--- Log opened Tue Jul 07 00:00:03 2015
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04:00 < kanzure> you all died on me?
04:17 < Adlai> almost
04:17 < Adlai> tesla pissed on a power strip
04:17 < Adlai> shock made him clench and i hope maybe taught him a little lesson too
04:29 < kanzure> what's up
04:30 < Adlai> ah so today is "answer answers with their question" day?
04:32 < Adlai> http://i.imgur.com/cO95AwG.jpg
04:34 < kanzure> how would i know what day it is? days are stupid anyway.
04:34 < Adlai> interestingly enough the power strip still works
04:35 < Adlai> and tesla lives, making me >epsilon curious to try this stunt myself someday
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06:40 < wrldpc1> sooo … Henry Markram
06:40 < wrldpc1> On a scale of 1 to Steve Jobs what’s his RDF rating?
06:41 < wrldpc1> Also … Nikola didn’t delete my comment .. I was an idiot and forgot I posted it on his YouTube post of his video and not his Facebook post.
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06:46 < kanzure> wrldpc1: http://diyhpl.us/wiki/transcripts/markram-2006/
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07:00 < Adlai> on random unrelated nonsense, anybody read Inferno?
07:00 < Adlai> (not the epic, the fanfic screenplay-in-book's-clothing)
07:01  * Adlai read it over a slow weekend and found the ending a little... disappointing
07:01 < Adlai> there are so many ways to do what was being attempted, which are both more effective, and more ethical
07:02 < Adlai> for somebody with such a flair for plot twists and language puzzles, i would've expected a slightly more imaginative grasp of macrobiology
07:02 < Adlai> s/or/rom/
07:07 < kanzure> this one? http://www.amazon.com/Inferno-Larry-Niven/dp/0765316765
07:09 < kanzure> https://en.wikipedia.org/wiki/Inferno_(Niven_and_Pournelle_novel)
07:11  * Adlai isn't aware that larry is a screenwriter in denial
07:12 < Adlai> https://en.wikipedia.org/wiki/Inferno_(Dan_Brown_novel)
07:12 < kanzure> i got lost on https://en.wikipedia.org/wiki/Niven%27s_laws
07:12 < Adlai> dan brown takes potshots at transhumanism and has characters with H+ tattoos
07:13 < Adlai> the "villian" (if you can call him that, which you can't quite) is a gone-insane genius who sets out to releaze a bioweapon/salvation for population control
07:14 < kanzure> you don't need a genius for that though
07:14 < Adlai> well that's how he's presented
07:14 < Adlai> one of the aspects i really didn't like about the book is his portrayal of "geniuses" and child prodigies
07:15 < Adlai> one aspect i did like is that there aren't really any bad guys, just good guys who haven't recognized eachother as such
07:15 < Adlai> (and a couple of gals)
07:16 < Adlai> hmm, the wikipedia article seems to have been written with the primary goal of spoiling every single plot twist
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07:18 < Adlai> my tl;dr for the book is that if you've enjoyed any of dan brown's previous books, you'll enjoy this one more. i've read most of them (skipped the previous one, about the freemasons), and this one was far better than the others, except for maaaybe A&D
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08:18 < kanzure> .title http://www.pnas.org/content/early/2015/07/01/1506264112
08:18 < yoleaux> Quantification of biological aging in young adults
08:19 < kanzure> "However, most human aging research examines older adults, many with chronic disease. As a result, little is known about aging in young humans." sigh
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08:47 < wrldpc1> I’ve heard it said Umberto Eco’s “Foucault’s Pendulum” is the “DaVinci Code” for smart people.
08:48 < wrldpc1> Da Vinci Code is basically pop fiction, right?  I never read it and half-watched the movie.  Someting about vatican secret societies.
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09:04 < eudoxia> god bless libgen
09:24 < kanzure> "Mousera is Heroku for mouse studies," oh man... let's see.
09:24 < kanzure> https://www.mousera.com/
09:24 < kanzure> giant web 3.0 pic of a mouse... off to a wonderful start already, blah.
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09:25 < kanzure> https://synaptic.nyc/ "Others like Synaptic allow universities that have expensive research equipment sitting idle to more effectively lease time on the equipment to researchers"
09:26 < kanzure> i regret reading this article
09:27 < kanzure> https://github.com/yarrick/pingfs
09:43 < CaptHindsight> http://www.epson.com/cgi-bin/Store/jsp/Product.do?sku=C11CB53201#Specifications  6 active channels on the printhead (of 8, 2 not guaranteed))
09:44 < CaptHindsight> 180 nozzles per channel, 1.5pL drop size (grey scale) so 1.5pL is the native drop size
09:45 < CaptHindsight> $300 to cannibalized for the head, not too bad, the ~$100 heads have only 4 channels active of the 8
09:46 < CaptHindsight> it's sort of like some older AMD processors that had more cores that you had to unlock
09:46 < CaptHindsight> but they were not guaranteed to work
09:48 < CaptHindsight> so 1080 working nozzles
09:48 < CaptHindsight> out of 1440 for 8 channels
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09:50 < CaptHindsight> 1" print swath, 0.0055" nozzle pitch
09:50 < CaptHindsight> ~141um
09:59 < nmz787_i> but can you control individual nozzles, or do they all fire at once within a channel?
