| --- Log opened Mon Apr 09 00:00:27 2012 | ||
| diginet | how does one get PCR'd DNA into a plasmid vector, do you simply design the primers to correspond to splice sites of the primer? | 00:17 |
|---|---|---|
| yashgaroth | basically, yes | 00:18 |
| diginet | ah okay, that's less obnoxious than I thought | 00:19 |
| diginet | do you have any suggestions on which vector to use for pichia? | 00:19 |
| diginet | (I've decided to try pichia first, as according to a few papers, it seems it should be viable for my purposes) | 00:20 |
| yashgaroth | nope, never worked with pichia | 00:21 |
| diginet | ah okay | 00:21 |
| diginet | I'm excited, I'm pretty sure I might be able to pull this off :) | 00:21 |
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| kanzure | beep boop | 06:49 |
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| ThomasEgi | kanzure, blibblib.. plingding | 06:55 |
| kanzure | ah yes that is completely comprehensible | 06:56 |
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| archels | http://quincybioscience.com/files/MadisonMemoryStudy.pdf | 07:09 |
| ThomasEgi | kanzure, whisteling and beeping is quite a good interface to machines. a lot better than natural language | 07:17 |
| kanzure | archels: hi | 07:17 |
| katsmeow-afk | it's slow but unambiguously error free? | 07:18 |
| archels | hello kanzure | 07:20 |
| kanzure | archels: what have you been up to? | 07:20 |
| ThomasEgi | katsmeow-afk, not error free. but a lot less interpretation and processing is needed to make some sense from the input | 07:20 |
| * katsmeow-afk nods | 07:21 | |
| archels | kanzure: nothing mindboggling, some electronics hobby work on making a "digital poster" for showcasing my research. | 07:21 |
| kanzure | haha.. "Well, my poster is about how I spent all this time making this poster.." | 07:21 |
| archels | :) lots of fun building it, though | 07:22 |
| archels | last time I looked at my actual research was 3 days ago, when I found that my problem was so stiff that none of the solvers built into the package I'm using can handle it. | 07:23 |
| kanzure | hmm "People who receive organ donations from "living" donors are more likely to survive than those who receive organs from "deceased" donors." | 07:27 |
| kanzure | maybe dead organs aren't useful | 07:27 |
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| archels | meh, how long are we even going to be messing with donor organs still? A few decades at most, surely. | 07:28 |
| katsmeow-afk | "the donor died of kidney failure, so did the recipient of the kidney, can anyone find the connection?" | 07:28 |
| katsmeow-afk | i was/am desperately trying to not use chlorine in a potable water system, but seems it's a good idea even after 0.5 micron filters and carbon filters,, else i haveto do reverse osmosis or distillation | 07:34 |
| * katsmeow-afk sighs | 07:34 | |
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| kanzure | F7: yo | 07:40 |
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| audy | Has anyone attempted to purify their own active T. aquaticus DNA polymerase holoenzyme? | 08:03 |
| kanzure | holoenzyme? | 08:03 |
| nmz787 | holoenzye is enzyme with multiple subunits | 08:04 |
| nmz787 | intact | 08:04 |
| kanzure | so.. does that just mean multiple purifications from lysate? | 08:05 |
| nmz787 | didnt kno pol was holoenzyme, is that just T. aq/? | 08:05 |
| nmz787 | oloenzyme | 08:07 |
| nmz787 | [hol′ō·en′zīm] | 08:07 |
| nmz787 | Etymology: Gk, holos + en, in, zymos, ferment | 08:07 |
| nmz787 | a complete enzyme-cofactor complex that gives rise to full catalytic activity. | 08:07 |
| audy | they all are | 08:08 |
| audy | oh neat you can precipitate it from cell lyase | 08:10 |
| audy | using polyethylenimine which creates balls of condensed, positively charge DNA. | 08:11 |
| audy | that's way easier than HPLC | 08:11 |
| audy | Step 1 - Go camping in Yellowstone. Bring a centrifugre | 08:12 |
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| Utopiah | http://www.technologyreview.com/blog/arxiv/27689/ | 08:21 |
| archels | Shannon an _unsung_ hero? What rock does this blogger live on? | 08:38 |
| delinquentme | who KentuckyFC @ arxivblog.com ? | 08:49 |
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| kanzure | roksprok_: hi | 09:01 |
| roksprok_ | hello kanzure | 09:02 |
| roksprok_ | how are things going? | 09:02 |
| kanzure | pretty good | 09:02 |
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| delinquentme | kanzure, how does one monitize reproducibility | 09:47 |
| roksprok_ | doesn't that take care of itself if you do useful stuff? | 09:53 |
| kanzure | roksprok_: nope.. a lot of biology is "try 20 times, it works once, let's roll with it" | 09:54 |
| roksprok_ | like if your stuff is reproducable and useful you can start a company or license it or people will cite you a lot | 09:54 |
| kanzure | you can license it even if it is barely reproducible, haha | 09:54 |
| roksprok_ | that's frusturating | 09:54 |
| roksprok_ | i guess its nice for people whose stuff isn't reproducable | 09:55 |
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| nmz787 | that techreview article really doesn't say anything useful at all | 09:59 |
| delinquentme | kanz TLDRed it | 10:00 |
| Mariu | I agree with kanzure on the biology thing :p | 10:01 |
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| nmz787 | the whole DNA info theory thing about shotgun sequencing kidnof gets blow out of the water if nanopore seq turns out to work as well as it sounds like it should | 10:22 |
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| kanzure | fenn: ping | 10:39 |
| F7 | Just reading through datasheets over here, I just got caught up on the log in this channel | 10:49 |
| F7 | delinquentme: did you ask the resolution on an analog distance sensor earlier? hahahahaha | 10:51 |
| F7 | Resolution is one pixel, the distance resolution is defined by your ADC | 10:52 |
| F7 | and to a degree, the physical properties of the object you're pointing at | 10:52 |
| F7 | It's a little light and a detector | 10:53 |
| F7 | you tell distance by the amount reflected back | 10:53 |
| F7 | It's not meant to do anything accurate, or beyond like a foot | 10:53 |
| F7 | What did you want it for? | 10:54 |
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| delinquentme | F7, yeah I was looking for that information | 11:09 |
| delinquentme | i need accuracy thats the thing | 11:09 |
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| delinquentme | F7, what do you know about sensors | 11:21 |
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| F7 | I know many things about sensors | 11:30 |
| F7 | What kind of accuracy do you need? | 11:30 |
| F7 | consider quadrature if it's linear or rotational encoding | 11:30 |
| F7 | Old dot matrix printers are built like tanks, for example. they're heavy enough that backlash isn't such a problem, and the linear axes are generally good to a twentieth of a mm. | 11:31 |
| F7 | And those are ooooold printers | 11:31 |
| F7 | A quadrature encoder gets 4 times the accuracy of the CPI of the encoder strip it is designed for | 11:35 |
| nmz787 | delinquentme: what are you doing that needs distance sensing? | 11:36 |
| delinquentme | pumps | 11:36 |
| F7 | that's odd | 11:36 |
