| --- Log opened Thu Jan 26 00:00:32 2012 | ||
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| utopiah_ | any project of 3D printer controlled by EEG? | 04:53 |
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| archels | How stoned are you? | 05:51 |
| utopiah_ | is that question for me? | 05:57 |
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| archels | yes, but don't worry, it was rhetorical. | 06:15 |
| utopiah_ | tbh Im sure both are at the same time too low resolution and too expensive but Im sure it would give a nice exciting feeling to just "make" something tangible without moving | 06:20 |
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| archels | relevant http://www.technologyreview.com/blog/mimssbits/27526/?p1=blogs | 07:32 |
| delinquentme | so I think it would be a HUGe resource to create some app to help people select out projects they want to work on selected out via skillsets | 07:54 |
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| delinquentme | ಠ_ಠ http://www.grg.org/ | 08:13 |
| archels | heh neat | 09:07 |
| kanzure | delinquentme: grg might look lame, but their mailing list has a lot of the big names | 09:28 |
| delinquentme | kanzure, yeah that website could use some improvement ... I've just written up an email to shoot over to him :D | 09:29 |
| delinquentme | archels, i know man thats some cutting edge web app axions | 09:29 |
| delinquentme | http://www.usc.edu/dept/gero/research.shtml ?? | 09:29 |
| delinquentme | lolol computational biogerontology | 09:30 |
| delinquentme | its such a mouthful | 09:30 |
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| delinquentme | here you go : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1877880/ | 10:05 |
| delinquentme | metabolic yeast aging | 10:06 |
| * kanzure cracks the whip | 10:12 | |
| kanzure | delinquentme: you should get back to reading http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/ | 10:12 |
| delinquentme | so i saw an opening somewhere in CA for someone with experience in solidworks to work on microfluidics | 10:14 |
| kanzure | were they asking for a cad monkey? | 10:14 |
| delinquentme | i didnt go through it fully | 10:24 |
| delinquentme | i think it was off of genome webs job sits | 10:24 |
| AlonzoTG | om | 10:26 |
| AlonzoTG | there is just enough data to suggest that working on a retrocausal quantum cascade of some sort that can send a signal roughly a hundred or so milliseconds back in time is not a total waste.... | 10:27 |
| AlonzoTG | If I can get it done for the few $ I still have on hand, I might never be poor again! =P | 10:27 |
| kanzure | um.. | 10:28 |
| AlonzoTG | wut? | 10:32 |
| kanzure | https://thepiratebay.org/torrent/6984445/Assorted_Printables_by_Cathal_Garvey | 10:32 |
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| delinquentme | aubreys doing the live chat on life extension now | 12:06 |
| kanzure | ask him why he fired lorenzo | 12:07 |
| kanzure | :( | 12:07 |
| delinquentme | aubrey fired lorenzo? | 12:12 |
| delinquentme | who is lorenzo? :P? | 12:12 |
| delinquentme | also humans and our fucking coping mechanisms | 12:13 |
| kanzure | lorenzo was one of the people working on SENS stuff | 12:13 |
| kanzure | previously there was also john schloendorn, but he dropped out and did biocurious (sort of) and then his company (which peter dumped money into) | 12:14 |
| delinquentme | yeah john is kicking ass solo | 12:15 |
| delinquentme | another reason why i <3 halcyon | 12:15 |
| delinquentme | how many awesome scientists are they employing | 12:16 |
| kanzure | john isn't at halcyon iirc | 12:16 |
| kanzure | well, they fired lorenzo.. which is bad.. lorenzo does pretty good work | 12:16 |
| delinquentme | correct hes @ immune path | 12:16 |
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| delinquentme | ALL RIGHT | 12:30 |
| delinquentme | im gonna go troll /r/psychology | 12:30 |
| kanzure | wait | 12:30 |
| delinquentme | and ask specifically why they want to die | 12:30 |
| delinquentme | YAYAYAYAYA | 12:30 |
| kanzure | why? why not do some of that reading you're not doing | 12:30 |
| delinquentme | lol i did do some reading | 12:30 |
| delinquentme | im spreading the word | 12:30 |
| kanzure | o.o | 12:31 |
| archels | kanzure: How does diyhpl.us work, does it auto-aggregate papers or do you manually post? | 12:31 |
| kanzure | manually upload | 12:32 |
| delinquentme | archels, its general AI | 12:32 |
| kanzure | presumably it's slightly more currated than something that auto-aggregates, but maybe not | 12:32 |
| archels | You're the second google hit for 'neuron membrane mesh'. | 12:32 |
| kanzure | i'm a lot of hits on scholar.google.com for, ah, interesting things | 12:32 |
| archels | brining up Lassere's paper (which I already read). | 12:33 |
| AlonzoTG | =P Why is this channel called h+ roadmap when the roadmap is never discussed but rather people discuss fine-grained details of specific projects without ever arguing that they are even on-topic for transhumanism at all or what the near-term (much less long-term) goals are... | 12:33 |
| delinquentme | kanzure, was actually relocated from his flesh vessel into a more suitable home for someone changing humanity | 12:33 |
| kanzure | AlonzoTG: because the original roadmap really sucks | 12:33 |
| delinquentme | AlonzoTG, I think we're pretty on point as to "the rubber meets the road" shit | 12:33 |
| kanzure | AlonzoTG: and presumably this is an experiment in shaming me into writing a better one | 12:33 |
