sourcing that | 16:42 |
| yashgaroth | I could just go to mexichina and do it there if I was that worried | 16:42 |
| AirmanEpic | DNA synthesis. How do you do that? | 16:43 |
| @fenn | what about site specific mutation of ... monkey pituitary or something | 16:43 |
| @fenn | nevermind that's stupid | 16:43 |
| @kanzure | AirmanEpic: http://diyhpl.us/wiki/dna-synthesis.html | 16:43 |
| yashgaroth | no, I considered it; that's a whole lot of mutations and the primers you need for that would also indicate you're working with HGH | 16:43 |
| @kanzure | AirmanEpic: http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf | 16:43 |
| AirmanEpic | holy wall of text *gets reading* | 16:43 |
| yashgaroth | even a 20 basepair primer for site mutations would pinpoint which gene you're working on | 16:44 |
| @fenn | oh, it's genomic so you don't need pituitary tissue | 16:45 |
| @fenn | *bonk* | 16:45 |
| yashgaroth | I meant pituitary so you could get the cDNA | 16:45 |
| yashgaroth | if you take it from genomic you'll just need a lot more incriminating primers | 16:45 |
| @fenn | huh? it's not rocket science to screen for the complementary sequence as well | 16:46 |
| yashgaroth | yeah, it's just a fuckton of sequencing and cloning and libraries | 16:46 |
| @fenn | hold on, let me read up on cDNA | 16:47 |
| @fenn | why can't you just clone the genomic DNA and let the target (human) cell do all the intron/exon crap after electroporation | 16:48 |
| @fenn | is it to get good expression? | 16:49 |
| yashgaroth | that would make the vector extremely large, which means low expression | 16:49 |
| yashgaroth | and still requires HGH-specific primers, which we're being paranoid about ordering | 16:49 |
| AirmanEpic | my cells can make copies of my genome all day long for $0.00001/genome. This shows that lower costs are at least imaginable. | 16:49 |
| AirmanEpic | xD | 16:49 |
| yashgaroth | copies are cheap | 16:50 |
| yashgaroth | the only way you'd be able to do it without ordering hgh-related primers is to make a library of all RNAs in a human pituitary, clone those into bacteria, and sequence several thousand until you find HGH | 16:51 |
| yashgaroth | maybe lower that to a few hundred with some creative size-based separation of the cDNAs | 16:52 |
| @kanzure | for the record, i never explored the costs or mechanisms of a non-microfluidic dna synthesizer so nobody should assume i covered those bases. | 16:52 |
| @fenn | iirc the main cost in bulk DNA synthesis was the initial five or six bottles of phosphoramidites | 16:53 |
| @fenn | the actual mixing and stirring is relatively inexpensive | 16:53 |
| @kanzure | no i mean the machines | 16:53 |
| @fenn | the machines dont come with reagents do they? | 16:53 |
| @kanzure | i haven't figured out if they are just extraordinarily expensive because of bullshit or if the components are actually really that expensive | 16:53 |
| yashgaroth | they do need to be fairly high-purity | 16:54 |
| @fenn | depends on how long the oligos you're making need to be | 16:54 |
| @kanzure | 'cause it might turn out that ubilding a bigger synthesizer might make more sense, especially since those sorts of components can be found at hardware stores | 16:54 |
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| yashgaroth | there's also the cost of sequencing each ~50bp fragment to make sure they're correct before you string them together | 16:54 |
| @fenn | just for cloning, not gene synthesis i meant | 16:55 |
| yashgaroth | oh, then it's much easier yeah | 16:55 |
| @fenn | gene synthesis is currently expensive for precisely this reason, the cost of bulk synthesis reagents | 16:55 |
| @kanzure | that doesn't explain why the machines cost a lot too | 16:56 |
| @fenn | oh that's just the usual business to business scam paradigm | 16:56 |
| AirmanEpic | Kanzure: how can you make channels that small? | 16:56 |
| yashgaroth | that seems odd since you use such a tiny amount, I mean you only need microgram yields on the oligo | 16:56 |
| @kanzure | lasers | 16:56 |
| @fenn | "call and ask us for a quote" | 16:56 |
| @fenn | yashgaroth: it's true, if there were a good method of accurately synthesizing micrograms of DNA it would drop the cost of gene synthesis | 16:57 |
| @fenn | this is what cambrian genomics is trying to do | 16:57 |
| yashgaroth | yes how is anselm these days | 16:57 |
| @fenn | i haven't talked to him for a long time | 16:57 |
| yashgaroth | I still have no idea exactly what technique(s) they're using so I can't really say how realistic or useful his methods will be | 16:58 |
| yashgaroth | except the whole lasers thing | 16:58 |
| @fenn | i kind of want to go back to the bay area, but so do 9 million new yorkers | 16:58 |
| AirmanEpic | Does DIYbio have the equipment to make that? | 16:58 |
