| --- Log opened Sun Jul 03 00:00:46 2016 | ||
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| CaptHindsight | anyone have access to this? http://pubs.acs.org/doi/abs/10.1021/nl502626s?source=cen | 04:17 |
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| Jawmare | CaptHindsight, libgen, noob | 04:37 |
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| CaptHindsight | Jawmare: that site that was taken down recently? | 05:05 |
| Jawmare | CaptHindsight, alright | 05:07 |
| Jawmare | 1sec | 05:07 |
| Jawmare | https://www.sendspace.com/file/t1hby5 | 05:08 |
| CaptHindsight | thanks | 05:10 |
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| c0rw1n- | http://gen.lib.rus.ec/ looks pretty functional for a site that was taken down | 06:16 |
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| kanzure | it depends on your isp etc | 06:24 |
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| CaptHindsight | yeah lets focus on this | 06:33 |
| CaptHindsight | why does this channel attract so many asshats? | 06:34 |
| CaptHindsight | bbl | 06:35 |
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| kanzure | "weaponized crispr" | 11:20 |
| kanzure | there is funding available if anyone wants to do open-source GMP production of (amgen-style) erythropoietin | 11:21 |
| kanzure | "The world's technological capacity to store, communicate and compute information" http://www.uvm.edu/~pdodds/files/papers/others/2011/hilbert2011a.pdf | 11:31 |
| yashgaroth | what, like a biosimilar for EPO? I don't get what open source really means in that context | 11:32 |
| kanzure | that probably means all the hardware necessary to produce it | 11:32 |
| yashgaroth | well I wouldn't mind an open source bioreactor, HPLC, FPLC, and bioprofile analyzer | 11:33 |
| kanzure | right.. | 11:33 |
| yashgaroth | there's already a dozen companies making biosimilars for EPO, and if they want it "GMP" I hope they understand what that means | 11:33 |
| yashgaroth | it's going to be as cheap from one of those companies as from this, if they want it actually GMP | 11:34 |
| yashgaroth | wait, more expensive since we need to design and build and publish a bunch of new open source lab equipment | 11:34 |
| yashgaroth | I mean there are better ways to spend fifty million dollars | 11:36 |
| kanzure | https://www.src.org/program/grc/semisynbio/ | 11:36 |
| kanzure | https://www.src.org/program/grc/semisynbio/semisynbio-consortium-roadmap/ | 11:37 |
| CaptHindsight | 1. DNA-based Massive Information Storage heh, who's brilliant idea is this? | 11:40 |
| xentrac | .g cockroaches lanier times | 11:41 |
| yoleaux | xentrac: Sorry, that command (.g) crashed. | 11:41 |
| xentrac | that's the earliest concrete proposal I've seen, CaptHindsight | 11:42 |
| xentrac | but the JCV-syn series of genomes include a list of credits and a copyright statement | 11:42 |
| xentrac | .t http://www.jaronlanier.com/roach.html | 11:43 |
| yoleaux | xentrac: Sorry, I don't know what timezone that is. If in doubt, see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones for a list of options. | 11:43 |
| xentrac | oh right it's pre-saxo | 11:43 |
| xentrac | 1999-05-03, "A Time Capsule that will survive One Thousand Years in Manhattan" | 11:43 |
| xentrac | although I remember people in the 1990s talking about information exfiltration via DNA | 11:44 |
| CaptHindsight | Error correction of microchip synthesized genes using Surveyor nuclease http://nar.oxfordjournals.org/content/early/2011/11/29/nar.gkr887.full | 11:45 |
| xentrac | "now you have to slip an exabyte tape cartridge in your shirt pocket before leaving the facility, but at some point you could just drip a drop of DNA on each of your fingernails" | 11:45 |
| CaptHindsight | "With two iterations, we were able to reduce errors in synthetic genes by >16-fold, yielding a final error rate of ∼1 in 8700 bp" | 11:45 |
| kanzure | CaptHindsight: also these things... http://groups.google.com/group/enzymaticsynthesis | 11:46 |
| CaptHindsight | lots of these articles look like they come from a modern version of Omni Magazine | 11:47 |
| kanzure | CaptHindsight: i still want to do a dna synthesizer with you at some point | 11:48 |
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| xentrac | CaptHindsight: Wired is the modern version of Omni, right? | 11:48 |
| kanzure | CaptHindsight: btw i started funding this thing https://docs.google.com/document/d/1xvLWDbp0x6z0Ft3AsfxjIsLUNsg5smkTcYb1g4WVo5U/edit | 11:48 |
| kanzure | (ultrasound imaging device) | 11:48 |
| CaptHindsight | kanzure: I'm going to make a working cheapo version inkjet for ChinaCo to copy | 11:50 |
| CaptHindsight | Epson DNA Inkjet Synthesizer on alibaba for a few $k | 11:51 |
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| kanzure | CaptHindsight: there needs to be a pipette tip to move all the samples around, for DNA assembly (like gibson assembly). | 11:52 |
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| CaptHindsight | nah, channels built into the slide | 11:53 |
| kanzure | valves ?? | 11:53 |
| CaptHindsight | controlled cleave/nicking | 11:54 |
| kanzure | how do you prevent the reaction material from draining down the channels immediately after inkjetting? | 11:54 |
| CaptHindsight | http://www.rsc.org/images/loc/2013/PDFs/Papers/638_0077.pdf | 11:59 |
| kanzure | "Subarrays were physically isolated from the rest of the chip by being located in individual wells, eliminating the need for post-synthesis partitioning of the oligo pool. We then integrate array oligo synthesis; amplification and gene assembly steps in physically isolated wells on the same chip." | 12:01 |
| kanzure | okay well that's the same thing as my "flooding" idea i guess... | 12:02 |
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| CaptHindsight | when you start building/printing/stacking each base you can couple/anchor/bond it to something to hold it there while you build the oligo | 12:06 |
| kanzure | that's right. | 12:06 |
| kanzure | "flooding" like in that paper does not require channels | 12:06 |
| kanzure | you just increase liquid content and physically rise above boundaries on the surface (like dams) | 12:06 |
| CaptHindsight | you can then cleave them from whatever you coupled/bonded/stuck from in each well | 12:07 |
| kanzure | yes that's right. | 12:07 |
| CaptHindsight | one well or multiple wells at a time | 12:07 |
| CaptHindsight | and then couple them together with an oligo from a different well | 12:08 |
| CaptHindsight | you can keep a cap on one end so it only grows in one direction | 12:10 |
| CaptHindsight | or like Silicon Valleys compression grow it from the middle out | 12:11 |
| kanzure | CaptHindsight: http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/ | 12:14 |
| CaptHindsight | https://www.alibaba.com/product-detail/2015-newest-A4-UV-printer-cell_60395368065.html | 12:17 |
| CaptHindsight | motorize the Z-axis | 12:17 |
| CaptHindsight | replace their controller | 12:18 |
| CaptHindsight | add the wash and dry nozzles | 12:18 |
| CaptHindsight | put it in a sealed enclosure | 12:18 |
| CaptHindsight | don't let them engineer anything | 12:19 |
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| kanzure | "Reading single DNA with DNA polymerase followed by atomic force microscopy" http://pubs.acs.org/doi/abs/10.1021/ja5063983 | 12:27 |
| kanzure | "Single-molecule imaging of DNA polymerase I (Klenow fragment) activity by atomic force microscopy" http://pubs.rsc.org/en/content/articlelanding/2016/nr/c5nr06544e#!divAbstract | 12:28 |