| AlonzoTG | What original roadmap? | 12:33 |
| archels | kanzure: Do you use mesh representations yourself (in your CAD apps)? | 12:34 |
| kanzure | delinquentme: yeh, i haven't heard that much disagreement between people who know hardware | 12:34 |
| kanzure | archels: most of the available open source "CAD" stuff is "mesh-based", | 12:34 |
| kanzure | archels: but opencascade is an example of one that is not.. so no, i try not to use tessellated meshes | 12:34 |
| archels | kanzure: I have a ball-and-stick model and would like to create a smooth mesh extrusion for it, any ideas on algorithms? | 12:35 |
| kanzure | depends on what your actual task is- what are you using the mesh for? | 12:35 |
| archels | neurons! | 12:35 |
| kanzure | AlonzoTG: so, the other day we were discussing a dna synthesizer project, do you think this is off-topic? | 12:35 |
| AlonzoTG | Maybe. | 12:35 |
| kanzure | archels: yes but.. visualization only? | 12:36 |
| kanzure | AlonzoTG: ok. any reason why? | 12:36 |
| archels | kanzure: let's stick with that for now, yes. | 12:36 |
| kanzure | archels: then it doesn't matter if it's mesh-based or not | 12:36 |
| AlonzoTG | Because it is not connected to a network of requirements that leads towards meaningful human enhancement.... | 12:36 |
| kanzure | archels: graphics cards convert everything down to triangles for visualization, so you don't need NURBS really.. | 12:36 |
| kanzure | AlonzoTG: humans are biological machines at the moment. these machines run programs based on DNA and lots of other shit. | 12:37 |
| AlonzoTG | Okay, Lets see how many question marks can be filled in: | 12:37 |
| kanzure | AlonzoTG: so being able to control your own DNA seems super-important to me.. | 12:37 |
| kanzure | but i could be wrong | 12:37 |
| kanzure | it's been known to happen | 12:37 |
| AlonzoTG | DNA synthesizer to synthesize ?????? that will be applied by ?????? to accomplish ?????? which is deemed to be a desirable human enhancement. | 12:37 |
| kanzure | DNA synthesizer synthesizes DNA | 12:38 |
| delinquentme | AlonzoTG, so anything which brings in $$ to a trans human project | 12:38 |
| delinquentme | is progress | 12:38 |
| kanzure | you can use many different (and standard) lab techniques to move this DNA into cells of all colors and types | 12:38 |
| archels | kanzure: Let me show you what I mean. I want to make this transition taper smoothly from the big to the small cylinder (so adding a single big sphere would not help). http://turingbirds.com/temp/mesh_cylinders.png | 12:38 |
| delinquentme | anything which discusses granular steps in the right direction is progress | 12:38 |
| AlonzoTG | I would be unable to use such a device because I don't have any DNA to sythesize. I don't at all discount the value of a DNA synthesizer, only that I can't use it at the moment. | 12:38 |
| delinquentme | would you agree? | 12:38 |
| kanzure | archels: loooading.... | 12:38 |
| kanzure | AlonzoTG: actually, there are publicly available genomes (including many human genomes) on NCBI's site | 12:39 |
| rkos | isn't it fairly cheap these days to just order your sequence from china or someplace? | 12:39 |
| delinquentme | AlonzoTG, and we know that there are people working on somatic cell nuclear transfer atm | 12:39 |
| kanzure | AlonzoTG: you can also sequence your own genome, and then synthesize parts that you want to fix | 12:39 |
| kanzure | rkos: sorta | 12:39 |
| kanzure | rkos: $0.35/bp for custom synthesis, $0.01/bp on a microarray if you don't care wtf comes out | 12:39 |
| kanzure | rkos: but i want a machine that i can build. and control. | 12:40 |
| delinquentme | youve got a shitty gene for liver cancer .. lets fix that .. put the fix in a stem cell and grow a solid portion of cellular material to offset the existing busted genes | 12:40 |
| kanzure | archels: weird. um. so what formats do you have for this data at the moment? | 12:40 |
| kanzure | delinquentme: right.. although it's of course a bit harder than that ;) | 12:40 |
| delinquentme | SO MUCH of the issue lies in this distinct idea that " IM OK AS I AM" | 12:40 |
| delinquentme | FUCK THAT up the ass | 12:40 |
| delinquentme | EVOLVE | 12:40 |
| delinquentme | become BETTER | 12:40 |
| kanzure | or what about these genes? | 12:40 |
| kanzure | http://diyhpl.us/~bryan/papers2/gene_doping_for_sports_enhancement.png | 12:40 |
| delinquentme | you dont still piss your pants you dont still need mommy to feed you | 12:41 |
| archels | kanzure: MATLAB matrix of (x, y, z) and faces, essentially. | 12:41 |
| kanzure | holy shit. i'm sorry man. | 12:41 |
| AlonzoTG | yeah, I agree with kanzure, actual gene therapies are MUCH harder. | 12:41 |
| kanzure | archels: so do you need some automatic way of doing this? | 12:41 |
| archels | kanzure: Yeah, I'm not going to do this by hand for all branchpoints. ;) | 12:41 |
| AlonzoTG | I'm pretty much despondent that it will work without nanotech or some way to systematically replace tissues. | 12:41 |
| archels | kanzure: The paper I mentioned above covers one method for doing this, but I was wondering if you had any ideas. | 12:42 |
| kanzure | archels: hrm hrm.. so let me think of (1) a moderately sane mesh library, and (2) something that will have a good tapering function | 12:42 |
| kanzure | archels: openscad, cgal, opencascade, blender all have things to do tapering like this | 12:42 |
| kanzure | you should find a matlab plugin to export your data to .stl | 12:42 |
| archels | kanzure: Automated, too? | 12:43 |
| archels | (scriptable) | 12:43 |
