| --- Log opened Fri Apr 12 00:00:55 2013 | ||
| @kanzure | someone stole my fucking github contributions calendar idea https://github.com/will | 00:08 |
|---|---|---|
| @kanzure | release the pitchforks | 00:08 |
| @kanzure | oh well at least he did it better | 00:10 |
| brownies | what does it say? | 00:24 |
| brownies | oh. "Will" ? | 00:24 |
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| @kanzure | brownies: seems to. | 00:32 |
| @kanzure | or possibly illwi | 00:32 |
| brownies | ah yes. that does make more sense. | 00:39 |
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| @kanzure | kajetan: hello. | 10:53 |
| eudoxia | so kanz now that you've been outdone, what was your github contributions calendar thingee supposed to say? | 11:03 |
| @kanzure | "HIRE ME" but then i realized that was the last thing i wanted | 11:03 |
| eudoxia | hehe | 11:03 |
| brownies | "HIRE ME BUT ONLY IF THE JOB MEETS THE FOLLOWING EIGHT QUALIFICATIONS:" | 11:03 |
| @kanzure | also his idea of using gradients is better than my idea of just doing darker cells | 11:03 |
| eudoxia | and inject a little javascript that hacks the canvas and makes the text scroll | 11:04 |
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| @archels | https://gist.github.com/anonymous/5374094 | 11:29 |
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| @kanzure | /win 13 | 12:05 |
| @kanzure | aacckkk | 12:05 |
| @ParahSailin | needs to be a way to use alt- something to get past window 10 | 12:07 |
| @kanzure | there is. you can use alt-letters. | 12:11 |
| @kanzure | except they are sometimes mapped to gnome things. | 12:11 |
| @kanzure | also alt-n is mapped to actual windows in my terminal. | 12:12 |
| kajetan | kanzure, hi, hello | 12:53 |
| jrayhawk | archels: the Surface Pro looks okay | 12:57 |
| jrayhawk | Chromebook Pixel might also do | 13:00 |
| @archels | jrayhawk: thanks, but it violates the storage space requirement | 13:00 |
| @archels | yeah the Pixel would be really nice, but it's not available yet in NL | 13:00 |
| jrayhawk | oh, right, missed that part. sorry. | 13:00 |
| jrayhawk | high density displays are hard to find on the x86 market :( | 13:01 |
| jrayhawk | i guess there's also the macbook pro 13" retina displays | 13:02 |
| @archels | yep, but no touchscreen | 13:02 |
| @fenn | why "no USB 2.0 ports" | 13:03 |
| @archels | I think that 1920x1080 will probably be sufficient for 13.3" and below though | 13:03 |
| @archels | because USB 3.0 | 13:03 |
| @archels | I don't want to invest in already-outdated hardware | 13:03 |
| jrayhawk | Is x86 actually a requirement? There's crap like the Transformer Pad Infinity | 13:04 |
| jrayhawk | oh, i guess that's bettery under the screen | 13:06 |
| jrayhawk | nevermind | 13:06 |
| @archels | sadly Windows 8 does not run natively on ARM yet | 13:08 |
| @archels | s/yet// | 13:09 |
| jrayhawk | SVZ131190X? | 13:10 |
| jrayhawk | would only work if the drives are replaceable | 13:10 |
| @archels | looks like a yes. Quite a feat of engineering, there's also an optical drive in there. http://forum.notebookreview.com/sony/274083-photos-taking-vaio-z-apart.html | 13:16 |
| jrayhawk | huh, cool | 13:17 |
| nmz787 | paperbot: http://www.computer.org/csdl/trans/tp/preprint/06487512-abs.html | 13:17 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/16fa585bb1ec67fec704da356a620bee.txt | 13:17 |
| jrayhawk | that is a comically dinky mainboard | 13:18 |
| @archels | jrayhawk: the Asus Zenbook Prime is currently on top of the list | 13:20 |
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| @archels | but if you come across a good alternative do let me know, I appreciate the input | 13:33 |
| jrayhawk | Yeah, most of the nerds I know are looking for pixel-dense x86s, but it's a remarkably underserved market | 13:40 |
| jrayhawk | unfortunately most of them are trackpoint-addicted | 13:41 |
| jrayhawk | only boring business laptops have those anymore | 13:41 |
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| jrayhawk | https://github.com/panicsteve/cloud-to-butt | 13:52 |
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| juri_ | HR displays? look toward fujitsu. | 15:32 |
