2015-07-19.log

--- Log opened Sun Jul 19 00:00:15 2015
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abetuskhttp://www.gaudi.ch/GaudiLabs/?page_id=39201:03
abetusksaran wrap + rain x01:05
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streetykanzure, I think it is one bead. There will be some droplets with zero or more than one, but it is the droplets with just one bead that are the useful droplets05:02
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fenn.wik ibutamoren05:47
yoleaux"Ibutamoren (INN) (developmental code names MK-677, MK-0677, L-163,191) is a non-peptidic, potent, long-acting, orally-active, and selective agonist of the ghrelin/growth hormone secretagogue receptor (GHSR) and a growth hormone secretagogue, mimicking the growth hormone (GH)-stimulating action of the endogenous hormone ghrelin." — https://en.wikipedia.org/wiki/Ibutamoren05:47
fenn"Restoring HGH in "normally-aging" people is not a function that the Food and Drug Administration (FDA) considers to be a legitimate function of a medicine; therefore, Merck (the pharmaceutical company) stopped all further development of MK-0677."05:49
EnLilaSkoIbutamoren seems to promote a more bleed-like GH release, meh05:50
fennsounds like sour grapes05:51
kanzurehm05:54
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kanzurehttp://untappedcities.com/2013/03/15/nycs-pneumatic-tube-mail-network/06:08
kanzure.title http://www.gaudi.ch/GaudiLabs/?page_id=39206:12
yoleauxWelcome to » OpenDrop – Digital Microfludics Plattform06:12
kanzurei'm still not convinced about electrowetting as a viable method for our projects06:12
fenni think there would be too much cross contamination06:13
kanzuredo you think cross-contamination matters for the ligase steps?06:14
kanzurealso, you could just leave open-spaces i think06:14
fennthe third pneumatic cylinder "had a black cat in it, for reasons unknown"06:15
fennearly quantum cryptography experiment06:15
kanzure.title https://www.youtube.com/watch?t=71&v=C677yPYXWIs06:16
yoleauxElectrowetting - Digital Microfluidics on Printed Circuit Board - Prototype - YouTube06:16
kanzure.title https://www.youtube.com/watch?v=53JiNYVzzHM06:16
yoleauxOpenDrop Digital Microfluidics on Printed Circuit Board - YouTube06:16
kanzurehttp://www.bioflux.eu/06:18
kanzurehttp://hackteria.org/wiki/Elektrowetting06:18
fennit looks like the drop is too big06:19
kanzureapparently this is all recent http://hackteria.org/wiki/index.php?title=Elektrowetting&action=history06:20
kanzureand here is their source code and schematics https://github.com/waagsociety/OpenFluxl06:20
kanzurehttps://github.com/waagsociety/OpenFluxl/blob/master/Components/OpenFluxl%20Components%20v.0.1.md06:21
kanzureoh this is pieter boheeman... i see.06:21
kanzureboheemen.06:21
fennso the idea is that you print your oligos directly on one of these arrays?06:22
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kanzureyes06:23
kanzurebut i still like the idea of just pushing the droplets around with a giant metal stick06:24
fennyeah that's super scalable~~~06:24
kanzureweb scale06:24
fennwouldnt you need like 100,000 sticks all perfectly aligned06:25
kanzureyou could also have a giant metal comb and push the droplets around like you're cutting lines of cocaine06:25
fennok so that's only 1000 razor blades at least06:26
fenn.c 100000^0.506:26
kanzurehm06:26
yoleaux100000^(1/2) = 100 sqrt(10) ≈ 316.22776601683793306:26
fennso the big idea behind cambrian genomics was to select known good sequences early in the assembly process by doing on-slide sequencing; droplet manipulation could work just as well as bead manipulation06:28
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fenninstead of firing beads around you just move droplets around06:29
fennunfortunately then your oligo synthesis substrate becomes a giant microfluidic chip06:29
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fennlately i seem to be having trouble stating things in a straightforward way06:30
kanzureelectrowetting at least does not have all the other problems of microfluidics06:30
fennit's definitely easier to think about06:31
kanzurei am ok with lasers but where are you going to be launching stuff, and then after it lands how will you combine some of the results?06:31
fenncan EWOD arrays handle droplets of varying size?06:31
fenni remember one demo where they separated droplets from a "reservoir" that was made up of many pixels06:32
kanzure.ttile https://www.youtube.com/watch?v=jpbUvSyeRg006:33
kanzureyoleaux: i command you!06:34
fenni dont get why each EWOD pixel requires its own dedicated transistor06:34
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kanzure.title https://www.youtube.com/watch?v=jpbUvSyeRg006:34
yoleauxDroplet Dispensing and Mixing in Digital Microfluidics - YouTube06:34
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fennthat's the wrong video06:35
fenn.title http://youtu.be/WxpQyqoukpc06:36
yoleauxProgrammable large area digital microfluidic array with integrated droplet sensing for bioassays - YouTube06:36
fennok i guess they are moving the large drops around too06:36
kanzureah i remember their test setup (exposed electrodes) https://www.youtube.com/watch?v=k9YE4jf-wzo06:40
fenn"FluxMux-Device06:40
fennBased on two crosswise flat ribbon cable the FluxMux device is an easy way to create a digital microfluidic device. An array of power leds shines through the grid to make drops visible.06:40
fennThe control is multiplexed.06:40
fennso i dont get why they think they need individual transistors06:40
kanzure.ttile https://www.youtube.com/watch?v=hVAa41qTIqg06:41
kanzure.title https://www.youtube.com/watch?v=hVAa41qTIqg06:41
yoleauxTwo-plate digital microfluidics for dispensing, mixing, and merging droplets - YouTube06:41
fenninstead of printing directly on the array you can print on a glass slide, then flip the slide over and put it on the array06:42
fenni'm not sure how to get a thin layer of oil on top of tiny droplets without disturbing the position of the droplets06:43
fennis the oil really necessary?06:44
kanzurewell you were complaining about evaporation06:45
fennyes but that may not be a problem if there's a cover slide06:45
kanzurewell it would suck for adding more ligase reaction reagents later06:46
kanzurei guess oyu could have "supply droplets" that you pre-printed06:46
kanzurefor later.06:46
kanzure(unless you had a hole in the cover slide)06:46
fennthe oligos would be dried up by the time you remove them from the machine, so you will have to add water and ligase anyway to re-dissolve them. and also probably add something to cleave the oligos from the surface06:47
fennso there would have to be 2 inkjet printers06:47
fennone to make the oligos, and one to make reaction droplets06:48
kanzuredo you mean two printheads?06:48
fennno, because one of them must be maintained in a completely water-free environment, and the other one is shooting water06:48
fennyay chemistry!06:48
fennyou can get away with a lower resolution on the second printer though, because you're going to be combining 10+ droplets anyway06:49
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kanzureif the surface is hydrophobic then i think you're better able to remove the water, as long as there's no evaporation06:51
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fennmaybe you can use an LCD TFT for the array06:53
fennif the oligos are cleaved and hybridized on the array, you can put down a sparse grid of small droplets, then move the droplet around to each oligo in sequence06:59
fennthis makes better use of the printed area because otherwise you'd have to waste a lot of margin between large circular drops, because it's printed on a square grid and circles don't tile very well07:00
fennit would be really nice to be able to separate long oligos form short ones directly on the array07:02
fennotherwise reaction byproducts will build up and make a mess07:02
fennmis-hybridized strands that got ligated, or badly synthesized oligos with no overhanging ends07:02
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fenni made a drawing http://fennetic.net/irc/dna_printer_EWOD_oligo_resuspension.png07:46
fennat each step you raise temperature to 95C then slowly lower it to 60C to allow stringent hybridization, then move to the next pixel; step 10 is to combine the nearest 9 droplets07:48
