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jrayhawk | https://www.flickr.com/photos/kylemcdonald/19266856649/sizes/o/ | 02:46 |
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kanzure | .title https://news.ycombinator.com/item?id=9836336 | 03:27 |
yoleaux | Hacking Team hacked, attackers claim 400GB in dumped data | Hacker News | 03:27 |
kanzure | "Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces" http://www.bakerlab.org/system/files/Gonen_2DArrays_Baker2015.pdf | 03:44 |
kanzure | "We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design ... | 03:44 |
kanzure | ... proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering." | 03:45 |
kanzure | "Accurate design of co-assembling multi-component protein nanomaterials" http://www.bakerlab.org/system/files/King_Nature2014A.pdf | 03:47 |
kanzure | figure 4 "Electron micrographs of designed two-component protein | 03:47 |
kanzure | nanomaterials." | 03:47 |
kanzure | no wait, figure 5 is better | 03:47 |
kanzure | "Automating human intuition for protein design" http://www.bakerlab.org/system/files/Niv%C3%B3n_prot24463_13M.pdf | 03:51 |
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kanzure | a more general review of de novo protein design (open access) http://www.sciencedirect.com/science/article/pii/S0959440X1500069X | 03:54 |
kanzure | a grammar for protein backbone structure using "protein blocks" http://onlinelibrary.wiley.com/doi/10.1002/pro.2581/pdf | 03:55 |
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kanzure | eudoxia: same request goes for you (regarding listmaking of useful molecular machines) | 05:52 |
eudoxia | hmm | 05:54 |
eudoxia | MNT style machines or just anything useful? | 05:54 |
kanzure | anything useful | 05:59 |
kanzure | not necessarily molecular nanoprobe stuff | 05:59 |
eudoxia | right, also proteins and shit | 06:00 |
kanzure | well, protein-equivalent machines could count, but let's skip proteins themselves here | 06:02 |
kanzure | having a molecular differential gear is nice, but only if you have other components to make use of it. meanwhile there are probably simple molecular machines that are useful in isolation. | 06:02 |
eudoxia | sort of like what the parts library of NE was meant to become | 06:04 |
kanzure | huh? | 06:05 |
kanzure | the parts library was full of differential gears | 06:06 |
eudoxia | .title http://crnano.org/interview.freitas.htm | 06:06 |
yoleaux | Nanotechnology: Robert Freitas Interview | 06:06 |
eudoxia | >We’d expect the library of designed machine systems to rapidly expand from the current 1-2 dozen items (including mostly just a few bearings, gears, and joints) into the hundreds or thousands in just a few years. | 06:06 |
eudoxia | oh bobbie | 06:06 |
kanzure | so you're saying the only simple molecular machines you are aware of are the ones listed here? https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib | 06:07 |
eudoxia | not really, there's also a nanotube linear motor and this rack and pinion system that's not there | 06:08 |
eudoxia | then there's all sorts of bespoke binding sites people have designed over the years | 06:09 |
eudoxia | wait a sec who did this https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib/schafmeister | 06:09 |
justanotheruser | kanzure: do you have a list started? | 06:10 |
justanotheruser | All I know of are drexlers designs | 06:10 |
kanzure | well the files in nanoengineer.git are a list beyond just drexler's designs | 06:11 |
kanzure | here are some protein things that are interesting, if that's what you're asking about http://diyhpl.us/wiki/dna/projects/#proteins | 06:11 |
justanotheruser | yes, that is interesting | 06:12 |
justanotheruser | wasn't aware of all the designs that come with nanoengineer | 06:12 |
* justanotheruser bookmarks | 06:13 | |
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kanzure | i'm surprised at the lack of responses- i was expecting obvious things like antennae arrays, rod arrays (for sensors or even dna separation), polymerase clamps, springs, spheres or beads, machine tools... | 06:26 |