| delinquentme | ultrasound are ehh | 11:36 |
| F7 | syringe pump? | 11:36 |
| delinquentme | lasers could be expensive ( havnt looked into it ) | 11:36 |
| delinquentme | yeahh and the LH | 11:36 |
| F7 | why does it have to be contactless? | 11:37 |
| delinquentme | magnetic sensors are fairy accurate but they've got interaction issues | 11:37 |
| delinquentme | it doesnt | 11:37 |
| F7 | oh | 11:37 |
| F7 | how accurate does it need to be? | 11:37 |
| nmz787 | pump i was working on a while ago was for sterile solutions | 11:37 |
| nmz787 | was calculating the delta V of a hanging droplet | 11:38 |
| nmz787 | that was in a closed drip tube | 11:38 |
| nmz787 | getting nanoliter precision with wideVGA camera | 11:38 |
| F7 | I don't know why you're thinking along the lines of these esoteric sensing solutions | 11:40 |
| F7 | If you can do contact, you can do cheap, easy, accurate stuff | 11:40 |
| F7 | I don't know if it's just your unfamiliarity, delinquentme, or if I'm missing some kind of big limiting factor inherent to your setup | 11:41 |
| ThomasEgi | F7, pumping nanoliters means.. moving veryveryveryvery little, mechanical setups simply have a hard time keeping up with that | 11:42 |
| F7 | I'm assuming the syringe pump is being driven with rotational to linear means? | 11:43 |
| F7 | like, some kind of mechanical advantage? | 11:43 |
| F7 | The same mechanical advantage can be used to advantage of the sensor | 11:43 |
| ThomasEgi | that wont take mechanical problems into account. backlash, slip, etc. | 11:43 |
| F7 | I am unsure of the exact setup, so I cannot be sure whether or not that would be advantageous | 11:44 |
| F7 | the syringe could just be very overbuilt, or it could be dependent on some slip-shod springy plastic parts. | 11:45 |
| F7 | Okay, some info about linear encoders | 11:46 |
| F7 | 500 CPI strips are about four bucks per inch | 11:47 |
| F7 | the encoder that goes with it is like 30 bucks | 11:47 |
| ThomasEgi | .. compare to a camera chip. | 11:47 |
| F7 | both can be scrapped from cheap printers | 11:47 |
| nmz787 | ThomasEgi: yeah it was r&d for a blood infusion pump | 11:47 |
| F7 | that nets 1/2000th of an inch | 11:48 |
| nmz787 | they have a really wide dynamic range | 11:48 |
| F7 | What is this camera volumetric stuff y'all are talking about? | 11:48 |
| ThomasEgi | F7, a scanner chip can has 4800dpi | 11:48 |
| nmz787 | F7, basically just pointing a camera at a hanging droplet in a closed tube, watching as it grows, calculating delta V from frame to frame (filtering the noise was where I basically left the project) | 11:49 |
| delinquentme | everyone loves scraping shit from printers for some reason | 11:50 |
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| delinquentme | i guess its bc they're only making 1 off robotics? | 11:50 |
| nmz787 | we were basically finding the edge of the droplet and rotating each row of pixels to get volume | 11:50 |
| ThomasEgi | delinquentme, until the day where you want to print something and notice... crap. my printer is all butched | 11:50 |
| delinquentme | ^ | 11:50 |
| delinquentme | but yes F7 i know little about sensors | 11:51 |
| nmz787 | each row was diameter, since pi*r^2 = area, the row gave us area and since we knew the height we got slices of volumes | 11:51 |
| delinquentme | F7, where would I get this sensor for the 500 CPI strips | 11:52 |
| nmz787 | then added the slices together to get drop vol | 11:52 |
| nmz787 | then looked at the differential of those | 11:52 |
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| delinquentme | nmz787, am I wrong in thinking that all you need is a single side view of a droplet? | 11:52 |
| nmz787 | nope | 11:52 |
| delinquentme | as the droplet will be uniform size | 11:52 |
| nmz787 | well | 11:53 |
| nmz787 | when the drop detaches, it actually jumps around | 11:53 |
| nmz787 | so there was talk about adding a second view | 11:53 |
| delinquentme | so you just need the 'footprint' to determine the vol | 11:53 |
| delinquentme | oh sure | 11:53 |
| nmz787 | or using structured light | 11:53 |
| nmz787 | when the drop detaches, it actuallt sends a ringing/oscillation of pressure up the orifice and into the feed tuube | 11:54 |
| kanzure | stereographic drop images? heh | 11:54 |
| nmz787 | but yeah like I said, i left the project when we were finally getting somewhere with the theoretical stuff and moving into cleaning up the real signals | 11:54 |
| F7 | www.usdigital.com has quadrature encoders | 11:54 |
| F7 | I've never bought one ever, they're easy to scrap | 11:55 |
| F7 | A cheap laser mouse will have about a 2000 dpi sensor, and run at over 10K FPS | 11:55 |
| F7 | something like that would be amazing for sensing | 11:56 |
| F7 | the 'gamer' mice are probably much better | 11:56 |
| ThomasEgi | F7, yeah but they have rather low resolution and for most models, there is no way to access the actual image data | 12:00 |
| ThomasEgi | just the final motion vector of the overall image. | 12:00 |
| diginet | so, bio-rad has cuvettes for $15, but Invitrogen has them for $150, am I missing something, or there just insane mark-up going on there? | 12:00 |
| diginet | oh wait, nevermind, bio-rad is selling a pack of 5, rather than 50 | 12:02 |
| nmz787 | kanzure: http://eclecti.cc/hardware/blinded-by-the-light-diy-retinal-projection | 12:02 |
| F7 | ThomasEgi, let me check you on that. I'm pretty sure most of those sensors send info to a separate microcontroller to extract the vector. | 12:04 |
| ThomasEgi | these days, sensors, motion extraction and usb controllers usualy are on one-chip | 12:07 |
| kanzure | nmz787: what's the resolution | 12:10 |
| kanzure | neat the guy also did lytro's file format.. http://eclecti.cc/computervision/reverse-engineering-the-lytro-lfp-file-format | 12:14 |
| kanzure | oh neat. he's friends with randallagordon (who used to hang out here?) | 12:18 |
| F7 | I'm looking through datasheets, and most low resolution ones I can find go offboard | 12:18 |
| F7 | I haven't found any sheets for 'gamer' mice yet | 12:18 |
| nmz787 | kanzure: for the retina projector? the image was only 1.5mm, so if he was using the whole DLP chip, i'd say pretty good | 12:19 |
| F7 | it actually looks pretty straightforward to piece the high speed video together with a micro | 12:19 |
| nmz787 | i dont think it really quite works though | 12:19 |
| nmz787 | the eye is supposed to be the focus, and the image rests on your retina | 12:20 |
| nmz787 | so to get a seemingly big image, the incoming light needs to have a pretty wide angle | 12:20 |
| kanzure | i would love to have per-cone addressable input to my eye :( | 12:22 |
| kanzure | er.. cone-addressable | 12:23 |
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| F7 | I'd love to have one for other people's eyes | 12:41 |
| F7 | with long distance retinal lasers, one could be the master of illusion | 12:42 |
| jrayhawk | I have a G500 that I'm not sure I care about | 12:42 |
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| nmz787 | kanzure: maybe we're pitching the DNA synthesizer in the wrong way | 12:51 |
| nmz787 | kanzure: maybe we should pitch it as an aide to solve developing world drug synthesis and production, or something | 12:52 |