| kanzure | "Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms" http://nar.oxfordjournals.org/content/43/12/5998.short | 12:28 |
| kanzure | hm. | 12:31 |
| CaptHindsight | oh and don't work with anyone that mentions *duino, GRBL or reprap | 12:36 |
| xentrac | hah | 12:39 |
| CaptHindsight | kanzure: if someone could write an app to use the .json files from http://mix.bio/ and create proper G-code ot would be handy | 12:41 |
| CaptHindsight | ot/it | 12:41 |
| CaptHindsight | the idiots used a poopieboard | 12:42 |
| CaptHindsight | how do you add printheads, lasers, machine vision to a poopieboard? | 12:42 |
| CaptHindsight | I'm glad the hype from reprap is finally dying | 12:44 |
| xentrac | yeah, FDM is not going to get us to self-replicating machinery | 12:44 |
| CaptHindsight | it caused so much myopia in CNC designs | 12:44 |
| xentrac | I'd say rather the opposite | 12:45 |
| xentrac | it brought a huge number of novices into CNC designs | 12:45 |
| xentrac | naturally the first thing that novices do is that they copy existing designs | 12:45 |
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| xentrac | but some fraction of them will progress, and there are a bunch of innovative CNC and robotics designs as a result of this huge influx | 12:46 |
| xentrac | polar3d, deltabots, parallel SCARA, and whatnot | 12:46 |
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| xentrac | I agree that CNC designs are myopic but that's not a novel phenomenon. CNC designs have been myopic since the beginning half a century ago | 12:47 |
| xentrac | a lot of them are still, you know, slides, gantry, rails, ballscrews, bullshit like that | 12:47 |
| xentrac | enormous rigidity in place of feedback | 12:48 |
| xentrac | stuff you absolutely need to get high precision when it's 1890 and you're operating the machine by turning handles by hand | 12:49 |
| xentrac | (they didn't have ballscrews in 1890 but they also didn't get high precision) | 12:49 |
| CaptHindsight | contact vs non-contact applications | 12:51 |
| xentrac | definitely a factor | 12:51 |
| CaptHindsight | big iron is cheap and easy for contact | 12:52 |
| CaptHindsight | it was humorous at first to see repraps for cutting applications | 12:53 |
| xentrac | well, it's easy compared to things we haven't developed yet | 12:53 |
| xentrac | and it's cheap compared to computer control in 1960 | 12:54 |
| xentrac | not so much in 2020 | 12:54 |
| xentrac | I mean a kilogram of steel costs more than a microcontroller | 12:54 |
| xentrac | a 10-MIPS microcontroller | 12:54 |
| CaptHindsight | bbl | 12:55 |
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| chris_99 | Anyone used Murashige and Skoog Medium out of interest, i want to try plant tissue culturing in a simple fashion, i found sigma aldrich sell it fairly cheaply 1l for £5 i believe, then i'd need agar, but can i get away without a fancy hood etc.? | 13:35 |
| superkuh | Sure. But it's easy to build a glove box out of transparent storage container and some rubber gloves + pvc tube. | 13:38 |
| superkuh | For the seal you can cut apart a towel into strips, soak them in bleach, the lay them around the top rim. | 13:39 |
| chris_99 | aha, interesting! | 13:39 |
| superkuh | You don't necessarily need to buy that media anyway. You can make a decent one from potatoes. | 13:39 |
| xentrac | that won't offgas so much chlorine that it kills the tissue? | 13:39 |
| chris_99 | also is it fairly likely to succeed providing you follow the protocol? | 13:40 |
| xentrac | the bleach, I mean, not the potatoes | 13:40 |
| superkuh | I hadn't have issues with it in the past, xentrac. | 13:40 |
| superkuh | I mean, you don't want it dripping or anything. | 13:40 |
| superkuh | Just damp. | 13:40 |
| chris_99 | i just found which seems to explain it quite nicely - http://www.apsnet.org/edcenter/k-12/teachersguide/plantbiotechnology/documents/planttissueculture.pdf | 13:40 |
| chris_99 | *found this | 13:40 |
| chris_99 | that mentions bleach too | 13:41 |
| superkuh | http://erewhon.superkuh.com/library/Biology/Agrobacterium/Plants%20from%20test%20tubes_%20an%20introduction%20to%20micropropagation_%20Lydiane%20Kyte_%20John%20G%20Kleyn_%201996.epub is one of my go-to books for this. Lots of practical advice. | 13:41 |
| chris_99 | oh cheers | 13:41 |
| chris_99 | ill have a look | 13:41 |
| chris_99 | what kind of plants have you tried this on btw? also is the particular part of the plant that important, like leaf etc? | 13:42 |
| superkuh | I imagine you'd want the meristem or the like. | 13:43 |
| superkuh | I was not working with plants. | 13:43 |
| chris_99 | aha gotcha | 13:44 |
| archels | .title http://terencebroad.com/convnetvis/vis.html | 13:45 |
| yoleaux | Visualisation of Convolutional Neural Networks Topology | 13:45 |
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| chris_99 | heh finally got that book opened superkuh, forgot what epub reader i had, that book looks very nice | 13:56 |
| superkuh | I have a hard copy. | 13:57 |
| superkuh | Bought it from the university library for 50 cents. | 13:57 |
| chris_99 | haha | 13:57 |
| chris_99 | nice | 13:57 |
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| Paul-_ | and why wouldn't you filter sterilize your broth? | 14:35 |
| Paul-_ | just get a decent bunsen, they're not even that expensive | 14:36 |
| Paul-_ | or an alcohol burner if you're scared of bunsens | 14:36 |
| Paul-_ | we had to improvize mammalian cell cultures once when all the flow hoods were contaminated with myco | 14:41 |
| Paul-_ | of course everything breaks down just before you need to organize a practical for 130 students | 14:41 |
| chris_99 | darn | 14:42 |
| chris_99 | if that was to me, yeah i'm not adverse to fire, will look into a simple way to setup a bunsen, as i don't have a gas tank | 14:42 |
| Paul-_ | no need | 14:42 |
| Paul-_ | well of course you need gas | 14:42 |
| Paul-_ | but you have the small ones | 14:42 |
| Paul-_ | I think they're also used for blow torches | 14:43 |
| Paul-_ | you just screw on the bunsen piece | 14:43 |
| chris_99 | ah interesting, do you nee a regulator too | 14:43 |
| chris_99 | or..? | 14:43 |
| Paul-_ | nope | 14:43 |
| chris_99 | do you mean the kind of dispoasable gas canisters that you just clip a blow torch head onto | 14:44 |
| Paul-_ | we used to use them in my old lab too, because the building was just falling apart and aparently the gas mains were shut off in parts or sth | 14:44 |
| Paul-_ | yeah | 14:45 |
| Paul-_ | well it's not the tanks you puncture | 14:45 |
| Paul-_ | there's a little valve and a screw thread | 14:45 |
| Paul-_ | I've seen the same thread on canisters for those weed killer blowtorches, but they are too tall | 14:45 |
| chris_99 | ahh | 14:46 |
| Paul-_ | tbh I just asked our technician and he slipped me one of those tanks, but I can't imagine they're hard to come by | 14:46 |
| chris_99 | mmm i'll look into that, as it'd be handy to have bunsen burner | 14:47 |
| Paul-_ | any decent camping/outdoor store should have them, and it shouldn't be too hard to find the bunsen attachment | 14:47 |
| Paul-_ | I got mine on ebay, but that was already quite a while ago | 14:47 |
| chris_99 | just found this - https://www.fishersci.com/shop/products/self-contained-lpg-burner/s41872 | 14:48 |
| chris_99 | might be better to get a normal bunsen though | 14:49 |
| Paul-_ | why, that thing looks pretty sweet | 14:49 |