| kanzure | or you can write your own .stl exporter- the file format is pretty easy | 12:43 |
| kanzure | yes, all of these options are scriptable | 12:43 |
| delinquentme | AlonzoTG, kanzure i guess Im missing out on what falls short in replacing busted cells in organs? | 12:43 |
| kanzure | if you ultimately choose blender, there's a headless mode where you can run scripts, but the main "use mode" is the blender ui for animators to sit around cleaning up meshes | 12:43 |
| delinquentme | what am I missing ? | 12:43 |
| rkos | might it everr be possible to get rid of the common cold by designing a completely new system of various proteins into your cells which can scan for virus dna/rna signatures and jam them/mark them for destruction | 12:43 |
| archels | kanzure: Any preference as to which of those four tools I should check up first? | 12:43 |
| archels | (open source would be nice) | 12:43 |
| rkos | then you'd occasionally just have to get virus signature updates into your genome | 12:44 |
| kanzure | AlonzoTG: you don't need nanotech to do gene therapy | 12:44 |
| kanzure | rkos: i'm not that familiar with the common cold, are there known cell markers for it? | 12:44 |
| AlonzoTG | Furthermore, I am concerned that the benefits from simple gene therapies will almost never justify the costs unless you are making a significantly long jump in your genetic capabilities; such a long jump would require an integration of chemical/physics/biology/nanotech/compsci that are so vastly beyond my capabilities that I feel that my best choice is to focus on build a lever big enough to move the problem: AI. | 12:44 |
| kanzure | rkos: you wouldn't send updates to your genome for that.. the immune system doesn't work like that | 12:45 |
| rkos | well i think its the rhinovirus that causes it and it keeps mutating so fast that your natural immune system cant recognize it for more than a few weeks or something like that | 12:45 |
| kanzure | rkos: your immune system includes lots of stuff that is not passed down to your offspring in your germline cells | 12:45 |
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| kanzure | this is why you can "train" someone's immune system, and see how vaccinations work, etc.. | 12:46 |
| * archels stumbles across the marching cubes algorithm | 12:46 | |
| rkos | yes i dont mean the bodys immune system, i just thought you could include a different immune system inside the cells | 12:46 |
| kanzure | archels: all of the options i listed are open source | 12:46 |
| kanzure | archels: honestly, you shouldn't have to implement your own tapering algorithm | 12:46 |
| kanzure | archels: you should look up tapering in cgal/openscad first.. if that fails, look it up in opencascade/pythonocc; and if *that* fails, then blender will definitely have it. | 12:47 |
| rkos | the way you have some proteins checking dna for mistakes couldn't you have some proteins checking the dna that gets into the cell for some sequences that can be identified to come from a virus | 12:47 |
| archels | kanzure: Will do, thankies. | 12:47 |
| kanzure | rkos: there's a lot of protein engineering problems that would have to be solved | 12:47 |
| kanzure | rkos: but in addition to this, how do you know that the dna is "bad"? most viruses use some very simple proteins | 12:48 |
| kanzure | it's just that, in their specific combination, they are the worst | 12:48 |
| kanzure | so how would you "remember" that there's been gene x, y and z recently produced, and not to produce gene w which might indicate a virus has infected the cell, etc. | 12:48 |
| kanzure | especially since gene x, y and z were probably copied/built by a different polymerase/ribosome somewhere, etc. etc. | 12:49 |
| rkos | well i heard about people spotting fragments of virus dna in our own genome, so i thought theres something about virus dna that makes it possible for us at least to spot it | 12:49 |
| rkos | how a protein would do it though i have no idea | 12:49 |
| kanzure | it's possible for /us/ to spot parts of virus genomes because we have large databases to query against | 12:50 |
| kanzure | but the immune system itself just recognizes the shape and structure of virus capsids | 12:50 |
| kanzure | also, have a dose of crazy science: | 12:51 |
| kanzure | http://diyhpl.us/~bryan/papers2/AFM/ViriChip%20-%20a%20solid%20phase%20assay%20for%20detection%20and%20identification%20of%20viruses%20by%20atomic%20force%20microscopy.pdf | 12:51 |
| kanzure | and http://diyhpl.us/~bryan/papers2/AFM/Imaging%20of%20viruses%20by%20atomic%20force%20microscopy.pdf | 12:51 |
| eudoxia | is there anything atomic force microscopes _can't_ do? | 12:52 |
| rkos | the US should put a good part of its defense budget into fighting viruses instead | 12:52 |
| AlonzoTG | =( | 12:53 |
| Urchin | did they get it to move atoms? | 12:53 |
| rkos | few things are more annoying than a rhinovirus | 12:53 |
| AlonzoTG | Unfortunately, they're creating bio-weapons. =((( | 12:53 |
| delinquentme | eudoxia, find me pener | 12:54 |
| delinquentme | =/ | 12:54 |
| kanzure | Urchin: yes you can move atoms with an afm.. just, in bulk | 12:54 |
| delinquentme | lulz | 12:54 |
| AlonzoTG | http://boundarytech.com/bi/articles/Physics_without_Causality.pdf | 12:54 |
| kanzure | delinquentme: you might enjoy this one.. http://diyhpl.us/~bryan/papers2/AFM/Single%20cell%20transfection%20using%20plasmid%20decorated%20AFM%20probes%20-%2030%20percent%20efficiency.pdf | 12:54 |
| delinquentme | i recently saw a document talking about AFMs resolving a single carbon hexagonal mesh | 12:54 |