fennit's worth noting that each pixel can be much larger than the size of the individual oligo sequence spots, so you could crap 10 of them in each pixel for example07:57
fenncram* heh07:58
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fennthen in the droplet there would be a population of 1,2,3...9 double strands each 225bp long (25 bp single stranded overhang on either end, assuming 50bp oligos)08:01
fennyou want to combine them in the last step because short strands have lower melting points than long strands08:02
fennmaybe it's easier to move the droplet in an outward spiral, because then you don't have to traverse over oligos on your way to the droplet combination location08:10
fennactually it doesn't have to be a spiral at all, it can be linear08:11
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streetyafter you have combined the closest two 9's, would you not then need to repeat with the closest two 10's, 11's etc?08:32
streetywould you leave some pixels blank to allow for merging corridors?08:33
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fennhierarchical linear combination http://fennetic.net/irc/dna_printer_EWOD_oligo_resuspension_linear.png08:39
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streetyspeedy diagramming08:40
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fenni had been drawing it already08:42
kanzureoh look a drawing08:43
kanzurethat's not fair why do you have a good drawing08:43
fennbecause i used inkscape instead of gimp08:43
kanzurefucker08:44
kanzureyeah i probably should have realized something was wrong when i was using gimp instead of inkscape...08:44
kanzureand you are not worried about water evaporation?08:44
kanzurei'm not sure whether ewod works for small droplets on big electrodes08:45
fennhaving a slide on top reduces the surface area significantly08:45
fenni don't know if evaporation will be a problem or not08:45
fenn95C is pretty hot08:46
kanzureisn't there some trick to this like "as you increase the temperature, lower the pressure to avoid evaporation"?08:46
fennraise partial pressure of h2o08:46
fennhmm08:47
kanzurewhat was the drop transfer mechanism you wanted?08:48
kanzurei don't see how you would transition from the inkjet to this08:48
fennwhich inkjet08:49
kanzure"the surface already has electrodes when you synthesize the oligos the first time around, so you just transfer the plate into the other machine and add a coverslip after printing water/reagents"?08:49
fennyes08:49
kanzuredid this require direct contact with the electrode?08:50
fennthey have to be pretty close to the surface but there is a dielectric film over the electrodes(?)08:50
kanzureok so the film would have to be compatible with the phosphoramidite chemistry, acetonitrile, etc.08:51
fennyes08:51
kanzureso does this mean we need an electrode grid the size of the inkjetted spot array?08:53
fennyes, i think an LCD panel could work but it would need new electronics to drive it at high voltage08:53
fennsomething like a TI-85 calculator display would be easier to work with because of the larger dot pitch, but those dont typically have TFT built in08:55
kanzureyes we have been over this before i think08:55
kanzurehttp://teitell-lab.com/wp-content/uploads/2014/02/2010_4_Park.pdf08:55
fennalternatively we could make a PCB that just does this08:55
fennthe electronics will be simpler because of the linear layout08:56
fennyou only need 3 phases08:56
fennthey can all be driven in parallel at the same time08:57
fennso i guess that's only 3 transistors08:57
fenninstead of 1 million or whatever08:58
kanzure.title https://www.youtube.com/watch?v=u_Be2awFf0c08:59
yoleauxSingle-sided continuous optoelectrowetting (SCOEW) for droplet manipulation with light patterns - YouTube08:59
kanzure(related to that last paper link)08:59
kanzurenot a good video09:00
fenn"optical electrowetting" sounds like just laser tweezers09:01
kanzurehere's one where they move droplets using suction https://www.youtube.com/watch?v=Qjeb_3y6RU809:01
kanzurehuh... https://www.youtube.com/user/labonachipVideos/videos09:02
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fenndown the microfluidics rabbit hole...09:03
kanzure"Instantaneous room temperature bonding of a wide range of non-silicon substrates with poly(dimethylsiloxane) (PDMS) elastomer mediated by a mercaptosilane" https://www.youtube.com/watch?v=FIwX28dRkVI09:03
kanzureyes perhaps i shouldn't look09:03
kanzureheh, a "bubble pump" https://www.youtube.com/watch?v=3WOop8-jcjY09:03
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kanzure.title https://www.youtube.com/watch?v=a-28gvw8WkQ09:07
yoleauxMicro Propulsion by Acoustic Bubble for Navigating Microfluidic Spaces - YouTube09:07
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fennits like a pulse jet09:08
fennwater gets sucked in from all directions but goes out in only one direction09:09
fennok so maybe this could be done with a bunch of razor blades09:10
fenninstead of electrowetting09:11
fennelectrowetting actually seems simpler though09:11
kanzureyes it is closer to solid state stuff09:11
kanzureand more solid state stuff is better and makes life simpler09:12
kanzureoh, razor blades are also solid state09:12
kanzurerealistically we are not going to have a 2000-drop wide razor blade that we move only 50 microns (so that it doesn't slide them into the next line/row)09:13
kanzureunless we get some really small paperclips09:13
kanzurethis wont work for our purposes but there was a way of grating a surface so that droplets move at variable speeds in certain directions. if you could control that sufficiently well you could have it also timed to the ligation protocol steps.09:16
kanzure(they would move up the gradient or grooves because of surface tension caused by the patterning on the surface)09:17
juri_have you thought of using the razorblade as 'ground', and forcing the droplets around that way?09:18
kanzurethe droplets have a diameter of <20 microns09:18
juri_ok, so the finest razorblade is just too blunt.09:20
juri_even if you were trying to hold it a fraction from the surface, getting it between droplets just isn't feasable.09:20
juri_and i can't find wire in sizes that small...09:27
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kanzureman if star wars 7 doesn't have a new superweapon (or the death star) i'm going to be grump10:10
chris_99heh10:16
streetydoes anyone have any recommendations for a good laptop? My backup has just failed, and my main is less reliable than I would like10:33
chris_99i just saw https://news.ycombinator.com/item?id=9911699 on HN, may be helpful?10:33
chris_99.title10:33
yoleauxAsk HN: Most hacker friendly laptop in market(2015) | Hacker News10:33
kanzurestreety: thinkpad w520 has been serving me well. there'a w530 also.10:34
streetyvery relevant, thanks10:35
kanzureoh they claim "HP Zbook 15 G2" can do 64 GB RAM. hmm. maybe i should upgrade.10:36
kanzurehmm hp seems to disagree10:37
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justanotheruserI have a w530, love everything about it except the battery life10:47
kanzureget battery extension pack thingy10:49
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fennwow at the end of the Park SCOEW paper they just use a LCD monitor to move droplets around11:02
fennalso i am a dumbass and didn't realize the obvious implication that a droplet handling system can make a bunch of small droplets from one large blob, so you don't need a second inkjet printer11:05
fennit might be possible to get rid of the first inkjet printer too11:16
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kanzurefenn: with a large enough blob i guess you could make sub droplets in parallel?11:48
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kanzurefinger actuation of electrowetting / EWOD by using a piezoelectric element http://pubs.rsc.org/en/content/articlelanding/2014/lc/c3lc51223a11:53
kanzure"Instead of requiring an external power supply, our F-DMF uses piezoelectric elements to convert mechanical energy produced by human fingers to electric voltage pulses for droplet actuation. Voltage outputs of over 40 V are provided by single piezoelectric elements, which is necessary for oil-free EWOD devices with thin (typically <1 μm) dielectric layers. Higher actuation voltages can be provided using multiple piezoelectric elements ...11:54
