--- Log opened Sun Jul 03 00:00:46 2016
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04:17 < CaptHindsight> anyone have access to this?  http://pubs.acs.org/doi/abs/10.1021/nl502626s?source=cen
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04:37 < Jawmare> CaptHindsight, libgen, noob
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05:05 < CaptHindsight> Jawmare: that site that was taken down recently?
05:07 < Jawmare> CaptHindsight, alright
05:07 < Jawmare> 1sec
05:08 < Jawmare> https://www.sendspace.com/file/t1hby5
05:10 < CaptHindsight> thanks
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06:16 < c0rw1n-> http://gen.lib.rus.ec/ looks pretty functional for a site that was taken down
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06:24 < kanzure> it depends on your isp etc
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06:33 < CaptHindsight> yeah lets focus on this
06:34 < CaptHindsight> why does this channel attract so many asshats?
06:35 < CaptHindsight> bbl
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11:20 < kanzure> "weaponized crispr"
11:21 < kanzure> there is funding available if anyone wants to do open-source GMP production of (amgen-style) erythropoietin
11:31 < kanzure> "The world's technological capacity to store, communicate and compute information" http://www.uvm.edu/~pdodds/files/papers/others/2011/hilbert2011a.pdf
11:32 < 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
11:33 < 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
11:34 < 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
11:36 < yashgaroth> I mean there are better ways to spend fifty million dollars
11:36 < kanzure> https://www.src.org/program/grc/semisynbio/
11:37 < kanzure> https://www.src.org/program/grc/semisynbio/semisynbio-consortium-roadmap/
11:40 < CaptHindsight> 1. DNA-based Massive Information Storage   heh, who's brilliant idea is this?
11:41 < xentrac> .g cockroaches lanier times
11:41 < yoleaux> xentrac: Sorry, that command (.g) crashed.
11:42 < 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
11:43 < 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"
11:44 < xentrac> although I remember people in the 1990s talking about information exfiltration via DNA
11:45 < 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"
11:46 < kanzure> CaptHindsight: also these things... http://groups.google.com/group/enzymaticsynthesis
11:47 < CaptHindsight> lots of these articles look like they come from a modern version of Omni Magazine
11:48 < kanzure> CaptHindsight: i still want to do a dna synthesizer with you at some point
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11:48 < 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)
11:50 < CaptHindsight> kanzure: I'm going to make a working cheapo version inkjet for ChinaCo to copy
11:51 < CaptHindsight> Epson DNA Inkjet Synthesizer on alibaba for a few $k
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11:52 < kanzure> CaptHindsight: there needs to be a pipette tip to move all the samples around, for DNA assembly (like gibson assembly).
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11:53 < CaptHindsight> nah, channels built into the slide
11:53 < kanzure> valves ??
11:54 < CaptHindsight> controlled cleave/nicking
11:54 < kanzure> how do you prevent the reaction material from draining down the channels immediately after inkjetting?
11:59 < CaptHindsight> http://www.rsc.org/images/loc/2013/PDFs/Papers/638_0077.pdf
12:01 < 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."
12:02 < kanzure> okay well that's the same thing as my "flooding" idea i guess...
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12:06 < 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)
12:07 < 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
12:08 < CaptHindsight> and then couple them together with an oligo from a different well
12:10 < CaptHindsight> you can keep a cap on one end so it only grows in one direction
12:11 < CaptHindsight> or like Silicon Valleys compression grow it from the middle out
12:14 < kanzure> CaptHindsight: http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/
12:17 < CaptHindsight> https://www.alibaba.com/product-detail/2015-newest-A4-UV-printer-cell_60395368065.html
12:17 < CaptHindsight> motorize the Z-axis
12:18 < CaptHindsight> replace their controller
12:18 < CaptHindsight> add the wash and dry nozzles
12:18 < CaptHindsight> put it in a sealed enclosure
12:19 < CaptHindsight> don't let them engineer anything
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12:27 < kanzure> "Reading single DNA with DNA polymerase followed by atomic force microscopy" http://pubs.acs.org/doi/abs/10.1021/ja5063983
12:28 < 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
12:31 < kanzure> hm.