| kanzure | it's an aide to scratch my butt | 12:52 |
| kanzure | oh, well. | 12:52 |
| nmz787 | http://newyork.craigslist.org/mnh/sci/2921681357.html | 12:53 |
| nmz787 | i could get that internship, then pitch ourselves | 12:53 |
| nmz787 | get you to come 'demo' something | 12:53 |
| kanzure | haha | 12:53 |
| kanzure | yeah there's a lot of vectors once we have a prototype | 12:54 |
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| diginet | what is the general protocol for preparing a lysate from a tissue sample? | 13:40 |
| ParahSailin__ | bead beater and lysis buffer | 13:41 |
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| nmz787 | if you want to torture yourself you can get our LN2 and a mortar and pestle.... it can be tough though | 13:44 |
| diginet | what is the lysis buffer composed of? | 13:45 |
| ParahSailin__ | depends on your sample | 13:46 |
| ParahSailin__ | you google it | 13:46 |
| diginet | could I use laundry detergent, or would that not provide good enough quality? | 13:46 |
| kanzure | it would probably be more specific? | 13:47 |
| ParahSailin__ | normally theres tris involved | 13:48 |
| diginet | ah | 13:48 |
| diginet | now, another thing I was thinking about: let's say I manage to transfect the genes into a cell, and I am able to culture a sizable quantity of them in some sort of tank, is there anyway to extract the protein (provided it is excreted of course) without disrupting the rest of the mixture? | 13:49 |
| ParahSailin__ | since i know what you are doing, you would go on mobio and their dna extraction kits come with bead beaters and all the buffers you need | 13:50 |
| diginet | okay thanks | 13:50 |
| ParahSailin__ | you did not really provide enough context for a naive observer to answer your question | 13:51 |
| diginet | I'm sorry | 13:52 |
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| ParahSailin__ | mobio gives free samples of *na extraction kits | 13:52 |
| diginet | oh, wow | 13:53 |
| diginet | thanks | 13:54 |
| ParahSailin__ | might need to use an institutional mailbox, which i still have | 13:54 |
| diginet | thank you so much, again | 13:54 |
| diginet | but yeah, if I were the CEO of some corporation, which was trying to produce a recombitant protein on an industrial scale, how would I go about it? I could culture the transgenic cells, and then desctructively extract the protein, but that seems a waste. Is there anyway to efficiently get it out of the tank with minimal disturbance to the culture? | 13:56 |
| ParahSailin__ | that spidroin has a golgi secretion tag on it | 13:57 |
| kanzure | hairy root cultures | 13:57 |
| ParahSailin__ | it will be in the supernatant | 13:57 |
| kanzure | in some biofuel operations they do secreting oils and then you harvest the oils from the pond scum (or something) | 13:57 |
| F7 | Just press it like it were olives? | 13:57 |
| nmz787 | i know some transgenics use secretion tags, so the golgi apparatus exports the proteins in vesicles which fuse to the cell membrane, releasing their contents into the extracellular medium (broth) | 13:58 |
| kanzure | what's wrong with regularly sacrificing a part of your culture? | 13:58 |
| nmz787 | wasteful | 13:58 |
| diginet | I know, it should excrete it, but is it trivial to extract the protein from the broth efficienctly? | 13:58 |
| nmz787 | more overhead | 13:58 |
| nmz787 | its a lot easier to extract from broth than intracellular | 13:59 |
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| nmz787 | you centrifuge the cells out first, and then purify for whatever you need | 13:59 |
| diginet | is the centrifugation destructive? | 13:59 |
| nmz787 | to? | 14:00 |
| diginet | the cells? | 14:00 |
| nmz787 | generally not | 14:00 |
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| diginet | Is there any sort of available membrane which could act like a sieve for the cells and just let the broth through? One of the benefits of Pichia, so I've read, is that it doesn't secrete very much protein naturally | 14:04 |
| ParahSailin__ | centrifuge | 14:05 |
| nmz787 | nanopore membranes | 14:12 |
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| nmz787 | http://www.simpore.com/products.html | 14:12 |
| ParahSailin__ | if you are doing pichia and you dont have a centrifuge, they will settle pretty quickly on their own | 14:12 |
| ParahSailin__ | like 1 cm/hr | 14:13 |
| nmz787 | looks like cofactorbio.com and seqify.com are offline | 14:26 |
| nmz787 | testing or dead? | 14:26 |
| kanzure | haven't heard from mac in a while | 14:27 |
| kanzure | last i heard he and josh were doing something | 14:27 |
| nmz787 | i thought seqify was it | 14:27 |
| kanzure | but then josh is going out to china with $50k openpcr money or something | 14:27 |
| nmz787 | to make cheaper PCR machines? | 14:28 |
| kanzure | haha no i doubt it | 14:28 |
| kanzure | fulfilling the backlog of orders | 14:28 |
| nmz787 | backlog? | 14:28 |
| nmz787 | weird | 14:29 |
| kanzure | yeh apparently they have a few ordes for openpcr boxes that they haven't satisfied | 14:29 |
| nmz787 | seems like it should be production by now | 14:29 |
| nmz787 | like, churn them out easily | 14:29 |
| nmz787 | are they taking new orders still? | 14:29 |
| kanzure | yes | 14:31 |
| diginet | one nice benefit is that the spidroin proteins are very heavy | 14:31 |
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| fenn | guh so much email | 14:34 |
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| fenn | that table looks familiar.. http://fennetic.net/irc/IMG_4615.JPG | 14:41 |
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| kanzure | wut did they grab it off ebay | 15:00 |
| kanzure | damn | 15:00 |
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| fenn | ah nice http://eclecti.cc/hardware/blinded-by-the-light-diy-retinal-projection | 15:26 |
| fenn | the newport table came from "centurian surplus" for i don't know how much | 15:27 |
| kanzure | nmz787 posted a very similar link the other day | 15:28 |
| kanzure | to such a table. | 15:28 |
| fenn | apparently this place has tons of equipment sitting around | 15:28 |
| fenn | yeah i know | 15:28 |
| kanzure | " know of people who have done silencing work on themselves, and one chap who has self inoculated. There are others who have created autoimmune responses against targets." | 15:35 |
| kanzure | "RNA interference was last autumn, Self inoculation was over a year back, and the autoimmune induction was jan this year, although I suspect that it has been going on for a few years." | 15:36 |
| kanzure | "As for who, they are all bodybuilders bar one who is a pro in combat sports." | 15:36 |
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| kanzure | nmz787: fenn is around | 15:50 |
| kanzure | how long will a channel cut take on the cutter? like 1min/mm? | 15:50 |
| kanzure | uh | 15:50 |
| kanzure | 1mm/min | 15:50 |
| fenn | that's ridiculously slow | 15:51 |
| kanzure | well. it's worth knowing. | 15:52 |
| kanzure | i think the total channel length will probably add up to multiple millimeters so.. it's important to know how long it would take | 15:52 |
| nmz787 | I think fenn said 1000rpm / 60 s/min * (635microns/turn) | 15:52 |
| kanzure | yes but it also depends on the material/laser | 15:53 |
| nmz787 | Pdms comes off fast | 15:53 |