| @kanzure | AirmanEpic: http://diyhpl.us/laser_etcher/laser_etcher | 16:58 |
| eudoxia | hi AirmanEpic | 16:59 |
| eudoxia | welcome | 16:59 |
| AirmanEpic | oh thanks eudo. | 16:59 |
| AirmanEpic | I'm stefan, I'm very, very new at biohacking but would like to get further into it | 16:59 |
| @fenn | yashgaroth: they're doing UV directed synthesis on beads, then sequencing each bead (which should be a single strand that's been cloned on the surface of the bead) to verify that each oligo is correct | 16:59 |
| eudoxia | hi cpopell, sorry about your job | 17:00 |
| yashgaroth | single strand, as in single molecule per bead? | 17:00 |
| @fenn | yes at first | 17:00 |
| @fenn | you can't sequence a single molecule though so they amplify it on the bead | 17:00 |
| @fenn | it's like having a lot of little wells on a plate, but you use beads instead of wells | 17:01 |
| @fenn | i forget the buzzword | 17:01 |
| @fenn | clonal amplification? | 17:01 |
| yashgaroth | sure, but I mean they'd need to have literally a single molecule that gets amplified, otherwise you can't get an accurate read on the sequence | 17:01 |
| AirmanEpic | still in awe of this picture. http://gyazo.com/e5c31102fbcaf21f99c27f8256ad3a60. all you'd really need to do is laser ech a whole bunch of super thin slides | 17:02 |
| yashgaroth | I can see what they're going for, just seems like several technologies that we don't have need to come together | 17:03 |
| @fenn | apparently everything is standard tech in sequencers already | 17:03 |
| @fenn | except for the bead handling | 17:03 |
| yashgaroth | well you can do single-molecule sequencing, sort of/sometimes | 17:04 |
| @fenn | "All second-generation platforms (except Helicos) rely on some clonal amplification method. Bridge amplification (two-dimensional PCR)" | 17:04 |
| @fenn | http://seq.molbiol.ru/sch_clon_ampl.html has some nice drawings | 17:05 |
| yashgaroth | I've still no idea how they ensure literally a single strand is grown on each bead | 17:05 |
| yashgaroth | how do you enforce a single atomic nucleation point | 17:06 |
| @fenn | uh, i could be wrong about the process | 17:06 |
| yashgaroth | this is why I wish he'd release some info, though I grudgingly accept why he doesn't | 17:07 |
| @fenn | this say they use emulsion PCR http://www.laserfocusworld.com/blogs/spectralbytes/2012/12/how-laser-printing-builds-dna.html | 17:07 |
| @fenn | oh i get it | 17:08 |
| @fenn | 1) synthesize dna on a plate 2) release dna into solution 3) bind single molecule to bead | 17:08 |
| yashgaroth | it's the " single molecule to bead" part that gets me | 17:08 |
| @fenn | that's just statistics | 17:08 |
| @fenn | if you have two dissimilar sequences on a single bead your sequencing comes out as garbage | 17:09 |
| @fenn | so aim to have just enough dna in solution that you aren't wasting beads by letting them go empty, but not too much to keep from having more than one strand per bead | 17:09 |
| yashgaroth | even cutting-edge single-molecule sequencing still has an obscenely high error rate what with the signal/noise | 17:10 |
| @fenn | you sequence multiple points in the gene synthesis assembly process, so that should weed out any PCR errors | 17:11 |
| yashgaroth | but you're relying on reads on the short oligos to determine which ones to use for the longer gene synthesis | 17:11 |
| @fenn | yes, and you sequence the larger constructs too | 17:12 |
| yashgaroth | and with the short oligos on beads you either have a crappy signal from single-molecule, or you have ambiguity about which sequence you get by using multiple templates | 17:12 |
| yashgaroth | in that case it's just traditional gene synthesis at a smaller scale | 17:12 |
| @fenn | hm | 17:13 |
| yashgaroth | he's a smart guy and so is Church, so hopefully they have something | 17:14 |
| @fenn | i assume the error rate of new polymerases is lower than the error rate of UV directed synthesis | 17:14 |
| yashgaroth | it's not the polymerase you have to worry about, it's the signal-reading method | 17:14 |
| yashgaroth | assuming you even have a single molecule that's bound to a trackable bead, your read won't be more accurate than your synthesis process | 17:15 |
| @fenn | of course | 17:16 |
| @fenn | wait, don't you mean "read wont be more accurate than your amplification process" | 17:16 |
| yashgaroth | pcr amplification is pretty okay with new high-fidelity polymerases, like 1/30,000bp or something | 17:17 |
| yashgaroth | the error rate, that is | 17:17 |
| @fenn | sure but if you're amplifying 10^5 times it adds up | 17:17 |
| yashgaroth | yes and that's another problem, but since those errors are distributed across many molecules you still get a clean read | 17:17 |