12:36 < CaptHindsight> oh and don't work with anyone that mentions *duino, GRBL or reprap
12:39 < xentrac> hah
12:41 < 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
12:42 < CaptHindsight> the idiots used a poopieboard
12:42 < CaptHindsight> how do you add printheads, lasers, machine vision to a poopieboard?
12:44 < 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
12:45 < 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
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12:46 < 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
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12:47 < 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
12:48 < xentrac> enormous rigidity in place of feedback
12:49 < 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)
12:51 < CaptHindsight> contact vs non-contact applications
12:51 < xentrac> definitely a factor
12:52 < CaptHindsight> big iron is cheap and easy for contact
12:53 < 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
12:54 < 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
12:55 < CaptHindsight> bbl
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13:35 < 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.?
13:38 < superkuh> Sure. But it's easy to build a glove box out of transparent storage container and some rubber gloves + pvc tube.
13:39 < 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?
13:40 < 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
13:41 < 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
13:42 < 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?
13:43 < superkuh> I imagine you'd want the meristem or the like.
13:43 < superkuh> I was not working with plants.
13:44 < chris_99> aha gotcha
13:45 < archels> .title http://terencebroad.com/convnetvis/vis.html
13:45 < yoleaux> Visualisation of Convolutional Neural Networks Topology
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13:56 < chris_99> heh finally got that book opened superkuh, forgot what epub reader i had, that book looks very nice
13:57 < 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
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14:35 < Paul-_> and why wouldn't you filter sterilize your broth?
14:36 < 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
14:41 < 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
14:42 < 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
14:43 < 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
14:44 < 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
14:45 < 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
14:46 < 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
14:47 < 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
14:48 < chris_99> just found this - https://www.fishersci.com/shop/products/self-contained-lpg-burner/s41872
14:49 < 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
14:50 < 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
14:54 < Paul-_> I have this one: (search bunsen, first hit) http://www.eurofysica.nl/media/113493/catalogos%20eurofysica%202012-2013%20website.pdf
14:55 < 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?
14:56 < Paul-_> what would you want a stand for?
14:57 < chris_99> for putting a flask on it
14:57 < Paul-_> why put a flask on a bunsen?
14:58 < chris_99> isn't that a usual thing to do with bunsens
14:58 < Paul-_> no
14:58 < Paul-_> 50 years ago maybe
14:59 < 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
15:00 < chris_99> wait so what did you mean to use the bunsen for
15:01 < 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
15:02 < chris_99> interestin
15:02 < chris_99> *interesting
15:02 < Paul-_> well the occasional one, but not for heating anything in glass
15:03 < 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
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15:03 < Paul-_> a decent bunsen reaches 1500C easily
15:04 < 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
15:05 < 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/
15:06 < 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
15:07 < 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
15:08 < 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
15:10 < 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?
15:11 < Paul-_> I should have a picture somewhere
15:12 < 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
15:13 < 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?
15:14 < 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
15:15 < 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
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15:16 < Paul-_> a three neck roundbottom flask
15:16 < chris_99> cheers, is that lab in your house then
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15:17 < 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
15:18 < 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
15:19 < 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 ;)
15:20 < 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
15:21 < 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
15:22 < Paul-_> I assume you have more than just a condenser? ;)
15:22 < chris_99> yeah
15:23 < Paul-_> I measure the temperature of the vapor at the point just before it's going to the condenser
15:24 < 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
15:25 < 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
15:26 < 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
15:27 < 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
15:28 < 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?
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15:28 < 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
15:29 < 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 ;)
15:30 < 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
15:31 < 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
15:32 < 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?
15:33 < 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?)