kanzure... connected in series when needed. Using this energy conversion scheme, we confirmed basic modes of EWOD droplet operation, such as droplet transport, splitting and merging. Using two piezoelectric elements in series, we also successfully demonstrated applications of F-DMF for glucose detection and immunoassay."11:54
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kanzure.title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079775/11:57
yoleauxPicoliter DNA Sequencing Chemistry on an Electrowetting-based Digital Microfluidic Platform11:57
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kanzure.title lindsay salis12:01
yoleauxkanzure: Sorry, that command (.title) crashed.12:01
kanzurefjoiefjeqreq12:01
kanzure.title https://www.youtube.com/watch?v=UQbqvqn7BSE12:01
yoleauxActive thermal management of on-chip hot spots using EWOD-driven droplet microfluidics - YouTube12:01
kanzureis that something i should expect to cool the chip?12:01
CaptHindsightI wonder how many Irish Folk Dancers it would take to power a cluster of these arrays?12:01
kanzure"biomems" lectures https://www.youtube.com/playlist?list=PLqYqvTonHe8-ok_aryb6UQlshRMVL_96L (27 videos)12:08
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streetyMy current thoughts on a replacement laptop are that the HP Zbook at 6lb is way too heavy. I'm actually tempted to go as light as possible this time around and see how it works for me. The laptop that has just failed was a lenovo but it took a lot of punishment so would definitely consider sticking with lenovo. The W series looks good, but again probably too heavy at 5.5lbs. The X1 looks to be a possibility. http://zareason.com/shop/U12:24
kanzureif you want light as possible then use a smartphone and a portable keyboard12:25
archelsstreety: which one just failed?12:26
archelsI just fixed my Lenovo U43012:27
streetylenovo G550, a cheap model but worked well for me for many years12:27
streetyit still starts but windows is corrupted somehow and the CD drive isn't being picked up by the BIOS to repair/re-install12:28
archelshaha if it has an optical drive it is definitely ripe for replacement12:28
archelsalthough I have to admit I never looked into the 15"+ segment much12:29
streetywell, DVD drive, but still true. I replaced it 3 years ago as my main computer but kept it around for those rare times when a windows machine comes in useful and as a backup12:31
CaptHindsightis it worth swapping in a used working G550 motherboard?12:33
archels.title https://wada-main-prod.s3.amazonaws.com/resources/files/wada-2015-prohibited-list-en.pdf12:35
yoleauxarchels: Sorry, that doesn't appear to be an HTML page.12:35
archelsindeed it isn't12:35
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archelsThe World Anti-Doping Code: The 2015 Prohibited List12:36
streetyfor what I have been using it for it wouldn't be worth the effort. If my main computer was humming along nicely I would just put it up on a shelf and not even consider taking any further action12:38
streetyonly considering buying a new laptop because my principal laptop is less than 100% as well12:38
ParahSailin_asus zenbook is ok, just got one of those12:42
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archelsParahSailin_: what OS are you running?12:48
ParahSailin_win 8.112:48
archelsargh Asus is doing that power-button-in-the-corner-of-keyboard thing now as well12:49
ParahSailin_ive forgotten where a power button is supposed to go12:50
streetylooks interesting, thanks12:51
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archelshttps://en.wikipedia.org/wiki/Born_alive_laws_in_the_United_States12:59
ParahSailin_what the hell is misprision13:01
archels.ety misprision13:17
yoleauxmisprision (n.): ""wrong action, a failure on the part of authority," early 15c., from Anglo-French mesprisioun "mistake, error, wrong action or speech," from Old French mesprision "mistake, wrongdoing, fault, blame, crime," from mespris, past participle of  …" — http://etymonline.com/index.php?term=misprision13:17
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fenn"a member of the species Homo sapiens, at any stage of development, who is carried in the womb"13:34
fennso we can experiment all we like with superbabies right?13:34
drethelinheh13:34
fennto say nothing of artificial wombs13:35
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FourFirefenn, I like the cut of your jib: "so we can experiment all we like with superbabies right?"14:24
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mginyo14:24
fennsup14:24
mginanyone here trying to achieve immortality?14:25
kanzurenah we're already dead14:25
fennalready achieved it...14:25
FourFiremgin, I'm intending on dedicating my useful healthspan to researching biological indefinite lifespan14:25
mginFourFire: good man!14:25
kanzureFourFire: that's insane; who wants to be biological indefinitely?14:25
FourFireimmortality is a problem for us to work on in a thousand years or so14:25
mginfinally someone serious14:25
mginwhat's your strategy?14:26
FourFirekanzure, well I'd like to stick as close to what I know works, just with improvements until the kinks are worked out of more... transcending methods14:26
kanzureFourFire: i don't think you know whether biology can last indefinitely. that's not a good idea.14:26
fenni'm thinking along the lines of that mutant in "total recall" that has a baby embedded in his abdomen14:26
kanzuremgin: http://diyhpl.us/wiki/declaration14:26
kanzurei seem to have missed a conversation14:26
FourFiremgin current plans involve brute forcing some proteins I need in probability space with some tweaked evolutionary algorithms, but I haven't made much progress towards that yet so I don't want to toot my horn much about it.14:27
FourFirebrute forcing the genes for those proteins, I mean.14:27
mginwhat does that mean?14:27
mginyou want to figure out which genes code for which proteins? why?14:28
FourFirekanzure, of course it can't, but it can be improved to last, say twice as long?14:28
FourFirethat's all I need, i reckon14:28
kanzureokay that's not the same thing as indefinite14:28
FourFirethe cybernetics and nanotechnology approaches will be quite far along by the 2060s14:28
mginkanzure: what's that for?14:29
FourFire"working on" and "working towards" != reached14:29
kanzuremgin: it's for reading...?14:29
kanzurefenn: i am writing a helpwanted job ad for some chemists. what should i mention?14:29
mginso i read it. what of it?14:29
kanzuremgin: you asked where the serious people are, then i gave you the link14:29
mginso?14:29
FourFirekanzure, I have a low probability for Cryonics and a slightly higher probability for plastination strategies working, so that's not really an option14:29
kanzuremgin: so nothing, you're welcome to ignore it, although i think you would be doing yourself a disservice14:30
FourFireI also don't want to lose all he stuff you start losing once you reach biological 5014:30
mginyou're trying to suggest this link implies that you are serious about achieving immortality?14:30
kanzurehave you read the document?14:30
mginFourFire: you want to figure out which genes code for which proteins? why?14:30
mginkanzure: yes14:31
mgini've seen all this stuff a thousand times, what of it?14:31
kanzurei think you'll have to provide better criticism than that14:31
kanzuresomething like "this is not serious because x"14:31
mginhow am I criticizing anything?14:31
mgini'm asking you what's this in reference to14:31
kanzurewe already established that14:32
FourFiremgin, no, I want to "invent" (really just find) proteins which aren't know and probably don't exist in nature which do simple, low hanging fruit things which are useful14:32
FourFirebut very unlikely to have come about due to evolution14:32
FourFirearen't known*14:32
mginFourFire: things like what?14:32
FourFireand test with simulations, animals etc. until they can be integrated in the human genome without too bad side effects14:33
kanzure14:29 < kanzure> mgin: you asked where the serious people are, then i gave you the link14:33
kanzurethis already answers your question:14:33
kanzure14:31 < mgin> i'm asking you what's this in reference to14:33
mgin[05:32.30] <mgin> you're trying to suggest this link implies that you are serious about achieving immortality?14:33