| yashgaroth | randomly across many molecules, I should say | 17:18 |
| @fenn | okay so what's the problem | 17:18 |
| @fenn | that there's no single perfect gene anywhere? | 17:18 |
| yashgaroth | well you've got your single molecules, and you bind them to single beads somehow: any sequencing method you use on them won't be accurate enough to rely on | 17:18 |
| yashgaroth | so you shuttle in the "good" ones for gene synthesis, but that makes it no better than traditional methods | 17:19 |
| @fenn | oh, btw you can use yeast cloning which has fantastically low error rates | 17:19 |
| yashgaroth | even e.coli has super-low error rates | 17:19 |
| yashgaroth | the errors come from the CCD or nanopore or whatever method you use | 17:20 |
| @fenn | sure, so once you've got something large enough that it makes sense to clone, you clone it and then sequence it, and all the DNA in that blob of goo is the same sequence | 17:20 |
| yashgaroth | cloning into a cell is gonna be extremely involved with that many sequences, and no one's really miniaturized it | 17:21 |
| @fenn | the longer the sequence the more likely it has an error, so it's a tradeoff between cost of synthesis and cost of cloning | 17:21 |
| @fenn | i'm not worried about sequencing fidelity | 17:22 |
| yashgaroth | you should be | 17:22 |
| yashgaroth | and that's traditional synthesis, where they get a 50bp oligo and clone+sequence it before moving it into a larger assembly anyway | 17:22 |
| @fenn | sequencing read errors are random error, not systematic error | 17:22 |
| yashgaroth | well, usually, but yes | 17:23 |
| @fenn | why bother cloning a 50bp sequence? just pretend it's good and concatenate enough oligos until you start getting errors | 17:23 |
| yashgaroth | that's what trad methods probably do these days anyway, I don't know | 17:24 |
| @fenn | the other thing you're forgetting is this is happening massively parallel, there's no need to miniaturize the cloning step | 17:25 |
| yashgaroth | if they can get a single molecule+bead into a well, and then amplify it, and then sequence that amplification product, then it'd work, so that's what I assume they're doing | 17:25 |
| yashgaroth | massively parallel, *and* disruptive? my god | 17:25 |
| @fenn | heh | 17:25 |
| yashgaroth | all they need is some genetic algorithms and bam | 17:26 |
| @fenn | heh | 17:26 |
| @fenn | grr | 17:26 |
| yashgaroth | I guess my main concern is their ability to get single molecules onto single beads | 17:26 |
| yashgaroth | I don't know how the hell they catalyze single sites, and/or ensure that's happening reliably enough to count on | 17:27 |
| @fenn | no that's not what's happening | 17:27 |
| yashgaroth | then [my previous concerns] | 17:27 |
| @fenn | you UV synthesize on a plate, then transfer individual molecules to beads | 17:27 |
| yashgaroth | how do they get a bead with a single functional group on the whole bead | 17:28 |
| @fenn | the bound oligos are amplified on the bead surface with "2d" surface-bound pcr | 17:28 |
| yashgaroth | yes that part works in my mind | 17:28 |
| @fenn | generic primers are bound to the bead surface | 17:28 |
| yashgaroth | sure you can use vanishingly small concentrations of DNA to hope that only one binds per bead, but that sounds like a technical clusterfuck | 17:29 |
| @fenn | 33% of the time there's nothing on the bead but primers, 50% of the time there's one molecule, the rest of the time there's more than one molecule (numbers made up for conversation's sake) | 17:30 |
| yashgaroth | but it's more like 99.9% have nothing but primers | 17:30 |
| @fenn | why you say that? | 17:30 |
| yashgaroth | because otherwise you'd end up with 99.9% having 2+ molecules | 17:31 |
| yashgaroth | this is where the money would be going, not the PCR steps | 17:31 |
| -!- lolcat is now known as Mikel | 17:31 | |
| @fenn | i'm really not sure how the statistics work out here | 17:31 |
| yashgaroth | everything after "single molecules on single beads" is relatively simple | 17:32 |
| yashgaroth | I don't do statistics I'm a biologist | 17:32 |
| @fenn | in the article it says "synthesize 10^6 oligos, sequence 10^9 beads, laser eject 10^6 beads" | 17:32 |
| @fenn | so you're right, 99.9% of the beads are wasted | 17:32 |
| @fenn | how many nines is that | 17:32 |
| yashgaroth | ok if they're categorizing and saving each single-molecule bead I can see it working, where they just build libraries of single sequences | 17:33 |
| yashgaroth | and dole them out as needed for a gene, like what our project is hopefully going to do | 17:33 |
| yashgaroth | also, 10^9 sequences per oligo seems expensive compared to traditional methods, no matter how massively parallel it is | 17:34 |
| @fenn | yeah i don't really get that part | 17:34 |
| yashgaroth | or 10^6 whatever it's still a lot | 17:34 |