15:34 < 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
15:35 < 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
15:36 < 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
15:37 < 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
15:38 < 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
15:39 < 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
15:40 < 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
15:41 < 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
15:42 < 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
15:43 < 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/
15:44 < 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
15:45 < Paul-_> just buy oak chips, small casks are super expensive
15:46 < 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
15:47 < 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
15:48 < 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
15:49 < 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
15:50 < 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
15:51 < 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
15:52 < 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
15:53 < 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
15:54 < 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
15:55 < Paul-_> ok makes sense
15:55 < kanzure> if you were paid, would you have tie?
15:55 < kanzure> ... time
15:55 < Paul-_> no
15:56 < 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
15:57 < kanzure> school is lame
15:57 < Paul-_> I agree
15:57  * kanzure wanders off
15:58 < Paul-_> after nine years of studying you're kind of.. done with it
15:58 < CaptHindsight> well there is school and there is learning
15:59 < 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
16:00 < 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?
16:01 < 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
16:02 < 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
16:04 < 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
16:05 < 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
16:06 < Paul-_> me and 2 other biologists, and some "converted" chemists
16:06 < Paul-_> I have never been in a nastier lab
16:07 < 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
16:08 < 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
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16:09 < Paul-_> and she calmly replies it was ok, it was her 10% sodium azide stock but she had to make new anyway
16:10 < CaptHindsight> well she paid or borrowed for her tuition so whats the problem?  :)
16:11 < 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
16:12 < 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
16:13 < 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
16:15 < Paul-_> so the list is: 1. ultracentrifuges, 2. azide, 3. senior professors wearing lab coats in the lab
16:18 < Paul-_> I saw plans for a "dremelfuge"
16:18 < Paul-_> you need some serious guts to use that
16:19 < 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
16:20 < 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
16:21 < Paul-_> I'm very happy I was not in the room at that moment, because the rotor ended up embedded in a wall
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16:21 < streety> so no stability check,
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16:22 < 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
16:23 < 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
16:24 < 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
16:25 < 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
16:26 < Paul-_> only usually I only hear that sound at ~4k, which could hurt you, but 300k is in a league of its own
16:28 < 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
16:29 < Paul-_> well no
16:29 < Paul-_> when you never had to consider if your tubes are forming a condensation on them
16:30 < 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
16:32 < Paul-_> oh yeah, and NMRs
16:32 < Paul-_> don't like NMRs
16:33 < Paul-_> don't like the complicated data they produce, and I definetely don't like magnetic quenching
16:34 < Paul-_> we were evacuated once because one of the NMRs quenched, and I could hear it from a different wing
16:36 < Paul-_> but if you like chemistry glass chris_999, check out my latest score
16:37 < 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
16:38 < 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
16:39 < 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
16:40 < 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
16:41 < 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
16:42 < 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
16:43 < Paul-_> ooh I love glassblowing
16:44 < 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
16:45 < Paul-_> it's all very pornographic
16:46 < Paul-_> she repaired my claisen adapter just this week
16:46 < Paul-_> and a good job too
16:47 < 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
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16:51 < Paul-_> very nice video
16:51 < Paul-_> I tried it once
16:51 < Paul-_> it all looks so easy when they show you
16:53 < 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
16:54 < 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
16:55 < 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
16:56 < Paul-_> that's just beyond belief
16:56 < Paul-_> especially because it doesn't look dificult at all
16:57 < 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
16:59 < 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
17:00 < 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
17:01 < Paul-_> but the flame just isn't hot enough
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17:01 < 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/
17:02 < CaptHindsight> sshhhh
17:02 < kanzure> "Genome engineering with TALE and CRISPR systems in neuroscience" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821859/
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17:03 < 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
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17:04 < 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
17:05 < 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
17:06 < 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
17:07 < 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
17:08 < 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
17:09 < 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
17:10 < Paul-_> that idiot was our seniour professor synthetic organic chemistry
17:11 < 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
17:12 < 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
17:13 < 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
17:14 < 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
17:15 < 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?
17:16 < 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
17:17 < 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?