| jrayhawk | i haven't seen anything particularly impressive from the lifebook line; what did you have in mind | 15:43 |
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| juri_ | i've seen some impressive stuff from them in the past.. but you have to order it from their japanese site. | 16:15 |
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| nmz787 | kanzure: if you want something to watch these talks are really fun http://alumni.media.mit.edu/~dlanman/ | 16:43 |
| nsh | is bout what? | 17:22 |
| @kanzure | i wonder if httpetrified/httprettified/httpretty works with libmproxy | 17:22 |
| nsh | reminds me of the guy hwo did the "magnets how do they work?!!" talk | 17:23 |
| @kanzure | attached wsgi apps bypass handle_request.. which was not what i intended. | 17:23 |
| nsh | which the crazy modelling system | 17:23 |
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| @kanzure | nmz787: well here's one answer... | 17:29 |
| @kanzure | 17:26 <@ggreer> kanzure: going for a run. we can pair after that | 17:29 |
| @kanzure | 17:27 <@ggreer> err | 17:29 |
| @kanzure | 17:27 <@ggreer> sorry wrong channel. and wrong person. autocomplete. | 17:29 |
| @kanzure | 17:27 <@ggreer> (kansface is the nick of my cofounder. we usually pair program in the evenings) | 17:29 |
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| ParahSail1n | lol kansface | 17:46 |
| @kanzure | ParahSail1n: because of | 17:47 |
| @kanzure | 2013-04-09.log:14:41 < nmz787> i wonder if kansface is some attempt to digitally slap you kanzure | 17:47 |
| @kanzure | from https://news.ycombinator.com/item?id=5519676 | 17:47 |
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| eudoxia | it's the face kanzure makes when sending hatemail | 17:47 |
| eudoxia | le angry kanzure face | 17:47 |
| @kanzure | all email is hatemail | 17:48 |
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| @fenn | Injectable, Cellular-Scale Optoelectronics with Applications for Wireless Optogenetics http://www.sciencemag.org/content/340/6129/211.abstract | 18:49 |
| @fenn | paperbot: http://www.sciencemag.org/content/340/6129/211.full | 18:50 |
| paperbot | error: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/Injectable%2C%20Cellular-Scale%20Optoelectronics%20with%20Applications%20for%20Wireless%20Optogenetics.pdf | 18:50 |
| ParahSail1n | has anyone built a lyman extruder? | 18:53 |
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| ParahSail1n | what, wood filament? http://www.lulzbot.com/?q=products/laywoo-d3-wood-filament-3mm | 19:31 |
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| jrayhawk | huh | 21:13 |
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| @kanzure | yashgaroth: lab update? | 22:30 |
| yashgaroth | last meeting was a weird sbir grant-writing-brainstorming-clusterfuck | 22:30 |
| @kanzure | ha ha sbir | 22:30 |
| yashgaroth | the one guy who brought in a couple 3d printers kept sassing the entire meeting | 22:30 |
| @kanzure | a heckler? | 22:30 |
| yashgaroth | sorta, yeah, like 'oh I've applied for plenty of sbir's and it's a crapshoot and these ideas are stupid' | 22:31 |
| @kanzure | nice | 22:31 |
| @kanzure | he's my hero | 22:31 |
| yashgaroth | admittedly he wasn't wrong | 22:31 |
| @kanzure | shouldn't kevin lustig have some pharma connections that could drop a few hundred grand on it? | 22:31 |
| yashgaroth | but then he was at odds with the guy who brought in the 28-foot van full of lab equipment, who was all offering to help review grant applications and such | 22:31 |
| yashgaroth | kevin wasn't even there for this one, it was odd | 22:32 |
| @kanzure | i feel like kevin should have some dark sith connections or some shit | 22:32 |
| yashgaroth | idk if kevin has pharma connections outside of his assaydepot-related stuff | 22:32 |
| @kanzure | well even if it's through assaydepot | 22:32 |
| @kanzure | i mean, that's probably how he knows pharma people | 22:32 |
| yashgaroth | aside from the whole 'PhD from UCSF' which I assume is good for at least a dozen primo connectz | 22:32 |
| @kanzure | haha.. no. | 22:32 |
| yashgaroth | yeeeah | 22:33 |
| yashgaroth | also kevin not being there meant no food and barely any alcohol, which I think hurt it more than any heckling | 22:33 |