FourFireI'm only going to realistically work on a tiny aspect of one subproblem, but I'm betting on people like me who are already working on other aspects of the same and different problems at least being partially successful14:33
kanzuremgin: i don't think that's a fair question14:34
kanzureFourFire: you should just use subunits to make structures, problem solved, no protein folding needed14:34
mginhow is it fair or unfair? it's just a question. is that what you're trying to do? you're saying you are serious about achieiving immortality? i don't know, hence the question14:34
mginmy follow up question is "how?", if you are14:34
kanzurequestions can be fair or unfair based on their context. i gave you a link, and now you're interrogating me about my beliefs about immortality.14:35
FourFiremgin, well for my part, mechanism for increased time before cellular asphyxiation, mechanism to increase physical information robustness of the genome by at least factor of Three14:35
FourFirethose are the two main goals ATM, with a preference for the second14:35
kanzuremgin: i think that the ideas expressed on that link are much more serious than the rest of the immortality literature out there14:36
FourFirebut I have ideas (and not much more) for further potential "upgrades"14:36
kanzurei have nfc why you would jump so weirdly with reasoning to such a distant conclusion14:36
FourFire(of course by the time I get around to developing someone else will have built something much better with nanotech or just good enough robotics)14:36
mginFourFire: so you're trying to generate proteins which help with that? which could potentially be synthesized?14:36
FourFireI'm trying to find the genes, not just the proteins14:37
mginwhat genes?14:37
FourFireand integrate into the genome, so that they are "naturallY" synthesized14:37
mginoh14:37
FourFireI want to discover robust technology14:37
FourFirenot silly elven fairytale magic which fails the instant the power goes out14:38
mginso how do you know which proteins need to be synthesized?14:38
FourFireI'd like my enhancements to remain at least partially useful even in a loss of civilization scenario14:38
FourFiremgin, I don't, I need to find them, all I know is what I need the to do14:39
FourFirethis is where the evolutionary algorithm comes in14:39
mginwhat do they need to do?14:39
FourFireand I'd prefer not to talk much more about it since I haven't really made much progress so far14:39
FourFirePM?14:39
mginwell i'm just wondering generally14:42
mginhow do your two goals fit into life extension research?14:42
mgindo you think they will have significant impact on aging?14:42
mgini mean, "mechanism for increased time before cellular asphyxiation, mechanism to increase physical information robustness of the genome by at least factor of Three"14:43
FourFiremgin, well one14:43
FourFirethe first method: delay mechanism for cellular asphyxiation would improve healthspan outcomes for metabolism degeneration, extend it basically, and also decrease sudden death incidence (because if you take 20 minutes to drown/die of blood loss/take permanent brain damage from stroke, heart attacks etc. then someone could rescue you in time)14:45
FourFirethe second mechanism, if it works, would allow you to retain the complete information of your genome in stem cells (where it's important) because rate of mutation from all non-nucleus-destructive sources would be orders of magnitude rarer14:47
mginwhy does that matter?14:48
FourFiremgin, why are mutations bad?14:48
FourFire(and don't give me crap about "muh evolutions will stahp")14:48
mginso your approach is to identify individual proteins which will somehow have these beneficial effects, and the genes which code for them, and then to what, insert these genes into the DNA of cells somehow so that they will get expressed?14:49
FourFiremaybe not individuals proteins, possibly tertiary or even Quaternary structures in one mechanism14:51
FourFirewhatever works and deson't break something else inside the cell14:51
FourFireI don't need something perfect on the first try, just something that works better than my base biology14:51
mginhow are you going to go about doing all of this?14:52
FourFiremgin, yes though other people are working on the gene insertion technology right now14:52
FourFirelots of computers, and simulations14:52
mginsimulating what?14:52
FourFirea freaking buttonne of computational power, the likes of which doesn't currently exist on this planet, but which will be available in the near decades14:53
FourFireRunning an evolutionary algorithm which selects against arbitrary amino acid sequences and their fitness against a specific fitness function14:53
FourFirerecombining the best 10 (or possibly 100) out of generations somewhere between 10⁵ and 10⁷ in size14:54
mginwhat fitness function?14:55
FourFirerecombining he best candidates into the next ~10⁵-10⁷ camndidates14:55
FourFiremgin I haven't written it yet, which is why frankly it's embarrassing for me to have explained this much already, for the DNA mechanism, see how well it can cross check the same basepair triplett against three sets of the same chromosome and then replace one which doesn't match if only one doesn't match, with the one the other two are14:57
FourFirethen slide down the three chromsome copies three baspairs and repeat14:57
FourFirefor the asphyxiation delay mechanism, 1, an organelle which can contain potentially highly reactive oxygen rich molecules, 2, a protein + chemical mechanism which, depending on environmental acidity outside the organelle membrane either, integrates O² molecules into a more stable but still fairly dense molecule which stores the oxygen (while requring a capped amount of chemical energy to decompose), OR, reverses the process15:01
FourFire unlocking O² molecules and letting them into the cell for metabolic use15:01
mginso the premise is that we are developing the ability to insert genes into the genome, so you want to start figuring out what genes it would be helpful to add15:01
FourFireof course that last one is rather more ambitious and not quite as useful as the first, which is why I'm preferring to focus on it15:01
FourFireon the first, seems like more low hanging15:02
FourFiremgin, we have developed, look into CRISPR15:02
mginsure15:02
mginbut how the hell do you simulate something like that?15:02
FourFireit's sorta unreliable, but it works to some extent and it's only going to be improved upon15:02
FourFirewell I've not gotten that far yet15:02
FourFirebut my intentions are not to simulate an entire cell, ala Wholecell.stanford.edu15:03
FourFirejust one small area of the environment15:03
mginso you're trying to figure out how to build some complex protein structure which checks DNA for anomalies and replaces them?15:05
FourFireand when I begin to get highly functional candidates for my molecules, I'll add the the fitness function that it must not react with x,y,z,a,b,c,fiz,buz molecules, and add one or to of each of the molecules inside the human cell to the simulation15:05
FourFirebut by the time I'm that far along, computers I will have access to will be so much more powerful15:05
FourFiremgin, yep15:05
FourFireand I hope, that if it can overcome, with the help of native dna repair mechanism, single and double strand breaks, it will only fail in two situations15:06
FourFire> each of the three copies of the genome have different triplets at the given spot15:06
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FourFire> two of the three copies are mutated to the same different triplet15:07
FourFirein the first scenario, the protein should just pass on, that's an incorrectable data loss15:07
FourFirea silent hard error, if you like15:07
FourFirein the second, that's a bit flip15:08
FourFireand again, that's fine, reducing mutation rate by several orders of magnitude is Good enough for me15:08
mginand you plan to do this with simulated proteins? can we even simulate proteins?15:10
FourFirewell yes and no15:10
FourFiredepends what detail of resolution you want, how many frames per nanoecond and whatnot15:11
mginso we can approximately simulate them?15:11
FourFireall stuff I don't know the requiremnts for yet, but I'm going to be working on it for the next five years at least to get my proof of concept working15:11