| @fenn | maybe they meant "stain for DNA" | 17:35 |
| yashgaroth | nah it still needs to be sequenced, I'd think | 17:35 |
| yashgaroth | oh right for determining which beads have DNA, then yeah maybe | 17:36 |
| @fenn | dont you love publically funded science | 17:36 |
| yashgaroth | haha | 17:36 |
| @fenn | :( | 17:36 |
| AirmanEpic | @fenn, if you have .1% of all your beads wasted, isn't it easy to copy the working ones? | 17:36 |
| AirmanEpic | sorry 99.9% wasted | 17:37 |
| @fenn | AirmanEpic: sort of, there's still the problem of polymerase errors in amplifying the single molecule | 17:38 |
| AirmanEpic | What is a polymerase? | 17:39 |
| yashgaroth | oh dear | 17:39 |
| @fenn | an enzyme that copies DNA | 17:39 |
| @fenn | but if you don't know that you aren't going to understand what we're talking about anyway | 17:39 |
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| AirmanEpic | =/ I'm trying but I really suck at memorizing all the terms | 17:40 |
| @kanzure | ArmilusDajjal: http://www.youtube.com/watch?v=teV62zrm2P0 | 17:40 |
| yashgaroth | it's not about memorizing, it's about 'oh good there's a word for this thing so I don't need to use 10 words to describe it each time' | 17:40 |
| AirmanEpic | it's always a freakin long and latinish name. | 17:41 |
| yashgaroth | 4 years of latin did spoil me, I'll admit | 17:41 |
| AirmanEpic | why can't we just be like coding. "oh, that's a copier" | 17:41 |
| @fenn | huh they actually sequence the beads on the slide | 17:41 |
| yashgaroth | kanzure I think you username-autofinished one too few/many times | 17:41 |
| ArmilusDajjal | lol | 17:42 |
| @kanzure | yashgaroth: ? | 17:42 |
| yashgaroth | yes but once you get a hundred different enzymes "copier" becomes too simplistic | 17:42 |
| @kanzure | oh right | 17:42 |
| @kanzure | AirmanEpic. | 17:42 |
| AirmanEpic | oh yes, I get it. I remember this from high school now | 17:42 |
| AirmanEpic | just didn't remember the term | 17:42 |
| @kanzure | you went to high school? get the hell out. | 17:43 |
| @fenn | AirmanEpic: there actually is a naming system that makes a bit of sense.. usually the enzyme is named after its substrate, and ends with -ase | 17:43 |
| AirmanEpic | Gah damng it | 17:43 |
| AirmanEpic | dang it* | 17:43 |
| AirmanEpic | sorry fenn, I gotta run 'cause I went through highschool. | 17:43 |
| @fenn | it's actually called "DNA polymerase" | 17:43 |
| AirmanEpic | and there are multiple polymerases? dear god | 17:44 |
| @fenn | there's RNA polymerase, and about ten different versions of each | 17:45 |
| AirmanEpic | my dreams of world domination may have to wait for a while while I wrap my head around these terms | 17:45 |
| AirmanEpic | and the concepts | 17:45 |
| yashgaroth | it happens | 17:45 |
| yashgaroth | but hey I don't know the difference between the many types of RNA pol, because fuck that, I can look it up | 17:46 |
| yashgaroth | also because I don't really work with RNA, thank fuck | 17:46 |
| @fenn | fuck welcomes you | 17:47 |
| yashgaroth | RNA is just an annoying intermediate between the glorious DNA and proteins, but that's a whole other thing | 17:47 |
| @fenn | i think you've got it backwards | 17:48 |
| @fenn | DNA is just an annoying intermediate between RNA and proteins :P | 17:48 |
| AirmanEpic | fuck has been really active today | 17:48 |
| yashgaroth | "ooh look at me I'm RNA I can carry information and perform enzymatic functions" well that's what DNA and proteins are for you asshole RNA | 17:49 |
| yashgaroth | p.s. fuck | 17:49 |
| @fenn | maybe you can invent DNA based life and shock the world | 17:50 |
| yashgaroth | wow I am bizarrely biased against a molecule | 17:50 |
| @fenn | straight from genome to protein in one step | 17:50 |
| AirmanEpic | nah, I feel like DNA based life is a little too over the top | 17:51 |
| AirmanEpic | like hipster glasses | 17:51 |
| @fenn | you'd have to have a very wide array of promoters to make different amounts of protein | 17:52 |
| @fenn | also there's that whole tRNA thing | 17:52 |
| yashgaroth | 5' UTRs and RNAi are just RNA's way of trying to keep itself relevant | 17:53 |
| yashgaroth | yeah it's not a realistic proposal, my plan of a superior DNA->protein master race will have to wait | 17:53 |
| @fenn | you're so eukaryo-centric | 17:53 |
| yashgaroth | nuclei4lyfe | 17:53 |
| @fenn | how can you have a dna based life with a nuclear membrane? it's hopeless | 17:54 |
| yashgaroth | it's an RNA conspiracy | 17:54 |
| @kanzure | check the eukaryotic privilege | 17:54 |
| @fenn | yashgaroth: so i guess they can sequence 10^6 beads at once because there's enough optical signal from millions of oligos on each bead | 17:59 |
| @fenn | pacific bio had problems with optical SNR because they were doing single molecule sequencing | 18:00 |