| delinquentme | it was brewtiful | 12:54 |
| rkos | problem is that even if we can identify viruses with our technology the viruses keep mutating so fast that there's never going to be any fool proof way of targeting them | 12:55 |
| rkos | interesting paper though | 12:55 |
| kanzure | that's why you have a learning immune system. | 12:56 |
| delinquentme | so this is like another option other than electroporation? | 12:56 |
| kanzure | delinquentme: yes, it's called "stab the fucking cell with your fucking plasmid" | 12:57 |
| delinquentme | lololol | 12:57 |
| delinquentme | "forcibly introduced" | 12:57 |
| kanzure | yes | 12:57 |
| delinquentme | rkos, but this idea that viruses will always lead the game is | 12:57 |
| delinquentme | limited | 12:57 |
| kanzure | delinquentme: here's the same thing, except for a human stem cell | 12:58 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/High-efficiency%20DNA%20injection%20into%20a%20single%20human%20mesenchymal%20stem%20cell%20using%20a%20nanoneedle%20and%20atomic%20force%20microscopy.pdf | 12:58 |
| delinquentme | do you know about the experiments basically pitting viral evolution against one another in a graduated field | 12:58 |
| delinquentme | kanzure, can you make a new technique | 12:58 |
| delinquentme | and call the process "DNA STABBING" | 12:59 |
| delinquentme | that'd b aweso | 12:59 |
| delinquentme | cite 50 cent in the refs | 12:59 |
| kanzure | delinquentme: yeah, "directed evolution".. right? | 12:59 |
| delinquentme | :P~ | 12:59 |
| delinquentme | kanzure, something like that .. but i think directed evolution is more of a broad term | 12:59 |
| kanzure | on a related note, there was also a paper that explored single-plasmid PCR | 13:00 |
| delinquentme | this specific one was basically pit viruses in a crazy war and so long as they stay isolated we're running ahead of the curve | 13:00 |
| kanzure | http://diyhpl.us/~bryan/papers2/bio/Recovery%20and%20amplification%20of%20plasmid%20DNA%20with%20AFM%20and%20PCR%20-%20single-plasmid%20PCR.pdf | 13:00 |
| kanzure | so you can both copy a plasmid on your afm tip and inject it into cells. | 13:00 |
| delinquentme | kanz i like how elsevier papers are free | 13:00 |
| delinquentme | :D | 13:00 |
| kanzure | eh? | 13:01 |
| kanzure | AlonzoTG: what costs are you talking about? money? or "risk-related" "costs" | 13:03 |
| AlonzoTG | risk. | 13:04 |
| AlonzoTG | I mean you aren't going to get a 100% conversion with these techniques, | 13:04 |
| AlonzoTG | and, you won't be 100% done after your first change. | 13:04 |
| kanzure | the original issue was that you didn't know what you can do with DNA | 13:04 |
| AlonzoTG | so you'll end up with lots and lots of different genomes. | 13:04 |
| AlonzoTG | Not exactly, | 13:05 |
| delinquentme | ok switching off brb | 13:05 |
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| kanzure | not "If i was going to try gene therapy, i would not get 100% cell transfection/transformation" | 13:05 |
| kanzure | you usually just inject a plasmid with your target gene + an antibiotic resistance gene, and then you kill the rest of the cells | 13:05 |
| AlonzoTG | It's just that DNA synthesis is a few hundred miles away from a practical treatment and even further from interesting forms of transhumanism. | 13:05 |
| kanzure | cells that did not get antibiotic resistance gene then die when you do the selection step of the transfection protocol | 13:06 |
| archels | AlonzoTG: What is your point? Should we stop developing the technology? | 13:06 |
| AlonzoTG | not at all, | 13:06 |
| AlonzoTG | All technologies are perfectly worthy to be developed. | 13:06 |
| AlonzoTG | It's just I can't see any way to use it for anything. | 13:07 |
| kanzure | AlonzoTG: 100 miles away? there are many things that are immediately applicable, like curing color blindness | 13:08 |
| kanzure | AlonzoTG: http://diyhpl.us/~bryan/papers2/bio/Emergence%20of%20novel%20color%20vision%20in%20mice%20engineered%20to%20express%20a%20human%20cone%20photopigment.pdf | 13:08 |
| archels | AlonzoTG: So you feel that only *current* technology should be discussed in a transhumanism channel? | 13:08 |
| AlonzoTG | okay, that's wonderful for ppl with color blindness. | 13:08 |
| archels | maybe we should just rename ourselves #magnetsinfingers | 13:08 |
| AlonzoTG | =P | 13:08 |
| kanzure | AlonzoTG: yes but, you don't see infrared; so if you want infrared vision, this is applicable | 13:09 |
| AlonzoTG | That would clear up quite a bit of confusion. | 13:09 |
| eudoxia | oh not lepht anonym | 13:09 |
| eudoxia | I sense a shitstorm on the horizson | 13:09 |
| eudoxia | horizon* | 13:09 |
| archels | god dammit kanzure stop dangling this carrot in front of my face | 13:09 |
| kanzure | archels: hrm? your marching cube algorithm is going to suck anyway man ;) | 13:09 |
| archels | :( | 13:09 |
| archels | kanzure: Any idea what software this is? (just out of curiosity) http://api.ning.com/files/NFcL64Dhixe*6slwkGTyhY8zV6aanouHenqTV7tmfmC8gOMd*xz*74WDL-tbZ1updfKWUIN3iTc6pRNuJD1m-WKZdxrg8fRh/NeuronMetaballslices.png | 13:10 |
| kanzure | possibly blender on the left | 13:10 |
| archels | specifically on the right | 13:11 |
| kanzure | labview? | 13:11 |
| kanzure | nope.. | 13:11 |
| archels | Seems like you can make pretty fancy pipelines with it, whatever it is. | 13:12 |
| eudoxia | I think blender lets you make those pipelines | 13:12 |
| eudoxia | though I've never seen them looking like that | 13:13 |
| kanzure | "Reference curves from Rhino" might refer to Rhino3d | 13:13 |