FourFire(I intend to evolve some form of the human histone proteins without actually inputting any specific basepair data besides the apporximate length of the DNA sequence which encodes for it15:13
FourFire)15:13
kanzurefenn: plz check http://diyhpl.us/~bryan/papers2/DNA/chemistry-hiring-ad.txt15:14
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FourFireif I succeed and the artificially evolved histones work as well, or possibly even better than human ones, then the method works and I won't be wasting the next decades of my life15:14
FourFireif not, well I spent 5 years doing science related stuff instead of becoming a politician or a stock broker or something15:15
FourFireand then I can reevaluate my life goals and jump on the next most likely looking approach for me to help15:16
mginwell i'm just asking how this works, you're saying it's possible to approximately simulate proteins?15:16
FourFiremgin yes, I'm using a program called GROMACS, and a visualization tool called PyMOL15:16
FourFireboth open source, both on linux (of course)15:16
FourFiremgin yes, but I, personally, don't yet know what degree of precision is required of the simulation in order to get "correct" answers to interaction questions15:17
FourFirefrankly the complexity of things like chaperonin scare me15:18
FourFirebut the way I see it, it's like the Human genome project15:18
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mginyeah i imagine proteins are insanely complex, let alone trying to simulate their behavior..15:18
FourFirewhen they started it was literally an impossible task15:18
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kanzureit was hardly impossible, venter was already half-way done15:18
fenni read the ad but i don't have any insight15:19
kanzurefenn: so "not completely shit"?15:19
kanzurefenn: what would you want out of a chemistry person in here?15:19
fenn"Hourly OK, milestone payments OK, other schedules OK. Upfront payments also OK" might be confusing, "so what exactly am i being paid to do???"15:19
mgini think your approach generally makes sense at least, gene therapy is starting to become feasible... so if we can figure out which genes to code for to help enhance biology / solve aging problems, that could be a big help15:20
kanzuremgin: using gromacs would be a big help why?15:20
kanzurefenn: maybe i should just make up some arbitrary goal ("a document") and demand that they produce it....?15:20
fennYOU MUST ... write this15:21
fennhaha15:21
mginit's a pretty hard problem though... we need to know which proteins will have beneficial effects, and how to code for them genetically15:21
fennpersonally i would like to know more about the safety of phosphoramidite nucleotides15:22
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kanzurethere's nothing like exposing people to the harsh love of reality, so maybe the goal should be "a working oligonucleotide synthesis, either from your premises or ours"15:22
QuadIngibut the technology improved, and after a few years, it was only a year of work until they were done15:22
QuadIngidid I miss anything?15:22
fenndo they cause cancer, how terrible, etc15:22
QuadIngilast I saw is xx:21:2415:22
mginFourFire: even if you figure out a helpful protein, how do you figure out the genetic sequence to synthesize it?15:23
kanzurealso i was considering something like just a "collaborators wanted" ad. instead of paying anyone. i mean paying people is good, but i think there might be one or two individuals that would be willing to poke their heads in here anyway without pay.15:23
QuadIngimgin, ah that's the question15:23
kanzuremgin: you can use something called reverse transcriptase. do you even biology? :-)15:23
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fennyes paying people tends to make things awkward15:23
QuadIngiI'm searching probability space for genes, not proteins15:23
kanzurewait, er15:23
kanzurenot reverse transcriptase15:23
QuadIngiand I'm rating the fitness of the genes, but how the proteins they synthesize perform15:23
fennprotein sequencer15:23
kanzurewhat's the one for .. yes, protein sequencing, sure.15:23
QuadIngis/but/by15:24
mginhow do you know what proteins are generated by a given gene sequence?15:24
kanzuremgin: you don't care; you start with the protein and then sequence the protein.15:24
QuadIngiit's a relatively simple program to write15:24
mginoh15:24
fennit's pretty straightforward to translate DNA sequence to the protein it produces, there's a small lookup table15:24
QuadIngiso simple the even I that can't code could write it in speudocode15:24
fenn.wik code of life15:24
yoleauxfenn: Sorry, that command (.wik) crashed.15:24
fenn.wik codon15:24
yoleaux"The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells." — https://en.wikipedia.org/wiki/Codon15:24
mgini know genes code for amino acids right15:25
kanzure-_-15:25
mginer15:25
mginright?15:25
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fenngenes code for gene products :P15:25
fennbiology is messy15:25
fennthe simplified version is that one gene makes one protein from one strand of dna15:26
mgini'm just asking, how well do we really understand the mapping between genes and proteins?15:26
fenner, and the gene is the one strand of dna15:26
FourFirefenn, which is another thing I'm uncertain about, do I reduce the search space by searching for genes, or do I increase it?15:26
kanzuremgin: are you asking about protein folding, or are you asking about the "central dogma"?15:26
mginright, isn't protein folding a huge problem by itsefl??15:26
kanzureyou didn't answer my question15:26
mginin other words you code for XYZ amino acids but how do you know what protein is the result15:27
FourFirebecause I imagine the the kinds of mechanisms required to do the stuff I want requires more than one part (so tertiary structures at least)15:27
kanzuremgin:  you look up what protein it made last time, then you know15:27
kanzurealthough amino acids don't always fold into the same proteins in all conditions15:27
mginthat's what i'm saying, you would have to try it experimentally, that's not something we can simulate is it?15:27
FourFiregtg15:28
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mginthat seems like a huge gap in his approach, no?15:28
kanzure.wik central dogma of molecular biology15:28
yoleaux"The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It was first stated by Francis Crick in 1956 and re-stated in a Nature paper published in 1970:" — https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology15:28
kanzuremgin: yes, but previously he wasn't doing anything at all. i think this is his first project.15:29
kanzureand i haven't had the heart to stop him yet15:30
kanzurefenn: i'm afriad the ideological "OPEN-SOURCE ALL THE THINGS" or "HACK THE PLANET" "help wanted" ad wont go over well.15:31
kanzuremaybe i should just pose it as an "academic credit" thing...... but then that will attract people that care about academic credit.15:31
kanzurewhich i'm not sure i want to deal with15:32
kanzure"The team also calculated the planet's equivalent of computing power: the speed of DNA transcription. Given the average rate of genetic transcription for different organismal groups, they found that the biosphere processes more than 10^24 subunits of DNA per second."15:33
mgindid anybody see that article on turning bacteria into computing components? that shit is fascinating to me15:35
mginimagine if we could just grow a massive computer out of bacteria in a petri dish15:36
kanzureit would be the slowest computer ever15:36
kanzurethere are much more interesting things to do with bacteria in a petri dish15:36
kanzurelike nanotechnology15:36
kanzurehttps://github.com/kanzure/nanoengineer15:36
mginit wouldn't necessarily be slow15:36
mginwhat's this?15:37
kanzurenanotech stuff15:37
kanzureinstead of using diamondoid mechanosynthesis you could use ribosomes to construct fusion proteins and protein subunits that form atomically-precise mechanical machinery15:37
fenn" Jacques Monod pointed out to me that I did not appear to understand the correct use of the word dogma, which is a belief that cannot be doubted. I did apprehend this in a vague sort of way but since I thought that all religious beliefs were without foundation, I used the word the way I myself thought about it, not as most of the world does ... that a dogma was an idea for which there was no15:37