| @kanzure | i also feel like ryan bethencourt probably knows a bunch of san diego people with deep pockets | 22:33 |
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| yashgaroth | who is | 22:33 |
| @kanzure | but ryan is probably trying to get them to fund east bay diybio or his fibroalzheimerohshit npo | 22:33 |
| yashgaroth | nm google's filling me in | 22:33 |
| @kanzure | ryan is just some pharma/biotech sales guy who hangs out in the community | 22:34 |
| yashgaroth | there was talk about a peter blank I think | 22:34 |
| @kanzure | i'm not completely sure about his background, there's supposed to be other things, he's been around in diybio/transhumanism since forever | 22:34 |
| yashgaroth | something * blank, some bigwig business silicon valley guy | 22:34 |
| yashgaroth | yeah I'd heard the name | 22:34 |
| @kanzure | "- Humanity + Caltech conference (2010) - talk titled "2020 the Future of the Biopharmaceutical industry "" | 22:34 |
| @kanzure | ""Open, cheap and fast: New Models of biotechnology entrepreneurship" " | 22:34 |
| @kanzure | "- Singularity University, Biotech track, July 2012" | 22:34 |
| @kanzure | "- Open Science Summit 2012, “Guerilla” style biotech for ALS" | 22:34 |
| @kanzure | "Co-founder, Rawflow.com - VC funded by Benchmark Capital £2M" | 22:35 |
| @kanzure | "Genescient Pharma division - Adviser and former P/T COO (helped close first external angel round)" | 22:35 |
| @kanzure | wtf genescient too? well ok. | 22:35 |
| @kanzure | ah right pfizer sales | 22:35 |
| @kanzure | well anyway. he probably knows people who hang out in san diego and spend lots of biotech money. | 22:35 |
| yashgaroth | "combines evolutionary genomics with massive selective screening to analyze and exploit the" hmm yeah | 22:35 |
| yashgaroth | I defer all bigwig-knowingness to jojack | 22:35 |
| yashgaroth | and I thought the whole meeting would be about writing an sbir for the actual lab, but everyone all like 'oh who wants to write that pfft' | 22:36 |
| @kanzure | jojack has a really weird ability to get around and find the right people, but the deals don't always close | 22:36 |
| @kanzure | yeah, i think for a sbir you might want to consider just hiring someone else to write it | 22:36 |
| yashgaroth | with all that money we have | 22:37 |
| @kanzure | i think grants are leagues better than membership fees for the hackerspace | 22:37 |
| @kanzure | but grants also suck in the scheme of things | 22:37 |
| yashgaroth | yeah I dunno what the actual output requirements are for grants like that | 22:38 |
| @kanzure | in terms of bang-for-the-buck i think the gates foundation grants are worth pursuing in your situation | 22:38 |
| ParahSail1n | do you know anyone who's gotten gates bucks? | 22:38 |
| @kanzure | darren zhu | 22:39 |
| yashgaroth | jojack seems unwilling to write the grants for some reason | 22:39 |
| yashgaroth | maybe he's bad at writing, who knows | 22:39 |
| @kanzure | actually my records indicate that i know darren via jojack, weird | 22:39 |
| @kanzure | no, he's very good at writing (but i think this is because he spends an extreme amount of time at it because obsession) | 22:39 |
| @kanzure | evidence: http://jetpress.org/v19/jackson.pdf | 22:40 |
| yashgaroth | well there you go, but when I mention writing the application he's very dismissive | 22:41 |
| yashgaroth | sure it's not a traditional sbir type of proposal, but hey | 22:42 |
| yashgaroth | also idk if I mentioned but jcline thinks there's big money in kombucha | 22:42 |
| @kanzure | something about algae? | 22:43 |
| yashgaroth | and algae, but kombucha is like yeast + bacteria forming these globs that ferment tea or some shit | 22:43 |
| yashgaroth | it's the new wholefoods thing | 22:43 |
| @kanzure | genspace likes to make money by giving presentations in-house | 22:44 |
| @kanzure | but this ends up hijacking a big portion of the space (lots of chairs, lots of scheduling issues, etc.) | 22:45 |
| @kanzure | in san diego i think it would be more efficient to bring the presentations to different companies that want to support a hackerspace | 22:45 |
| @kanzure | in exchange they would get professional talks about cool biotechnology projects | 22:45 |