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10:01 < nmz787_i> kanzure: heard of these folks? I wonder how they compare to Halcyon (at first glance it seems they were around before Halcyon, and still exist) http://www.zsgenetics.com/
10:01 < CaptHindsight> each nozzle is individually controlled
10:02 < CaptHindsight> channels is this case means "ink channels"
10:02 < CaptHindsight> so 6 fluid channels, each with 180 addressable nozzles
10:03 < CaptHindsight> you might get lucky and get 8 working channels from a 6 channel printer
10:03 < CaptHindsight> they all use the same head
10:03 < CaptHindsight> they just QC the ones they need
10:04 < Adlai> wrldpc1: dan brown books are conspiracy stories, foucoult's pendulum is more of a story about conspiracy theorists
10:06 < kanzure> i thought we needed more than six chemicals
10:08 < nmz787_i> CaptHindsight: are all channels focused on same zone?
10:08 < nmz787_i> such that nozzle 1 of all channels will land on same spot?
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10:22 < CaptHindsight> nmz787: yes, to be clear let me find a good pic
10:23 < CaptHindsight> if X axis is the side to side scanning you notice on a typical desktop inkjet....
10:23 < CaptHindsight> then if you scan in X, each channel will overlap
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10:31 < CaptHindsight> http://members.shaw.ca/hargravep/images/nozzles.jpg  here's a closeup of one channel made up of 2 rows of 90 nozzles each
10:31 < CaptHindsight> so the actual nozzle pitch is 2x 141um
10:32 < CaptHindsight> each channel has 2 rows of 90 nozzles staggered/interlaced
10:34 < CaptHindsight> http://www.mbsdirect.com/current/images/stories/epson/epson-printhead.gif this is an older model with 4 channels
10:35 < CaptHindsight> sorry 8 channels but it's not zoomed in to see the stagger
10:36 < CaptHindsight> http://www.northlight-images.co.uk/content_images_2/epson_sp3880/3880-print-head.jpg
10:40 < kanzure> well we might have to chemically switch and repurpose channels outside of the head, oh well
10:40 < kanzure> lots of cleaning steps...
10:40 < CaptHindsight> how many fluids in total?
10:41 < CaptHindsight> I thought 6
10:41 < CaptHindsight> Epson is up to 8 fluid channels per head
10:41 < CaptHindsight> we can also stitch heads
10:43 < CaptHindsight> http://www.epson.com.sg/resource/mediacenter/image_library/events/Micro_Piezo_Tour_Photos_zip/Micro_Piezo_Tour_Photos/Epson_SurePress_Micro_Piezo_print_head_array_2_N.jpg  16 heads stitched
10:44 < CaptHindsight> for example  16 heads x 8 channels = 128 fluids  x 180 nozzles = 23,040 nozzles
10:45 < CaptHindsight> overkill for synthesis but handy for printing
10:45 < kanzure> there's a list on page 2 http://diyhpl.us/~bryan/papers2/DNA/abi391/Chemical%20Storage%20Conditions.pdf
10:45 < CaptHindsight> that's how Agilent does it
10:46 < kanzure> lolz "Coupling efficiency drops below 90% after 4 days"
10:46 < kanzure> double lolz "Last updated May 1996"
10:46 < CaptHindsight> so his old mix must have spoiled by now
10:47 < kanzure> you may be interested in reading around page 24 ish http://diyhpl.us/~bryan/papers2/DNA/abi391/ABI%20391-manual.pdf
10:47 < kanzure> or i guess you might prefer to read the list of chemicals from the posam project... see page 4 http://bioinformatics.org/pogo/POSAM_Man_Ch2_User_v1-0_040414.pdf
10:48 < kanzure> and page 10
10:49 < CaptHindsight> heh, slides with Rain-X, lucky break
10:49 < nmz787_i> CaptHindsight: so without moving the head, the channels don't target and identical location
10:49 < nmz787_i> s/and/an/
10:49 < kanzure> moving the head is not a problem
10:49 < kanzure> (or moving the slide) (whichever is fine)
10:50 < CaptHindsight> can work either way
10:50 < CaptHindsight> even if we have the heads on a stage the stage can park and the slides may be moved by a 2nd 2 axis stage
10:51 < CaptHindsight> you usually want the heads to move since you want to cap them when not printing
10:51 < CaptHindsight> or when you perform cleaning or purge cycles
10:51 < kanzure> capping the nozzles is a better reason (cleaning and purge cycles can still work even when moving the slide out of the way)
10:52 < CaptHindsight> you don't want anything that has a high enough vapor pressure to be left idle and uncapped
10:52 < nmz787_i> ok, just making sure... there would be higher accuracy if the head didn't have to move between reaction steps
10:53 < CaptHindsight> probably the #1 reason heads get clogged
10:53 < CaptHindsight> I can control repeatability to a few microns pretty cheaply and easily
10:54 < kanzure> er what sort of accuracy problems are you anticipating? what's the per-step additional misaccuracy accumulation factor... if we are using 10 pL drops we can tolerate more float.