kanzureit was an example of what to do with bacteria in a petri dish15:37
mginthis looks legit15:37
fennreasonable evidence. You see!?"15:37
mginholy shit15:37
fennwhat does nanoengineer have to do with bacteria in a petri dish?15:38
kanzurei was giving him examples of molecular things to build with bacteria15:39
kanzurehe wanted to do computation instead15:39
mgini've seen this nanofactory video many times over the years15:39
kanzureyes, well, now you know who made it15:39
mginand the animations of molecular machines15:39
mginyou really made this stuff?15:39
fennlol15:39
kanzurethe original developers of nanoengineer were responsible for the nanofactory animations15:39
kanzurethe README specifically says this........15:40
kanzure(although the nanoengineer devs did not make the animation itself, they were involved/responsible/culpable)15:40
fennkanzure was saddled with upkeep and archival of a dead project15:40
kanzure((the foresight challenge))15:40
mginoh15:41
kanzure.wa mass of adenosine in grmas15:41
kanzure.wa mass of adenosine in grams15:41
yoleauxconvert adenosine: molar mass to grams: 267.241 g/mol (grams per mole); Additional conversion: 0.267241 kg/mol (kilograms per mole); Comparisons: ~0.37 × molar mass of fullerene (~721 g/mol); ~1.4 × molar mass of caffeine (~194 g/mol); ~4.6 × molar mass of sodium chloride (~58 g/mol); Corresponding quantities: Mass of a molecule m from m = M/N_A:: 4.4×10⁻²² grams: 4.4×10⁻²⁵ kg (kilograms): 267 u (unified atomic mass units15:41
yoleaux): 267 daltons15:41
yoleauxconvert adenosine: molar mass to grams: 267.241 g/mol (grams per mole); Additional conversion: 0.267241 kg/mol (kilograms per mole); Comparisons: ~0.37 × molar mass of fullerene (~721 g/mol); ~1.4 × molar mass of caffeine (~194 g/mol); ~4.6 × molar mass of sodium chloride (~58 g/mol); Corresponding quantities: Mass of a molecule m from m = M/N_A:: 4.4×10⁻²² grams: 4.4×10⁻²⁵ kg (kilograms): 267 u (unified atomic mass units15:41
yoleaux): 267 daltons15:41
fennthere's nothing wrong with the software really, but they never really developed a user base15:41
kanzure.wa 4*(10^(-25)) grams * (10^24 / second)15:42
fenni wish wolfram alpha would just shut the fuck up and give you the answer you asked for instead of all this other crap15:42
yoleaux4×10⁻²⁵ grams×10²⁴/(second): 0.4 g/s (grams per second); Unit conversions: 4×10⁻⁴ kg/s (kilograms per second); 24 g/min (grams per minute); 0.024 kg/min (kilograms per minute); 24000 mg/min (milligrams per minute); 2.4×10⁷ µg/min (micrograms per minute); Basic unit dimensions: [mass] [time]⁽⁻¹⁾15:42
mginso15:42
kanzurethe whole biosphere is only making 0.4 grams/second of nucleotides??15:42
mginhow is this sort of nanoscale modeling useful?15:43
kanzurewait shouldn't this be exponential or something15:43
mginsounds like it isn't given that it's a dead project with no user base15:43
kanzurewhy is tihs a linear rate >:(15:43
fennis 10^-25 supposed to be avogadro's number?15:43
kanzureoh it said kilograms15:44
kanzure.wa 4*(10^(-25)) kilograms * (10^24 / second)15:44
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yoleaux4×10⁻²⁵ kg (kilograms)×10²⁴/(second): 0.4 kg/s (kilograms per second); Unit conversions: 400 g/s (grams per second); 24 kg/min (kilograms per minute); 24000 g/min (grams per minute); 2.4×10⁷ mg/min (milligrams per minute); 2.4×10¹⁰ µg/min (micrograms per minute); Basic unit dimensions: [mass] [time]⁽⁻¹⁾15:44
kanzure0.4 kg/sec sounds better15:44
kanzurealthough not really. hrm.15:44
kanzureperhaps i should do this the other way around: what would be a reasonable guestimate for the mass per second of dna being produced by the biosphere?15:45
fenn"subunit" is a vague word15:46
kanzurei think they meant nucleotide15:46
kanzurehttp://www.nytimes.com/2015/07/21/science/counting-all-the-dna-on-earth.html15:47
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kanzureyashgaroth: yo15:48
yashgarothsup15:48
kanzurestuff15:48
kanzureyou?15:48
yashgarothsame15:48
fennyo/sup protocol completed15:48
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kanzureyashgaroth: we have someone willing to build an inkjet dna synthesizer, but we need a chemist i think15:49
fennbegin transmitting data on port 69889615:49
yashgarothah was about to ask: so rather than read through a megabyte of electrowetting, how's the new dna synth project going?15:49
yashgarothyes a chemist would be the missing link in the group15:49
kanzureyashgaroth: also for gene assembly we are thinking of a cycling ligase reaction on an electrowetting surface for moving and merging droplets (although it's possible that this system would also be used for phosphoramidite chemistry too...?)15:49
kanzure"cycled ligation assembly" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.010732915:50
yashgarothfine I'll find out what electrowetting is15:50
kanzurehydrophobic drops on a surface and then electrodes under the thin surface, electrodes cause drops to move15:50
fennelectrowetting is just moving tiny drops around on a slide15:50
yashgarothok cool do that15:51
fennhere's a dumb video http://youtu.be/jpbUvSyeRg015:52
fenn.title15:52
yoleauxDroplet Dispensing and Mixing in Digital Microfluidics - YouTube15:52
yashgaroththat linked article still requires rather large pieces of dna though15:52
kanzure40 bp?15:52
yashgarothisn't that just for the linker bit? lemme see15:53
kanzureyes, but i don't know if they tested the requirement of length for the non-linker strands15:53
kanzure"The efficiency of CLAs decreases as the size of the assembled DNA fragments grows above 5–6 kb"15:54
kanzure"This effect is likely due to the probabilistic nature of CLAs" (so can be fixed with heat and time and stuff)15:54
yashgaroththey become far less likely to randomly orient and line up and behave yeah15:54
fenni was thinking the first ligation reaction would be all linkers (50 bp oligos say) that overlapped by half15:54
kanzure"At the scale of the most common DNA assembly goals, using fragments from <500 bp to 5 kb, cycled-ligation assemblies are efficient"15:55
kanzuredoesn't say how much smaller than 500 bp15:55
yashgarothI really should just order a bunch of t4 ligase and 10bp oligos and test that out before I try to preach it any more15:56
fenn10 is pretty short15:56
kanzureok well let me know what the total amounts to15:56
yashgaroth10's a lot better than we were planning to work with, when a million seemed too high for microplates15:57
kanzurehave you ever done emulsion pcr?15:57
fennoh well 10 is not much larger than 615:57
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yashgarothI avoid pcr whenever possible, and no15:57
fennwhy dont you like pcr?15:58
yashgarothbiology's already enough hopes and guesses and frustration without pcr15:58
yashgarothalso I mostly do protein work these days, lot fewer shrines at the sds-page bench than a pcr station15:59
fennso you dont have good luck with primer design?15:59
yashgarothno I'm great at that shit, usually it works for me, pcr is just a pain15:59
yashgarothjust because I dislike something doesn't mean I'm not good at it16:00
kanzurethermocyclers should do pcr prep16:00
yashgarothanyway! iirc 10 was much closer to being feasible for t4 ligase recognition than 6, will try and find some data16:01
fenndo you think it would work if there were a lot of other nicks along the strand16:01
kanzurefenn: i would worry about spot density in the electrowetting approach.16:02
yashgarothhow many nicks we talking here16:03
fennlike if you had a strand made entirely of 10bp oligos overlapping by 5bp each16:03
fennor 6bp oligos overlapping by 316:03
yashgarothwell the hope was to do them one at a time, with that many nicks it'd fall apart if you did them all at once16:03
kanzureif you overlap by 3 on both ends then you have no unique content16:03
fennit falls apart because there is more force tugging on the longer strand?16:06
yashgarothjust a long-ish strand composed of overlapping 10mers seems unstable, and the more you add at once the higher chance that you get unwanted combination between the wrong strands16:07
yashgarothpossibly you could add a few oligos into the mixture at a time, depending on their sequences, if that'd help speed it up16:08
yashgarothand then there was something about washing in between 10mers just so trace amts. of previous oligos don't hang around and fuck their way into the chain later on16:09