| @kanzure | uh i mean in exchange for their bags of money per presentation | 22:45 |
| @kanzure | or training session (off site) | 22:45 |
| yashgaroth | very few of these companies care about hackerspaces, and who would be talking at these talks? | 22:45 |
| yashgaroth | because if it's our usual bunch of presentations like last night, it'll just be 'so we get some stem cells right, and then alzheimers is cured' | 22:46 |
| yashgaroth | because stem cells, you see | 22:46 |
| @kanzure | well, not jojack because he doesn't seem to think he's capable of giving highly technical talks | 22:46 |
| yashgaroth | about biotechnology? then I might agree with him to be honest | 22:47 |
| @kanzure | heh | 22:47 |
| @kanzure | he really needs to sit down and get to the point where he feels confident about biotechnology | 22:47 |
| @kanzure | he just... hasn't? for some reason? | 22:47 |
| @kanzure | anyway, i dunno what the mechanics would be. but speaking at companies is a known thing that happens that they might be receptive to. you could possibly recruit other people with careers and give them free publicity in the process. dunno. | 22:48 |
| yashgaroth | well jojack could organize that pretty easily, but most companies have a tech/patent that they're pursuing, and ignore anything else unless it's a direct and immediate competitor to them | 22:49 |
| yashgaroth | at least in biotech I guess | 22:49 |
| @kanzure | uh by recruit i mean "hey go speak at this event on behalf of jerkwad biohack incorporated, in exchange you get your name out to these companies and we get some money to support the space". and then they go off and give some talk about whatever biotech topic. | 22:49 |
| @kanzure | yeah, i don't know how bad it is in the biotech industry | 22:50 |
| @kanzure | i know there's a lot of companies that just hire pipette drones | 22:50 |
| @kanzure | which would be less receptive. | 22:50 |
| yashgaroth | well they need a few paper drones at the top | 22:50 |
| @kanzure | what sorta biotech company density is there in san diego anyway? | 22:51 |
| yashgaroth | generally the talk culture is conference-oriented, where if you've been a good little drone you get to fly to cincinnati for proteinchat 2013 | 22:51 |
| yashgaroth | density? super high | 22:51 |
| yashgaroth | mira mesa/sorrento valley, every other building is biotech | 22:51 |
| yashgaroth | ah apparently sorrento mesa is the region name | 22:53 |
| @kanzure | i guess gates foundation is my only immediately-relevant suggestion. i think they expect just one or two pages of typed information on their application. | 22:57 |
| yashgaroth | on paper the whole thing looks like a great funding recipient | 22:58 |
| brownies | what're you trying to fund? | 22:59 |
| @kanzure | does it? i expect that (for gates foundation money) there would be some specific project that would require evidence of at least one or two people being committed to the project, its progress and completion. i'm not sure if you can demonstrate that at the moment? | 22:59 |
| yashgaroth | our local diybio lab space | 22:59 |
| yashgaroth | (brownies) | 22:59 |
| @kanzure | the city of san diego granted world heavyweight champion jojack a $1 lease on a 6000 sq ft lab facility for biohacking adventures | 23:00 |
| yashgaroth | we have a whole bunch of half-baked projects that could occur in the space, I guess, so those mashed together may add up to one good project | 23:00 |
| yashgaroth | the city of carlsbad, ahem | 23:00 |
| brownies | heh really? that's pretty awesome | 23:00 |
| @kanzure | and now they are trying to figure out how to make money | 23:00 |
| yashgaroth | also it's not a lab facility yet, just an office building | 23:01 |
| brownies | lease me half of it for $3 | 23:01 |
| brownies | that's a 400% ROI | 23:01 |
| yashgaroth | add three zeros to that and you've got a deal | 23:01 |
| @kanzure | $0.003 | 23:01 |
| @kanzure | done | 23:01 |
| yashgaroth | sold! | 23:01 |
| yashgaroth | your square inch of leased space is bound by all applicable restrictions | 23:01 |
| yashgaroth | ...once we figure out what those are | 23:02 |
| @kanzure | "code of ethics" | 23:02 |
| yashgaroth | pffft haha | 23:02 |