| nmz787 | But that would be our upper limit | 15:53 |
| nmz787 | I need to look at black acrylic with a spectrometer | 15:53 |
| kanzure | nmz787: do you have access to a micron laser on campus | 15:54 |
| nmz787 | We might be able to use a NIR diode laser, which would be smaller and a little less complex optics/gantry-wise | 15:54 |
| nmz787 | Nope | 15:54 |
| nmz787 | No one makes these things | 15:55 |
| nmz787 | Someone converse with me... I'm bored in a liberal arts class | 15:57 |
| fenn | nmz787: do you think mcmaster part 6350K137 is a good lead screw? | 15:57 |
| nmz787 | The one you originally chose? | 15:58 |
| fenn | 3/8-40 acme | 15:58 |
| nmz787 | Yeah, looked like the best | 15:59 |
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| kanzure | Kev_ant: hello | 16:03 |
| nmz787 | hi keg | 16:03 |
| nmz787 | Kev | 16:04 |
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| nmz787 | Kanzure... Remeber we roughly calculated 20000 drops would take at least 50cm | 16:06 |
| kanzure | yep | 16:07 |
| kanzure | so ideally it would take <30min of cutting | 16:07 |
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| nmz787 | So thats significantly more than your few mm comment earlier | 16:07 |
| kanzure | ah true | 16:08 |
| nmz787 | At 1000rpm that's 16.66 turns per sec, which is about 10.5mm per sec | 16:09 |
| nmz787 | Or 1cm per sec | 16:09 |
| nmz787 | So I think less than 5 or 10 mins per layer for.cutting | 16:09 |
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| kanzure | yo juul | 16:11 |
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| nmz787 | If we have 3 layers, 15 mins, plus time to prep those layers (spin coat, bake)... Say 10 min per layer (we'll do these in bulk in advance) | 16:11 |
| juul | hey kanzure | 16:11 |
| kanzure | nmz787: yeah i imagine we'd have a stock of uncuts | 16:11 |
| fenn | nmz787: am i missing something? 50cm*50micron = 0.25 cm^2 | 16:11 |
| nmz787 | and I figure 30 mins to bond 2 layers, at least in beginning | 16:12 |
| fenn | if so, why do we need such a big stage? | 16:12 |
| kanzure | no this was just a storage area | 16:12 |
| nmz787 | Fenn you need space between the channels | 16:12 |
| fenn | yeah, 50 microns ought to be enough, no? | 16:12 |
| fenn | anyway it increases linearly with spacing between channels | 16:12 |
| fenn | to a first order approximation | 16:13 |
| nmz787 | I calf 3.55 cm per side for the 20000 drop column/pipe | 16:14 |
| nmz787 | Calc | 16:14 |
| fenn | let's go over those calculations | 16:14 |
| kanzure | the calculation was something like 20 micron diameter per drop * 50,000 drops | 16:14 |
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| kanzure | and at least 20 microns in between each channel (like if it's zigzagging or something, no "infinitely thin" walls) | 16:14 |
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| fenn | and spacing between drops? | 16:15 |
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| fenn | how wide is the channel? | 16:16 |
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| fenn | i'm assuming the area required is roughly the same whether it's a zigzag or a straight line with a given width | 16:17 |
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| kanzure | let's say 5 or 10 microns in between drops? | 16:18 |
| kanzure | channel is as wide as the drop | 16:18 |
| nmz787 | 20 Micron drop * 25000 drops = 50000 microns long | 16:18 |
| fenn | and spacing between drops is what? | 16:18 |
| nmz787 | 20 Micron wide channel, plus 2.5 Micron wall on each side | 16:18 |
| kanzure | yeah that's 50mm not 50cm | 16:18 |
| nmz787 | So 25 micron width per channel | 16:19 |
| kanzure | 2.5 micron wall will probably break, but it's worth exploring | 16:19 |
| fenn | no it's 50 cm | 16:19 |
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| kanzure | how is 50,000 microns = 50 cm? | 16:19 |
| fenn | 50cm * 25 micron = 0.125 cm^2 | 16:19 |
| kanzure | oh woops | 16:21 |
| nmz787 | Huh | 16:21 |
| nmz787 | 20 microns | 16:22 |
| fenn | people mess up the square conversions all the time | 16:22 |
| nmz787 | 20 microns/drop * 25000 drops is not a sq | 16:22 |
| fenn | 10000 microns per cm => (10000)^2 microns^2 per cm^2 | 16:23 |
| fenn | ok back up a second, what's the volume of the drop? | 16:23 |
| nmz787 | Doesn't matter | 16:24 |
| kanzure | it's some weird oblique blob.. not quite a sphere | 16:24 |
| fenn | rough estimate | 16:24 |
| fenn | enough DNA for maybe 100 PCR reactions right? | 16:25 |
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| kanzure | what are we talking about now? | 16:25 |
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| kanzure | in the library scheme we would have beads in each drop | 16:25 |
| fenn | how big each droplet is | 16:25 |
| kanzure | and the dna is attached to the beads | 16:26 |
| fenn | ok how big are the beads? | 16:26 |
| kanzure | so there's probably a few million strands attached to each bead, and however many beads we want for whatever size we buy | 16:26 |
| n_bentha | small | 16:26 |
| kanzure | we can buy all sorts of beads | 16:26 |
| kanzure | 1 micron beads, 100 micron beads.. 0.1 micron beads.. | 16:26 |
| fenn | paralyzed by choice! :) | 16:26 |
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| kanzure | we will probably just test a bunch of things | 16:26 |
| kanzure | "load droplet with beads" is a big test | 16:27 |
| kanzure | anyway, let's say 1 to 5 picoliters | 16:27 |
| n_bentha | so all this spiffy lab voodoo. where will it be done? | 16:28 |
| n_bentha | in a biosafety hood? | 16:28 |
| fenn | ok 1pl is about 8 micron radius | 16:28 |
| fenn | who cares about biosafety | 16:28 |
| fenn | this is DNA | 16:29 |
| kanzure | this isn't even DNA yet | 16:29 |
| nmz787 | So to get a square of snaking channel, (25x)*(50000/x)=1250000 | 16:29 |
| yashgaroth | safety for the dna, not for the user | 16:29 |
| nmz787 | That's not including the turns on the ends to connect each row, actually | 16:29 |
| n_bentha | u just don't want contamination of dust, bacteria, etc | 16:30 |
| fenn | the system's sealed, it's not open to the air | 16:30 |
| n_bentha | oh ok. cool | 16:30 |
| kanzure | bacteria! i'd love bacteria to get into the drops. dam. | 16:30 |
| kanzure | *dam | 16:30 |
| kanzure | moIDKfaa *damn | 16:30 |
| fenn | nmz787: if you think about it, the turns add to the path length | 16:31 |
| fenn | imagine a spiral instead of a zigzag | 16:31 |
| kanzure | where does the spiral exit ? | 16:31 |
| fenn | nowhere | 16:31 |
| fenn | why would it need to exit? | 16:32 |
| fenn | okay, two spirals | 16:32 |
| kanzure | oh you could do a double spiral, right.. | 16:32 |
| kanzure | heh | 16:32 |
| fenn | we'll have to have 2 zigzags | 16:32 |
| nmz787 | Exit through the top layer? | 16:32 |
| fenn | it just needs a volume in the center to collect working fluid | 16:32 |
| kanzure | 2x spiral means once it gets to the "center" it starts going "out" | 16:32 |
| fenn | anyway the point is that the formula for area is the same whether it's a long line or a zigzag | 16:33 |
| fenn | kanzure: oh, like a bifilar coil | 16:33 |
| kanzure | double spiral: http://www.prodigyquilter.com/ProductImages/double%20spiral.gif | 16:34 |
| kanzure | has an entrance and exit | 16:34 |