| eudoxia | the left isn't blender, the axes aren't right | 13:13 |
| kanzure | archels: how did you generate your mesh data anyway? | 13:14 |
| archels | kanzure: Just geometrical primitives, although I'm basing it on neuron data from ModelDB. | 13:15 |
| kanzure | i see | 13:15 |
| kanzure | i think NEURON visualizes modeldb data | 13:15 |
| archels | yes, but it looks like absolute crap. | 13:16 |
| archels | All NEURON knows is cylinders. | 13:16 |
| kanzure | superkuh: any ideas? | 13:16 |
| kanzure | oh there was a recent markram paper that released some visualization tool, right? | 13:16 |
| kanzure | http://diyhpl.us/~bryan/papers2/neuro/A%20neuron%20membrane%20mesh%20representation%20for%20visualization%20of%20electrophysiological%20simulations%20-%20Markram%20-%202012.pdf | 13:16 |
| kanzure | feb 2012 | 13:17 |
| archels | Yes, that's the one where you're Google hit #2. ;) | 13:17 |
| kanzure | look on the right here- | 13:20 |
| kanzure | http://people.epfl.ch/154037 | 13:20 |
| kanzure | sebastien.lasserre@epfl.ch | 13:21 |
| kanzure | just call him up.. [+0041] 76 530 21 90 | 13:21 |
| kanzure | it's only 10:21pm where he is.. he's probably awake | 13:22 |
| archels | Why would I want to call him? | 13:25 |
| kanzure | to ask him for his code | 13:25 |
| archels | I'm not actually sure I want to use his method. | 13:26 |
| archels | It could come in handy, but I can always e-mail him later. | 13:26 |
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| archels | kanzure: Looking at metaballs now. | 13:34 |
| archels | alright, saving the rest for tomorrow. Night! | 13:37 |
| kanzure | seeya | 13:38 |
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| Mariu | see you guys | 13:47 |
| kanzure | hi _0bitcount | 13:47 |
| _0bitcount | Hello kanzure | 13:47 |
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| kanzure | lianchao han recommended this in 2010: | 15:31 |
| kanzure | High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing | 15:31 |
| kanzure | Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips | 15:31 |
| kanzure | don't think i grabbed those pdfs yet.. | 15:32 |
| kanzure | nope i'm wrong | 15:33 |
| kanzure | http://diyhpl.us/~bryan/papers2/DNA/High-fidelity%20gene%20synthesis%20by%20retrieval%20of%20sequence-verified%20DNA%20identified%20using%20high-throughput%20pyrosequencing%20-%202010.pdf | 15:33 |
| kanzure | http://en.wikipedia.org/wiki/Picotiter_plate | 15:37 |
| kanzure | "The picotiter plate platform enables parallel sequence analysis of 1.7 million of separate DNA fragments and thus is capable of sequencing entire genomes within a couple of hours." | 15:37 |
| kanzure | pictotiter plate image: http://www.ikmb.uni-kiel.de/cms/uploads/pics/pico_titer_plate_01.png | 15:38 |
| kanzure | i see. so they insert beads into each well plus polymerase and some other stuff for sequencing enzymes | 15:39 |
| kanzure | "454 Sequencing uses a large-scale parallel pyrosequencing system capable of sequencing roughly 400-600 megabases of DNA per 10-hour run on the Genome Sequencer FLX with GS FLX Titanium series reagents" | 15:40 |
| kanzure | "Each DNA-bound bead is placed into a ~29 μm well on a PicoTiterPlate, a fiber optic chip" | 15:40 |
| kanzure | "enzymes such as DNA polymerase, ATP sulfurylase, and luciferase" ok typical pyrosequencing | 15:41 |
| kanzure | i wonder how much a picotiter plate costs | 15:42 |
| kanzure | https://www.roche-applied-science.com/servlet/RCProductDisplay?storeId=10202&catalogId=10202&langId=-1&countryId=us&forCountryId=us&productId=3.8.8.2.3.1 | 15:53 |
| kanzure | bleh "call for pricing information" | 15:53 |
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| delinquentme | ok todays WTF moment | 16:00 |
| delinquentme | ACT advanced cell technologies did a reverse merger with a utah based company called Two Moons Kachinas | 16:01 |
| delinquentme | which sold native american dolls... | 16:01 |
| delinquentme | ???? | 16:01 |
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| delinquentme | nice! http://www.cirm.ca.gov/ | 16:06 |
| delinquentme | hitting these guys up! | 16:06 |
| kanzure | "David joined Xeotron in March, 2001, from Motorola Life Sciences were he was the Sr. Manager, Business and Market Development. He was responsible for the Business Unit's strategic alliances & acquisition, licensing, equity investment and collaborations." | 16:10 |
| kanzure | "Motorola Life Sciences"? | 16:10 |
| kanzure | delinquentme: yeh they have a few billion that california voted for back in 2007 or something | 16:11 |
| delinquentme | yeh! | 16:11 |
| delinquentme | reading this bamf article about ACT atm | 16:11 |
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| delinquentme | does it piss anyone else off that bioethicists exist? | 16:13 |
| delinquentme | seriously | 16:13 |
| delinquentme | who the F are you to say that your moral compass is any better than someone elses | 16:13 |
| kanzure | "He was most recently Director of Applied Genomics and BioInformatics at Motorola Life Sciences and Chairman of the SNP Consortium's Scientific Management Committee. Prior to Motorola, Dr. Wang was head of human genetics at Bristol-Myers Squibb (BMS)" | 16:13 |
| kanzure | the existence of motorola life sciences really confuses me | 16:14 |
| delinquentme | motorola life sciences??? | 16:14 |
| kanzure | was this included in google's recent acquisition of motorola? | 16:14 |
| delinquentme | @_@ | 16:14 |
| kanzure | wtf | 16:14 |
| delinquentme | state of the art | 16:15 |