| yashgaroth | yeah it's probably something like pacbio's deal | 18:00 |
| yashgaroth | I don't know about millions if they only have a single template molecule though | 18:00 |
| yashgaroth | it just seems like the kind of thing they'd need millions for to get the whole thing working | 18:01 |
| yashgaroth | millions of $ I mean | 18:01 |
| @fenn | it's pyrosequencing | 18:01 |
| @kanzure | "This weekend is Ushicon, an 18+ anime convention. By 18+, we mean *no teenagers*, not adult content. This will be held from Feb 8 to 10 in Round Rock, TX. | 18:02 |
| @kanzure | It'll be fun." | 18:02 |
| @kanzure | do i dare.. | 18:02 |
| yashgaroth | uguu~~ | 18:02 |
| yashgaroth | also, more like 10s-100s of million $s | 18:02 |
| @fenn | do you have a sailor moon costume :\ | 18:03 |
| @fenn | yashgaroth: why would you need that much money for development? | 18:03 |
| yashgaroth | because biotech | 18:03 |
| @fenn | to pay 5 guys and their robots? | 18:04 |
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| yashgaroth | well sure if they want to take a hundred years to develop it | 18:04 |
| @fenn | money doesn't automatically speed things up | 18:05 |
| yashgaroth | it don't hurt | 18:05 |
| yashgaroth | I kind of feel like all this speculating is for naught when I don't have access to their specific methods | 18:06 |
| @fenn | it does if you lose all your equity | 18:06 |
| yashgaroth | I don't really know what equity is, so | 18:06 |
| @fenn | stock in your own company | 18:06 |
| yashgaroth | oh, yeah | 18:07 |
| yashgaroth | well I wish them the best of luck | 18:07 |
| @fenn | VC's don't just give you money, they buy stock. if you sell all your stock you don't get rich when the company goes big (presumably when you're done making X gizmo work) | 18:07 |
| yashgaroth | oh right the whole rich thing | 18:08 |
| @fenn | there's also maintaining control of your company | 18:09 |
| yashgaroth | see this is why I'm not in business...this and many other reasons | 18:11 |
| @fenn | this is a bit ridiculous (list of companies co founded by george church) http://arep.med.harvard.edu/gmc/tech.html | 18:12 |
| yashgaroth | he really needs to get around to adding this channel to that list | 18:13 |
| @kanzure | he probably doesn't remember that he handed me a penny at a conference in 2009 | 18:13 |
| yashgaroth | maybe we could work out a deal with just his beard | 18:13 |
| yashgaroth | legally it operates independently of his body | 18:14 |
| @fenn | aubrey de grey has a patent on autonomous beard technology | 18:14 |
| yashgaroth | aubrey is simply a puppet for his sweet beard | 18:14 |
| @fenn | then the beard has the patent | 18:14 |
| yashgaroth | I'm no expert in beard law | 18:15 |
| @kanzure | http://diyhpl.us/~bryan/irc/aubrey.jpg | 18:15 |
| @fenn | hey it's not any crazier than patenting genomes | 18:15 |
| @kanzure | ah he's on the board of sigma and NEB | 18:17 |
| @kanzure | pfft "Edge Foundation 1988 (2005-present; science communication) " | 18:17 |
| @fenn | jealous? | 18:17 |
| @fenn | you could be part of the "third culture" | 18:17 |
| @kanzure | :( | 18:17 |
| @kanzure | i | 18:18 |
| @kanzure | i'm gestalt, i swear. | 18:18 |
| yashgaroth | oh huh cambrian is listed under "past advisory roles", 2011-2012 | 18:18 |
| @kanzure | third culture always sounded like protoculture to me | 18:18 |
| @kanzure | yashgaroth: interesting detail | 18:19 |
| @kanzure | he is still listed on | 18:19 |
| @kanzure | https://angel.co/cambrian-genomics | 18:19 |
| @fenn | church was estimating $1500 per genome (40x coverage) in 2009, what happened there? | 18:19 |
| yashgaroth | I've no idea what that means, but george church getting *out* of an advisory role must take something serious, considering | 18:20 |
| @kanzure | we should track changes to this page. he seems to keep it somewhat updated. | 18:21 |
| yashgaroth | fenn: that's black market prices, I've got a guy in hong kong who can sequence your genome for $1000 no questions asked | 18:21 |
| @kanzure | well fuck you too | 18:21 |
| @kanzure | i'll take one | 18:21 |
| @kanzure | what coverage? | 18:21 |
| yashgaroth | oh you know, enough | 18:21 |
| @fenn | he was estimating consumable costs and with labor it's more like $4k | 18:22 |
| @fenn | "for bulk orders of 50 or more" | 18:22 |
| yashgaroth | also the 'no questions asked' part was on the consumer end | 18:22 |
| @fenn | hm? | 18:23 |
| yashgaroth | oh, nothing | 18:23 |
| @fenn | like if you have obama's napkin or something? | 18:23 |
| yashgaroth | guys don't worry, the government sequenced everyone's genomes back in the 2000s as part of operation Omeg | 18:24 |
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| yashgaroth | :V | 18:24 |
