| --- Log opened Tue Jul 07 00:00:03 2015 | ||
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| kanzure | you all died on me? | 04:00 |
|---|---|---|
| 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 | 04:17 |
| kanzure | what's up | 04:29 |
| Adlai | ah so today is "answer answers with their question" day? | 04:30 |
| Adlai | http://i.imgur.com/cO95AwG.jpg | 04:32 |
| kanzure | how would i know what day it is? days are stupid anyway. | 04:34 |
| Adlai | interestingly enough the power strip still works | 04:34 |
| Adlai | and tesla lives, making me >epsilon curious to try this stunt myself someday | 04:35 |
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| wrldpc1 | sooo … Henry Markram | 06:40 |
| wrldpc1 | On a scale of 1 to Steve Jobs what’s his RDF rating? | 06:40 |
| 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. | 06:41 |
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| kanzure | wrldpc1: http://diyhpl.us/wiki/transcripts/markram-2006/ | 06:46 |
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| Adlai | on random unrelated nonsense, anybody read Inferno? | 07:00 |
| Adlai | (not the epic, the fanfic screenplay-in-book's-clothing) | 07:00 |
| * 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 | 07:01 |
| 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/ | 07:02 |
| kanzure | this one? http://www.amazon.com/Inferno-Larry-Niven/dp/0765316765 | 07:07 |
| kanzure | https://en.wikipedia.org/wiki/Inferno_(Niven_and_Pournelle_novel) | 07:09 |
| * Adlai isn't aware that larry is a screenwriter in denial | 07:11 | |
| 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 | 07:12 |
| 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 | 07:13 |
| 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 | 07:14 |
| 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) | 07:15 |
| Adlai | hmm, the wikipedia article seems to have been written with the primary goal of spoiling every single plot twist | 07:16 |
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| 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 | 07:18 |
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| kanzure | .title http://www.pnas.org/content/early/2015/07/01/1506264112 | 08:18 |
| yoleaux | Quantification of biological aging in young adults | 08:18 |
| 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 | 08:19 |
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| wrldpc1 | I’ve heard it said Umberto Eco’s “Foucault’s Pendulum” is the “DaVinci Code” for smart people. | 08:47 |
| wrldpc1 | Da Vinci Code is basically pop fiction, right? I never read it and half-watched the movie. Someting about vatican secret societies. | 08:48 |
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| eudoxia | god bless libgen | 09:04 |
| 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. | 09:24 |
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| 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" | 09:25 |
| kanzure | i regret reading this article | 09:26 |
| kanzure | https://github.com/yarrick/pingfs | 09:27 |
| 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)) | 09:43 |
| CaptHindsight | 180 nozzles per channel, 1.5pL drop size (grey scale) so 1.5pL is the native drop size | 09:44 |
| CaptHindsight | $300 to cannibalized for the head, not too bad, the ~$100 heads have only 4 channels active of the 8 | 09:45 |
| 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 | 09:46 |
| CaptHindsight | so 1080 working nozzles | 09:48 |
| CaptHindsight | out of 1440 for 8 channels | 09:48 |
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| CaptHindsight | 1" print swath, 0.0055" nozzle pitch | 09:50 |
| CaptHindsight | ~141um | 09:50 |
| nmz787_i | but can you control individual nozzles, or do they all fire at once within a channel? | 09:59 |
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| 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 | 10:01 |
| CaptHindsight | channels is this case means "ink channels" | 10:02 |
| CaptHindsight | so 6 fluid channels, each with 180 addressable nozzles | 10:02 |
| 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 | 10:03 |
| Adlai | wrldpc1: dan brown books are conspiracy stories, foucoult's pendulum is more of a story about conspiracy theorists | 10:04 |
| kanzure | i thought we needed more than six chemicals | 10:06 |
| 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? | 10:08 |
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| CaptHindsight | nmz787: yes, to be clear let me find a good pic | 10:22 |
| 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 | 10:23 |
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| 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 | 10:31 |
| CaptHindsight | each channel has 2 rows of 90 nozzles staggered/interlaced | 10:32 |
| CaptHindsight | http://www.mbsdirect.com/current/images/stories/epson/epson-printhead.gif this is an older model with 4 channels | 10:34 |
| CaptHindsight | sorry 8 channels but it's not zoomed in to see the stagger | 10:35 |
| CaptHindsight | http://www.northlight-images.co.uk/content_images_2/epson_sp3880/3880-print-head.jpg | 10:36 |
| 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? | 10:40 |
| CaptHindsight | I thought 6 | 10:41 |
| CaptHindsight | Epson is up to 8 fluid channels per head | 10:41 |
| CaptHindsight | we can also stitch heads | 10:41 |
| 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 | 10:43 |
| CaptHindsight | for example 16 heads x 8 channels = 128 fluids x 180 nozzles = 23,040 nozzles | 10:44 |
| 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 | 10:45 |