eudoxia | regarding springs | 06:27 |
eudoxia | drexler mentioned in the design of rod logic that you'd need springs to bring the rods back into place | 06:27 |
eudoxia | not knowing if there were small spring molecules like that, i imagined the way it would work would be something like | 06:27 |
eudoxia | a rotor with a cam would push the rods back into place, and travel perpendicular to a stack of identical rod-logical circuits | 06:27 |
eudoxia | but there are probably small linear spring molecules, no? | 06:28 |
kanzure | here is a more chemistry-oriented review of molecular machines http://www.researchgate.net/profile/Alberto_Credi/publication/12237218_Artificial_Molecular_Machines/links/0a85e531aec5618f45000000.pdf | 06:28 |
kanzure | i don't think that small-scale rod logic is likely to work for a while-- you need lots of other machinery to make use of it | 06:30 |
eudoxia | certainly, just asking cause it came to mind | 06:30 |
justanotheruser | http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002086 | 06:32 |
justanotheruser | .title | 06:32 |
yoleaux | PLOS Biology: Open Labware: 3-D Printing Your Own Lab Equipment | 06:33 |
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kanzure | steganography framework https://github.com/bramcohen/DissidentX | 07:20 |
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CaptHindsight | kanzure: the Agilent inkjet may be used for more than oligo probe hybridization, they are just focusing on that with their NextGen | 07:31 |
CaptHindsight | HP makes lots of printheads that they don't resell | 07:32 |
kanzure | it's not the inkjet which limits it; it's the lack of sample recovery | 07:33 |
CaptHindsight | it looks like they have made some just for printing oligos | 07:33 |
CaptHindsight | what's stopping/preventing the sample recovery? | 07:34 |
CaptHindsight | it's a stack of oligos in wells | 07:34 |
kanzure | see pm | 07:34 |
kanzure | wells are problematic because the only way to recover dna from wells (in this scenario) is pipetting, and if you have 2 million pores/wells then uh.. well.. pipetting will take forever. | 07:35 |
CaptHindsight | drop the bottom out | 07:36 |
kanzure | to where? you need to keep the samples separated. | 07:36 |
CaptHindsight | you have to start connecting them somewhere | 07:37 |
kanzure | now would be an okay time for a phone call if you're up for it | 07:37 |
archels | hmm, these guys coded their spiking neural network in Julia. I wonder why | 07:44 |
archels | 447 SLOC, pretty tight | 07:44 |
archels | no parallelism though | 07:44 |
archels | if spiked[cc] #spike occurred | 07:46 |
archels | spiked[cc] = true; | 07:46 |
archels | # make **REALLY REALLY** sure that this variable is set to true | 07:46 |
kanzure | CaptHindsight: good talking with you capt'n | 08:24 |
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kanzure | win 5 | 08:39 |
kanzure | eijroeqjrqi whoops | 08:39 |
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kanzure | https://np.reddit.com/r/IAmA/comments/38jawf/im_the_president_of_the_liberland_settlement/crw1d0f?context=10 | 09:06 |
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nmz787_i1 | kanzure: so what does CaptHindsight want to improve on specifically, just cost to manufacture a POSAM clone? | 10:36 |
nmz787_i1 | if that's the case, then I think replicating the POSAM chemicals list would be the best idea | 10:37 |
nmz787_i1 | and send me an email for the items that are no longer available with direct replacements... and we can search for a substitute | 10:38 |
nmz787_i1 | kanzure: a more interesting question to me is, who here would want to help with a micro/nano device? | 10:38 |
kanzure | why bother with micro or nano if you can get enough scale without it? inkjet printing can do picoliter droplets. | 10:39 |
nmz787_i1 | yeah but eww | 10:39 |
nmz787_i1 | you want to do offsite sequencing | 10:39 |