| -!- kanzure changed the topic of ##hplusroadmap to: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA | http://gnusha.org/logs http://diyhpl.us/wiki http://groups.google.com/group/diybio | banned by the Federal Death Administration | 3.5 kidneys for sale | no questions asked | 18:24 | |
| AirmanEpic | can I get a third of a kidney please? | 18:25 |
| yashgaroth | 'federal death administration' sounds like an alex jones thing, I wonder if we could get him to sponsor as well | 18:25 |
| @kanzure | yashgaroth: sadly people might take that one seriously, so no thanks | 18:25 |
| yashgaroth | heh | 18:25 |
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| @kanzure | gene_hacker: welcome back | 18:57 |
| gene_hacker | kanzure is this article paywalled for you? :http://nar.oxfordjournals.org/content/32/18/5409.full | 19:00 |
| gene_hacker | anyway, I just figured something out | 19:02 |
| @kanzure | paperbot: http://nar.oxfordjournals.org/content/32/18/5409.full | 19:02 |
| gene_hacker | you know that microfluidics thread in diybio where they showed you can use a diy laser cutter to make microfluidics? | 19:02 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences.pdf | 19:02 |
| gene_hacker | it should be free isn't it? | 19:02 |
| @kanzure | hey wait i published in this journal before | 19:02 |
| gene_hacker | what? | 19:03 |
| @kanzure | this is nar | 19:03 |
| gene_hacker | oh on aptamers? | 19:03 |
| @kanzure | nah on bioinformatics things | 19:03 |
| @kanzure | anyway that paper seems to be open access | 19:03 |
| gene_hacker | anyway, that diy lasercutter has sufficient resolution to make a kilobase level DNA synthesizer | 19:03 |
| @kanzure | also it's in my collection already, | 19:04 |
| @kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf | 19:04 |
| gene_hacker | figured as much | 19:04 |
| @kanzure | gene_hacker: have you seen http://diyhpl.us/laser_etcher/laser_etcher | 19:04 |
| gene_hacker | hacketeria laser cutter is simpler | 19:05 |
| @kanzure | it had a cutting area of only 45 mm^2 | 19:05 |
| @kanzure | is this it? http://hackteria.org/wiki/index.php/DIY_Micro_Laser_Cutter | 19:06 |
| gene_hacker | yup | 19:06 |
| gene_hacker | it is sufficient for microfluidics | 19:06 |
| @kanzure | nmz787: are you around? | 19:06 |
| AirmanEpic | man, that's sweet. Do you just epoxy each layer of glass together? | 19:07 |
| gene_hacker | nah, you use pdms and electrical tape | 19:08 |
| gene_hacker | though I wonder if the process could be adapted to use something more solvent resistant | 19:08 |
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| @kanzure | gene_hacker: there are other things worth reading here, http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/ | 19:26 |
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| gene_hacker | picoarray is nice because it's massively parallel | 19:39 |
| gene_hacker | and uses up very small amounts of oligos | 19:39 |
| @kanzure | damn it i should seriously stop writing annotations about papers in irc, it makes it hard to find my notes | 19:40 |
| @kanzure | 16:18 < kanzure> ok i don't get it. xeotron made this microfluidic picoarray dna synthesizer in 2003ish | 19:41 |
| @kanzure | 16:18 < kanzure> had $45mil in sales | 19:41 |
| @kanzure | 16:18 < kanzure> got bought by invitrogen. and now no such product is on the market. | 19:41 |
| @kanzure | 16:18 < kanzure> warning: this paper is written very poorly | 19:41 |
| @kanzure | also you mentioned this same paper last year | 19:43 |
| @kanzure | http://gnusha.org/logs/2012-01-25.log | 19:43 |
| @kanzure | also here's a new compressed archive of logs, | 19:50 |
| @kanzure | http://gnusha.org/logs/archives/hplusroadmap-2013-02-02.tar.gz | 19:50 |
| @kanzure | http://gnusha.org/logs/archives/ | 19:50 |
| @kanzure | also here's a new dump of links from the logs, | 19:55 |
| @kanzure | http://gnusha.org/logs/meta/hplusroadmap-2013-02-02-links.url.txt | 19:55 |
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| @kanzure | "Reality must take precedence over public relations." - RICHARD FUCKING FEYNMAN | 20:14 |
| @kanzure | argument from authority, but bite me | 20:14 |
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| @kanzure | "Trust me, if dental composites took 15 minutes to cure, or had to be baked at all, no dentist would ever use them. A typical dental composite might take under a minute's exposure to high-intensity blue light. Other systems can be much, much faster." | 20:32 |
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| heath | humor (scene from time bandits) :: http://www.youtube.com/watch?v=R6OKLgLZHFk | 21:37 |
| @kanzure | more javascript funkery http://christmasexperiments.com/23/ | 21:44 |
| @kanzure | http://christmasexperiments.com/23/js/ | 21:49 |