| Paul-_ | pretty expensive tho | 14:49 |
| chris_99 | yeah, the price, and woudln't i need a longer stand | 14:50 |
| Paul-_ | those disposable gas tanks go for a few euros here I'm told, and I got the bunsen for $20 or something from china | 14:50 |
| Paul-_ | I have this one: (search bunsen, first hit) http://www.eurofysica.nl/media/113493/catalogos%20eurofysica%202012-2013%20website.pdf | 14:54 |
| Paul-_ | and they go on the little gray tanks a bit further on the page | 14:55 |
| chris_99 | ah cool, but as it fits straight on the tank, doesn't the bunsen stand need longer legs than normal? | 14:55 |
| Paul-_ | what would you want a stand for? | 14:56 |
| chris_99 | for putting a flask on it | 14:57 |
| Paul-_ | why put a flask on a bunsen? | 14:57 |
| chris_99 | isn't that a usual thing to do with bunsens | 14:58 |
| Paul-_ | no | 14:58 |
| Paul-_ | 50 years ago maybe | 14:58 |
| Paul-_ | I've never seen anyone in an actual lab use a bunsen to heat flasks/reactions | 14:59 |
| yashgaroth | not since microwaves were invented | 14:59 |
| chris_99 | oh interesting | 14:59 |
| Paul-_ | or hotplates, waterbaths, oilbaths, etc | 14:59 |
| chris_99 | wait so what did you mean to use the bunsen for | 15:00 |
| Paul-_ | create updraft to create an environment where you don't get anything from the air contaminating your cultures | 15:01 |
| Paul-_ | or flame sterilizing innoculation loops | 15:01 |
| Paul-_ | stuff like that | 15:01 |
| chris_99 | ahh | 15:01 |
| chris_99 | gotcha | 15:01 |
| chris_99 | ive only used a bunsen burner in highschool before | 15:01 |
| Paul-_ | chemistry labs don't even have bunsens | 15:01 |
| chris_99 | interestin | 15:02 |
| chris_99 | *interesting | 15:02 |
| Paul-_ | well the occasional one, but not for heating anything in glass | 15:02 |
| chris_99 | say for distillation with glassware, would they just use a hotplate | 15:03 |
| Paul-_ | borosilicate can withstand about a 160C difference in temperature, so if you put something that's 0C in borosilicate in an oilbath that's 160C you should be ok but cutting it close | 15:03 |
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| Paul-_ | a decent bunsen reaches 1500C easily | 15:03 |
| yashgaroth | distillation is mostly in heating mantles, but I'm not a chemist | 15:04 |
| Paul-_ | I personally prefer oilbaths | 15:04 |
| Paul-_ | well technically not oil but a very large ethoxylated alcohol | 15:04 |
| Paul-_ | no smell, you can heat it up to 200C no problem and you rinse it off with water | 15:05 |
| Paul-_ | and you have a very accurate control over your temperature | 15:05 |
| ybit_ | http://blogs.plos.org/synbio/2016/06/28/why-plants-part-i-feynman-and-flowers/ | 15:05 |
| ybit_ | http://openplant.org/ | 15:05 |
| Paul-_ | heating mantles are convenient but you need a different size for every different size flask and if you fuck up and spill and it's not a very modern one it either catches fire or shorts out | 15:06 |
| Paul-_ | and only the really expensive ones have stirring | 15:06 |
| chris_99 | is the oil recirculated at all? | 15:07 |
| ybit_ | http://openplant.org/openplantforum/ | 15:07 |
| Paul-_ | yeah, I use a hotplate with a magnetic stirrer and a temperature controller | 15:07 |
| Paul-_ | so that's basically a fancy thermostat with a pt1000 sensor you put in the oil which determines the heat capacity and dT so it keeps it within a tenth of a degree of the set temperature | 15:08 |
| Paul-_ | if you overshoot your temperature by much with distillation shit can go sideways very fast | 15:10 |
| chris_99 | oh gotcha, so just so i can picture this, what's the stirrer in?, so you have hotplate ---> flask with oil + stirrer in ----> then something else in that, that's actually getting heated? | 15:10 |
| Paul-_ | I should have a picture somewhere | 15:11 |
| Paul-_ | https://www.dropbox.com/s/wf1s23hdwn1lw7m/2016-06-04%2003.45.30.jpg?dl=0 | 15:12 |
| Paul-_ | https://www.dropbox.com/s/c06ctjroxh7drzk/2016-06-04%2005.54.18.jpg?dl=0 | 15:12 |
| Paul-_ | the grey disk around the flask is a flap I casted out of silicone because this was before I got the nice heating medium | 15:13 |
| Paul-_ | the paraffin oil smells up the place and if a drop of water falls in it splashes | 15:13 |
| chris_99 | ok, in your second one, i guess the metal above the hot plate is the bath? and you have magnetic stirbar in that? | 15:13 |
| Paul-_ | yes, and another one in my flask | 15:14 |
| Paul-_ | it's a little tricky using 2, it's not made for that, but with some trial and error it works | 15:14 |
| chris_99 | ok, so i assume the glassware is suspended above the stirbar right with a clamp thing | 15:14 |
| Paul-_ | yeah | 15:14 |
| chris_99 | gotcha, that makes sense now, cool | 15:14 |
| Paul-_ | and the hotplate is raised on a platform, so if at some point the temperature gets too high I can immediately remove the heat source | 15:15 |
| chris_99 | what do you call that piece of glass out of interest, with the 3 ports | 15:15 |
| Paul-_ | all the tin foil is to insulate the fractioning column | 15:15 |
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| Paul-_ | a three neck roundbottom flask | 15:16 |
| chris_99 | cheers, is that lab in your house then | 15:16 |
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| Paul-_ | the right one has a tube on it because I was doing a distillation that had the tendency to foam and I could release pressure through the valve | 15:17 |
| chris_99 | neat | 15:17 |
| kanzure | page 10 "Single molecule approaches for studying DNA polymerase" http://digitalcommons.wayne.edu/cgi/viewcontent.cgi?article=1861&context=oa_dissertations | 15:17 |
| Paul-_ | yup, I've been hoarding handoffs and trash from the uni for 7 years now | 15:17 |
| chris_99 | cool :) | 15:17 |
| B3nszy | Hello | 15:17 |
| Paul-_ | so bizarre the things they throw out | 15:17 |
| B3nszy | Can someone help me decide what to major in | 15:17 |
| B3nszy | I was told I have similar interests to this chat | 15:18 |
| Paul-_ | biochemistry | 15:18 |
| chris_99 | i've got a PID i use with a pt100, for brewing, so i could re-appropiate that, for stuff should i need too :) | 15:18 |
| Paul-_ | yeah the blue thermometer connected to the hotplate is basically a PID | 15:18 |
| chris_99 | ah cool | 15:19 |
| Paul-_ | and I use a mercury thermometer in my crude material because unfortunately I can't hook up 3 thermometers to the hotplate ;) | 15:19 |
| Paul-_ | here I'm actually distilling just alcohol from fermented sugarwater | 15:20 |
| B3nszy | What are new scientific fields immersing that would satisfy someone who is into sci fi like concepts | 15:20 |
| B3nszy | A field open to a lot of huge discoveries of the world | 15:21 |
| B3nszy | and ideas | 15:21 |
| Paul-_ | I know that for this volume and percentage of alcohol the oil bath needs to be 102C to run optimally, but the booze boils at ~89 degrees | 15:21 |
| chris_99 | aha neat Paul-_, i bought a cheap SS liebig condenser to play with | 15:21 |
| Paul-_ | I assume you have more than just a condenser? ;) | 15:22 |
| chris_99 | yeah | 15:22 |
| Paul-_ | I measure the temperature of the vapor at the point just before it's going to the condenser | 15:23 |
| chris_99 | nice, sounds like a good idea | 15:24 |
| Paul-_ | this way I can exactly see when the methanol is out, and when I'm past the azeothrope of the alcohol, so I end up with 96% alcohol in one go, with minimal contamination of unwanted aromas | 15:24 |
| Paul-_ | it just takes a while | 15:25 |