| fenn | right | 16:34 |
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| fenn | so i guess we can forget about building a motion stage | 16:35 |
| kanzure | why | 16:35 |
| kanzure | piezo+mirror? | 16:36 |
| n_bentha | lol | 16:36 |
| fenn | because it only needs to be 5mm on a side, so we can just use one of the readily available 50mm microscopy positioning stages | 16:36 |
| kanzure | no we might want features longer than 5mm :( | 16:37 |
| kanzure | in fact i'm sure of it | 16:37 |
| fenn | longer than 50mm? | 16:37 |
| kanzure | centimeters! | 16:38 |
| fenn | gosh | 16:38 |
| nmz787 | That's only for drop storage | 16:38 |
| nmz787 | For 25k drops | 16:38 |
| nmz787 | We could do a million drops | 16:38 |
| nmz787 | In late stages tho | 16:39 |
| kanzure | that will be our 1028 bit version :) | 16:39 |
| nmz787 | But we definitely need some longer straight tubes for silica columns and or agarose | 16:39 |
| nmz787 | We shouldnt under build | 16:40 |
| fenn | even for a million drops, drop storage is only 30mm on a side | 16:40 |
| kanzure | the chip isn't 30mm x 30mm | 16:41 |
| kanzure | it's 5cm x 5cm or something, at least | 16:41 |
| kanzure | you have all sorts of features including world interconnects | 16:42 |
| nmz787 | Plus we need room to fit valving pistons or whatever on top, so they need mm between each | 16:42 |
| kanzure | which you don't want crammed into a 30mm^2 area | 16:42 |
| nmz787 | Rift | 16:42 |
| nmz787 | Right | 16:42 |
| n_bentha | shit will evaporate! | 16:42 |
| kanzure | n_bentha: in oil | 16:43 |
| nmz787 | Plus I think the cutter resolution specs are good | 16:43 |
| n_bentha | oh | 16:43 |
| kanzure | fenn: http://www.nature.com/nature/journal/v442/n7101/images/nature05058-f1.2.jpg | 16:43 |
| nmz787 | Also on chip perstaltic pumps could happen, more space required | 16:43 |
| fenn | kanzure: a dime is 18mm diameter, so that chip's not more than 30mm on a side | 16:44 |
| nmz787 | That's also a really simple chip | 16:44 |
| kanzure | i should probably know what this chip does before i keep citing it | 16:44 |
| nmz787 | With basically no onboard stuff but pipes | 16:44 |
| kanzure | ah this was whitesides' chip.. from http://www.nature.com/nature/journal/v442/n7101/full/nature05058.html#B65 | 16:45 |
| kanzure | oh hell no | 16:46 |
| kanzure | http://lesswrong.com/lw/b98/minicamps_on_rationality_and_awesomeness_may_1113/ | 16:46 |
| kanzure | fff “I do not say this lightly... but if you're looking for superpowers, this is the place to start.” | 16:46 |
| fenn | SUPERPOWERS | 16:46 |
| kanzure | rationality superpowers? god damn it | 16:46 |
| nmz787 | http://m.sciencemag.org/content/309/5731/137/F1.expansion.html | 16:47 |
| nmz787 | Ttyl8r, driving | 16:47 |
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| fenn | i wonder why the channel width varies so much | 16:50 |
| kanzure | between labs? | 16:51 |
| fenn | well, that too, but if you look at the image, the red channels seem to shrink and grow as they cross other channels | 16:52 |
| fenn | this image http://m.sciencemag.org/content/309/5731/137/F1.large.jpg | 16:52 |
| kanzure | pressure valves.. where they cross, you're trying to increase the amount of pressure to drive down the membrane to cover the other channel | 16:52 |
| kanzure | oh also it looks like they might be trying to control pressure or concentration? | 16:53 |
| kanzure | like look under the word "loop" in green on the bottom left | 16:53 |
| fenn | F7: the EZ430 is really chunky.. i'm not sure i want to wear it all the time | 16:53 |
| fenn | under "loop", is that a valve? | 16:54 |
| fenn | the one above "pump" looks like it's valving something | 16:55 |
| kanzure | the one under loop is idk | 16:55 |
| fenn | F7: for example it's hard to reach into my pocket with it on | 17:05 |
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| kanzure | fenn: did you get the parts all picked uot | 18:03 |
| kanzure | out | 18:03 |
| bkero | kanzure: ping | 18:06 |
| bkero | Anything I should see while in Copenhagen? | 18:07 |
| kanzure | juul: superping | 18:07 |
| kanzure | whatever juul recommends | 18:07 |
| kanzure | copenhagen suborbitals. go steal his submarine. | 18:07 |
| kanzure | bioligigaragen | 18:08 |
| bkero | fwah? | 18:08 |
| juul | bkero, Kristiania and Labitat | 18:08 |
| kanzure | Mogens Hvidtfeldt <mogens@hvidtfeldt.dk> | 18:08 |
| kanzure | Lasse Nørfeldt <lasse@norfeldt.dk> | 18:08 |
| juul | yeah and if you can get a tour of copenhagen suborbitals but i don't really have contacts for that | 18:08 |
| kanzure | Tobias H. Michaelsen | 18:08 |
| kanzure | Martin Malthe Borch | 18:08 |
| juul | yeah and biologigaragen is in Labitat | 18:08 |
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| kanzure | oh | 18:08 |
| kanzure | right then! labitat. | 18:08 |
| kanzure | bkero: yeah you should definitely check out his submarine | 18:09 |
| juul | then there's Illutron which is an old tiny ferry-type boat | 18:09 |
| juul | also hacker/maker types | 18:09 |
| bkero | Who?'s submarine? | 18:09 |
| juul | there's actually three submarines | 18:09 |
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| kanzure | http://forums.somethingawful.com/showthread.php?threadid=3005279&userid=0&perpage=40&pagenumber=2 | 18:09 |
| kanzure | http://forums.somethingawful.com/showthread.php?threadid=3271649&userid=0&perpage=40&pagenumber=1 | 18:09 |
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| juul | https://en.wikipedia.org/wiki/UC3_Nautilus | 18:10 |
| bkero | kanzure: that's super badass | 18:10 |
| bkero | kanzure: Who's Morgens, Lasse, Tobias, and Martin? | 18:11 |
| kanzure | i'm not really sure how i know them. i just talk with them about biohacking and they are in copenhagen. | 18:12 |
| bkero | haha cool | 18:12 |
| bkero | Members of the diybio list? | 18:12 |
| kanzure | no not to my knowledge | 18:12 |
| juul | http://biologigaragen.org/ | 18:12 |
| bkero | found that | 18:13 |
| bkero | juul, kanzure: don't know anybody at copenhagen suborbitals though? | 18:14 |
| kanzure | lemme check | 18:14 |
| juul | no, unfortunately not, but you should go talk to the illutron people as there is overlap in people and the space/tools they use | 18:15 |
| kanzure | aha | 18:15 |
| kanzure | this guy uc3nautilus@hotmail.com | 18:15 |
| kanzure | that's peter madsen's email | 18:16 |
| bkero | cool | 18:16 |
| * bkero is going to be in copenhagen for a mercurial code sprint next month and is staying an extra week for touring | 18:16 | |
| kanzure | mergecurial | 18:17 |
| juul | for regular touristy stuff you could go visit vesterbro + noerrebrogade (equivalent to the mission district in SF). I recommend that you rent a bike, as Copenhagen is an excellent bike city. | 18:17 |
| juul | cool | 18:17 |
| juul | tivoli is fun, but touristy | 18:17 |
| juul | take a bike ride / walk along the lakes | 18:18 |
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| bkero | yea | 18:19 |
| bkero | I'm looking on airbnb now for where to stay for the extra week | 18:19 |
| juul | labitat has meeting nights on tuesdays starting at around 7 pm and you can probably find someone to act as your guide | 18:19 |
| * bkero will try to do that | 18:19 | |
| juul | there's also couchsurfing :) | 18:19 |
| bkero | yea | 18:19 |