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| nmz787 | kanzure: back | 22:32 |
| @kanzure | gene_hacker: are you still around? | 22:33 |
| @kanzure | i wanted you two to meet a while ago | 22:33 |
| @kanzure | hrm well whatever. i think he's gone. | 22:34 |
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| nmz787 | hmm | 22:37 |
| @kanzure | i talked with my photopolymer guy | 22:39 |
| @kanzure | (david treadwell) | 22:39 |
| @kanzure | " can shop around, but the price seems reasonable for small-quantity purchases." | 22:39 |
| @kanzure | "I'd be interested exploring this further. If there is sufficient need in the community, I could work on a public-domain produce. I currently lack the facilities to do such formulation, however." | 22:39 |
| @kanzure | "I recall from some work I did ten years ago that making a decent UV/vis cure polymer is not especially involved, but the intricacies of making a polymer system which works in a rapid prototyping environment would take some experimentation." | 22:39 |
| @kanzure | nmz787: do you have anything you would say in response? i'm at least going to tell him "YES DO IT". | 22:40 |
| nmz787 | I dunno, I found a place offering 3D printable UV polymer for ~$250 per gallon | 22:42 |
| @kanzure | bucktown was $150/gal | 22:43 |
| nmz787 | was it? | 22:43 |
| @kanzure | maybe i didn't check the right product | 22:43 |
| nmz787 | this is prob what i'm gonna try out first http://www.solarez.com/productsnew/fly_tie_uv_resin_thin.html | 22:43 |
| nmz787 | bucktown was : gallon of vis curable $235, gallon of UV curable $1040 | 22:44 |
| @kanzure | what. | 22:44 |
| nmz787 | and sigma was around $1100 per gallon | 22:44 |
| nmz787 | kanzure: you can add to cart on their site to see prices | 22:44 |
| @kanzure | have we done any estimates on how much we would use per prototype? | 22:44 |
| nmz787 | very little | 22:45 |
| nmz787 | lemm calc | 22:45 |
| @kanzure | yeah but is 1 gallon only enough for 100 prototypes? 1000? | 22:45 |
| @kanzure | k | 22:45 |
| nmz787 | (50 microns) * (2 cm) * (2 cm) = 0.02 milliliters | 22:45 |
| @kanzure | haha | 22:45 |
| nmz787 | 189270.5892 prototypes per gallon at that rate | 22:46 |
| @kanzure | i'm not sure we'll be doing 50 microns, let's say we are sloppy and we pour enough for 500 microns | 22:46 |
| @kanzure | ok, 18927 prototypes | 22:46 |
| nmz787 | 1 gallon / (200 microns * 4 cm * 4 cm) = 11829.411825 | 22:46 |
| nmz787 | that's 2.2 cents each | 22:47 |
| nmz787 | so if you didn't need to prototype, like you were using a proven design, that seems pretty cheap | 22:47 |
| nmz787 | <10 cents for a multilayer design | 22:47 |
| nmz787 | plus PDMS costs of course | 22:48 |
| nmz787 | PDMS looks cheaper | 22:49 |
| nmz787 | http://www.amazon.com/Sylgard-Solar-Encapsulation-Making-Panels/dp/B004IJENBG | 22:49 |
| nmz787 | gonna assume that's 500mL worth | 22:49 |
| @kanzure | oh right spincoating | 22:50 |
| nmz787 | so at that price it's around 3.9 cents per PDMS prototype | 22:50 |
| @kanzure | how do you spincoat a visible curable polymer safely? | 22:51 |
| @kanzure | keep the spincoater dark? | 22:51 |
| nmz787 | red light | 23:01 |
| nmz787 | 'dark room lighting; | 23:01 |
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| gene_hacker | you called kanzure? | 23:26 |
| @kanzure | gene_hacker: yo meet nmz787, he's doing microfluidics/photocurable stuff | 23:29 |
| gene_hacker | with a DLP? | 23:29 |
| @kanzure | well sort of, i was supposed to buy him a dlp yesterday but i flaked out | 23:30 |
| gene_hacker | Oh, Nathan McCorkle | 23:30 |
| gene_hacker | you really should use a DL:P, met a german guy who hooked one up to a microscope to do micron sized printing | 23:31 |
| nmz787 | hi gene_hacker | 23:32 |
| gene_hacker | though, you might need to use some exotic stuff if you're going to run solvent resistant stuff | 23:32 |
| gene_hacker | sup | 23:32 |
| nmz787 | no need for solvent resistance | 23:32 |
| nmz787 | since i'm just gonna use the DLP printed stuff to cast PDMS on top | 23:32 |
| gene_hacker | so a one shot? | 23:32 |
| gene_hacker | PDMS is far from solvent resistant from what I've read | 23:33 |
| nmz787 | nah, expose then cure photoresin, lay PDMS on top, cure, peel, attach layers, hook up to macro | 23:33 |
| nmz787 | depends what solvent | 23:33 |
| nmz787 | for most of what I am aiming for, I can use PDMS no prob | 23:34 |
| gene_hacker | for DNA synthesis? | 23:34 |
| nmz787 | yes | 23:34 |
| gene_hacker | what type? | 23:34 |
| nmz787 | phosphoramidite | 23:35 |
| gene_hacker | well, if you're going to make a high resolution DLP system for curing photopolymer, you really should look into making a picoarry | 23:36 |
| nmz787 | hah | 23:36 |
| nmz787 | no way | 23:36 |