| 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 | 10:46 |
| 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 | 10:47 |
| kanzure | and page 10 | 10:48 |
| 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) | 10:49 |
| 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 | 10:50 |
| 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) | 10:51 |
| 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 | 10:52 |
| CaptHindsight | probably the #1 reason heads get clogged | 10:53 |
| CaptHindsight | I can control repeatability to a few microns pretty cheaply and easily | 10:53 |
| 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 | 10:54 |
| 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) | 10:55 |
| nmz787_i | I don't know what the rate/quantifier would be | 10:56 |
| 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) | 10:57 |
| CaptHindsight | step back a second | 10:58 |
| CaptHindsight | each layer is one drop | 10:58 |
| 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? | 10:59 |
| 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 | 11:00 |
| 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 | 11:01 |
| nmz787_i | sure | 11:02 |
| CaptHindsight | so we are using a fire hose vs ideally one molecule dropped onto the next | 11:02 |
| 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 | 11:04 |
| 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 | 11:05 |
| 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 | 11:06 |
| 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? | 11:07 |
| nmz787_i | depends on the reaction volume, temperature, concentration of the activating acid | 11:08 |
| 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 | 11:09 |
| CaptHindsight | yes, requires some tweaking (lots) | 11:10 |
| nmz787_i | I think most protocols just lower the concentration to avoid damage, and take the time lengthening hit | 11:11 |
| 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 | 11:13 |
| 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) | 11:14 |
| CaptHindsight | MEMS and being able to print electronics | 11:15 |
| CaptHindsight | or at least connect to MEMS devices | 11:16 |
| CaptHindsight | do both | 11:16 |
| CaptHindsight | inkjet and fab some nanopores | 11:16 |
| 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 | 11:18 |
| 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 | 11:19 |
| nmz787_i | blast in a controlled manner | 11:20 |
| kanzure | from what? | 11:20 |
| 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 | 11:21 |
| 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 | 11:22 |
| 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) | 11:23 |
| 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 | 11:24 |
| 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 | 11:25 |
| 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 | 11:26 |
| 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? | 11:27 |
| nmz787_i | sometimes | 11:28 |
| 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 | 11:29 |
| 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). | 11:30 |
| 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. | 11:31 |
| 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 | 11:32 |
| kanzure | (such a channel would naturally be named "maxwell's true demon") | 11:33 |
| 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 | 11:34 |
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| CaptHindsight | yeah, that is the goal | 11:35 |
| CaptHindsight | that would make things easier | 11:35 |
| nmz787_i | ssDNA or dsDNA? | 11:37 |
| kanzure | somebody got carried away when naming this one "Microoptomechanical pumps assembled and driven by holographic optical vortex arrays" | 11:38 |
| CaptHindsight | heh | 11:38 |
| 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 | 11:39 |
| CaptHindsight | fabricating a gate with coils around it could isolate single nucleotides | 11:40 |
| 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 | 11:41 |
| CaptHindsight | make those tools | 11:42 |
| 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. | 11:43 |
| CaptHindsight | need to make the low cost tools to make those | 11:44 |
| CaptHindsight | molecular machine shop | 11:44 |
| 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 | 11:45 |
| CaptHindsight | on the inkjet side the ink reservoirs behind the nozzles hold a few mL | 11:53 |
| CaptHindsight | so if they are expensive then you probably want to reclaim them | 11:54 |
| 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 | 11:56 |
| 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 | 11:57 |
| CaptHindsight | the pointy parts have a small orifice that pokes through the septum on the cartridge | 11:58 |
| CaptHindsight | for bulk feeding you just attach a line over them using friction | 11:59 |
| CaptHindsight | or use the cartridges with tubing back to a larger reservoir | 12:01 |
| CaptHindsight | the cartridges also act as a damper | 12:01 |
| CaptHindsight | one big industrial systems we have negative pressure regulators | 12:02 |
| CaptHindsight | just a few inches of water of negative pressure | 12:03 |
| CaptHindsight | and also degassing since some heads fire so fast that any trapped O2 cases cavitation vs drops | 12:04 |
| nmz787_i | then you still need to think of waste disposal | 12:09 |
| nmz787_i | no pouring acetonitrile into the backyard, kids | 12:09 |
| nmz787_i | and you don't really need a gate, you can just use dilute solutions and electrophoresis or just pressure to gate them | 12:10 |