| brownies | other than stuffing it full of lab equipment of some sort, what kinds of things are planned? | 23:02 |
| brownies | you could stuff it full of lab equipment and then turn it into a biocoworking space? rent out things to aspiring biotech startups? | 23:03 |
| yashgaroth | we've already stuffed it full of equipment, we need to tear up the existant carpet which is a no-no for labwork | 23:03 |
| brownies | perhaps you should've done that before the stuffing | 23:03 |
| yashgaroth | that was the original idea, hosting a bunch of startups | 23:03 |
| @kanzure | i think the problem with renting it out to biotech companies is that it quickly becomes a typical lab renting facility.. which is sorta boring and not going to end up facilitating yashgaroth's projects. | 23:03 |
| yashgaroth | ehh we can always stuff the stuff | 23:03 |
| yashgaroth | at this point I'd be okay with a studio apartment | 23:04 |
| @kanzure | and then they stop sharing equipment because it has to be calibrated perfectly for each company | 23:04 |
| @kanzure | and because SECRETS | 23:04 |
| yashgaroth | jcline's gonna help me with a bottle bioreactor, don't really *need* a centrifuge if I get creative | 23:04 |
| @kanzure | biotech startups are remarkably different in terms of their attitudes and beliefs | 23:04 |
| brownies | what kinds of things are " yashgaroth 's projects" | 23:04 |
| yashgaroth | yeah it's mostly secrets, and heavy mistrust of all other companies | 23:04 |
| @kanzure | direct electroporation of human muscle tissue | 23:04 |
| @kanzure | whole body electrophoresis | 23:05 |
| yashgaroth | "diy human genetic engineering" | 23:05 |
| yashgaroth | with plasmids that produce whatever gene/protein you would like more of | 23:05 |
| brownies | i think it's time for you to really buckle down and focus on serious work | 23:05 |
| brownies | it's been weeks and i still don't have a glowing cat | 23:05 |
| yashgaroth | you're right, I'll stem some cells | 23:06 |
| yashgaroth | honestly all I'd need from the official space is a place to ship reagents to, since many places want a commercial address | 23:06 |
| yashgaroth | but somewhere deep in my heart the dream of an actual diybio lab still lives | 23:07 |
| yashgaroth | despite how shit-useless the community is | 23:07 |
| @kanzure | my recommendation is to focus on specific projects | 23:07 |
| @kanzure | which seems to be the way that the los angeles group works | 23:07 |
| @kanzure | cory seems to get a lot of fun things done using this approach | 23:07 |
| brownies | what kinds of projects do they do? | 23:08 |
| @kanzure | although he often doesn't share what he's been up to until later | 23:08 |
| yashgaroth | I like his project even if it'll never go anywhere | 23:08 |
| @kanzure | well he has a neural tissue culture somewhere | 23:08 |
| @kanzure | and a deal with the chinese government to sequence basically anything he gives them | 23:08 |
| yashgaroth | his big thing is a biological haber process | 23:08 |
| @kanzure | and his nitrogenase high-pressure tank for directed selection? iirc. | 23:08 |
| @kanzure | nitrogenase? i hope i am remembering the right enzyme he's playing with.. | 23:09 |
| yashgaroth | well that's all a part of it, and yes that's the one | 23:09 |
| ParahSail1n | who's this? | 23:09 |
| yashgaroth | cory tobin | 23:09 |
| @kanzure | cory tobin at los angeles biohackers | 23:09 |
| @kanzure | http://www.biohackers.la/ | 23:09 |
| @kanzure | http://wiki.biohackers.la/Main_Page | 23:09 |
| yashgaroth | he apparently found a nitrogen-fixing bacterium in german charcoal pits that can fix N2 in the presence of oxygen | 23:09 |
| ParahSail1n | that's thermodynamically impossible | 23:10 |
| yashgaroth | or rather, read some abandoned research about it | 23:10 |
| ParahSail1n | like as in delta G shit | 23:10 |
| yashgaroth | yeah well don't let thermodynamics get in the way of things | 23:10 |
| yashgaroth | it's this bizarre species that only lives at like 60C or some shit | 23:11 |
| @kanzure | yeah he described his setup once and it seemed.. less than safe. | 23:11 |
| @kanzure | "Project Hindenburg -> streptomyces thermoautotrophicus" | 23:11 |
| yashgaroth | whole lotta H2 being pumped in | 23:11 |