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| bkero | I need something reliable since I won't really be taking any time off of work. | 18:20 |
| bkero | (I telecommute) | 18:20 |
| juul | ah | 18:20 |
| bkero | Or I could just take the week off, I have built up PTO | 18:20 |
| kanzure | haha i would hope mozilla lets you telecommute. geeze. | 18:20 |
| bkero | they might be relocating me to london | 18:21 |
| * bkero takes off for dinner | 18:21 | |
| bkero | Thanks for the info and if you're ever in Portland or the Bay Area let me know and I'll make sure you have a good time ) | 18:22 |
| bkero | :) | 18:22 |
| kanzure | he is in the bay area haha | 18:22 |
| bkero | juul: I'm Ben Kero by the way, don't think we've been introduced. I'm a hacker interested in ##hplusroadmap topics and general open sourcery. | 18:22 |
| bkero | I'm a sysadmin at Mozilla | 18:22 |
| bkero | juul: let's meet up next time I'm in the bay then, it'll only be a few months | 18:23 |
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| juul | bkero, cool, yeah let's | 18:37 |
| juul | I'm Marc Juul | 18:37 |
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| kanzure | hi klafka | 19:19 |
| klafka | sup | 19:19 |
| kanzure | SF startup shuffle.. always a fun ride | 19:20 |
| klafka | ? | 19:20 |
| klafka | what's that | 19:20 |
| kanzure | hustle and bustle | 19:21 |
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| kanzure | nmz787: hi | 20:23 |
| nmz787 | hey | 20:23 |
| nmz787 | whats new | 20:23 |
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| kanzure | yashgaroth: do you know the person who is doing diy RNAi? | 21:12 |
| yashgaroth | nope? | 21:12 |
| kanzure | me either. | 21:12 |
| yashgaroth | you mean that stuff you quoted earlier? where was it from | 21:13 |
| kanzure | i don't even remember | 21:13 |
| nmz787 | you just had it in a text file? | 21:13 |
| nmz787 | untagged? | 21:13 |
| kanzure | no it was from some dark part of the interwebs | 21:13 |
| nmz787 | ahh | 21:13 |
| nmz787 | so the price of the cutter isnt too bad | 21:14 |
| nmz787 | i still need to figure out the optics | 21:14 |
| kanzure | yes please :P | 21:14 |
| nmz787 | i dont have a frickin spectrometer to measure the damn acrylic | 21:14 |
| kanzure | what happened to your spectrophotometer | 21:15 |
| nmz787 | i guess i can just power this NIR laser on at some acrylic and see if it burns | 21:15 |
| nmz787 | etches | 21:15 |
| nmz787 | i need to design the optics | 21:15 |
| nmz787 | :P | 21:15 |
| kanzure | heh i sense a theme | 21:15 |
| nmz787 | yeaaahhh | 21:15 |
| nmz787 | time has been an issue | 21:16 |
| nmz787 | cant talk now actually | 21:16 |
| nmz787 | ttyl | 21:16 |
| kanzure | seeya | 21:16 |
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| yashgaroth | I can't imagine what target they'd pick for inducing autoimmunity, if they're sticking with the bodybuilding theme | 21:17 |
| yashgaroth | even inducing one to soluble myostatin would be rather dangerous | 21:18 |
| kanzure | might be bullshit | 21:18 |
| yashgaroth | nah, I'm sure someone's been doing it, at least the RNAi stuff | 21:18 |
| kanzure | RNAi at least doesn't cause AIDS | 21:19 |
| kanzure | or wait.. what's the self-rejection disease called | 21:19 |
| yashgaroth | there's many...lupus? | 21:19 |
| kanzure | it's not lupus | 21:19 |
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| yashgaroth | never | 21:19 |
| yashgaroth | wait were you referencing House or were you actually thinking of another one | 21:20 |
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| kanzure | yashgaroth: another one | 21:20 |
| kanzure | what is house? | 21:20 |
| yashgaroth | tv show with hugh laurie where he diagnoses diseases | 21:20 |
| yashgaroth | a semi-catchline of it is "it's never lupus" | 21:21 |
| kanzure | oh, you mean house the show | 21:21 |
| kanzure | right. yes. | 21:21 |
| kanzure | anyway, no, i think there's another autoimmune disease | 21:21 |
| yashgaroth | well, diabetes, MS, uh | 21:21 |
| yashgaroth | eczema | 21:22 |
| yashgaroth | and a hundred super-rare ones | 21:22 |
| yashgaroth | oh psoriasis | 21:23 |
| klafka | there are tons | 21:26 |
| yashgaroth | but inducing one would be rather insane | 21:27 |
| klafka | yes | 21:28 |
| klafka | that sounds like a really terrible idea | 21:29 |
| diginet | inducing autoimmune disorders? wat? | 21:33 |
| yashgaroth | indeed | 21:35 |
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| diginet | heh, if you want to be disturbed, read pro-anorexia forums. yes, they exist. | 21:38 |
| kanzure | surely that is not the most disturbing thing you can find on the internet | 21:40 |
| kanzure | you're not even trying | 21:40 |
| joshcryer | Don't Google Mexican chainsaw beheading. | 21:41 |
| kanzure | still not trying hard enough | 21:42 |
| joshcryer | I'm not sure I would want to see anything more disturbing than that. | 21:42 |
| diginet | the most disturbing thin on the internet is the weird parts of reddit | 21:45 |
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| diginet | like "PicsOfDeadChildren" | 21:46 |
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| yashgaroth | how I envy you | 21:46 |
| klafka | lol | 21:47 |
| diginet | I don't look at that stuff | 21:47 |
| kanzure | yashgaroth: hah | 21:52 |
| kanzure | diginet: yeah, that's unfortunately not the worst of the internet | 21:52 |
| klafka | not nearly | 21:53 |
| klafka | my friend works for youtube spamops | 21:54 |
| klafka | he definitely sees the worst of the internet | 21:54 |
| juul | my friend runs a Tor exit node | 21:55 |
| juul | also pretty bad | 21:55 |
| diginet | kanzure, I'm sure the guy who runs that I'm sure has something else up his sleeve | 21:56 |
| diginet | tor/freenet are pretty disgusting, about the only thing they are really uses for is CP, which is about the most vile thing I can think of | 21:56 |
| juul | diginet, wut? no that is definitely not true | 21:57 |
| juul | run an exit node and see for yourself | 21:57 |
| diginet | what else is it used for? | 21:57 |
| kanzure | holy carp | 21:58 |
| kanzure | yeah, tons of legitimate activity | 21:58 |
| diginet | every directyory I see on there is riddled with CP | 21:58 |
| diginet | or just porn | 21:58 |
| joshcryer | Wait, what is the worst of the internet? | 21:59 |
| diginet | I mean, there's porn, people claiming to be hitmen, Randroids, that's about all I see, but who knows | 21:59 |
| kanzure | joshcryer: 1000x worse than the dnepropetrovsk maniacs | 21:59 |
| kanzure | diginet: whatever you do don't type in anything you see from us in the past 20min or the next 20min | 22:00 |
| kanzure | diginet: you have been unscathed by the internet and you should cherish this | 22:00 |
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| ParahSailin__ | heh Randroids arent even close to the worst | 22:01 |
| joshcryer | No actually I agree that Randroids do ruin the internet. | 22:01 |
| diginet | kanzure, thanks L) | 22:01 |
| diginet | :) | 22:01 |
| diginet | I love all the Randroids on reddit, it's funny how all the chauvinists/eugenicists/racists/etc on there are probably losers in real life, who wouldn't live up to their own standards | 22:02 |
| * ParahSailin__ moderates /r/Objectivism | 22:03 | |