10:54 < kanzure> er the question was for nmz787_i i suppose
10:55 < CaptHindsight> each layer gets dropped directly over the other
10:55 < kanzure> right
10:55 < CaptHindsight> if they are off by a few microns the fluids will still cover the previous layer
10:55 < nmz787_i> if two droplets are not coincident, chemistry is less even (the droplets mixing start out by looking like a venn diagram, then need some time for diffusion to happen)
10:56 < nmz787_i> I don't know what the rate/quantifier would be
10:57 < nmz787_i> maintaining efficiency is all about having synchronous chemistry, even heating and cooling, no weird corners in the reaction vessel
10:57 < nmz787_i> and of course keeping out imposter molecules (like water)
10:57 < nmz787_i> (like water, in the phosphoramidite approach)
10:58 < CaptHindsight> step back a second
10:58 < CaptHindsight> each layer is one drop
10:59 < CaptHindsight> each drop is one link in the chain
10:59 < kanzure> nah some of the steps are things like capping the chain, cleaning the pore/well, etc.
10:59 < nmz787_i> priming the chain
10:59 < nmz787_i> 'activating'
10:59 < CaptHindsight> how many parallel links are forming at the same time?
11:00 < nmz787_i> millions
11:00 < kanzure> depends on how you initiated the process tho-
11:00 < CaptHindsight> we're not dropping one molecule at a time in 1.5pL
11:00 < nmz787_i> well, depends on well size and concentration
11:00 < CaptHindsight> but the point is "several"
11:00 < nmz787_i> 'well' meaning reaction chamber
11:00 < nmz787_i> the point is 'too damn many to keep track of completely'
11:00 < CaptHindsight> so drop to drop variation is also a factor
11:01 < nmz787_i> yep
11:01 < CaptHindsight> sometimes the links get built, so get missed
11:01 < nmz787_i> yep
11:01 < nmz787_i> sometimes the link gets burned by one of the other steps and is no longer usable in next steps
11:01 < CaptHindsight> so lets just say for this discussion 1 million at a time in parallel
11:02 < nmz787_i> sure
11:02 < CaptHindsight> so we are using a fire hose vs ideally one molecule dropped onto the next
11:04 < nmz787_i> yes, thus my affection for smaller devices
11:04 < CaptHindsight> or dropping a swimming pool onto the top of the previous
11:04 < CaptHindsight> well sure
11:04 < nmz787_i> you have a ton of waste, and even more when you go to clean up after a bunch of cycles
11:05 < CaptHindsight> yes
11:05 < CaptHindsight> ideally you print a molecule at a time and QC each step and it should happen at 10Ghz so entire complete stands can be made in <1 sec
11:06 < CaptHindsight> so thats the ultimate goal
11:06 < CaptHindsight> but back here in 2015 where do we start
11:06 < nmz787_i> IMO just not do 10GHz
11:07 < nmz787_i> I already have a friggin nanomill
11:07 < nmz787_i> which can zap a hole in something that a DNA can pass through but not an enzume
11:07 < nmz787_i> enzyme
11:07 < CaptHindsight> whats the time required for each link?
11:08 < nmz787_i> depends on the reaction volume, temperature, concentration of the activating acid
11:09 < CaptHindsight> yeah something small and accurate/repeatable, and either fast or parallel
11:09 < nmz787_i> concentration of activating acid can also cause destructive activity of some of the side-bases, destroying information capacity of the link
11:10 < CaptHindsight> yes, requires some tweaking (lots)
11:11 < nmz787_i> I think most protocols just lower the concentration to avoid damage, and take the time lengthening hit
11:13 < CaptHindsight> I think inkjet is low cost and a good start
11:13 < CaptHindsight> next might be DLP or using FIB to create an array
11:14 < CaptHindsight> we need some low cost nano-cnc tools to make more complex nano machines
11:14 < nmz787_i> FIB is pretty much free other than my time, unless we really start to need lots of time on the machine (which I wouldn't imagine would happen with the first-try)
11:15 < CaptHindsight> MEMS and being able to print electronics
11:16 < CaptHindsight> or at least connect to MEMS devices
11:16 < CaptHindsight> do both
11:16 < CaptHindsight> inkjet and fab some nanopores
11:18 < nmz787_i> inkjet heads might be more accessible to normal people than a FIB or higher-volume planar fab technologies, but the reagents for a water/green-chemistry based approach is a lot cheaper and less headache ridden
11:19 < CaptHindsight> inkjet is low cost and won't take long
11:19 < nmz787_i> not only would the cost be less, but shelf life is phenomenally longer
11:19 < CaptHindsight> yeah, the easy chem is the trade-off
11:19 < CaptHindsight> but the longer term plan is to make FIB low cost
11:19 < nmz787_i> and you could even DIY the reagents, you can't really do that with the phosphoramidite approach
11:19 < kanzure> i don't think the tdt nanopore protocol has been written down anywhere. your plan is to just blast nucleotides at it?
11:19 < nmz787_i> unless you're already having a B.S. in organic chemistry and are top-notch
11:20 < nmz787_i> blast in a controlled manner
11:20 < kanzure> from what?
11:21 < nmz787_i> either dilute stock solutions, such that one pump is one molecule (chamber would have to be large then, increasing cycle time, but who knows could still be quite low time due to microfluidic nature)
11:21 < nmz787_i> or find the right electronic sensing technique with some localized wires/traces
11:22 < CaptHindsight> how many different nucleotides?
11:22 < nmz787_i> (you can sputter coat the device on an angle to coat walls of the chamber to make capacitor-like electrode plates)
11:22 < nmz787_i> 4
11:22 < kanzure> i don't think a syringe pump is enough to make that work. you'd pump too many nucleotide molecules out, they'd get incorporated.