| delinquentme | in 98 | 16:15 |
| kanzure | aha | 16:15 |
| kanzure | "Founded as a unit of Motorola in 1998. They have sold off the CodeLink unit to Amersham Biosciences, but are currently keeping the eSensor group (in Pasadena) (10/2002). It now appears that this group no longer exists as a separate entity." | 16:15 |
| delinquentme | beat u to it :D | 16:15 |
| delinquentme | sounds like they're mfg things to use in something like that tricoder | 16:15 |
| delinquentme | Motorola Life Sciences (MLS), a business unit of Motorola, Inc., develops products that enable scientists and healthcare professionals to quickly and accurately analyze DNA, RNA and proteins from living cells. | 16:16 |
| kanzure | nate's old prof's dna synthesizer did 3min/bp apparently | 16:16 |
| kanzure | so +1bp/min should be doable these days | 16:16 |
| kanzure | ok i don't get it. xeotron made this microfluidic picoarray dna synthesizer in 2003ish | 16:18 |
| kanzure | had $45mil in sales | 16:18 |
| kanzure | got bought by invitrogen. and now no such product is on the market. | 16:18 |
| kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Synthesis%20-%20Microfluidic%20PicoArray%20synthesis%20of%20oligodeoxynucleotides%20and%20simultaneous%20assembling%20of%20multiple%20DNA%20sequences%20(10%20kb).pdf | 16:18 |
| kanzure | warning: this paper is written very poorly | 16:18 |
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| kanzure | hrm it would be fun if we could do DMD photolithography for DNA synthesis, and pyrosequencing in the same well | 16:26 |
| kanzure | the wash step complicates things.. | 16:26 |
| delinquentme | umm | 16:32 |
| delinquentme | if you could gather a group of individuals who are willing to donate gametes for embryonic stem cell research | 16:32 |
| delinquentme | would you effectively be able to bypass laws ? | 16:33 |
| kanzure | bleh you don't need embryonic stem cells, | 16:33 |
| kanzure | just use pluripotent stem cells. | 16:33 |
| delinquentme | they're not there yet | 16:33 |
| kanzure | embryonic stem cells are useful because they are pluripotent | 16:33 |
| kanzure | that's the whole point | 16:33 |
| kanzure | you can induce pluripotency: http://en.wikipedia.org/wiki/Induced_pluripotent_stem_cells | 16:34 |
| kanzure | http://diyhpl.us/~bryan/papers2/stem-cells/ | 16:34 |
| kanzure | ok so the xeotron thing.. looks like they only had a few thousand wells at most. a picoliter array should do millions of wells simultaneously, imo | 16:37 |
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| delinquentme | kanzure, but the embryonic stem cells are less problematics than IPPs | 16:43 |
| kanzure | anyone know if photomasked-based dna synthesis can occur in water exposed to atmosphere? | 16:48 |
| kanzure | it would make micropipette actuation and picking of beads from wells pretty easy.. | 16:49 |
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| delinquentme | messing with the expressions of a single gene would be done how in a worm model? | 17:13 |
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| kanzure | delinquentme: it depends on how that gene is expressed, no? | 17:24 |
| kanzure | like if it has another gene that serves as a promoter | 17:24 |
| kanzure | you would copy-and-paste that gene some more heh | 17:30 |
| delinquentme | YES | 17:32 |
| delinquentme | lol | 17:32 |
| delinquentme | kanz you've got logs of this channel right? | 17:33 |
| delinquentme | systems biology break down of yeast aging models: http://ouroboros.wordpress.com/2009/02/04/systems-biology-of-aging-understanding-yeast-cr-by-network-inference/ | 17:33 |
| delinquentme | #HotShit | 17:33 |
| jrayhawk | in the topic, even | 17:33 |
| delinquentme | Yeah I was looking for a general log | 17:33 |
| delinquentme | bc it would be handy to have a dump area | 17:33 |
| delinquentme | and i could just re search that shit | 17:33 |
| kanzure | there's the .tar.gz backup | 17:34 |
| delinquentme | kanzure, >> https://www.destroyallsoftware.com/talks/wat | 17:39 |
| kanzure | yes i saw it.. | 17:39 |
| delinquentme | kanz you dont have the logs as public? | 17:39 |
| kanzure | delinquentme: http://gnusha.org/logs/ | 17:39 |
| kanzure | hrm, i need a polymerase with a conformational change switching between "capture a nucleotide & wait (no incorporation)" v. "polymerize (non-accepting)".. | 17:42 |
| kanzure | the "non-accepting" state is easy: mess up the finger motif (or whatever motif is responsible for accepting new nucleotides) | 17:44 |
| kanzure | the "no-polymerization" state is harder.. you need it to capture a nucleotide, and then wait. iirc the default is more like "nuleotide floats around, polymerase may or may not icorporate it" | 17:45 |
| kanzure | but if that much can be accomplished, you can use pyrosequencing and have light generated after polymerase incorporates a nucleotide (like if you're using phospholinked dNTPs.. which, i guess, would also be photocleavably-capped ugh) | 17:53 |
| kanzure | damn. pacbio mutated ΦDNA polymerase to better-accept their phospholinked dNTPs.. | 17:58 |
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| * delinquentme passes the joint to kanzure | 18:05 | |
| delinquentme | so. | 18:05 |
| delinquentme | if open source software is to become more prevalent ( safe assumption ) | 18:06 |
| delinquentme | we've got more specific tailored languages ( in this example S lang for R ) | 18:06 |
| delinquentme | there should be TONS of value in the ability to stitch particular programs together noe? | 18:06 |