| * diginet quickly tries to avoid massive argument | 22:03 | |
| kanzure | also, can we stop talking about reddit | 22:04 |
| kanzure | let's ban reddit | 22:04 |
| diginet | sorry I brought it up | 22:04 |
| joshcryer | Reddit will make you rich dude. Get on the front page, profit! | 22:04 |
| klafka | so guys did you see reddit last night? | 22:04 |
| diginet | no | 22:05 |
| joshcryer | From an H+ perspective, probably the neo-Luddites are the worst. | 22:09 |
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| fenn | mmm dead children | 22:11 |
| kanzure | fenn: optics? | 22:12 |
| fenn | afraid i'm too stupid to function today | 22:12 |
| fenn | think i caught some sort of flu | 22:12 |
| diginet | I hate radiation fear-mongers | 22:13 |
| fenn | i definitely don't want an RS485 stepper controller | 22:13 |
| kanzure | diginet: you surround yourself with the oddest people. maybe if you stop visiting reddit your circle of friends will improve. like.. for instance, not radiation fearmongerers | 22:14 |
| diginet | oh, I hate reddit | 22:14 |
| diginet | I don't go there | 22:14 |
| kanzure | fenn: why do you say that | 22:14 |
| fenn | also, i work hard to keep the price down so that people who want to reproduce our results are able to do so without massive engineering | 22:14 |
| fenn | a $225 stepper motor driver is just dumb | 22:15 |
| diginet | I don't really have "friends" per se, anyhow though | 22:15 |
| kanzure | ah didn't know the price | 22:15 |
| kanzure | diginet: i'll be your friend. | 22:15 |
| diginet | awwww :) | 22:15 |
| fenn | anyway, i'd rathe run EMC, and serial comms is not compatible | 22:15 |
| kanzure | you can even facebook me. http://facebook.com/kanzure | 22:15 |
| kanzure | fenn: sure. i'd prefer emc too. | 22:15 |
| diginet | I'm kind of a loner IRL | 22:15 |
| fenn | diginet: aside from diamonds, what is there you _do_ like? | 22:15 |
| fenn | oh, and spiders | 22:16 |
| kanzure | diamonds and spiders | 22:16 |
| kanzure | because he's spiderman | 22:16 |
| diginet | spider diamonds? | 22:16 |
| diginet | Umm | 22:16 |
| diginet | let me think | 22:16 |
| diginet | I like physics, dead languages, Roman and Byzantine history | 22:16 |
| fenn | maybe a role model | 22:16 |
| ParahSailin__ | diginet, i want to go to tx-rx but i wanna bring someone along in case its weird | 22:17 |
| diginet | kanzure: requested | 22:17 |
| diginet | ParahSailin__, if you don't mind me asking: how old are you? | 22:18 |
| kanzure | hmm my guess is at least 23 | 22:18 |
| diginet | I'm 18, but I look about 15-16 | 22:18 |
| joshcryer | I'm 35 and look about 20. | 22:18 |
| ParahSailin__ | im 26 | 22:18 |
| kanzure | i'm eternally 12 | 22:18 |
| joshcryer | I got carded for lottery tickets recently. | 22:19 |
| diginet | I'm immature and mature at the same time, I've always enjoyed the company of older people rather than my peers, but yet at the same time I like doing "childish" things, and am somewhat (well very) naive | 22:19 |
| diginet | ParahSailin__, how much does it cost? | 22:19 |
| ParahSailin__ | dunno, i think ill go to the next open house, but not this week because im out of town then | 22:20 |
| kanzure | ParahSailin__: you should go with F7 | 22:20 |
| kanzure | F71: ping | 22:20 |
| kanzure | diginet: attendance is free | 22:21 |
| diginet | ah okay | 22:21 |
| joshcryer | What is tx-rx? | 22:21 |
| kanzure | membership probably costs | 22:21 |
| kanzure | joshcryer: some hackerspace | 22:21 |
| diginet | well kanzure if you accept my friend request you'll get to enjoy all my acerbic status updates | 22:21 |
| diginet | I do love that word | 22:21 |
| kanzure | diginet: dude you have rage comics and "literally hitler" everywhere. you're from reddit. | 22:22 |
| joshcryer | Oh Houston. | 22:22 |
| klafka | LOL | 22:22 |
| diginet | Rage comics? | 22:23 |
| diginet | wat | 22:23 |
| diginet | no | 22:23 |
| yashgaroth | hiterally litler | 22:23 |
| klafka | kanzure is eternally 12 | 22:23 |
| diginet | also my last name isn't Palaiologos, it's Keith. The Palaiologos comes from the last dynasty of the Byzantine Empire | 22:23 |
| diginet | the "literally hitler" was sarcasm | 22:23 |
| klafka | i feel like an adult because i'm going to buy furniture from ikea soon | 22:23 |
| * joshcryer contemplates friending kanzure | 22:23 | |
| klafka | :( | 22:23 |
| joshcryer | Are you a frequent updater kanzure? | 22:24 |
| diginet | kanzure, did you know my scumbag byzantine memes? | 22:24 |
| diginet | I feel like such a loser | 22:24 |
| klafka | i bet he posts a lot to linkedin | 22:24 |
| klafka | just chatting all the time there | 22:24 |
| kanzure | joshcryer: i update like once a year | 22:24 |
| joshcryer | OK, that's good. | 22:25 |
| kanzure | i have more friends on google+ :( | 22:25 |
| joshcryer | I now have 24 friends. | 22:25 |
| diginet | GOOGLE+ IS LITERALLY SATAN | 22:25 |
| kanzure | https://plus.google.com/102967708777429109844/posts | 22:25 |
| diginet | no, but seriously I hate Google with a fiery passion | 22:25 |
| klafka | why? | 22:25 |
| diginet | because, they're monopolist bastards | 22:26 |
| klafka | how are they monopolist? | 22:26 |
| joshcryer | Wait who is Eudoxia and how do we both know them kanzure? | 22:26 |
| diginet | DON'T QUESTION ME | 22:26 |
| diginet | I'm weird, I hate communism, but I also hate most big businesses | 22:26 |
| klafka | why do you hate communism? | 22:26 |
| yashgaroth | eudoxia is the resident uruguayan | 22:26 |
| klafka | or big businesses? | 22:26 |
| diginet | well, I'm weird in general, that is merely one facet of my hatred | 22:26 |
| kanzure | klafka: don't poke the troll | 22:26 |
| diginet | I'm not trolling :( | 22:27 |
| diginet | sorry | 22:27 |
| klafka | so you just irrationally dislike these things? | 22:27 |
| klafka | or do you have reasons | 22:27 |
| diginet | I go off on tangents | 22:27 |
| kanzure | you hate like all of us | 22:27 |
| joshcryer | yashgaroth, ahh yes I recall now. | 22:27 |
| diginet | no, you guys are awesome | 22:27 |
| diginet | I have rational and irrational reasons | 22:27 |
| klafka | illuminative | 22:27 |
| diginet | I more hate relativism/cultural marxism than communism itself | 22:27 |
| diginet | but I think I already articulated that before | 22:28 |
| diginet | but I do have TONS of irrational hatreds | 22:28 |
| diginet | like flip flops | 22:28 |
| diginet | I LOATHE THOSE VILE EXCUSES OF "SHOES" | 22:28 |
| diginet | sorry | 22:28 |
| diginet | you don't understand how much I hate flip flops, or open shoes in general | 22:29 |
| joshcryer | So you hate toes? | 22:29 |
| diginet | I also hate alcohol | 22:29 |
| diginet | I hate visible feet | 22:29 |
| kanzure | ParahSailin__: http://diyhpl.us/~bryan/images/aubrey.jpg | 22:29 |
| klafka | so do you have any fetishes? | 22:29 |
| klafka | what are your kinks? | 22:29 |
| klafka | do you like to tie people up? | 22:29 |
| yashgaroth | man you're gonna hate college, no flip flops or alcohol | 22:29 |
| diginet | I'm asexual, so I don't have any I guess | 22:29 |
| ParahSailin__ | lol | 22:29 |
| diginet | oh, I already do | 22:29 |
| diginet | colleges are full of douchebags, ugh | 22:30 |
| klafka | i didn't drink or wear flip flops all through college | 22:30 |
| klafka | it was pretty awesome | 22:30 |