11:22 < CaptHindsight> well that's why the need for low cost nano tools to make these
11:23 < nmz787_i> though in more advanced medicine and biochem research, they like to use 8 or 12 or 16 types (roughly)
11:23 < CaptHindsight> this goes back to the single molecule canon
11:23 < nmz787_i> (mostly variations, change something to a heavier version, or a larger atom, but some are novel 'bits' or whatever)
11:24 < kanzure> as far as i know nobody has demonstrated a single molecule syringe pump
11:24 < nmz787_i> you can just coat the nanopore in metal and sense it to count moleucles
11:24 < CaptHindsight> let me give that some thought
11:24 < kanzure> counting molecules wasn't the problem
11:24 < kanzure> releasing too many molecules was the problem
11:24 < nmz787_i> get a femtoamplifier
11:25 < nmz787_i> yeah but when you can count them, you've got a closed loop feedback system to control them
11:25 < CaptHindsight> maybe a sieve
11:25 < nmz787_i> essentially a sieve with a counter
11:25 < CaptHindsight> more than one pore with a gate
11:25 < kanzure> so your claim is that you can make a syringe pump that has a minimum step size of one molecule? how
11:25 < kanzure> like, it doesn't matter if you count too many molecules- that's too late
11:26 < CaptHindsight> whats the diameter of a nucleotide?
11:26 < nmz787_i> depends on the way you measure it
11:26 < CaptHindsight> once you get them single file do they want to agglomerate?
11:26 < nmz787_i> maybe 2nm
11:27 < CaptHindsight> just for discussion say you had them single file in tube
11:27 < nmz787_i> yeah after like 5 or 20 they start acting wonky in that sense
11:27 < kanzure> width of a dna molecule is 2 nm
11:27 < kanzure> so nucleotide is not 2 nm
11:27 < nmz787_i> so confinement is another trick at the nano scale
11:27 < CaptHindsight> will they want to link to each other?
11:28 < nmz787_i> sometimes
11:29 < CaptHindsight> say you had a gate/pore of the proper diameter
11:29 < CaptHindsight> how polar are they?
11:29 < nmz787_i> you can think of each outwardly facing atom on the side-bases as magnets, and their polarity is not always the same, and sometimes there are 2 or sometimes 3 outwardly-facing atoms per base
11:29 < nmz787_i> they like water
11:30 < CaptHindsight> can they be steered/attracted or repulsed?
11:30 < nmz787_i> yeah
11:30 < nmz787_i> electrophoresis
11:30 < nmz787_i> one easy and common way
11:30 < CaptHindsight> ok
11:30 < kanzure> i want an hna, tna, gna, pna, xna, dna alternative with a larger backbone and larger nucleotides. each step requires a mutant polymerase (and other enzymes) that can process the different chemistry. but you could make the size slightly larger each time. you could eventually work up to a very large dna-equivalent molecule. the building blocks would be large enough to manipulate through other means. then you would use the mutant polymerase ...
11:30 < kanzure> ... to get back to dna (or some other oligo).
11:31 < CaptHindsight> since that is big picture anyway
11:31 < kanzure> although there might be a practical size limit to how large a polymerase enzyme can become
11:31 < CaptHindsight> mutations
11:31 < nmz787_i> "The width of a single DNA molecule is approximately 22 to 26 Angstroms and the length of one repeating nucleotide chain link (phosphate, sugar, base) is about 3.4 Angstroms. Around 10.4 nucleotide units are required to complete one full twist of the DNA helix."
11:31 < CaptHindsight> vs complete custom DNA
11:31 < kanzure> one thing that i might accept from nmz787_i is if he claims something about a single-molecule-wide nanochannel that you pump the nucleotides out of.
11:32 < nmz787_i> so 2.2 to 2.6 nm for 2 nucleotides next to each other, long ways
11:32 < nmz787_i> .34nm for the 'height' short ways
11:33 < kanzure> (such a channel would naturally be named "maxwell's true demon")
11:34 < nmz787_i> i have a video somewhere that shows a single molecule of DNA with fluorophores bound in a nanochannel, travelling back and forth from the ends with electrphoresis
11:34 < nmz787_i> (not my work)
11:34 < kanzure> no i want a nucleotide trapped in a nanochannel, not dna
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11:35 < CaptHindsight> yeah, that is the goal
11:35 < CaptHindsight> that would make things easier
11:37 < nmz787_i> ssDNA or dsDNA?
11:38 < kanzure> somebody got carried away when naming this one "Microoptomechanical pumps assembled and driven by holographic optical vortex arrays"
11:38 < CaptHindsight> heh
11:39 < kanzure> you could probably find a membrane protein that has a single-molecule-wide channel that could be conformationally switched to activate/deactivate. and then you'd pump a nucleotide through.
11:39 < kanzure> i mean switched to open/close
11:40 < CaptHindsight> fabricating a gate with coils around it could isolate single nucleotides
11:41 < CaptHindsight> 2 approaches
11:41 < CaptHindsight> nature vs full synthetic
11:41 < CaptHindsight> I want to make those proteins on demand
11:41 < CaptHindsight> in the shape I want
11:42 < CaptHindsight> make those tools
11:43 < kanzure> anyway, unfortunately i don't have a single-molecule syringe pump, or a membrane channel that can be electronically opened and closed or activated to sense whether a nucleotide is being transported, etc.