| streety | so it is the alcohol you are after? What were you using it for? | 15:25 |
| chris_99 | i was wondering that | 15:25 |
| Paul-_ | making clandestine gin | 15:25 |
| chris_99 | heh cool | 15:25 |
| chris_99 | did you put the botanicals in the vapour path | 15:25 |
| chris_99 | or in the wash | 15:25 |
| Paul-_ | actually I do two distillations | 15:25 |
| Paul-_ | first I go for the purest possible clear ethanol | 15:26 |
| chris_99 | you mean, one to create a 30-40% spirit? | 15:26 |
| streety | B3nszy: I think any STEM subject would be good. Find professors doing work that interests you and get involved | 15:26 |
| Paul-_ | then I do another distillation where I remove the fractioning column, because that actually removes the majority of the aromas | 15:27 |
| CaptHindsight | was looking into a federal distillers license recently | 15:27 |
| CaptHindsight | lots of hoops and you have to fully build out your plant before inspection and approval | 15:27 |
| Paul-_ | so I dilute the 96% to about 40% and then I run another distillation at a higher temp and boil it almost dry | 15:28 |
| chris_99 | is that something you have to pay a lot for? | 15:28 |
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| chris_99 | cool Paul-_ , i read if you have above 40% it ignites right? | 15:28 |
| CaptHindsight | depending on the size of your plant some have spent $500k | 15:28 |
| chris_99 | eek | 15:28 |
| Paul-_ | depends on the temperature | 15:28 |
| Paul-_ | I don't know when you can light it tbh | 15:29 |
| CaptHindsight | the catch is you have to have it all built before they grant the license | 15:29 |
| Paul-_ | 40-50% at room temp sounds about right | 15:29 |
| chris_99 | so you could have built it, and they reject it? | 15:29 |
| CaptHindsight | yup | 15:29 |
| chris_99 | darn | 15:29 |
| CaptHindsight | yeah | 15:29 |
| Paul-_ | which is why using a bunsen would be suboptimal ;) | 15:29 |
| chris_99 | heh | 15:30 |
| CaptHindsight | some states are easier than others, but it eventually ends up with the feds | 15:30 |
| CaptHindsight | I was looking at Wisconsin | 15:30 |
| Paul-_ | I'm now starting a new brew and I'm gonna try a different way, because it takes a few days to distill 5 liters of sugarwine into alcohol | 15:31 |
| chris_99 | the distillation takes a few days? | 15:31 |
| Paul-_ | I recently salvaged a rotavap | 15:31 |
| Paul-_ | well, I don't leave it running day and night | 15:31 |
| chris_99 | heh gotcha | 15:32 |
| chris_99 | would you be distilling for alcohol, or other chemicals, CaptHindsight? | 15:32 |
| Paul-_ | but this was a 1 liter flask and you don't want to fill it for more than 2/3 | 15:32 |
| CaptHindsight | whiskey is my main interest | 15:32 |
| chris_99 | nice :) | 15:32 |
| chris_99 | do you brew beer? | 15:32 |
| Paul-_ | I love whisky, but its such an investment | 15:33 |
| CaptHindsight | no | 15:33 |
| Paul-_ | unaged whisky tastes like old boots | 15:33 |
| CaptHindsight | at best | 15:33 |
| chris_99 | i don't find it that bad, i tried some from yamazaki (sp?) | 15:33 |
| CaptHindsight | hard to find in the US | 15:34 |
| Paul-_ | so only after a few years you know if you did it right, and then you can adjust and try again | 15:34 |
| CaptHindsight | how to rapid age? | 15:34 |
| chris_99 | for single malt, are they not allowed to blend casks | 15:34 |
| Paul-_ | I heard some things about cheating with wood chips and extracts | 15:34 |
| CaptHindsight | what is it about the fusel oils? | 15:35 |
| chris_99 | you can use smaller casks for larger surface area too | 15:35 |
| Paul-_ | that is a nuisance | 15:35 |
| CaptHindsight | well it's not cheating if it works :) | 15:35 |
| Paul-_ | but for the whisky it's actually part of the flavor profile | 15:35 |
| Paul-_ | that's why it tastes so horrible if it's not aged | 15:35 |
| Paul-_ | if I'm too impatient with my distillation the result tastes like moldy wet carpet | 15:36 |
| chris_99 | there seems to be a lot of art in choosing the heads etc during distillation i think | 15:36 |
| CaptHindsight | take Ardbeg, Lagavulin etc, what is the flavor? | 15:36 |
| chris_99 | peat | 15:36 |
| Paul-_ | lots | 15:36 |
| CaptHindsight | yeah but how much of the peat flavor is lost during distillation? | 15:37 |
| chris_99 | i'd like to get some peated malt to play with, for beer | 15:37 |
| Paul-_ | the barley, the yeast strain, the way they distilled, the air the cask was in, the wood the cask was made of, if something else was in the cask | 15:37 |
| CaptHindsight | I made some | 15:37 |
| chris_99 | cool | 15:37 |
| Paul-_ | that depends how you distill it | 15:37 |
| Paul-_ | and I don't know what the way to go is for whisky to be honest, because you want to retain some flavor but definetely not everything | 15:38 |
| CaptHindsight | can you start with everclear and add scotch flavor? | 15:38 |
| Paul-_ | and the flavor you retain changes completely through the aging | 15:38 |
| Paul-_ | no | 15:38 |
| chris_99 | no, which is why they use pot stills | 15:38 |
| chris_99 | or tend to | 15:39 |
| kanzure | | 15:39 |
| kanzure | ~> | 15:39 |
| Paul-_ | but this is why I do gin | 15:39 |
| CaptHindsight | how much of the flavor comes along during the distillation? | 15:39 |
| Paul-_ | well that depends entirely on how you do it | 15:39 |
| CaptHindsight | all those 100+ year old secrets | 15:40 |
| Paul-_ | almost all distilleries use fractioned distillation | 15:40 |
| Paul-_ | and also a continuous distillation, look it up on wikipedia, pretty complicated | 15:40 |
| chris_99 | the Japanese seemed to quite well at learning those CaptHindsight, when creating their whisky | 15:40 |
| Paul-_ | but what I do is I fractionate it as accurately as I can | 15:41 |
| Paul-_ | the thing that does that is called a vigreux column | 15:41 |
| CaptHindsight | yeah, I like Yamazaki when I'm in the mood for something sweeter | 15:41 |
| chris_99 | yeah it's nice | 15:41 |
| chris_99 | i tried octomore | 15:42 |
| chris_99 | recenlty | 15:42 |
| CaptHindsight | I'm partial to Islays | 15:42 |
| Paul-_ | you can't see it in my photo because it's wrapped in pyrex wool and tin foil | 15:42 |
| CaptHindsight | but i get in the mood for rye whiskeys | 15:42 |
| Paul-_ | but I would seriously consider starting with something easier | 15:42 |
| Paul-_ | getting a feel for how distillation actually works, because believe me, the first few times are going to taste horrible | 15:43 |
| CaptHindsight | I just finished an unpeated https://www.bruichladdich.com/ | 15:43 |
| chris_99 | interesting CaptHindsight | 15:44 |
| Paul-_ | we have a really nice store here, everyone in the NL gets their stuff there | 15:44 |
| chris_99 | i used an airstill on some of my beer a while ago Paul-_, i want to try aging it in a teeny tiny cask see if it tastes an better | 15:44 |
| Paul-_ | just buy oak chips, small casks are super expensive | 15:45 |
| Paul-_ | airstills are the things that americans use to distill tapwater right? | 15:46 |
| CaptHindsight | oak chips without any sap | 15:46 |
| Paul-_ | the kind of teapot ooking things | 15:46 |
| CaptHindsight | or bark | 15:46 |
| kanzure | Paul-_: : take a look at http://diyhpl.us/wiki/dna/synthesis/notes/ is this something that you would like to work on | 15:46 |
| Paul-_ | well yes, you have specific chips for aging whisky | 15:46 |
| chris_99 | yeah they're used for tap water | 15:46 |
| Paul-_ | chopped up cherry barrels, stuff like that | 15:46 |