kanzure | elaborate? | 10:39 |
nmz787_i1 | how gross | 10:39 |
kanzure | yes, i want to do offsite sequencing for now | 10:39 |
kanzure | v2 can include other components | 10:39 |
nmz787_i1 | you need sequencing after every 1 to 10 or 50 additions | 10:39 |
kanzure | putting all work upfront is not good.... likewise, putting everything off until later is also bad. | 10:40 |
nmz787_i1 | tdt plus nanopore would be more interesting | 10:40 |
kanzure | i thought that required a mutated/not-yet-existing version of tdt | 10:40 |
nmz787_i1 | na | 10:40 |
nmz787_i1 | just some wires to sense the nanopore for when a nucleotide passes through | 10:41 |
nmz787_i1 | impedanceometry or whatever | 10:41 |
kanzure | i'm not sure why you think that is easier than working with off-the-shelf inkjet heads? | 10:41 |
nmz787_i1 | because I have access to a FIB and silicon and gas-injection... I don't have inkjets, know their interfaces aren't stable for offlabel use | 10:42 |
kanzure | fib is not the hard part when confining an enzyme in a nanopore | 10:45 |
nmz787_i1 | you don't want the enzyme in the nanopore though | 10:47 |
nmz787_i1 | the nanopore is just to limit diffusion and tunnel molecules past your molecule-counter electrodes | 10:47 |
nmz787_i1 | so you can know when to turn off the nucleotide pump | 10:47 |
nmz787_i1 | but anyway, yeah I'd say just replicate the POSAM chem list, and shoot me an email if there are items with questions or supply problems | 10:48 |
kanzure | one thing you might be able to convince me about is single-molecule emulsions | 10:49 |
nmz787_i1 | the HO on water looks like the HO on the 2' site on the nucleotide rings, that's why it lowers efficiency... so anything with a similar HO can have that effect | 10:50 |
nmz787_i1 | (just FYI) | 10:50 |
nmz787_i1 | https://en.wikipedia.org/wiki/Directionality_(molecular_biology) | 10:50 |
nmz787_i1 | err | 10:50 |
nmz787_i1 | the 3' | 10:50 |
nmz787_i1 | https://en.wikipedia.org/wiki/Nucleotide | 10:51 |
nmz787_i1 | (the first link shows the hidden polymer form) | 10:51 |
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kanzure | .title http://www.sciencemag.org/content/333/6042/613.short | 10:55 |
kanzure | "A Single Molecule of Water Encapsulated in Fullerene C60" | 10:56 |
yoleaux | A Single Molecule of Water Encapsulated in Fullerene C60 | 10:56 |
kanzure | https://scholar.google.com/scholar?hl=en&q=%22organic+cage%22+&btnG=&as_sdt=1%2C44&as_sdtp= | 10:57 |
kanzure | or nanopipette stuff.. hm. | 11:00 |
kanzure | huh i'm surprised that single-molecule emulsions are not a thing | 11:07 |
archels | superkuh: the website is down :( | 11:08 |
archels | this should be fun https://www.youtube.com/watch?v=7u8mheM2Hrg | 11:17 |
archels | .title | 11:17 |
yoleaux | RESPONSE TO ROBOT DUEL CHALLENGE. - YouTube | 11:17 |
nmz787_i1 | I think I'd basically just need some help with CAD models and idea putting-together... then I could convert them to FIB files or mask files, do the micro/nano work... then maybe send that off to someone with a machine shop to make the macro to micro manifold, hookup the pumps and chemicals. Before that the sensing board would need to be built or a good analog frontend (amplifier) would need purchased | 11:17 |
kanzure | which cad models? | 11:18 |
CaptHindsight | nmz787: what do you want to fabricate? the manifold? | 11:19 |
nmz787_i1 | I'd do the actual micro and nano device (on-chip peristaltic pumps, some mixing areas, a nanopore for each nucleotide, a chamber for tdt, a nano-lattice/pore-matrix to retain tdt so waste can flow, some purification areas) | 11:20 |
superkuh | Uh oh. Something didn't come back up from the lightning strike. | 11:21 |
nmz787_i1 | the manifold I'm guessing will look something like this http://www.ifitjams.com/images/f4-11.jpg | 11:21 |
superkuh | Oh, no, just another IP change. | 11:21 |
CaptHindsight | a zero insertion force socket | 11:22 |
nmz787_i1 | the microchip just compresses onto the steel manifold, with some rubber or teflon between | 11:22 |