kanzurehmm a wash step with electrowetting. or even with the flood group method. uhh...16:10
kanzureif we were using magnetic beads then we could turn on a magnet and then blast away all the surrounding liquids16:11
kanzurebut i dunno if beads could be transported in the droplets16:11
kanzure.title https://www.youtube.com/watch?v=P-LsWmy6hqo16:12
yoleauxConcentration of polystyrene beads - YouTube16:12
yashgarothanother fun project would be to investigate salt/pH/temp conditions that improve the ligation accuracy/efficiency/speed for this, maybe apply the inkjetted array approach somehow16:13
fennyashgaroth: what's a good way of removing everything but the longest strand in a droplet that doesn't involve beads?16:14
* fenn sick of hearing about beads16:14
yashgarothdroplet? um feed it into a tiny capillary gel and electrophorese the smaller stuff out maybe16:14
fennthat was my first thought but it seemed complicated16:15
yashgarothwell when your choice is between complicated and impossible...16:15
fennalternatively remove only the longest strand and come back for it later16:15
yashgarothincomprehensibly small ultracentrifuge16:15
fennor some sort of process that causes longer strands to precipitate faster than shorter strands do16:15
yashgarothwhat's the g-force on atp synthase?16:16
fennheh16:16
fennit's actually more like a crankshaft than a turbine16:16
yashgarotha guy can dream16:16
yashgaroththe precipitation one is a possibility, depends how absolutely selective you need to be16:17
fennjust to get rid of accumulating side products and mismatched/malformed oligos16:18
kanzureother than beads and linking to a surface, and complex gel/hplc shit that nobody wants, i'm not sure how to not wash away oligos16:18
fennhm i should clean my desk16:20
yashgarothyeah I always assumed they'd be attached to a surface16:20
kanzurethey can be attached to a surface (and not a bead), but then moving droplets is not as useful16:20
yashgarothwait are we moving the chain between places on the oligo board? I thought it was stationary chain and then you droplet the oligos onto it16:21
kanzureuh.. undecided i think?16:22
fennit's a lot simpler to move the oligos around: http://fennetic.net/irc/dna_printer_EWOD_oligo_resuspension_linear.png16:23
kanzurei thought both were moving around16:23
fenner, uh, terminology fail16:23
fennis there a word for a combination of synthesized short strands that is slightly longer?16:23
kanzure"synthesized oligos (bound)" how are they going to be ligated to anything if everything prior in the path was also tied down...?16:23
kanzureoh, cleaved16:24
fennthat's why the droplet also contains a cleaving enzyme16:24
kanzureok. so everything gets cleaved.16:24
fennyes16:24
yashgarothcleaving or nicking?16:25
fennthe synthesized oligos are single stranded16:25
yashgarothyes16:25
yashgaroth.title http://www.biomedcentral.com/content/pdf/1756-0500-3-291.pdf16:27
yoleauxyashgaroth: Sorry, that doesn't appear to be an HTML page.16:27
yashgarothfuck you yoleaux16:27
yashgaroth.title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994885/16:28
yoleauxEfficient assembly of very short oligonucleotides using T4 DNA Ligase16:28
yashgarothdecent success with 8mers16:28
kanzure"From the ligation experiments, it was concluded that DNA synthesis was feasible with octamers. To improve the pace of such a method, a hierarchical approach was designed in which multiple intermediate fragments could be constructed from octamers in parallel and then combined in a repeated pair-wise manner. The solid-support used to anchor growing intermediate fragments was designed such that digestion with BbsI would release any ...16:30
kanzure... attached fragment while retaining a 4-nt overhang (Figure ​(Figure3a).3a). Released intermediates could then be used in further ligations. Four distinct bead sets were created each with a unique 4-nt overhang (Figure ​(Figure3b).3b). The overhangs for the solid support adaptors were constructed to be complementary to evenly distributed regions of the 128-bp target such that eight octamers, overlapping in 4-nt frame shifts, would ...16:30
kanzure... tile between each region."16:30
kanzurefigure 3 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994885/bin/1756-0500-3-291-3.jpg16:30
kanzureor er, better figure 3 link http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994885/figure/F3/16:30
kanzurehm.16:33
kanzure"Octamers that are complete palindromes will self-hybridize, and those with 4-nt palindromic ends will result in self-polymerization. Further, repetitive sequences longer than 8 bp cannot be synthesized from octamers, and cleavage from the solid support by BbsI digestions requires that the recognition site for this enzyme not be encoded elsewhere within the assembled sequence"16:35
kanzuretrying to figure out why no repetitive sequences16:36
kanzure"In principle, it is also possible to include in the design longer, custom oligos that span problematic sequences, although at increased cost" well ok16:36
kanzureyashgaroth: so no more electroporation plans? or did i misinterpret16:40
yashgarothpretty much for now yeah16:40
yashgarothrather high number of injections with a specialized device, probably not much mass appeal there16:41
kanzurenot with that attitude16:41
kanzuredid you see the cambrian genomics pics yesterday?16:41
yashgarotha couple of 'em I think, wanna get on that ebay firesale16:42
yashgarothalso if I can get like 100 mg/L of the protein in pichia instead, it should be cost effective, I mean I haven't worked out the break-even point but we'll see16:44
yashgaroth& some people have been having success with AAV therapy, I never looked into it since you need a clinic for the immunosuppression, but said people have that and it's supposedly working for them16:45
streetywhat's the protein?16:45
yashgarothfollistatin, a myostatin inhibitor, fusion to an antibody Fc region16:46
yashgarotherr, fused*16:47
streetywhats the reason for the Fc fusion? I've seen it done elsewhere but never knew why16:47
yashgarothextends the serum half-life from 1 hour to 2 weeks, roughly16:48
yashgarothalso makes it somewhat easier to purify, but mostly it's for the half-life16:48
streetythat is quite an improvement, thanks16:49
yashgarothand ideally it aids clearance of the target protein; so the follistatin-Fc binds the circulating myostatin, then that whole complex gets pinocytosed into cells, vesicle acidifies causing complex to separate, Fc-fusion protein gets recycled outside the cell by FcRn receptor, myostatin gets digested16:51
kanzureewod with microelectrodes (although the spacing seems to be 1 millimeter... er..) http://ir.nctu.edu.tw/bitstream/11536/15046/1/000298136700010.pdf16:59
kanzureah right, there was the picoliter ewod paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613134/17:01
kanzuremagnetic bead trapping seems to work, it's used in lots of papers and it seems to just require a giant magnet under the device17:08
kanzurenot sure why fenn doesn't like this17:08
fennSCOEW looks really cool http://teitell-lab.com/wp-content/uploads/2014/02/2010_4_Park.pdf17:09
kanzure"Dynal® MyOne™ Streptavidin magnetic beads (1.05 µm diameter)"17:09
fenni'm just tired of thinking about beads i guess17:10
fennit's really hot today17:12
fennwe just had a brownout17:13
kanzurei think i would die if texas had brownouts17:13
kanzurepath coordination planner thingy for scoew-stuff http://webpages.uncc.edu/sakella/papers/MaAkellaICRA12.pdf17:14
fennobviously they should swarm like boids17:16
fenneach droplet should be incentivized as a purely rational economic actor to improve its market value17:16
kanzurethere will probably be some % failure, so plans should have easy degradations available when there is a merge failure or w/e17:17
kanzurehere is one that uses a projector to move droplets ftp://222.18.54.49/Papers/ICRA%202013/media/files/papers_videos/2091.pdf17:18
kanzure"Recent work in optically activated microfluidic devices has focused on reducing the droplet actuation voltage and optical source intensity. Pei et al. [18] reported a lightactuated droplet manipulation (LADM) device in which the optical source is a conventional data projector (DELL 4210X) instead of a laser. The aggressive scaling of the dielectric thickness in the device fabrication helps them achieve high speed droplet manipulation (2 ...17:19