11:44 < CaptHindsight> need to make the low cost tools to make those
11:44 < CaptHindsight> molecular machine shop
11:45 < kanzure> well none of those things that i just said are well-specified, so even if you had a molecular machine shop it wouldn't matter
11:53 < CaptHindsight> on the inkjet side the ink reservoirs behind the nozzles hold a few mL
11:54 < CaptHindsight> so if they are expensive then you probably want to reclaim them
11:56 < CaptHindsight> flushing means you still mix fluids in those reservoirs
11:56 < kanzure> nah just only print when you know that you want to use everything
11:56 < CaptHindsight> yes, best
11:57 < CaptHindsight> print it all out and as many as you can
11:57 < CaptHindsight> http://www.qtparts.com/attachments/Image/Epson_4880_Print_Head.JPG  here is the backside of the head
11:58 < CaptHindsight> the pointy parts have a small orifice that pokes through the septum on the cartridge
11:59 < CaptHindsight> for bulk feeding you just attach a line over them using friction
12:01 < CaptHindsight> or use the cartridges with tubing back to a larger reservoir
12:01 < CaptHindsight> the cartridges also act as a damper
12:02 < CaptHindsight> one big industrial systems we have negative pressure regulators
12:03 < CaptHindsight> just a few inches of water of negative pressure
12:04 < CaptHindsight> and also degassing since some heads fire so fast that any trapped O2 cases cavitation vs drops
12:09 < nmz787_i> then you still need to think of waste disposal
12:09 < nmz787_i> no pouring acetonitrile into the backyard, kids
12:10 < nmz787_i> and you don't really need a gate, you can just use dilute solutions and electrophoresis or just pressure to gate them
12:11 < kanzure> waste disposal is not the end of the world
12:11 < nmz787_i> it's such a sad part of the process
12:12 < CaptHindsight> I'll have to start looking for surplus SEM parts and other components to make tools
12:13 < kanzure> http://www.popsci.com/science/article/2011-01/most-massive-synthetic-molecule-could-be-used-deliver-drugs-or-make-new-materials
12:13 < kanzure> 170k reactions is sort of unfortunate
12:16 < kanzure> https://en.wikipedia.org/wiki/Nucleic_acid_analogue
12:16 < kanzure> all of these seem to be roughly the same size as dna though. that's unfortunate.
12:17 < drethelin> yeah getting exact particle sizes can be tough
12:17 < drethelin> for whatever you need
12:17 < kanzure> drethelin: goal is very-super-large dna alternative
12:17 < kanzure> 10x larger would be nice
12:17 < drethelin> to what end?
12:18 < drethelin> oh wait there's a link
12:18 < kanzure> easier synthesis
12:18 < kanzure> no link is unrelated unfortunately
12:18 < kanzure> *no, link
12:18 < kanzure> anyway there are alternatives to dna that researchers have used with dna polymerase before (they just mutate the polymerase to work with the alternative backbone structure)
12:19 < kanzure> but a backbone that works with very large overwhelmingly massive nucleotides would be quite useful becuase an object that is 100 nm wide or thick is something that we could conceivably physically handle with machines
12:20 < CaptHindsight> that's giant
12:20 < kanzure> exactly
12:21 < nmz787_i> you guys are crazy
12:21 < kanzure> i'm not saying that method is easy
12:21 < kanzure> or that we should do it
12:21 < kanzure> although i do claim that larger nucleotides would be easier to work with
12:22 < nmz787_i> but then you'd need some translator to real nucleotides
12:22 < nmz787_i> some custom polymerase
12:22 < kanzure> polymerase already does that for xna (well maybe not xna- perhaps it's gna?)
12:23 < kanzure> right, and there might be some scaling limits to how big a polymerase can get
12:23 < kanzure> i mean at some point it's going to need to start consuming atp or something.... and that's much harder.
12:24 < CaptHindsight> plus this has other applications
12:24 < CaptHindsight> custom oligomers for coatings, inks, adhesives etc
12:25 < nmz787_i> 'this' meaning the printer?
12:25 < CaptHindsight> fabricate custom polymers with unique surfaces
12:25 < CaptHindsight> oh, synthesis of polymers in general
12:26 < CaptHindsight> the printer is like getting your first 100 pcs tool set with 27 screw drivers and 18 allen keys
12:27 < CaptHindsight> better than just having your fingers
12:32 < CaptHindsight> http://kilobaser.com/  got funding and went silent
12:35 < CaptHindsight> https://www.youtube.com/watch?v=08Ju95uwgt0  XY-Stage and SyringePumps Prototype Test
12:40 < CaptHindsight> https://youtu.be/WxpQyqoukpc?t=39s  Programmable large area digital microfluidic array
12:40 < CaptHindsight> whats the patent situation on these devices?
12:41 < CaptHindsight> is the tech being held hostage for 20 years?
12:56 < kanzure> probably, but the older tech is up for grabs
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13:05 < CaptHindsight> Sandia and a few others are all similar
13:06 < CaptHindsight> https://youtu.be/9GInRQYzSJg?t=2m32s  Sandia Digital Microfluidic Hub
13:09 < nmz787_i> this room doesn't have any managerial types, other than maybe jrayhawk as far as I can tell
13:09 < nmz787_i> and I don't even know why I say jrayhawk, other than that he's a sysadmin type
13:09 < kanzure> he's not managerial
13:10 < nmz787_i> he knows how to manage the computers
13:10 < CaptHindsight> just me then  :(
13:10 < CaptHindsight> or :)
13:10 < CaptHindsight> depending on your point of view
13:11 < nmz787_i> well someone that can tell you and me and kanzure what to do
13:11 < nmz787_i> with sequencing the ideas
13:11 < nmz787_i> doing forecasts, etc
13:11 < jrayhawk> maybe "loudmouthed" is managerial
13:12 < CaptHindsight> the Bio part of all this is tangential to what I usually do
13:12 < CaptHindsight> but it looks like the wild west
13:12 < kanzure> but.. we know what to do.