| delinquentme | im looking at this statistics package designed by this bigwig @ stanford | 18:07 |
| delinquentme | for SVMs | 18:07 |
| kanzure | haha animations.. http://www.youtube.com/watch?v=TC2mYWR8754 | 18:07 |
| delinquentme | huge benefits of getting something like that to jive turkey with python.. or other languages which are used in bio | 18:07 |
| kanzure | sure.. that's why there's horrible things like "swig" | 18:07 |
| delinquentme | but what inherently about it is horrible? | 18:08 |
| delinquentme | does this not sound akin to specialization within a task? | 18:08 |
| delinquentme | big companies hire specilists | 18:08 |
| delinquentme | specialists**** | 18:08 |
| kanzure | what? | 18:09 |
| kanzure | swig is a wrapper generator | 18:09 |
| kanzure | http://www.swig.org/ | 18:09 |
| kanzure | "SWIG is used with different types of target languages including common scripting languages such as Perl, PHP, Python, Tcl and Ruby. The list of supported languages also includes non-scripting languages such as C#, Common Lisp (CLISP, Allegro CL, CFFI, UFFI), D, Go language, Java, Lua, Modula-3, OCAML, Octave and R." | 18:09 |
| eudoxia | it gives me shit when trying to generate bindings for the GSL though | 18:10 |
| kanzure | gsl? | 18:10 |
| eudoxia | what bullshit | 18:10 |
| eudoxia | GNU scientific library | 18:10 |
| kanzure | you sometimes have to fix their header files | 18:10 |
| kanzure | by 'their' header files i mean 'your target library' :/ | 18:10 |
| eudoxia | :( | 18:10 |
| eudoxia | that is when when using the library or when generating it? (ie editing the module file) | 18:11 |
| kanzure | you write some stuff first, then you call swig on the stuff you wrote | 18:11 |
| kanzure | oh right they call it their "swig interface file" | 18:11 |
| kanzure | delinquentme: this what you're looking for? | 18:11 |
| delinquentme | eudoxia, you're working w swig? | 18:12 |
| eudoxia | delinquentme, I was trying to generate Common Lisp bindings for the GSL but gave up. typically, my solution was "start working on a VM with my own FFI" | 18:13 |
| eudoxia | because it's not like I have better things to do | 18:13 |
| kanzure | heh | 18:13 |
| delinquentme | kanzure, im saying offload statistical tasks to programs which are designed for statistical tasks | 18:14 |
| delinquentme | head hurts | 18:14 |
| kanzure | ah ok. so "R packages except as shell commands" | 18:14 |
| kanzure | *shell-accessible executables | 18:14 |
| delinquentme | brb | 18:15 |
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| kanzure | huh, someone has used an aptamer to block polymerase activity | 18:23 |
| kanzure | http://www.google.com/patents/US20110104678? | 18:23 |
| kanzure | "The polymerase inhibitors provide a double stranded nucleic acid portion that is recognized by a polymerase enzyme as a template for extension but is incapable of being extended by the polymerase enzyme. The polymerase binds to the polymerase inhibitor which sequesters the enzyme until the temperature achieves a level that denatures the double stranded portion of the inhibitor after which the polymerase is released and can then catalyze nucleic ac | 18:23 |
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| kanzure | http://www.sanken.osaka-u.ac.jp/labs/smbio/sanken/ronbun_pdf/2007LamLabChip.pdf | 18:56 |
| kanzure | page 2 figure 1b | 18:56 |
| kanzure | is a λDNA enzyme trapped in a femtoliter bubble | 18:57 |
| kanzure | erm wait | 18:58 |
| kanzure | why did i say enzyme :( | 18:59 |
| yashgaroth | λDNA | 18:59 |
| yashgaroth | + enzyme | 18:59 |
| kanzure | yes but obv. you aren't going to see an enzyme at 10 micron resolution | 18:59 |
| yashgaroth | I'm surprised they can see the lambda genome | 19:00 |
| kanzure | i think it was fluorescently labelled somehow | 19:01 |
| yashgaroth | oh right sybr stain | 19:01 |
| kanzure | why is a droplet with a diameter of 17 microns considered to be 'femtoliter' volume? | 19:04 |
| kanzure | isn't the volume more like 2500ish cubic microns | 19:05 |
| yashgaroth | ~5000 femtoliters | 19:05 |
| kanzure | oops. 1 cubic micron =~ 1 femtoliter | 19:08 |
| delinquentme | does this webpage flicker on and off for anyone else? v | 19:16 |
| delinquentme | http://blog.griddynamics.com/2010/03/apache-hadoop-on-amazon-ec2.html | 19:16 |
| delinquentme | in chrome | 19:16 |
| kanzure | so far no | 19:17 |
| kanzure | i'll stare at it for a few hours and let you know? | 19:17 |
| delinquentme | hmm | 19:17 |
| delinquentme | its cool | 19:17 |
| delinquentme | are you on ubuntu? | 19:18 |
| delinquentme | i get this weird behavior sometimes and usually its on websites which google runs | 19:18 |
| delinquentme | i blame it on too much integration | 19:18 |
| kanzure | i hate how i keep running into papers that show up on diyhpl.us | 19:20 |
| kanzure | delinquentme: i am on debian | 19:20 |
| delinquentme | kanzure, any HQ existential / machine animes you have links to on youtube? | 19:24 |
| delinquentme | serial experiments lain is stuck @ 50% | 19:24 |
| kanzure | delinquentme: http://diyhpl.us/~bryan/irc/fenn.anime.txt | 19:26 |
| delinquentme | lololol | 19:27 |
| delinquentme | fenn, this is awesome | 19:27 |
| delinquentme | kanzure, you dont happen to have pickup shit stashed do you? | 19:27 |
| kanzure | pua? i don't remember. probably not. | 19:28 |
| delinquentme | thats prob about the only unfilled spot I could contribute to | 19:28 |
| delinquentme | but this list is awesome | 19:28 |
| delinquentme | theres one 4 chan post which really stuck out for me | 19:28 |