nmz787_i1 | I think that is LGA | 11:22 |
nmz787_i1 | so not quite ZIF | 11:22 |
CaptHindsight | nmz787: LGA PGA | 11:22 |
nmz787_i1 | since there's no insertion | 11:22 |
CaptHindsight | yeah just the pores | 11:22 |
CaptHindsight | inlets | 11:23 |
CaptHindsight | CAD models are no problem | 11:26 |
CaptHindsight | kanzure: you have to decide which way you want to go | 11:27 |
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nmz787_i1 | I would prefer BRL-CAD personally | 11:28 |
CaptHindsight | nmz787: heh, well you can spend the time converting from Step or Iges | 11:28 |
nmz787_i1 | that seems like the only approach that is reliable | 11:29 |
nmz787_i1 | nah i'd just use my python interface ;) | 11:29 |
nmz787_i1 | To make the CAD automated for the FIB, I ultimated neem a .BMP type file | 11:30 |
nmz787_i1 | need* | 11:30 |
nmz787_i1 | but if the device is a one-off, I can do it by hand | 11:30 |
nmz787_i1 | but we still need to layout the components, break/fan them out to the macro manifold, and design the manifold | 11:31 |
CaptHindsight | I have all the design tools. I just don't bother with all the open source almost CAD tools | 11:33 |
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CaptHindsight | heh, how does a single molecule qualify as in emulsion? | 11:39 |
CaptHindsight | in/an | 11:39 |
nmz787_i1 | the cage would be the emulsifier | 11:39 |
CaptHindsight | kidding | 11:39 |
archels | superkuh: excellent | 11:39 |
CaptHindsight | low cost DIY FIB | 11:40 |
CaptHindsight | a handy tool of the nano machine shop | 11:41 |
nmz787_i1 | yeah it would work as a mass-spec too, if reversed | 11:41 |
nmz787_i1 | err, maybe the DIY SEM would be a better candidate | 11:42 |
CaptHindsight | what tools to build first? that was the discussion | 11:42 |
nmz787_i1 | but the DIY DUAL-BEAM would definitely be reversible for mass-spec | 11:42 |
CaptHindsight | well both, but where do we start | 11:42 |
CaptHindsight | build tools to build tools | 11:42 |
CaptHindsight | 3-axis inkjet is pretty simple | 11:43 |
CaptHindsight | also DLP micro printer | 11:44 |
CaptHindsight | there are lots of old SEM's around | 11:44 |
CaptHindsight | the electronics could all be modular, motion control, imaging etc can all be done on a PC | 11:45 |
kanzure | there really is no substitute at the moment for solidworks, really | 11:45 |
kanzure | brlcad has iges/step support, so just do it in solidworks then export to step/iges | 11:45 |
CaptHindsight | there are not really any open analog boards for drivers and sensors | 11:46 |
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CaptHindsight | NX, Catia, Creo, SW we run em all | 11:46 |
CaptHindsight | brl is coming along | 11:47 |
nmz787_i1 | BRL seemed to have better support for wide dynamic range in CAD models (they claim molecular to planetary scales) | 11:47 |
CaptHindsight | it's all the automated plug-ins and tools in the CAD package that save you so much time | 11:48 |
CaptHindsight | most on the surface act about the same | 11:49 |
nmz787_i1 | BRL doesn't have great support for harder to define curves, at least in terms of defining them with math/equations | 11:49 |
CaptHindsight | extrude, cut, rotate, chamfer etc | 11:49 |
CaptHindsight | it's when you need to blend from one surface to another or hold some inner diameter on a contorted tube or similar is when the extra features come in handy | 11:50 |
CaptHindsight | or generate a pattern of holes etc | 11:50 |
CaptHindsight | but that's not holding us back | 11:51 |
CaptHindsight | that's just a preference for tools | 11:51 |
CaptHindsight | and how much time you have | 11:52 |
nmz787_i1 | I just need a BMP file | 11:52 |
nmz787_i1 | :P | 11:52 |
CaptHindsight | yeah | 11:52 |
nmz787_i1 | 256-bit greyscale and single-layer per BMP | 11:53 |
kanzure | CaptHindsight: i'm a big fan of keeping it simple. nanopore stuff is fun, worth doing, but i still think keeping things simple can lead to good results. | 11:55 |