| CaptHindsight | oak microparticles | 15:47 |
| CaptHindsight | for max surface area | 15:47 |
| chris_99 | i found some 1l casks for £30 iirc, ive only got 1l of spirit alas, a 1l cask will probably age it far too fast though | 15:47 |
| CaptHindsight | then 1um filter before serving | 15:47 |
| chris_99 | haha | 15:47 |
| chris_99 | you can get oak essence too i think | 15:47 |
| Paul-_ | whatever you get, it needs to age | 15:48 |
| Paul-_ | otherwise you just have tannin | 15:48 |
| chris_99 | yeah, with a 1l cask i think it only takes a month or so iirc | 15:48 |
| Paul-_ | haha no | 15:48 |
| Paul-_ | 3 years | 15:48 |
| Paul-_ | minimum | 15:48 |
| chris_99 | that's in a hogshead | 15:48 |
| CaptHindsight | I think Suntory just acquired Jim Beam | 15:48 |
| chris_99 | with a small cask the aging time reduces | 15:49 |
| CaptHindsight | yeah they are #2 in the world now | 15:49 |
| chris_99 | oh interesting CaptHindsight | 15:49 |
| chris_99 | didn't know that | 15:49 |
| CaptHindsight | http://www.suntory.com/news/2014/11942.html | 15:49 |
| CaptHindsight | the Yamazaki disti told me that last week | 15:50 |
| Paul-_ | very neat idea kanzure | 15:50 |
| Paul-_ | I love the inkjet printer idea | 15:50 |
| CaptHindsight | they are making it harder to get in the USA to raise the price | 15:50 |
| chris_99 | harder to get yamazaki? | 15:50 |
| CaptHindsight | yeah | 15:50 |
| chris_99 | arn | 15:50 |
| chris_99 | *darn | 15:50 |
| CaptHindsight | increase exclusivity | 15:51 |
| CaptHindsight | already up to $100/bottle | 15:51 |
| CaptHindsight | from what $60 2 years ago | 15:51 |
| Paul-_ | it's pretty ambitious | 15:51 |
| CaptHindsight | Its combined portfolio of leading brands will include Beam's Jim Beam, Maker's Mark and Knob Creek bourbons, Teacher's and Laphroaig Scotch whiskies, Canadian Club whisky, Courvoisier cognac, Sauza tequila, and Pinnacle vodka, and Suntory's leading Japanese whiskies Yamazaki, Hakushu, Hibiki, and Kakubin, Bowmore Scotch whisky and Midori liqueur. | 15:52 |
| chris_99 | suntory owns Laphroaig? | 15:52 |
| CaptHindsight | heh, yeah | 15:52 |
| Paul-_ | it's very much like solid state peptide synthesis | 15:52 |
| chris_99 | wow, i didn't know that | 15:52 |
| chris_99 | i really like Laphroaig | 15:53 |
| CaptHindsight | it's not by a little old lady in Islay anymore :) | 15:53 |
| chris_99 | :'( | 15:53 |
| Paul-_ | but the twist with basically doing the reaction on "chip" and assembling it afterwards | 15:53 |
| Paul-_ | only the chip is paper | 15:53 |
| kanzure | Paul-_: yes, it's similar to solid state peptide synthesis. it's fro the sae era originally. | 15:54 |
| Paul-_ | I wish I had the time to get involved, I'm not a chemist but I have basic knowledge of organic synthesis | 15:54 |
| kanzure | the chip is not paper, usually a glass slide or a chip | 15:54 |
| Paul-_ | ok makes sense | 15:55 |
| kanzure | if you were paid, would you have tie? | 15:55 |
| kanzure | ... time | 15:55 |
| Paul-_ | no | 15:55 |
| Paul-_ | I'm going to finish my study past due, and this means every day after august 31 is going to be very expensive because I have to study full time and to be honest I'm usually drained after a day in the lab | 15:56 |
| kanzure | school is lame | 15:57 |
| Paul-_ | I agree | 15:57 |
| * kanzure wanders off | 15:57 | |
| Paul-_ | after nine years of studying you're kind of.. done with it | 15:58 |
| CaptHindsight | well there is school and there is learning | 15:58 |
| CaptHindsight | don't confuse the two | 15:59 |
| Paul-_ | but I'm only a few months removed from my MSc so quitting at this point, a few months short of that piece of paper, that's no option | 15:59 |
| Paul-_ | deep stuff | 15:59 |
| chris_99 | is that in chemistry? | 16:00 |
| Paul-_ | but I know | 16:00 |
| Paul-_ | no | 16:00 |
| Paul-_ | I'm a biologist | 16:00 |
| chris_99 | ah cool, are you doing a thesis for that then? | 16:00 |
| Paul-_ | I did a BSc biology and my MSc will officially be in life science and technology | 16:01 |
| CaptHindsight | I need to build programmable error checking Surveyor nuclease bots | 16:01 |
| Paul-_ | so basically still biology only they are in the building across the street and they have more cool stuff | 16:01 |
| chris_99 | nice | 16:02 |
| Paul-_ | actually I carefully avoided chemistry most of my life | 16:02 |
| Paul-_ | but I had to take organic chem for my master, and now I did it I'm astounded that they don't include this in the biology curriculum | 16:02 |
| CaptHindsight | they don't want you out building killer mutant zombie e.coli | 16:04 |
| Paul-_ | well there was a 3 week course taught by a very confused old man, I failed it twice and then decided to fck it and I ended up doing a summer course physical anthropology | 16:04 |
| Paul-_ | very cool | 16:04 |
| CaptHindsight | or curing anything | 16:04 |
| Paul-_ | chemists can't do biology | 16:04 |
| Paul-_ | they think they can, but they can't | 16:05 |
| Paul-_ | my previous project was with the chemical immunology group which was part of biosyn | 16:05 |
| Paul-_ | me and 2 other biologists, and some "converted" chemists | 16:06 |
| Paul-_ | I have never been in a nastier lab | 16:06 |
| CaptHindsight | avoid the academic types | 16:07 |
| Paul-_ | and I will never forget how the first week one of the supervisors calmly entered the bio lab and said that we should probably leave the door shut for a while because someone accidentally made mustard gas and didn't turn on his fumehood | 16:07 |
| chris_99 | heh 'accidentally' | 16:08 |
| Paul-_ | after only being almost killed the next day, when my neighbour knocks over a tube with who knows what, not alarmed at all | 16:08 |
| CaptHindsight | did the problem solve itself? | 16:08 |
| Paul-_ | so I back away, ask what it is | 16:08 |
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| Paul-_ | and she calmly replies it was ok, it was her 10% sodium azide stock but she had to make new anyway | 16:09 |
| CaptHindsight | well she paid or borrowed for her tuition so whats the problem? :) | 16:10 |
| Paul-_ | look up the safety sheet on sodium azide | 16:11 |
| Paul-_ | there's not a lot of things in the lab that scare me | 16:11 |
| streety | similar to cyanide | 16:11 |
| CaptHindsight | which you dump into the river and hope you don't get caught | 16:12 |
| Paul-_ | yeah, but the difference is that when you work with cyanide you are accutely aware you're doing something dangerous | 16:12 |
| Paul-_ | there's actually an emergency bucket which you need to have when you work with cyanides | 16:12 |
| CaptHindsight | everybody has a story in industry about how they went around the rules | 16:12 |
| Paul-_ | it has the "antidote" regime in it, and it's in a bucket because that's the first thing you'll need after administering it | 16:13 |
| Paul-_ | but they sprinkle azide on everything like it's sugar | 16:13 |
| Paul-_ | so the list is: 1. ultracentrifuges, 2. azide, 3. senior professors wearing lab coats in the lab | 16:15 |
| Paul-_ | I saw plans for a "dremelfuge" | 16:18 |
| Paul-_ | you need some serious guts to use that | 16:18 |
| streety | lol, ultracentrifuges can be interesting. I've been trying to impress on a new student the importance of balancing the rotor just this past week | 16:19 |
| Paul-_ | "interesting" is not how I'd put it | 16:19 |
| Paul-_ | I was on a summer course in france and I actually saw one go | 16:20 |
| Paul-_ | as in | 16:20 |