13:13 < kanzure> oh, you mean the person would be doing the task estimation
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13:15 < CaptHindsight> we could all be so much further along on this
13:15 < CaptHindsight> it's frustrating when you have to deal with Doc's that don't really have a clue
13:18 < nmz787_i> good thing we don't have many of them in here
13:18 < CaptHindsight> "The University of Washington patented propylene carbonate as a solvent for inkjet oligonucleotide synthesis, and granted Rosetta Inpharmatics (and then Agilent), exclusive rights to use propylene carbonate for oligoarray synthesis."
13:18 < CaptHindsight> what a joke
13:19 < CaptHindsight> sounds like Bio-med meets inkjet and they are both very controlling
13:19 < kanzure> yup, definitely a joke
13:21 < CaptHindsight> if China would have started sooner we'd be buying all this from them
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13:50 < kanzure> CaptHindsight: sorry about that; i'm in a very noisy environment at the moment.
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15:07 < kanzure> http://www.projectoberon.com/ "Project Oberon is a design for a complete computer system. Its simplicity and clarity enables a single person to know and implement the entire system, while still providing enough power to make it useful and usable in a production environment."
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16:03 < nmz787_i> new thrift-store targets "Before LCDs were advanced and cheap enough to include in video cameras, CRTs were the only show in town. These tiny black and white screens use high voltage to scan an electron beam across a phosphor screen just like their bigger brethren."
16:05 < nmz787_i> from http://hackaday.com/2015/07/07/headphone-amp-features-a-tiny-crt/
16:09 < jrayhawk> i think my parents might still have their VHS camera with the old tube viewfinder; lemme know if you want their number
16:09 < jrayhawk> they are the sort of people to keep it around
16:11 < jrayhawk> man, shoving my eye right up against a CRT just seems like a bad idea, in retrospect
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16:15 < nmz787_i> "The vertical drive is just a 555 circuit generating a sawtooth waveform at 75hz, the filament was also simple, this one ran on 3 volts, so I used a little tiny 3.3v linear regulator sample I had laying around. The HV to the anodes/grids was generated using the original little box flyback which was driven with a few BJTs along with the original driver IC that came off the viewfinder PCB, to control the focus and brightness, which, onc
16:15 < nmz787_i> the values I wanted, I used regular resistors for instead of pots to keep everything as small as possible. I tried to use as much of what was already there as I could, while making it as compact as possible. I didn't need all the video/NTSC chips and stuff, so I ended up doing a lot of reading, testing (and frying things in the process) before managing to pull what I needed and re-engineer it into working for this application."
16:15 < nmz787_i> jrayhawk and his one BIG and redeye
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17:04 < alu> What do you all see the difference as between a transhumanist and posthumanist?
17:04 < alu> Serious question
17:05 < nmz787_i> one is in transition, one has gotten past it?
17:05 < kanzure> is that important?
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17:42 < drethelin> why would you think thats a serious question
17:42 < drethelin> that's MY question
17:43 < drethelin> In the modern age of internet subcommunities and groups claiming identities for their own the specific definition of a word may vary from group to group
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17:44 < drethelin> it's not like there's eastern orthodox transhumanism and catholic posthumanism
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18:12 < juri_> alu: welcome. ;)
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18:30 < fenn> i know a catholic posthumanist
18:30 < fenn> also i think pasky runs or.cz
18:32 < fenn> uh, the orthodox church in czech republic, or something
18:33 < fenn> there are also a fair number of mormon transhumanists
18:34 < drethelin> you seem to have missed my point
18:35 < drethelin> which is that with internet communities there's generally not a pope or other patriarch because of how easy it is to start your own spin-off
18:35 < drethelin> ie asking if someone is a catholic or orthodox will give you a direct lineage
18:35 < drethelin> that they get their beliefs from
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18:38 < fenn> ok i guess max more is our pope then
18:38 < fenn> and anders sandberg is his prophet
18:39 < drethelin> I don't even know who those guys are
18:41 < fenn> here's some stuff then http://www.extropy.org/proactionaryprinciple.htm    http://www.aleph.se/Trans/
18:44 < fenn> hmm the extropian principles page went 404
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18:44 < kanzure> wait i thought aubrey was our space pope
18:44 < kanzure> older extropian principles doc http://www.aleph.se/Trans/Cultural/Philosophy/princip.html
18:45 < kanzure> fenn: CaptHindsight wants to use linuxcnc to control and motion plan an inkjet head. also, there would be mesa cards. what would the integration on linuxcnc look like for controlling some nozzle piezos?
18:45 < fenn> a digital i/o daughter card
18:46 < kanzure> no i mean from the software perspective
18:46 < kanzure> you have a bunch of dna -> split up into a bitmap -> somehow while the printhead is moving you tell it to fire based on some optical encoder feedback maybe? but where does my software get that feedback from. or is it all just pre-planned?