| nmz787 | i want to output >1kb DNA strands, not oligos | 23:37 |
| gene_hacker | in one step? | 23:38 |
| gene_hacker | without putting different strands together? | 23:38 |
| nmz787 | no | 23:38 |
| @kanzure | army.mil vulnerabilities http://pastebin.com/Cpgp9jHE | 23:39 |
| nmz787 | no, around 30 or 50bp is what i'm targeting for onchip oligos | 23:39 |
| gene_hacker | because otherwise, you can do the same with picoarrays can you not? | 23:39 |
| nmz787 | pico arrays are just microarrays, right? | 23:40 |
| @kanzure | no, he's referring to a specific paper | 23:40 |
| nmz787 | photobased synthesis? | 23:40 |
| gene_hacker | yes | 23:40 |
| @kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf | 23:40 |
| gene_hacker | but without fancy photolabile bases | 23:40 |
| gene_hacker | you use photogenerated acid instead | 23:40 |
| @kanzure | iirc this was a continuous flow device | 23:41 |
| nmz787 | nope wasn't planning on using photoacid | 23:42 |
| nmz787 | (haven't seen photolabile bases actually) | 23:42 |
| nmz787 | I think i saw something about photo-based activation being less efficient | 23:43 |
| @kanzure | gene_hacker: we were thinking of using bubbles to store beads with library dna | 23:43 |
| nmz787 | I can't really remember why i stopped considering it | 23:43 |
| nmz787 | but the reaction is pretty simple, so adding one extra valve seems trivial to me | 23:43 |
| gene_hacker | where you have nxn combinations of every possible DNA sequence and put them together right? | 23:44 |
| @kanzure | yes that type of library | 23:44 |
| @kanzure | of course, a basic oligo synthesizer would also be worth working on | 23:44 |
| nmz787 | also i am not considering continuous-flow | 23:44 |
| gene_hacker | are you sure that's going to scale well? | 23:45 |
| nmz787 | pretty sure, i have a few specific ideas on reducing the error rate of each oligo | 23:45 |
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| nmz787 | and there's been a lot of single-molecule work done, so each reactor can be really small, so you gain in parallelizing | 23:46 |
| nmz787 | not that i will be requiring single molecules | 23:46 |
| nmz787 | or aiming for work with thm | 23:46 |
| nmz787 | them | 23:46 |
| @kanzure | nmz787: is there any particular reason that neither of us has checked in how much it would cost to build a more traditional synthesizer? | 23:47 |
| nmz787 | i'm probably going to try using DLP to make molds that get edited with a FIB for nano features | 23:47 |
| gene_hacker_ | what sort of nanofeatures? | 23:48 |
| nmz787 | kanzure: reagent costs will go up, we won't really gain any benefit over existing systems | 23:48 |
| gene_hacker_ | and why? | 23:48 |
| nmz787 | nanocapillaries mainl | 23:48 |
| nmz787 | you can do gel-free separations | 23:48 |
| nmz787 | or pull a growing molecule back into a nanochannel to hide it from the active chemistry | 23:49 |
| gene_hacker_ | ok now that's neat | 23:49 |
| nmz787 | a significant error contributor is damage to early-added nucleotides | 23:49 |
| gene_hacker_ | is that actually done? | 23:49 |
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| @kanzure | cost per bp would be closer to existing systems, but the benefit is that we'd have an open source synthesizer (and one that might be slightly more practical to build for others who don't have a dlp setup) | 23:49 |
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| nmz787 | i think i read about someone mentioning it would help | 23:50 |
| nmz787 | kanzure: DLP is on everycraigslist | 23:50 |
| @kanzure | why early-added in particular ? | 23:50 |
| gene_hacker | how do you pull the DNA in and out? electrical charge? | 23:50 |
| nmz787 | well because they're gonna see more chances to interact | 23:50 |
| nmz787 | yeah electric | 23:50 |
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| nmz787 | you could also use an optical trap, but i have not looked into that | 23:51 |
| nmz787 | as it requires some fancy-ish optics | 23:51 |
| gene_hacker | now if only you could pull the DNA with varying degrees, you could make a DNA origami nanomechanism | 23:54 |
| @kanzure | diybio-eu is trying to decide on logos | 23:55 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo01.jpg | 23:55 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo02.jpg | 23:55 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo03.jpg | 23:55 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/diybio-eu-logo04.jpg | 23:55 |
| @kanzure | paperbot: http://www.sciencedirect.com/science/article/pii/S0962892402023516 | 23:57 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Chromosome%20positioning%20in%20the%20interphase%20nucleus.pdf | 23:57 |
| --- Log closed Sun Feb 03 00:00:49 2013 | ||
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