| Paul-_ | some poor bastard didn't correctly load the swinging basked rotor, and it wasn't a state of the art centrifuge | 16:20 |
| Paul-_ | I'm very happy I was not in the room at that moment, because the rotor ended up embedded in a wall | 16:21 |
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| streety | so no stability check, | 16:21 |
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| streety | I spent much of my PhD working at a bench beside a ultracentrifuge | 16:22 |
| Paul-_ | they probably made it with old citroen parts or something | 16:22 |
| streety | fortunately I was the only person using it | 16:22 |
| Paul-_ | the thing was ancient | 16:22 |
| streety | are you sure it was an imbalance and not the rotor tearing itself apart? If it really was that old | 16:23 |
| Paul-_ | and that's not a problem in itself, but if a whole department uses it someone is gonna fuck up | 16:23 |
| Paul-_ | I have no idea | 16:23 |
| Paul-_ | I was behind a window | 16:23 |
| Paul-_ | it started revving, and at first rattling and then whinnig | 16:24 |
| Paul-_ | then the vacuum broke and everything went very fast after that | 16:24 |
| streety | sounds like an imbalance | 16:25 |
| Paul-_ | I only heard that he screwed up, but to be honest I didn't stay around to find out | 16:25 |
| Paul-_ | yeah, it sounded very typical like a rotor resonating and then exceeding resonant speed | 16:25 |
| Paul-_ | only usually I only hear that sound at ~4k, which could hurt you, but 300k is in a league of its own | 16:26 |
| streety | We go up to 200k g. I try to make the point that each gram becomes equivalent to a 200kg weight when up to speed. Not sure the concept fully sinks in | 16:28 |
| Paul-_ | well no | 16:29 |
| Paul-_ | when you never had to consider if your tubes are forming a condensation on them | 16:29 |
| Paul-_ | or if you can only fill between certain ranges because otherwise the tube just collapses because it's not full enough or blows up because it's too full | 16:30 |
| Paul-_ | oh yeah, and NMRs | 16:32 |
| Paul-_ | don't like NMRs | 16:32 |
| Paul-_ | don't like the complicated data they produce, and I definetely don't like magnetic quenching | 16:33 |
| Paul-_ | we were evacuated once because one of the NMRs quenched, and I could hear it from a different wing | 16:34 |
| Paul-_ | but if you like chemistry glass chris_999, check out my latest score | 16:36 |
| chris_999 | just watched https://www.youtube.com/watch?v=tPqduF5xB-o 600 MHz NMR spectrometer quench | 16:37 |
| Paul-_ | https://www.dropbox.com/s/xsnclvq4qgyh1ft/2016-06-24%2017.11.57.jpg?dl=0 | 16:37 |
| chris_999 | cool :) is that a graham condenser? | 16:37 |
| Paul-_ | so now you know what the oxygen alarm sounds like? :p | 16:37 |
| Paul-_ | part of it is | 16:38 |
| Paul-_ | but I have no clue what this thing does | 16:38 |
| chris_999 | ah heh | 16:38 |
| Paul-_ | and nobody I asked knew | 16:38 |
| chris_999 | is it a reflux column in the centre? | 16:38 |
| Paul-_ | no | 16:38 |
| Paul-_ | well | 16:38 |
| Paul-_ | perhaps | 16:39 |
| Paul-_ | but the top is sealed | 16:39 |
| chris_999 | ah | 16:39 |
| Paul-_ | except for a little hooked tube with it's own ground joint | 16:39 |
| Paul-_ | and the thing on the right is a cold finger that condenses into a cup into that hooked tube | 16:39 |
| Paul-_ | it's bound to be some complicated solvent-gas reaction chamber or something | 16:40 |
| chris_999 | ah, i was wondering what the two ports on the right were for | 16:40 |
| Paul-_ | the cold finger condenser | 16:41 |
| Paul-_ | but the way it looks vapor has to come from the top, because the bottom of the condensor has a reservoir | 16:41 |
| Paul-_ | so thats already weird | 16:41 |
| chris_999 | heh | 16:42 |
| chris_999 | did you see the article on lab glassware posted here recently | 16:42 |
| Paul-_ | no | 16:42 |
| Paul-_ | I only found out about diy bio 2 days ago | 16:42 |
| chris_999 | http://www.latimes.com/local/education/la-me-caltech-glassblower-20160613-snap-story.html | 16:42 |
| Paul-_ | ooh I love glassblowing | 16:43 |
| Paul-_ | a friend of mine studies at the school for instrument makers | 16:44 |
| kanzure | there is such a school? | 16:44 |
| Paul-_ | roughly translated | 16:44 |
| Paul-_ | leidse instrumentenmakers school | 16:44 |
| chris_999 | what kind of instruments do they make, any scientific ones? | 16:44 |
| Paul-_ | yes | 16:44 |
| Paul-_ | mostly | 16:44 |
| Paul-_ | it's all very pornographic | 16:45 |
| Paul-_ | she repaired my claisen adapter just this week | 16:46 |
| Paul-_ | and a good job too | 16:46 |
| Paul-_ | a new one would have set me back at least $60 | 16:47 |
| Paul-_ | this cost me a bar of chocolate :p | 16:47 |
| chris_999 | hehe | 16:47 |
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| Paul-_ | very nice video | 16:51 |
| Paul-_ | I tried it once | 16:51 |
| Paul-_ | it all looks so easy when they show you | 16:51 |
| Paul-_ | and at first you think everything is going quite well, until your thing starts to cool down and all the stress points I created as a noob started to crack one by one | 16:53 |
| Paul-_ | and just to rub it in the instructor had secretly made a sketch while I was working showing exactly where the cracks would be | 16:54 |
| xentrac | Paul-_: haha, that's awesome | 16:55 |
| xentrac | it probably would have worked better trying it twice | 16:55 |
| Paul-_ | yeah, but just the level of skill that you only get wih the years of experience | 16:55 |
| Paul-_ | that's just beyond belief | 16:56 |
| Paul-_ | especially because it doesn't look dificult at all | 16:56 |
| Paul-_ | I can make a half decent T junction of two boro tubes, close an end, draw capilaries and bend them and thats about it | 16:57 |
| xentrac | 22:01 < Paul-_> or flame sterilizing innoculation loops | 16:59 |
| xentrac | maybe you could use one of those little handheld soldering torches for that? | 16:59 |
| Paul-_ | learning to draw a decent capilary was actually very useful, they are far superior to prefab capilaries for tlc spotting | 16:59 |
| Paul-_ | and actually even in vivo cell injection | 17:00 |
| Paul-_ | no | 17:00 |
| Paul-_ | that was the problem, I always used to play around with the glass pasteur pipettes in the bunsen | 17:00 |
| Paul-_ | and they are fairly forgiving | 17:00 |
| Paul-_ | but the flame just isn't hot enough | 17:01 |
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| CaptHindsight | 3d printed labware | 17:01 |
| Paul-_ | wouldn't use it | 17:01 |
| kanzure | "CRISPR-Cas9 as a powerful tool for efficient creation of oncolytic viruses" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810262/ | 17:01 |
| CaptHindsight | sshhhh | 17:02 |
| kanzure | "Genome engineering with TALE and CRISPR systems in neuroscience" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821859/ | 17:02 |
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| Paul-_ | I always get a little anxious when I draw a high vacuum on lab glass | 17:03 |
| CaptHindsight | you're giving away secrets to things hardly anyone can figure out how to do practically | 17:03 |
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| kanzure | "Establishment of a highly efficient virus-inducible CRISPR/Cas9 system in insect cells" http://www.sciencedirect.com/science/article/pii/S0166354216301474 | 17:04 |