| kanzure | waste disposal is not the end of the world | 12:11 |
| nmz787_i | it's such a sad part of the process | 12:11 |
| CaptHindsight | I'll have to start looking for surplus SEM parts and other components to make tools | 12:12 |
| 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 | 12:13 |
| 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. | 12:16 |
| 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? | 12:17 |
| 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) | 12:18 |
| 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 | 12:19 |
| CaptHindsight | that's giant | 12:20 |
| kanzure | exactly | 12:20 |
| 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 | 12:21 |
| 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?) | 12:22 |
| 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. | 12:23 |
| CaptHindsight | plus this has other applications | 12:24 |
| CaptHindsight | custom oligomers for coatings, inks, adhesives etc | 12:24 |
| nmz787_i | 'this' meaning the printer? | 12:25 |
| CaptHindsight | fabricate custom polymers with unique surfaces | 12:25 |
| CaptHindsight | oh, synthesis of polymers in general | 12:25 |
| CaptHindsight | the printer is like getting your first 100 pcs tool set with 27 screw drivers and 18 allen keys | 12:26 |
| CaptHindsight | better than just having your fingers | 12:27 |
| CaptHindsight | http://kilobaser.com/ got funding and went silent | 12:32 |
| CaptHindsight | https://www.youtube.com/watch?v=08Ju95uwgt0 XY-Stage and SyringePumps Prototype Test | 12:35 |
| CaptHindsight | https://youtu.be/WxpQyqoukpc?t=39s Programmable large area digital microfluidic array | 12:40 |
| CaptHindsight | whats the patent situation on these devices? | 12:40 |
| CaptHindsight | is the tech being held hostage for 20 years? | 12:41 |
| kanzure | probably, but the older tech is up for grabs | 12:56 |
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| CaptHindsight | Sandia and a few others are all similar | 13:05 |
| CaptHindsight | https://youtu.be/9GInRQYzSJg?t=2m32s Sandia Digital Microfluidic Hub | 13:06 |
| 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 | 13:09 |
| 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 | 13:10 |
| 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 | 13:11 |
| 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. | 13:12 |
| kanzure | oh, you mean the person would be doing the task estimation | 13:13 |
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| 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 | 13:15 |
| 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 | 13:18 |
| CaptHindsight | sounds like Bio-med meets inkjet and they are both very controlling | 13:19 |
| kanzure | yup, definitely a joke | 13:19 |
| CaptHindsight | if China would have started sooner we'd be buying all this from them | 13:21 |
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| kanzure | CaptHindsight: sorry about that; i'm in a very noisy environment at the moment. | 13:50 |
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| 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." | 15:07 |
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| 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." | 16:03 |
| nmz787_i | from http://hackaday.com/2015/07/07/headphone-amp-features-a-tiny-crt/ | 16:05 |
| 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 | 16:09 |
| jrayhawk | man, shoving my eye right up against a CRT just seems like a bad idea, in retrospect | 16:11 |
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| 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 | 16:15 |
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| alu | What do you all see the difference as between a transhumanist and posthumanist? | 17:04 |
| alu | Serious question | 17:04 |
| nmz787_i | one is in transition, one has gotten past it? | 17:05 |
| kanzure | is that important? | 17:05 |
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| drethelin | why would you think thats a serious question | 17:42 |
| drethelin | that's MY question | 17:42 |
| 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 | 17:43 |
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| drethelin | it's not like there's eastern orthodox transhumanism and catholic posthumanism | 17:44 |
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| juri_ | alu: welcome. ;) | 18:12 |
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| fenn | i know a catholic posthumanist | 18:30 |
| fenn | also i think pasky runs or.cz | 18:30 |
| fenn | uh, the orthodox church in czech republic, or something | 18:32 |
| fenn | there are also a fair number of mormon transhumanists | 18:33 |
| drethelin | you seem to have missed my point | 18:34 |
| 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 | 18:35 |
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| fenn | ok i guess max more is our pope then | 18:38 |
| fenn | and anders sandberg is his prophet | 18:38 |
| drethelin | I don't even know who those guys are | 18:39 |
| fenn | here's some stuff then http://www.extropy.org/proactionaryprinciple.htm http://www.aleph.se/Trans/ | 18:41 |
| fenn | hmm the extropian principles page went 404 | 18:44 |
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| 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 | 18:44 |
| 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 | 18:45 |
| 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? | 18:46 |
| 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 | 18:48 |
| 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 | 18:49 |