CaptHindsight | kanzure: we have to start somewhere | 11:55 |
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CaptHindsight | build a tool at a time, in a few years there will be a whole sub-micron CNC shop | 11:56 |
kanzure | oh regarding the emulsion question earlier: the idea was to use an emulsion where the contents of the emulsion is a single molecule | 11:58 |
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kanzure | the actual emulsifier could be many multiple molecules | 11:58 |
CaptHindsight | kanzure: whats the solvent or vehicle it's suspended in? | 12:00 |
nmz787_i1 | CaptHindsight: IMO the nanopore stuff is immensely less complicated from a success standpoint... no one is going to care if you make POSAM cheaper, because the reagents are so relatively unavailable, short shelf life, low value output (it creates stuff that was available mail-order 30 years ago) | 12:01 |
kanzure | no idea, i was just looking around for papers to see if the emulsion idea exists elsewhere, doesn't matter | 12:01 |
CaptHindsight | I'm translating from Bio to coating, ink, paint chemistry terminology | 12:01 |
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kanzure | nmz787_i1: whether "no one is going to care if you make POSAM cheaper" does not modulate whether "the nanopore stuff is immensely less complicated from a success standpoint"... | 12:02 |
kanzure | short shelf life is probably because of contamination | 12:02 |
kanzure | being available by mail-order is irrelevant | 12:02 |
nmz787_i1 | nope, that's why I included the chemistry point(s) | 12:02 |
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nmz787_i1 | tdt is all water-based, can be achieved with a few home-brew enzymes and purified molecules | 12:03 |
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CaptHindsight | nmz787: https://en.wikipedia.org/wiki/Terminal_deoxynucleotidyl_transferase making sure we are talking about this | 12:12 |
kanzure | yes | 12:12 |
kanzure | terrible diagram of tdt, it's essentially a donut | 12:13 |
kanzure | but the diagram fails to express this | 12:14 |
CaptHindsight | squished donut | 12:17 |
kanzure | a less delicious donut | 12:18 |
CaptHindsight | http://www.ebay.com/itm/Cambridge-Stereoscan-250-MK2-Scanning-Electron-Microscope-SEM-/400758845514 $800 as-is | 12:25 |
kanzure | working? | 12:25 |
CaptHindsight | looks like "untested" we have no clue how to either | 12:25 |
CaptHindsight | I usually spot one or two for a few $K that are in working condition | 12:28 |
nmz787_i1 | e-ink remote control on Sony's home-grown crowdfunding site https://first-flight.sony.com/pj/2/HUIS%20REMOTE%20CONTROLLER | 12:31 |
CaptHindsight | http://www.ebay.com/itm/Zeiss-Electron-Microscope-EM-109-/181783812468 $3500 was working | 12:32 |
drethelin | nice | 12:32 |
CaptHindsight | and another: This instrument was pulled from service many years ago and its operational status is not known, thus we are listing it as "for parts or not working" because we cannot guarantee its proper operation. http://www.ebay.com/itm/JEOL-JSM-35C-Scanning-Electron-Microscope-with-Spectrum-Analysis-/331482051373 | 12:33 |
CaptHindsight | $2500 | 12:33 |
CaptHindsight | with Spectrum Analysis | 12:33 |
CaptHindsight | http://www.ebay.com/itm/JEOL-T330A-Electron-Microscope-working/331599003517 $2500 working | 12:35 |
CaptHindsight | with video of it working https://www.youtube.com/watch?v=FVpqDrAeKLU | 12:35 |
CaptHindsight | https://www.youtube.com/watch?v=gejSPGIcWPo | 12:36 |
nmz787_i1 | the T330A looks pretty much like the scope I have (T200)... I think I might even have some schematics for the T330A too | 12:37 |
CaptHindsight | I should try to find surplus gun, chamber, detector assemblies | 12:40 |
nmz787_i1 | https://www.tedpella.com/calibration_html/SEM_Calibration.htm | 12:40 |
nmz787_i1 | I think that JSM-35C was on craigslist for a while | 12:41 |
nmz787_i1 | oh, maybe not | 12:42 |
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kanzure | .tell eleitl http://www.metzdowd.com/pipermail/cryptography/2015-July/025971.html | 12:58 |