| kanzure | "we disrupted a viral genome in infected insect cells in vitro as a defense against viral infection. We optimized the CRISPR/Cas9 system to edit foreign and viral genome in insect cells. Using Bombyx mori nucleopolyhedrovirus (BmNPV) as a model, we found that the CRISPR/Cas9 system was capable of cleaving the replication key factor ie-1 in BmNPV thus effectively inhibiting virus proliferation. Furthermore, we constructed a ... | 17:04 |
| kanzure | ... virus-inducible CRISPR/Cas9 editing system, which minimized the probability of off-target effects and was rapidly activated after viral infection." | 17:04 |
| Paul-_ | well, if you can get around pressure issues you could be on to something | 17:04 |
| CaptHindsight | 3, 2, 1 years until all the CRISPR patents get published | 17:05 |
| kanzure | "AAV-mediated CRISPR/Cas gene editing of retinal cells in vivo" http://biorxiv.org/content/early/2016/04/24/039156.abstract | 17:05 |
| Paul-_ | but even with thickwalled expensive boro vacuum stuff is always a little scary | 17:05 |
| xentrac | Paul-_: there was an interesting piece within the last year about high-resolution stereolithography to print in silicone, then firing it to get silica | 17:05 |
| xentrac | actually I think it was silicon carbide | 17:06 |
| xentrac | unfortunately I think I didn't bookmarket it | 17:06 |
| yashgaroth | it's only one atm of pressure difference c'mon | 17:06 |
| Paul-_ | I'm not saying it's not doable or even that it's not brilliant | 17:06 |
| Paul-_ | but it's not yet tried and true | 17:07 |
| xentrac | so far the things they demonstrated were all latticey though | 17:07 |
| CaptHindsight | Gorilla Glass | 17:07 |
| Paul-_ | that one atm is pretty scary if you're standing next to somebody doing a reaction with an organolithium in vacuum in an oil bath | 17:08 |
| yashgaroth | to me that's already scary enough, but I take your point | 17:09 |
| xentrac | are organolithiums toxic like organotins and stuff? | 17:09 |
| xentrac | or just inflammable? | 17:09 |
| Paul-_ | because I'm in that one atmosphere, but that atmosphere is not in that flask, so if it's scratched, like all glass is because chemists just stack their flasks 5 high in a pile | 17:09 |
| CaptHindsight | best to just not work around idiots | 17:09 |
| Paul-_ | that idiot was our seniour professor synthetic organic chemistry | 17:10 |
| Paul-_ | they'll set fire to the oil just before it flies everywhere | 17:11 |
| xentrac | aha | 17:11 |
| Paul-_ | and they're toxic | 17:11 |
| CaptHindsight | https://upload.wikimedia.org/wikipedia/commons/b/b7/Aviano_bomb_suit.jpg just wear this to lab | 17:11 |
| xentrac | and I suppose the oil isn't something innocuous like a fluorocarbon | 17:11 |
| CaptHindsight | safety first | 17:12 |
| xentrac | it's something with lots of C-H and C=C bonds in it? | 17:12 |
| Paul-_ | this is what I wear in the lab | 17:12 |
| Paul-_ | https://cdn.shopify.com/s/files/1/0149/3544/products/science_shirt_1_1024x1024.jpg?v=1449771515 | 17:12 |
| Paul-_ | no it's just mineral oil | 17:12 |
| Paul-_ | and not from sigma, but probably from an auto workshop or something :p | 17:13 |
| Paul-_ | it's black and it smells foul | 17:13 |
| xentrac | so it contains significant volatile components | 17:13 |
| xentrac | so it probably has a low flashpoint | 17:13 |
| Paul-_ | yes | 17:13 |
| kanzure | dna synthesis photolithography things on thin plastic sheets http://pubs.acs.org/doi/abs/10.1021/acs.analchem.5b02893 "The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based ... | 17:14 |
| Paul-_ | but chemists have an entirely different concept of danger than you me and everyone else | 17:14 |
| kanzure | ... nucleic acid synthesis." | 17:14 |
| xentrac | heh | 17:14 |
| Paul-_ | that's why I take a break and vacate the premises when I see professors in the lab wearing labcoats | 17:15 |
| xentrac | haha | 17:15 |
| xentrac | why are organolithium compounds toxic? | 17:15 |
| xentrac | I mean, more toxic than lithium salts | 17:16 |
| xentrac | which, while not something I want to snack on, still have >1000mg lethal doses | 17:16 |
| Paul-_ | I don't know how toxic they are | 17:17 |
| Paul-_ | they are very reactive | 17:17 |
| Paul-_ | probably it's already reacted before it can do any real harm | 17:17 |
| xentrac | depends on the reaction products, no? | 17:17 |
| xentrac | I mean chlorine is very reactive too, but part of the problem is that the reaction products are often toxic | 17:18 |
| Paul-_ | well yes, but the nice thing about organolithiums is that they're kind of legos | 17:18 |
| Paul-_ | yes, but chlorine likes to make radicals | 17:18 |
| Paul-_ | look up grignard reaction | 17:19 |
| xentrac | while e.g. H₂O₂ is just as happy to rip into organic molecules as chlorine is, but the results are generally minimally toxic | 17:19 |
| Paul-_ | it's basically the same principle, only the group is slightly different | 17:19 |
| Paul-_ | h2o2 oxidizes something and then it's done | 17:20 |
| xentrac | really? I didn't realize that chlorine would leave free radicals floating around in a way H₂O₂ wouldn't | 17:21 |
| Paul-_ | well I'm not going to contest you on this because I'm no chemist but that's how I thought it worked | 17:22 |
| xentrac | you could be right | 17:22 |
| Paul-_ | chlorine is a very nice leaving group | 17:22 |
| xentrac | I wrote a brief comment about this a couple of weeks ago, maybe you can tell me if I was saying grossly stupid things: https://news.ycombinator.com/item?id=11925118 | 17:23 |
| Paul-_ | so if you chlorinate an organic compound, it could be slightly more reactive towards another, and so on | 17:23 |
| xentrac | in the process of writing it I learned what leaving groups are | 17:23 |
| Paul-_ | well this is a little bit above my paygrade too | 17:24 |
| Paul-_ | but fluorine is a soft nucleophile | 17:25 |
| Paul-_ | meaning it has a very diffuse electron shell | 17:25 |
| Paul-_ | or organofluorines I should say | 17:25 |
| Paul-_ | and they like to react wih other soft electrophiles | 17:26 |
| xentrac | very diffuse? wouldn't that be more like cesium than like fluorine? | 17:26 |
| Paul-_ | am I confusing things? | 17:26 |
| Paul-_ | wait | 17:26 |
| Paul-_ | is it fluorine chlorine bromine iodine etc | 17:28 |
| Paul-_ | or the other way round | 17:28 |
| Paul-_ | ok sorry I flipped it, you're right | 17:28 |
| Paul-_ | which actually makes more sense | 17:29 |
| Paul-_ | delocalization is also a "soft" characteristic | 17:29 |
| Paul-_ | but fluorine is weird | 17:31 |
| Paul-_ | actually all halogens are | 17:31 |
| Paul-_ | QED | 17:31 |
| Paul-_ | https://en.wikipedia.org/wiki/Chlorine_pentafluoride | 17:31 |
| Paul-_ | or HFSbF6 | 17:34 |
| Paul-_ | "magic acid" | 17:34 |
| Paul-_ | always be weary of things that are "magic" in any way | 17:34 |
| Paul-_ | there were all these spray bottles with a piece of tape on it that said "magic mix" standing around | 17:35 |
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| kanzure | "CONFOLD: Residue-residue contact-guided ab initio protein folding" http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.714.5591&rep=rep1&type=pdf | 17:39 |
| xentrac | heh | 17:40 |
| kanzure | "Synthetic evolutionary origin of a proofreading reverse transcriptase" http://science.sciencemag.org/content/352/6293/1590 | 17:45 |
| kanzure | "DNA polymerase enzymes copy DNA into new strands of identical DNA. Reverse transcriptase (RT) enzymes copy RNA into DNA. Unlike many DNA polymerases, RT enzymes do not have a proofreading function that checks for errors in the newly synthesized DNA. Ellefson et al. use in vitro directed evolution and protein engineering to build an error-correcting RT from a prokaryotic DNA polymerase. The RT “xenopolymerase” shows increased ... | 17:45 |