17:18 < 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
17:19 < 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
17:20 < Paul-_> h2o2 oxidizes something and then it's done
17:21 < xentrac> really?  I didn't realize that chlorine would leave free radicals floating around in a way H₂O₂ wouldn't
17:22 < 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
17:23 < 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
17:24 < Paul-_> well this is a little bit above my paygrade too
17:25 < 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
17:26 < 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
17:28 < 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
17:29 < Paul-_> which actually makes more sense
17:29 < Paul-_> delocalization is also a "soft" characteristic
17:31 < 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
17:34 < Paul-_> or HFSbF6
17:34 < Paul-_> "magic acid"
17:34 < Paul-_> always be weary of things that are "magic" in any way
17:35 < Paul-_> there were all these spray bottles with a piece of tape on it that said "magic mix" standing around
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17:39 < 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
17:40 < xentrac> heh
17:45 < 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 ...
17:46 < 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."
17:47 < 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
17:48 < 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
17:49 < Paul-_> I can't stand his smug face
17:49 < Paul-_> and I can't stand militant atheists
17:51 < Paul-_> not because they're wrong, but they usually make things worse
17:54 < fenn> that UV inkjet printer looks pretty handy
17:55 < 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.
17:56 < yashgaroth> nor do I
17:58 < 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
17:59 < kanzure> probably nmz787 will dazzle us all with a very specific water flow control method to shoot nucleotides around with femtoliter droplet encapsulation
18:07 < kanzure> i don't think anyone has figured out a way to do polymerase ratcheting at 1 nt/step
18:09 < 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
18:11 < 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
18:12 < kanzure> "Confinement and manipulation of individual molecules in attoliter volumes"
18:13 < kanzure> wait that's too large
18:30 < kanzure> evaporative assembly https://www.semanticscholar.org/paper/Fast-High-throughput-Creation-of-Size-tunable-Choi-Jamshidi/79548bfd341ea066024a3d2125f16725718e585d/pdf
18:32 < 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.
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19:03 < streety> http://repository.tudelft.nl/assets/uuid:daac9a6d-63be-438d-be03-1990e52fe409/Master_thesis_Rick_de_Gruiter.pdf approach is mainly hollow cantilever AFM
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19:13 < CaptHindsight> kanzure: I have to build the tools to make that tool first
19:14 < CaptHindsight> I should have started on this 20-30 years ago, but better late than....
19:16 < CaptHindsight> I got a good laugh out of this  http://phys.org/news/2016-06-scientists-unveil-synthetic-human-genomes.html
19:20 < CaptHindsight> fenn: the ChinaCo UV inkjet has horrible software
19:21 < CaptHindsight> replace their controller and it's adequate for multipass printing
19:22 < CaptHindsight> motorize the Z-axis and you have a cheap polyjet printer as well
19:46 < CaptHindsight> http://phys.org/news/2016-06-tiny-dna-legs-fuel-efficiency.html  DNA that drags itself into the cell
19:49 < CaptHindsight> http://www.nature.com/articles/srep27413  Programmable DNA Nanosystem for Molecular Interrogation
19:53 < 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
20:02 < CaptHindsight> need to make this sooner than later http://www.nature.com/nnano/journal/v10/n12/full/nnano.2015.219.html
20:13 < 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
20:15 < 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
20:16 < CaptHindsight> not holding my breath
20:17 < CaptHindsight> yeah higher S:N for better vs faster reads
20:18 < CaptHindsight> I'm sure they will raise a ton of cash
20:20 < 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
20:21 < CaptHindsight> it would be nice if they can actually build something that works
20:21 < CaptHindsight> and is available outside of their group
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20:58 < 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
20:59 < CaptHindsight> long story short, they slow down the scan to get a better signal
20:59 < CaptHindsight> using a viscous media
21:01 < CaptHindsight> "maintaining a signal-to-noise ratio higher than 10." 10:1, 10db power or voltage?
21:01 < CaptHindsight> details details
21:04 < CaptHindsight> honestly, how does one build a nanopore for sequencing DNA and not understand how this works?
21:25 < xentrac> snr is standardly measured with power
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23:46 < 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
--- Log closed Mon Jul 04 00:00:47 2016