yoleaux | kanzure: I'll pass your message to eleitl. | 12:58 |
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kanzure | apparently firefly synchronization is a thing http://www.eecs.harvard.edu/ssr/projects/sync/ | 13:52 |
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kanzure | "Some viruses that infect Archaea have complex structures that are unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.[80]" | 13:59 |
kanzure | [80] Prangishvili D, Forterre P, Garrett RA. Viruses of the Archaea: a unifying view. Nature Reviews Microbiology. 2006;4(11):837–48. doi:10.1038/nrmicro1527. PMID 17041631. | 13:59 |
kanzure | http://www.nature.com/nrmicro/journal/v4/n11/full/nrmicro1527.html | 13:59 |
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kanzure | http://www.researchgate.net/profile/Patrick_Forterre/publication/6753226_Viruses_of_the_Archaea_a_unifying_view/links/53f5c8700cf2888a7491e75e.pdf | 13:59 |
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nmz787_i | .title http://hplusmagazine.com/2015/02/15/biology-technology-darpa-back-game-big-vision-h/ | 15:20 |
yoleaux | Biology is Technology - DARPA is Back in the Game With A Big Vision and It Is H+ - h+ Mediah+ Media | 15:20 |
nmz787_i | 'Most lenses are, by definition, curved. After all, they are named for their resemblance to lentils, and a glass lens made flat is just a window with no special powers.' | 15:26 |
nmz787_i | /me had no idea of the relation to lentils | 15:26 |
nmz787_i | =-O | 15:26 |
kanzure | "Well known Silicon Valley venture capitalist, rocketeer, transhumanist, and super guy Steve Jurvetson was spotted “high fiving” a DARPA funded telepresence robot developed at Johns Hopkins APL at the reception." | 15:27 |
kanzure | (jurvetson is the J and draper is the D in DFJ) | 15:27 |
kanzure | (draper is the one with the kid that is desperate to fund someone building an iron man exoskeleton) | 15:28 |
kanzure | didn't know that these were the organ-on-a-chip people http://emulatebio.com/ | 15:28 |
nmz787_i | .title http://keyssa.com/technology/ | 15:36 |
yoleaux | Our Technology - Keyssa | 15:36 |
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nmz787_i | .title http://www.voxel8.co/ | 15:45 |
yoleaux | Voxel8: 3D Electronics Printing | 15:45 |
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kanzure | .title https://news.ycombinator.com/item?id=9841209 | 18:08 |
yoleaux | Antibody wipeout relieves symptoms of chronic fatigue syndrome | Hacker News | 18:08 |
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kanzure | .wik treponema pallidum | 18:22 |
yoleaux | "Treponema pallidum is a spirochaete bacterium with subspecies that cause treponemal diseases such as syphilis, bejel, pinta, and yaws. The treponemes have a cytoplasmic and an outer membrane. Using light microscopy, treponemes are only visible using dark field illumination. They are gram negative, but some regard them too thin to be gram stained." — https://en.wikipedia.org/wiki/Treponema_pallidum | 18:22 |
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kanzure | oh cool we have the genome of neurosyphilis | 18:23 |
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drethelin | great, now we can synthesize it! | 18:29 |
kanzure | there are easier ways to get neurosyphilis | 18:30 |
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kanzure | "The metalloprotease Mpr1 has been demonstrated to be critical in blood-brain barrier penetration.[16]" | 18:40 |
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ryankarason | nmz787: ha! @ lentils.. nor did i.. | 19:25 |
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kanzure | hm | 20:09 |
kanzure | whatever happened to the brain preservation prize results. did that happen? or was it just a hit-and-run thing. | 20:10 |
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kanzure | hrm. | 21:06 |
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