| fenn | lol "one thousand artificial diamond disks the size of CDs will be hidden in locations in manhattan" will certainly not last 1000 years once people start hunting them | 17:46 |
| kanzure | ... fidelity as compared to natural RTs and should streamline and increase the precision of transcriptomics methods." | 17:46 |
| kanzure | "Most reverse transcriptase (RT) enzymes belong to a single protein family of ancient evolutionary origin. These polymerases are inherently error prone, owing to their lack of a proofreading (3′- 5′ exonuclease) domain. To determine if the lack of proofreading is a historical coincidence or a functional limitation of reverse transcription, we attempted to evolve a high-fidelity, thermostable DNA polymerase to use RNA templates ... | 17:46 |
| kanzure | ... efficiently. The evolutionarily distinct reverse transcription xenopolymerase (RTX) actively proofreads on DNA and RNA templates, which greatly improves RT fidelity. In addition, RTX enables applications such as single-enzyme reverse transcription–polymerase chain reaction and direct RNA sequencing without complementary DNA isolation. The creation of RTX confirms that proofreading is compatible with reverse transcription." | 17:46 |
| fenn | lanier doesn't seem to have understood selection pressure or the concept of a gene drive (which maybe didn't exist in 1999) | 17:47 |
| kanzure | gene drive is somewhat recent | 17:47 |
| fenn | i wonder what calculation he used to come up with "8 cubic feet of cockroaches" as the correct number | 17:47 |
| Paul-_ | don't say dawkins | 17:47 |
| Paul-_ | calculations? | 17:48 |
| Paul-_ | from what I gather 8 cubic feet of cockroaches is not uncommon in NYC | 17:48 |
| kanzure | to be fair, jaron lanier is probably worse than dawkins, although they are both awful | 17:48 |
| Paul-_ | I can't stand his smug face | 17:49 |
| Paul-_ | and I can't stand militant atheists | 17:49 |
| Paul-_ | not because they're wrong, but they usually make things worse | 17:51 |
| fenn | that UV inkjet printer looks pretty handy | 17:54 |
| kanzure | devrandom: someone asked about you today | 17:55 |
| kanzure | yashgaroth: these guys are really stuck on an electronically-controlled polymerase. but nobody has any reasonable ideas for how to make one happen. | 17:55 |
| yashgaroth | nor do I | 17:56 |
| fenn | ug why is opentrons $3k that is nowhere near $3k in parts | 17:58 |
| yashgaroth | wait, stuck as in they need to leap 20 years into the future and find out how to make it happen, or stuck as in we need to convince them of a better option | 17:58 |
| kanzure | fenn: probably because they want to make money... | 17:58 |
| kanzure | yashgaroth: kind of both! | 17:58 |
| yashgaroth | heh | 17:58 |
| kanzure | probably nmz787 will dazzle us all with a very specific water flow control method to shoot nucleotides around with femtoliter droplet encapsulation | 17:59 |
| kanzure | i don't think anyone has figured out a way to do polymerase ratcheting at 1 nt/step | 18:07 |
| yashgaroth | maybe with protecting groups on the nucleotides, but that sounds as painstaking and error-prone as any other method | 18:09 |
| kanzure | still needs ratcheting and pausing | 18:09 |
| yashgaroth | well, it implies washing, deprotecting, and flowing in new bases, same as traditional synthesis, but yeah the protein isn't really controlled in any sense | 18:11 |
| kanzure | "Confinement and manipulation of individual molecules in attoliter volumes" | 18:12 |
| kanzure | wait that's too large | 18:13 |
| kanzure | evaporative assembly https://www.semanticscholar.org/paper/Fast-High-throughput-Creation-of-Size-tunable-Choi-Jamshidi/79548bfd341ea066024a3d2125f16725718e585d/pdf | 18:30 |
| kanzure | a thesis regarding femtoliter water dispensing file:///home/kanzure/Downloads/Master_thesis_Rick_de_Gruiter.pdf | 18:32 |
| kanzure | ah fooey | 18:32 |
| kanzure | well fuck it. who cares. | 18:32 |
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| streety | http://repository.tudelft.nl/assets/uuid:daac9a6d-63be-438d-be03-1990e52fe409/Master_thesis_Rick_de_Gruiter.pdf approach is mainly hollow cantilever AFM | 19:03 |
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| CaptHindsight | kanzure: I have to build the tools to make that tool first | 19:13 |
| CaptHindsight | I should have started on this 20-30 years ago, but better late than.... | 19:14 |
| CaptHindsight | I got a good laugh out of this http://phys.org/news/2016-06-scientists-unveil-synthetic-human-genomes.html | 19:16 |
| CaptHindsight | fenn: the ChinaCo UV inkjet has horrible software | 19:20 |
| CaptHindsight | replace their controller and it's adequate for multipass printing | 19:21 |
| CaptHindsight | motorize the Z-axis and you have a cheap polyjet printer as well | 19:22 |
| CaptHindsight | http://phys.org/news/2016-06-tiny-dna-legs-fuel-efficiency.html DNA that drags itself into the cell | 19:46 |
| CaptHindsight | http://www.nature.com/articles/srep27413 Programmable DNA Nanosystem for Molecular Interrogation | 19:49 |
| CaptHindsight | https://www.osapublishing.org/optica/abstract.cfm?uri=optica-3-6-659 Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements | 19:53 |
| CaptHindsight | need to make this sooner than later http://www.nature.com/nnano/journal/v10/n12/full/nnano.2015.219.html | 20:02 |
| kanzure | CaptHindsight: i am hanging out with the organizer of that synthetic human genome project, i'm at his july 4th party at the moment | 20:13 |
| kanzure | .title | 20:15 |
| yoleaux | Identification of single nucleotides in MoS2 nanopores : Nature Nanotechnology : Nature Publishing Group | 20:15 |
| kanzure | oh, they mean polymerized nucleotides | 20:15 |
| CaptHindsight | not holding my breath | 20:16 |
| CaptHindsight | yeah higher S:N for better vs faster reads | 20:17 |
| CaptHindsight | I'm sure they will raise a ton of cash | 20:18 |
| kanzure | .title http://pubs.acs.org/doi/abs/10.1021/nl502626s?source=cen | 20:20 |
| yoleaux | kanzure: Sorry, that command (.title) crashed. | 20:20 |
| kanzure | .title http://pubs.acs.org/doi/abs/10.1021/nl502626s | 20:20 |
| kanzure | hmph | 20:20 |
| CaptHindsight | it would be nice if they can actually build something that works | 20:21 |
| CaptHindsight | and is available outside of their group | 20:21 |
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| fenn | .title http://www.nature.com/nnano/journal/v10/n12/full/nnano.2015.219.html | 20:58 |
| yoleaux | Identification of single nucleotides in MoS2 nanopores : Nature Nanotechnology : Nature Publishing Group | 20:58 |
| CaptHindsight | long story short, they slow down the scan to get a better signal | 20:59 |
| CaptHindsight | using a viscous media | 20:59 |
| CaptHindsight | "maintaining a signal-to-noise ratio higher than 10." 10:1, 10db power or voltage? | 21:01 |
| CaptHindsight | details details | 21:01 |
| CaptHindsight | honestly, how does one build a nanopore for sequencing DNA and not understand how this works? | 21:04 |
| xentrac | snr is standardly measured with power | 21:25 |
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| maaku | .title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323922/ | 23:46 |
| yoleaux | Fatigue is a Brain-Derived Emotion that Regulates the Exercise Behavior to Ensure the Protection of Whole Body Homeostasis | 23:46 |
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