| @kanzure | "hydrogen + oxygen growth chamber at 50 psi, explosive and very volatile, so we don't keep it in doors" | 23:11 |
| @kanzure | "Project Skynet -> Reverse engineering an in vivo neural network on a chip" | 23:12 |
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| rigel | how on earth could that be useful anyway | 23:12 |
| @kanzure | cory_: hi, we were discussing streptomyces thermoautotrophicus | 23:12 |
| rigel | if it requires h2 | 23:13 |
| @kanzure | ParahSail1n: please elaborate on your thermodynamic violation claims | 23:13 |
| cory_ | it can consume either CO or a combination of H2 and CO2 | 23:13 |
| ParahSail1n | kanzure, brb im looking up the crc tables | 23:13 |
| @kanzure | too bad crc is so god damn inaccessible | 23:14 |
| @kanzure | cory_: we were also trying to figure out what projects we should make the carslbad people look into | 23:15 |
| @kanzure | *carlsbad | 23:15 |
| yashgaroth | yea we're down to collaborate | 23:16 |
| cory_ | what kind of projects are you/they looking for? Like biotech startup type projects? | 23:17 |
| yashgaroth | sure, we haven't really decided on a theme yet | 23:17 |
| yashgaroth | biotech incubator, membership+rented bench space, teaching classes, any or all of those | 23:18 |
| @kanzure | do you need to focus on money? | 23:18 |
| yashgaroth | according to jojack, oh god yes | 23:18 |
| @kanzure | because carlsbad will kick you out? | 23:18 |
| yashgaroth | eventually, but the electric's only free for a year and -80s are power hogs | 23:18 |
| yashgaroth | I don't know how often the city's gonna come by and check on how we're progressing, what with us promising 8+ startups | 23:19 |
| @kanzure | haha wait what else have you promised | 23:19 |
| yashgaroth | damn I used to have the powerpoint somewhere | 23:19 |
| yashgaroth | ask jojack, he did the presentation | 23:19 |
| yashgaroth | general fostering innovation and whatnot, but the 8 startups within X years was the big one | 23:20 |
| @kanzure | out of curiosity... what? like 8 startups owned by the space? | 23:21 |
| brownies | perhaps you should talk to the local universities? | 23:21 |
| brownies | they're always producing startups 'n' things right? | 23:21 |
| yashgaroth | 8 inhabiting the space, paying rent and producing patentz | 23:21 |
| @kanzure | oh.. so it looks like your plan is already set then. good luck :P | 23:22 |
| yashgaroth | we're in talks with the local uni's, at least community colleges, but mostly about hosting lab classes for them since they have no space to run their own lab classes | 23:22 |
| yashgaroth | idk how many startups a CC will produce per year | 23:22 |
| yashgaroth | I guess there's enough biologists here that, say, someone with a marginal idea that wouldn't get VC funding would be able to maybe get off the ground at our space | 23:23 |
| ParahSail1n | hm, delta G comes out negative | 23:23 |
| ParahSail1n | i guess i was wrong | 23:23 |
| ParahSail1n | its just a question of activation energy rather than favorability | 23:24 |
| cory_ | @parahsailin is this in regard to the nitrogenase? | 23:25 |
| ParahSail1n | yes | 23:25 |
| cory_ | what were you calculating the delta-G of? | 23:25 |
| ParahSail1n | 1/2 N2 + 3/2 H2 -> NH3 | 23:26 |
| cory_ | oh, well that's not the reaction, it doesn't use H2 directly to do the reaction, I was just saying the bacteria either metabolizes CO or H2+CO2 | 23:27 |
| cory_ | I'll go look up the full reaction, brb | 23:27 |
| ParahSail1n | whatever the german guy's name for the law that chemical reactions are path independent | 23:28 |
| ParahSail1n | thats a cool sounding bug you got your hands on | 23:29 |
| ParahSail1n | oh that's interesting, CO is used as the electron donor and H+ and N2 are electron acceptors | 23:31 |
| cory_ | http://i.imgur.com/Ncg4qZW.png and http://i.imgur.com/dHAMdQj.png | 23:32 |
| cory_ | yeah, it's a pretty cool bug. Pain in the ass to grow though. Blew up one bioreactor before I got it right. | 23:33 |
| cory_ | It doesn't grow on any sort of carbon-based media. Won't eat sugars, carbohydrates, fats, etc. Only toxic gas :P | 23:34 |
| cory_ | *hot toxic explosive gas | 23:35 |
| ParahSail1n | http://imgur.com/beJ7pAQ | 23:36 |