| diginet | actually, colleges have basically everything I hate about the world in one nice little tidy package | 22:30 |
| klafka | learning? | 22:30 |
| kanzure | libraries? | 22:31 |
| klafka | academia? | 22:31 |
| kanzure | women? | 22:31 |
| klafka | frogs? | 22:31 |
| diginet | Okay I like those | 22:31 |
| klafka | you don't like women | 22:31 |
| klafka | you've already said that | 22:31 |
| diginet | I like women | 22:31 |
| joshcryer | They have feet. | 22:31 |
| diginet | I just don't like their feet | 22:31 |
| diginet | but women are all right | 22:31 |
| diginet | some of my favourite people are women | 22:31 |
| -!- mode/##hplusroadmap [+o kanzure] by ChanServ | 22:31 | |
| joshcryer | There are women without feet, true. | 22:31 |
| -!- joshcryer was kicked from ##hplusroadmap by kanzure [klafka diginet] | 22:31 | |
| @kanzure | fdklsadasfkaslda | 22:31 |
| @kanzure | what | 22:31 |
| klafka | LOL | 22:31 |
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| klafka | FINE | 22:32 |
| @kanzure | that went terribly | 22:32 |
| diginet | :( | 22:32 |
| diginet | were you meaning to kick me? | 22:32 |
| @kanzure | joshcryer: i am sorry bro | 22:32 |
| yashgaroth | what's going onnnn | 22:32 |
| joshcryer | I'm just glad to be first on the list. | 22:32 |
| klafka | i'm going to watch st:tng and fall asleep :P | 22:32 |
| diginet | does everyone hate me now? | 22:32 |
| klafka | since i have to get up at 630 tomorrow | 22:32 |
| klafka | no | 22:32 |
| klafka | i'm pretty apathetif | 22:32 |
| diginet | night night klafka | 22:32 |
| @kanzure | diginet: nobody hates you | 22:32 |
| klafka | apathetic | 22:32 |
| diginet | ah okay | 22:32 |
| @kanzure | but the signal to noise is all out of whack | 22:32 |
| diginet | I'm sorry, my meds wear off about this hour | 22:33 |
| joshcryer | I was barely contributing. But I was still the first to be listed in fail kick alias. :P | 22:33 |
| fenn | eat dark green leafy vegetables | 22:33 |
| klafka | i need to eat more of those | 22:33 |
| diginet | is it just me or are colleges STD infected cesspools or exposed feet, drunkenness, and date-rape? | 22:34 |
| katsmeow-afk | Adrafinil is being made again, if that helps | 22:34 |
| diginet | *of | 22:34 |
| -!- mode/##hplusroadmap [+o fenn] by ChanServ | 22:35 | |
| -!- mode/##hplusroadmap [-o kanzure] by ChanServ | 22:35 | |
| kanzure | fenn's problem now | 22:35 |
| diginet | because when I toured at Rice (no offense ParahSailin__) my guide person just seemed to brag about how they get drunk at parties and sleep around | 22:36 |
| diginet | two things absolutely no appeal to me | 22:36 |
| diginet | *with | 22:36 |
| diginet | alright back to business: does anyone here know anything about continuous bioreactors? | 22:38 |
| yashgaroth | yes | 22:39 |
| diginet | what can you tell me about them? would it be hard for me to build one? | 22:41 |
| yashgaroth | lots; yes | 22:41 |
| diginet | should I just give up on that and go for batch? | 22:42 |
| yashgaroth | yes, flasks are much easier unless you've got money to burn | 22:42 |
| diginet | I wonder what kind of yields I could get with batch | 22:43 |
| yashgaroth | absolute peak yields are 1-20 grams per liter, depending on cell type and how much effort you put into optimizing expression | 22:44 |
| diginet | do you think DIY growth medium would be feasible? | 22:44 |
| yashgaroth | for bacteria and yeast, sure | 22:45 |
| yashgaroth | cells from multicellular organisms need blood factors | 22:45 |
| diginet | I'm trying to use Pichia | 22:45 |
| diginet | what are good sources for the nutrients I would need? | 22:46 |
| yashgaroth | vegemite | 22:47 |
| diginet | seriously? | 22:47 |
| yashgaroth | yeast extract and salt, mixed with water | 22:47 |
| yashgaroth | but you can get the various ingredients in bulk and mix them yourself for fairly cheap | 22:48 |
| diginet | can one even buy that in the states? | 22:48 |
| diginet | haha | 22:48 |
| yashgaroth | it's sold as marmite | 22:48 |
| diginet | this may sound stupid: would plant fertilizer work? | 22:49 |
| ParahSailin__ | seriously i will borrow extra lb from my lab so that you dont have to do that | 22:49 |
| yashgaroth | no not plant fertilizer | 22:49 |
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| diginet | ParahSailin__, wow, thanks for being so nice to me :) | 22:49 |
| yashgaroth | but seriously it's pretty cheap for unicellulars, don't worry about that | 22:49 |
| diginet | I didn't think so | 22:49 |
| diginet | well, I'm going to need a fair amount of the spidroins to make any sizeable quantity of silk | 22:50 |
| ParahSailin__ | diginet, check pm | 22:51 |
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| ParahSailin__ | night | 22:56 |
| diginet | ah okay, night | 23:00 |
| diginet | oh, I also adore classical music | 23:02 |
| diginet | yashgaroth: one thing I'm potentially concerned about is the difficulty of purifying the protein | 23:03 |
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| yashgaroth | depends whether it'll start forming fibers in the media or during the purification | 23:04 |
| yashgaroth | I dunno what conditions cause them to start polymerizing, but especially when purifying they'll be at high concentrations and close to each other | 23:05 |
| yashgaroth | might be better off trying to dissolve one of those huge communal spiderwebs and weaving them into something else | 23:05 |
| diginet | I'm not concerned with that as much, you have to induce polymerization by lowering the pH | 23:06 |
| diginet | and extruding it | 23:06 |
| diginet | (the act of squeezing causes fibers to form | 23:07 |
| diginet | =) | 23:07 |
| diginet | I'm just wondering how hard protein purification is in general | 23:07 |
| yashgaroth | it can be easy | 23:07 |
| yashgaroth | ...ish | 23:08 |
| diginet | uh oh | 23:09 |
| yashgaroth | I'm sure you can find a suitable method | 23:13 |
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| ParahSailin__ | F71, you are in houston? | 23:16 |
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| ParahSailin__ | You're just jealous. This dropped a huge stage full of funding/legitimacy on both syn bio and this community. ... You're typing, for free, on Al Gore's Internet, which used to be called ARPANET, with the first D missing ... | 23:26 |
| ParahSailin__ | rage | 23:26 |
| yashgaroth | ? | 23:27 |
| ParahSailin__ | some thread on diybio list | 23:27 |
| diginet | could malt extract be used for a nutrient source for my yeast? | 23:28 |
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| yashgaroth | oh jcline | 23:29 |
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| yashgaroth | you'd need to hydrolyse the malt extract but sure why not | 23:30 |
| diginet | well it's really cheap, and pre-groud | 23:30 |
| diginet | so I thought it might be a good option | 23:30 |
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| diginet | as much as I hate alcohol, all of the DIY beer brewing information is really useful for my purposes | 23:36 |
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| skorket | hey folks | 23:39 |
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| --- Log closed Tue Apr 10 00:00:29 2012 | ||
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