18:48 < fenn> it might be possible to just shove binary bitmap data directly into the hardware abstraction layer, but to perfectly synchronize it with g-code movements i think you'd instead have to use a whole bunch of M-codes on each line, like one per nozzle so G0 X1 Y1 M0 M1 M2 ... M120
18:49 < kanzure> oh ok so it'd just be stuffed into the gcode
18:49 < fenn> hard to say if linuxcnc's parser and message passing code can keep up with that much traffic
18:49 < kanzure> ok i'm fine with that
18:50 < juri_> I'd worry about buffers in thi inkjet hardware.
18:50 < kanzure> custom board
18:50 < kanzure> no printer hardware left except the nozzles and head
18:50 < juri_> oh, you're fine then.
18:51 < fenn> "The 5I24 has 72 I/O bits available"
18:51 < fenn> you could directly bit bang it or use shift registers to expand even further
18:52 < fenn> actually i dont know what the print head control interface looks like
18:52 < kanzure> apparently he spends a bunch of time reverse engineering that
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18:53 < fenn> it's probably not just ~100 wires huh
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19:01 < juri_> we tried that on one at hacDC, but had the laptop with the data on it stolen.
19:03 < fenn> there's so much crap online about how to circumvent the anti ink refill electronics that i can't find anything about using the print head outside of a printer
19:04 < kanzure> might be in the posam docs
19:04 < kanzure> also links on bottom of http://reprap.org/wiki/Scratchbuilt_Piezo_Printhead
19:04 < fenn> that's just a speaker and a plate with a hole in it
19:05 < kanzure> .gc inkshield
19:05 < yoleaux> 14,000 (site), 1,810 (api)
19:06 < kanzure> .title https://www.youtube.com/watch?v=dzTCDMRv8bY
19:06 < yoleaux> InkShield: An Open Source Inkjet Shield for Arduino - YouTube
19:07 < fenn> that's thermal, no piezo
19:09 < kanzure> hmph
19:10 < fenn> honestly i thought there would be a million hackers doing this already
19:10 < fenn> .title http://techref.massmind.org/techref/pcb/etch/custom-vs.htm
19:10 < yoleaux> PCB Resist, InkJet Printing, Epson InkJet, By Volkan Sahin
19:10 < fenn> Epson inkjet head signals:
19:10 < fenn> COM: Trapezoidal drive signal 4-30Volts
19:10 < fenn> NCHG: Discharge all piezo (I don't know actual naming maybe Not CHarGe)
19:10 < fenn> CH: Increment waveform counter.
19:10 < fenn> LE: Latch enable
19:10 < fenn> CLK: Data clock (both edges used to sample data)
19:11 < fenn> and then one channel each for C, M, Y, K data
19:11 < kanzure> maybe patrik d'haeseleer has done this
19:11 < kanzure> didn't biocurious do this at some point
19:11 < fenn> i think they just put different liquids into a functioning printer
19:12 < kanzure> bleh
19:13 < fenn> "We’ve built our own functioning bioprinter from a couple of old CD drives, an inkjet cartridge, and an Arduino."
19:14 < fenn> http://biocurious.org/wordpress/wp-content/uploads/2015/04/8047589122_03a555c1a1_b.jpg
19:14 < drethelin> your MOM was a functioning bioprinter
19:14 < kanzure> yes but she didn't have 192 nozzles
19:14 < fenn> only 2
19:15 < kanzure> juul: did the biocurious people use a piezoelectric inkjet head?
19:19 < CaptHindsight> the inkjet industry is pretty tight lipped about specs for their heads
19:20 < CaptHindsight> they make most of their income from selling $5/L ink for $3k/L in 15mL plastic cartridges
19:20 < juri_> I've heard one of the later epson models was reverse engineered...
19:20 < drethelin> alas
19:21 < CaptHindsight> the old DX2 or 3 was
19:21 < CaptHindsight> the Epsons are pretty easy
19:22 < kanzure> http://www.instructables.com/id/Reverse-Engineering-to-Emulate-Ink-Cartridges-for-/
19:22 < CaptHindsight> http://global.kyocera.com/prdct/printing-devices/inkjet-printheads/  these would be tough without specs
19:24 < kanzure> 2656 nozzles haha
19:24 < CaptHindsight> 330 million drops per second from a head with 5,120 nozzles.   64,000 drops of ink per second per nozzle
19:24 < kanzure> can we use that one
19:24 < CaptHindsight> 330 millions drops per head per second + grey scale
19:25 < CaptHindsight> I have access to them
19:25 < CaptHindsight> $8k ea
19:25 < kanzure> are there older generations of this that do maybe >1 million drops/second?
19:26 < CaptHindsight> I'm under NDA so somebody else would have to make an open driver board
19:26 < CaptHindsight> the lowest cost piezo heads are Epson (since they sell the whole printer for $300)
19:27 < CaptHindsight> next are the Xaar 128/6 http://www.xaar.com/en/products/xaar-126
19:27 < CaptHindsight> they start at $300/head
19:27 < kanzure> not bad
19:28 < CaptHindsight> only 126 nozzles
19:28 < kanzure> 35 pL drop volume..
19:28 < CaptHindsight> 5-9Khz
19:28 < kanzure> and 9 kHz
19:28 < kanzure> hmm
19:29 < CaptHindsight> http://www.xaar.com/en/products
19:29 < CaptHindsight> http://www.fujifilmusa.com/products/industrial_inkjet_printheads/print-products/printheads/index.html
19:30 < fenn> ugh techref.massmind.org has the most obnoxious anti-spidering policy
19:30 < fenn> "i see that you are using wget -> BAN!"