| 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. | 18:50 |
| 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 | 18:51 |
| 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 | 18:52 |
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| fenn | it's probably not just ~100 wires huh | 18:53 |
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| juri_ | we tried that on one at hacDC, but had the laptop with the data on it stolen. | 19:01 |
| 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 | 19:03 |
| 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 | 19:04 |
| kanzure | .gc inkshield | 19:05 |
| yoleaux | 14,000 (site), 1,810 (api) | 19:05 |
| kanzure | .title https://www.youtube.com/watch?v=dzTCDMRv8bY | 19:06 |
| yoleaux | InkShield: An Open Source Inkjet Shield for Arduino - YouTube | 19:06 |
| fenn | that's thermal, no piezo | 19:07 |
| kanzure | hmph | 19:09 |
| 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) | 19:10 |
| 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 | 19:11 |
| kanzure | bleh | 19:12 |
| fenn | "We’ve built our own functioning bioprinter from a couple of old CD drives, an inkjet cartridge, and an Arduino." | 19:13 |
| 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 | 19:14 |
| kanzure | juul: did the biocurious people use a piezoelectric inkjet head? | 19:15 |
| CaptHindsight | the inkjet industry is pretty tight lipped about specs for their heads | 19:19 |
| 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 | 19:20 |
| CaptHindsight | the old DX2 or 3 was | 19:21 |
| CaptHindsight | the Epsons are pretty easy | 19:21 |
| 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 | 19:22 |
| 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 | 19:24 |
| 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? | 19:25 |
| 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) | 19:26 |
| 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 | 19:27 |
| 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 | 19:28 |
| CaptHindsight | http://www.xaar.com/en/products | 19:29 |
| CaptHindsight | http://www.fujifilmusa.com/products/industrial_inkjet_printheads/print-products/printheads/index.html | 19:29 |
| 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? | 19:30 |
| CaptHindsight | it's a flex pcb | 19:31 |
| 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 | 19:32 |
| kanzure | is the protocol known? | 19:33 |
| CaptHindsight | yes and no | 19:33 |
| kanzure | fenn: you should brag about linuxcnc things | 19:33 |
| CaptHindsight | there will be some tweaking to the drive pulse shape | 19:34 |
| CaptHindsight | http://dpnow.com/3762.html here is how Epson has the internals arranged | 19:40 |
| CaptHindsight | Epsons are pretty basic | 19:45 |
| 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 | 19:46 |
| CaptHindsight | they even sense temp and modify drive waveforms on the fly | 19:47 |
| CaptHindsight | some even have LVDS or HDMI type interfaces since the data rate is so high | 19:48 |
| fenn | yeech | 19:50 |
| fenn | what sort of application uses such a high data rate? | 19:51 |
| CaptHindsight | digital press | 19:51 |
| CaptHindsight | some use 64 of those Kyocera heads I posted | 19:52 |
| CaptHindsight | 64 x 330M/sec = 21GB/sec for the driver | 19:53 |
| fenn | so they just do the whole page in one pass? | 19:54 |
| CaptHindsight | yes | 19:54 |
| CaptHindsight | just like an offset press | 19:54 |
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| CaptHindsight | https://www.youtube.com/watch?v=3nYSJK_sy-k here's a slow one with only 16 heads | 19:58 |
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| fenn | we've created a fantastically adaptable technology capable of infinite variation, and we print repeating floral patterns... | 19:59 |
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| kanzure | well worst case for reverse engineering the control of the printhead, we can just intercept the signal and see what's going on | 20:30 |
| juri_ | Got funding? :P | 20:31 |
| kanzure | yes | 20:31 |
| juri_ | sounds like fun, then. | 20:32 |
| kanzure | are you offering? | 20:33 |
| juri_ | I could do that. | 20:33 |
| juri_ | it's been on my todo for some time. | 20:33 |
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| fenn | the epson looks like just a shift register in the techref page | 20:35 |
| 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 | 20:36 |
| drethelin | anyone in here know anything about regulon/lipoplatin? | 20:39 |
| 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 | 20:46 |
| drethelin | regulon inc, not regulon the cell biology term, sorry | 20:47 |
| kanzure | gah | 20:48 |
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| fenn | regulon is a terrible name for a company anyway | 20:50 |
| 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 | 20:51 |
| fenn | why do you care about a cancer drug | 20:52 |
| 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 | 20:53 |
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| kanzure | http://america.aljazeera.com/articles/2015/7/6/lax-sec-regulation-biotech-market.html | 21:02 |
| 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.” ... | 21:05 |
| 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." | 21:06 |
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| 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/ | 21:18 |
| kanzure | http://secondmarket.com/ | 21:19 |
| drethelin | fair | 21:19 |
| 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. | 21:21 |
| drethelin | hah | 21:24 |
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