kanzure... cm/sec) in low optical intensity (3 W/cm^2)"17:19
kanzurepdf of [18] http://www.colorado.edu/engineering/MCEN/MEMSII/LiteratureReview_2010/B_Light-actuated_microfluidic_2010.pdf17:20
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kanzurethey manipulated 5 nL droplets on a 1.65 cm^2 surface17:24
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kanzurenot sure how to combine a magnet with the lcd/dmd approach to "virtual electrodes". magnet seems likely to be disruptive to the other components? i guess you don't need "virtual electrodes" during a wash cycle so... just move the projector away.17:30
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kanzureoh also i think you have to plan to wash different drops at the same time, since you can't selectively isolate individual magnetic beads or droplets or whatever. so anything that isn't being "washed" needs to stay immobile until the wash cycle is done for the participating drops/beads.17:31
kanzurehere is how they used their projector eventually, http://nanophotonics.eecs.berkeley.edu/Publications/Conference/files/241/Pei%20et%20al.%20-%202013%20-%20Isothermal%20real-time%20polymerase%20chain%20reaction%20det.pdf17:32
kanzurethese are 1 mm diameter droplets :-/17:34
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kanzurehm he also claims to have done electroporation with this17:38
kanzurehe included a parts list, how nice of him17:41
fenni dont get how you're supposed to put thousands of samples collected from the wild on a chip, and if you're not doing large numbers then what's the point of using a chip in the first place17:42
fennthe herpes pcr detection paper17:43
fennanyway SCOEW looked simpler17:44
fennso many acronyms17:45
kanzurehow is it simpler than projecting light? heh17:46
fennwell, you can just put the slide on top of an lcd screen17:46
fennwhich is crazy but apparently it works17:46
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fennbut it's simpler because there's no cover slip and there are less layers to be deposited on the chip17:47
kanzurethe thesis with the bill of materials for the projector one is http://diyhpl.us/~bryan/papers2/microfluidics/Light-induced%20electrokinetics:%20A%20path%20to%20a%20versatile%20micro%20total%20analysis%20system%20(projector)%20-%20Justin%20K.%20Valley%20-%20thesis.pdf17:49
kanzure"Actuation at a distance of microelectromechanical systems using photoelectrowetting: proof-of-concept" http://arxiv.org/pdf/1201.2873.pdf (i guess someone figured they should confirm this shit)17:52
fennthe ftp...2091.pdf paper was the same basic physics as SCOEW17:53
fennwhy do people always have such terrible document names17:53
fenn"towards automated optoelectrowetting on dielectric devices for multi-axis droplet manipulation"17:54
kanzurethe thesis compares the physics17:55
kanzurein more detail17:55
kanzurewasn't there another photo radiation result that people were surprised about recently in another context17:56
fennwas it firing lasers through fiber optics at beads in sequencer wells17:59
kanzureah, optical lift http://gnusha.org/logs/2014-06-02.log17:59
kanzurefollowed by 15:07 < kanzure> why are people always more interested in cryonics? there are perfectly good brains still living that could continue to live18:01
fennyou are your own worst enemy :P18:01
kanzurehe has a good point18:02
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kanzure.wik optical lift18:09
yoleaux"Optical lift is an optical analogue of aerodynamic lift, in which a cambered refractive object with differently shaped top and bottom surfaces experiences a stable transverse lift force when placed in a uniform stream of light." — https://en.wikipedia.org/wiki/Optical_lift18:09
kanzure.wik optical force18:09
yoleaux"The optical force is a phenomenon whereby beams of light can attract and repel each other. The force acts along an axis which is perpendicular to the light beams. Because of this, parallel beams can be induced to converge or diverge. The optical force works on a microscopic scale, and cannot currently be detected at larger scales." — https://en.wikipedia.org/wiki/Optical_force18:09
kanzuremaybe egan was right, and everyone needs to stop doing math immediately lest we accidentally make the wrong branch of reality happen18:11
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fennquintillions of bits madly whirling hard drives spinning doom approches ever closer18:26
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juri_fenn: you know how to party.18:33
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juri_Have we thought of using electrical charge to increase the odds of our droplets landing on top of one another?18:35
fennthat's not really a problem from what the captain says18:37
juri_well, if we're using charge to move droplets of water around, might as well use the same equipment to help target droplets.18:38
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CaptHindsightI can make an electrostatic printhead18:58
CaptHindsightin the inkjet scenario droplets land on top of the previous material19:00
CaptHindsighthow the droplets behave is a matter of the temperature and surface tension or both the droplet and the previous layer19:00
CaptHindsightor/of19:01
CaptHindsightsince the glass slides are treated with siloxane that helps keep the initial drops from spreading19:02
CaptHindsightafter a layer or few of bases the drops are still contained if the drops spread down the sides of the previous oligo layers19:04
CaptHindsightI didn't see any comments about the surface tension of the previously completed oligo layers19:05
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kanzureyou can also have a pre-programmed surface where you etch a patter ninto the surface, such that droplets would be set on a specific program of movement thanks to surface tension19:54
kanzuresuch a pre-programmed surface tension path could also take into account things like "it takes a while to load the other droplets" (although i think you'd still have to time everything pretty well)19:54
kanzurei think it would also be compatible with wash steps (lock the magnetic beads to the surface with a giant magnet, wash, then put water droplets at the start, by the time they get to the place with the magnetic beads, unlock the beads, then let them continue down the path)19:56
kanzuresurface should be on a one degree incline or slant19:57
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kanzureor, instead of putting droplets at the same start position to go all the way back to the beginning and then pick up the beads, you can have shortcut spots in a few places although this may negatively effect your other route geometry20:00
kanzure"Inkjet patterned superhydrophobic paper for open-air surface microfluidic devices" http://pubs.rsc.org/en/content/articlelanding/2014/lc/c3lc51248g20:08
kanzureCaptHindsight: what do you think of that one?20:08
kanzurethis isn't droplets but here's one for "continuous flow" on paper over sharpied patterns http://repositorium.sdum.uminho.pt/bitstream/1822/24877/1/17612-artigo%20plataforma.pdf20:16
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kanzuresome droplet math modeling of sliding a droplet over alternating stripes of hydrophilic and hydrophobic surfaces http://arxiv.org/pdf/1310.4803.pdf20:24
kanzurewelp nevermind about the patterned surfaces thing. i thought i had seen that before but i guess i was making that up.20:26
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kanzureinkjet emulsion pcr http://ir.semi.ac.cn/bitstream/172111/26165/1/A%20novel%20picoliter%20droplet%20array%20for%20parallel%20real-time%20polymerase%20chain%20reaction%20based%20on%20double-inkjet%20printing%20.pdf20:32
juri_you give me such interesting reading assignments.20:38
kanzurei think you mean "everyone else i know is boring"20:41
juri_I might. ;)20:46
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fenni am reading this machine tool engineering thesis again http://pergatory.mit.edu/research/Cortesi/index.html20:50
fennbedtime stories20:50
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ebowdenhttp://www.smbc-comics.com/comics/1437229685-20150718.png20:56
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--- Log closed Mon Jul 20 00:00:16 2015

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