| ParahSail1n | seems like a bit of a curiosity unless you have carbon monoxide source | 23:37 |
| ParahSail1n | CO is its primary substrate? | 23:38 |
| cory_ | I think the CO-dehydrogenase is just there to produce more superoxide. I don't think the CO is critical for nitrogenase functionality since cells generate superoxide | 23:38 |
| ParahSail1n | for growth i mean? | 23:38 |
| cory_ | yeah, but it can also consume a combination of H2 and CO2 | 23:39 |
| @kanzure | paperbot: http://www.jbc.org/content/272/42/26627.short | 23:39 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/N2%20Fixation%20by%20Streptomyces%20thermoautotrophicus%20Involves%20a%20Molybdenum-Dinitrogenase%20and%20a%20Manganese-Superoxide%20Oxidoreductase%20That%20Couple%20N2Reduction%20to%20the%20Oxidation%20of%20Superoxide%20Produced%20from%20O2by%20a%20Molybdenum-CO%20Dehydrogenase.pdf | 23:39 |
| cory_ | in the case of CO it uses CO as both an energy souce and carbon source. Or it uses H2 for energy and CO2 for carbon since it has RuBisCO | 23:40 |
| yashgaroth | wait wtf it's photosynthetic too? | 23:41 |
| yashgaroth | oh wait nevermind | 23:43 |
| cory_ | no, but it can convert CO2 to sugar. Photosynthesis and CO2 sequestration aren't directly coupled | 23:43 |
| yashgaroth | right right I forgot that bit | 23:44 |
| ParahSail1n | its gotta keep O2 away from the nitrogenase otherwise it's just going to reduce it? | 23:48 |
| ParahSail1n | i think it has to sequester that nitrogenase in a low oxygen region like cyanobacteria do | 23:49 |
| cory_ | well, in the classical nitrogenases the enzymes were poisoned by O2, specifically the O2 oxidized the Fe cofactor or something like that. It is possible that this bug's nitrogenase is immune to O2 poisoning. But I haven't got that far yet. Still working on setting up biochemical experiments. | 23:50 |
| ParahSail1n | if the catalytic center is capable of activating nitrogen, it's gonna activate oxygen too | 23:50 |
| cory_ | yeah maybe. but it may be able to do so without destroying the enzyme. | 23:51 |
| cory_ | which is the case in most nitrogenases | 23:51 |
| cory_ | The original work on this bug showed that the nitrogenase works in vitro in the presence of oxygen | 23:52 |
| cory_ | but there is a lot of skepticisim that the work was nto wrong or fraudulent. I'm trying to re-do those experiments now | 23:53 |
| ParahSail1n | you expressing nitrogenase? | 23:53 |
| cory_ | no, just purifying it from S. thermoautotrophicus using sepharose columns | 23:54 |
| ParahSail1n | get that bug sequenced | 23:55 |
| @kanzure | haha well.. | 23:55 |
| cory_ | already did :) | 23:55 |
| cory_ | still assembling it. It's like 78% GC | 23:55 |
| ParahSail1n | you got a server with the reads? | 23:55 |
| @kanzure | could we get a copy of the reads? | 23:55 |
| @kanzure | yeah | 23:55 |
| ParahSail1n | ill assemble that shit | 23:56 |
| cory_ | they're on some server at harvard. I'll ask my collaborators for the link. We're re-doing the sequencing now because the original sample seems to be a micture of multiple strains | 23:57 |
| ParahSail1n | illumina? | 23:57 |
| cory_ | We're working on getting a purer line going to sequence. | 23:57 |
| cory_ | yeah | 23:57 |
| ParahSail1n | i have some tools that work well on microbiomes | 23:57 |
| cory_ | but we're also going to do some 454 or pacbio to get some longer reads | 23:57 |
| ParahSail1n | velvet chokes on those | 23:57 |
| ParahSail1n | nah you dont need that, just get lots of coverage on hiseq | 23:58 |
| @kanzure | what is lots of coverage? 30x? | 23:58 |
| ParahSail1n | 30x is a little low for bacteria | 23:58 |
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| cory_ | well, in the first run we had some areas with 100x coverage and some with zero. so we were hoping to maybe stitch together some of those gaps with longer reads | 23:59 |
| ParahSail1n | usually aim for a couple hundred | 23:59 |
| @kanzure | couple hundred :\ | 23:59 |
| ParahSail1n | couple hundred is like 2% of a hiseq lane | 23:59 |
| ParahSail1n | hiseq lane is like $3000 | 23:59 |
| @kanzure | haha i don't have a hiseq machine laying around | 23:59 |
| --- Log closed Sat Apr 13 00:00:02 2013 | ||
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