19:30 < CaptHindsight> http://www.rpsa.ricoh.com/
19:30 < CaptHindsight> http://www.siiprintek.co.jp/eg/
19:30 < kanzure> do you know the name of the connector that epson heads use?
19:31 < CaptHindsight> it's a flex pcb
19:32 < kanzure> we have someone that decaps chips and does gate-level scans so whatever it takes
19:32 < CaptHindsight> oh thats all been done
19:32 < CaptHindsight> we just need to make an open source board to drive it
19:33 < kanzure> is the protocol known?
19:33 < CaptHindsight> yes and no
19:33 < kanzure> fenn: you should brag about linuxcnc things
19:34 < CaptHindsight> there will be some tweaking to the drive pulse shape
19:40 < CaptHindsight> http://dpnow.com/3762.html here is how Epson has the internals arranged
19:45 < CaptHindsight> Epsons are pretty basic
19:46 < CaptHindsight> the complex heads are the ones that have integrated micros that you talk to
19:46 < CaptHindsight> and they have firmware that needs to be loaded on startup
19:47 < CaptHindsight> they even sense temp and modify drive waveforms on the fly
19:48 < CaptHindsight> some even have LVDS or HDMI type interfaces since the data rate is so high
19:50 < fenn> yeech
19:51 < fenn> what sort of application uses such a high data rate?
19:51 < CaptHindsight> digital press
19:52 < CaptHindsight> some use 64 of those Kyocera heads I posted
19:53 < CaptHindsight> 64 x 330M/sec = 21GB/sec for the driver
19:54 < fenn> so they just do the whole page in one pass?
19:54 < CaptHindsight> yes
19:54 < CaptHindsight> just like an offset press
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19:58 < CaptHindsight> https://www.youtube.com/watch?v=3nYSJK_sy-k  here's a slow one with only 16 heads
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19:59 < fenn> we've created a fantastically adaptable technology capable of infinite variation, and we print repeating floral patterns...
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20:30 < kanzure> well worst case for reverse engineering the control of the printhead, we can just intercept the signal and see what's going on
20:31 < juri_> Got funding? :P
20:31 < kanzure> yes
20:32 < juri_> sounds like fun, then.
20:33 < kanzure> are you offering?
20:33 < juri_> I could do that.
20:33 < juri_> it's been on my todo for some time.
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20:35 < fenn> the epson looks like just a shift register in the techref page
20:36 < juul> kanzure: in the beginning but they switched away from it. not sure why (clogging?)
20:36 < juul> now the use a suringe controlled by a stepper motor
20:39 < drethelin> anyone in here know anything about regulon/lipoplatin?
20:46 < kanzure> .wik regulon
20:46 < yoleaux> "In cell biology and genetics, a regulon is a collection of genes or operons under regulation by the same regulatory protein. This term is generally used for prokaryotic systems, for example quorum sensing in bacteria. It is a group of operons/genes spread around the chromosome but controlled by a common factor or stimulus." — https://en.wikipedia.org/wiki/Regulon
20:46 < kanzure> .wik lipoplatin
20:46 < yoleaux> "Lipoplatin (Liposomal cisplatin) is a nanoparticle of 110 nm average diameter composed of lipids and cisplatin (1). Liposome figure This new drug has successfully finished Phase I, Phase II and Phase III human clinical trials (2,3)." — https://en.wikipedia.org/wiki/Lipoplatin
20:47 < drethelin> regulon inc, not regulon the cell biology term, sorry
20:48 < kanzure> gah
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20:50 < fenn> regulon is a terrible name for a company anyway
20:51 < drethelin> sure but that doesn't really matter if they have a succesful anti-cancer drug
20:51 < drethelin> I dunno if regulon is terrible so much as Villain sounding
20:52 < fenn> why do you care about a cancer drug
20:53 < drethelin> apparently dad bought some shares in regulon some years ago
20:53 < drethelin> and I was idly trying to figure out whether the company is about to get important
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21:02 < kanzure> http://america.aljazeera.com/articles/2015/7/6/lax-sec-regulation-biotech-market.html
21:05 < kanzure> weird "This last part of Wysneski’s defense — that her trades were planned in advance and not intentionally made at the time the data were released — is part of a long-standing loophole under SEC rule 10b5-1 that allows automated trading to fall outside insider trading statutes. It allows executives to carry out “preplanned transactions at a later time, even if they later become aware of material nonpublic information.” ...
21:06 < kanzure> ... Planning of stock sales like this is done solely through a broker. There are no requirements for the trading plans to be registered with the SEC or, sometimes, disclosed at all."
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21:18 < drethelin> well they're not currently public
21:18 < drethelin> so it's not like we can immediately sell the shares
21:18 < kanzure> you can sell shares before it's public
21:18 < kanzure> http://sharespost.com/
21:19 < kanzure> http://secondmarket.com/
21:19 < drethelin> fair
21:21 < kanzure> equidate, microventures, .. i'm sure there's a few others i'm forgetting.
21:21 < kanzure> sharespost is really funny. they just have a form and you type in how many shares you own and they just accept that and put you straight into the process.
21:24 < drethelin> hah
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--- Log closed Wed Jul 08 00:00:04 2015