| delinquentme | chobits! | 19:29 |
| delinquentme | lol | 19:29 |
| delinquentme | there are two akiras? | 19:30 |
| delinquentme | where can I find this blame anime? | 19:38 |
| kanzure | it's a manga. i think there was an animation but i haven't seen it / confirmed its existence | 19:39 |
| kanzure | one sec.. | 19:39 |
| JayDugger | OT: Blame! had an anime. | 19:40 |
| JayDugger | I have a copy. | 19:40 |
| JayDugger | Stick with the manga. | 19:40 |
| kanzure | http://www.manga2u.com/BLAME/ | 19:40 |
| kanzure | oh he was kind enough to dump it into /torrents/images/manga/blame/ | 19:41 |
| JayDugger | On what server? | 19:42 |
| kanzure | the server under jrayhawk's toilet | 19:42 |
| JayDugger | Heh. | 19:42 |
| delinquentme | ahhh | 19:43 |
| delinquentme | well | 19:43 |
| delinquentme | is there a movie? | 19:43 |
| delinquentme | bc id prefer the moving pictures featured in technicolor | 19:44 |
| JayDugger | Of Blame! ? | 19:44 |
| kanzure | delinquentme: i suggest you start reading at http://www.manga2u.com/BLAME/9/01/ | 19:44 |
| kanzure | wait what | 19:44 |
| delinquentme | yeah | 19:44 |
| delinquentme | ive got issues with old media | 19:45 |
| kanzure | why is this colored o.o | 19:45 |
| delinquentme | i dont really care to explain | 19:45 |
| JayDugger | You can buy the video on DVD from Amazon. It has a 37 minute run time. | 19:46 |
| kanzure | delinquentme: it's worth it.. | 19:46 |
| kanzure | not the dvd though. don't know how bad that is. | 19:46 |
| delinquentme | i LOVE the concepts | 19:46 |
| delinquentme | but I'm looking for videos :D | 19:47 |
| JayDugger | Ehh...about 50¢ / minute. What worth has your time? | 19:47 |
| kanzure | $3/min | 19:47 |
| kanzure | is the going market rate | 19:47 |
| JayDugger | Then no, don't buy a copy. | 19:47 |
| kanzure | huh? so the idea is to only purchase content that costs as much to watch as it is for me to.. erm.. | 19:48 |
| JayDugger | No, the idea is to use the cost of buying content as a proxy for its worth to you. This can help conserve your attention. | 19:50 |
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| JayDugger | This assumes the price and the value of the content have something to do with each other. | 19:50 |
| kanzure | conserve.. attention? why do you need to conserve a non-scarce resource? | 19:50 |
| JayDugger | Obviously not always the case. | 19:50 |
| JayDugger | Individual attention is scarce. Human attention, no, not really. | 19:51 |
| delinquentme | ok so the manga is better than I expected | 19:51 |
| delinquentme | im at /1/01 not 9 ... it said 9 isnt there kanzure | 19:52 |
| kanzure | yeah that's very odd. | 19:52 |
| delinquentme | http://www.mangatoyou.com/BLAME/9.1/01/ | 19:54 |
| kanzure | this isn't what i remember | 19:55 |
| kanzure | it wasn't in color | 19:55 |
| delinquentme | thats just the first few pages | 20:01 |
| kanzure | heh google scholar inclusion checklist http://support.google.com/scholar/bin/request.py?hl=en | 20:05 |
| kanzure | "All article URLs can be read by any user without a login or payment" | 20:05 |
| kanzure | http://scholar.google.com/intl/en/scholar/inclusion.html | 20:05 |
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| kanzure | can anyone get me this? http://pubs.rsc.org/en/Content/ArticleLanding/2011/LC/c0lc00577k | 20:09 |
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| delinquentme | http://www.sciencemag.org/content/334/6062/1518 | 20:12 |
| delinquentme | ^^ can i get this ?D | 20:12 |
| kanzure | mitzenmacher? | 20:13 |
| kanzure | the stats prof is named mitzenmacher? | 20:13 |
| delinquentme | reshef | 20:13 |
| delinquentme | yeah | 20:13 |
| delinquentme | hes on there as well | 20:13 |
| yashgaroth | heh | 20:14 |
| kanzure | he might as well change his name to mixandmatcher | 20:14 |
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| delinquentme | OOC is research which is performed in say .. italy | 20:27 |
| delinquentme | looked upon as valid as research which is performed at say MIT here in the states? | 20:28 |
| delinquentme | im looking at this thing: http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&arnumber=5702936 | 20:28 |
| delinquentme | and im just like @_@ | 20:28 |
| delinquentme | grab bag of cool tech? | 20:28 |
| delinquentme | http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&arnumber=5702936 "Application of Evolutionary Game Theory on stem cells interaction in bio-active scaffolds" | 20:30 |
| delinquentme | derp! | 20:31 |
| kanzure | yashgaroth: have you seen LED-assisted transfection? | 20:48 |
| kanzure | yashgaroth: http://diyhpl.us/~bryan/papers2/bio/Violet%20diode-assisted%20photoporation%20and%20transfection%20of%20cells.pdf | 20:48 |
| yashgaroth | nope, lemme take a look | 20:49 |
| yashgaroth | looks impossible to use in vivo, but perfect for that nanoscale chip transfection stuff | 20:52 |
| yashgaroth | I'm telling you, electrotransfer is the way to go for in vivo stuff | 20:54 |
| kanzure | i have a thing for papers like that one.. "very standard thing used to do very cool thing" | 20:54 |
| yashgaroth | it's like "we have electro, sono, chemo, viral and kinetic transfection, why not photo" | 20:56 |
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| kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/synthesis/Optical%20tweezers%20directed%20one-bead%20one-sequence%20synthesis%20of%20oligonucleotides.pdf | 21:20 |
| kanzure | too bad it requires such a huge optical tweezer setup | 21:21 |
| kanzure | otherwise it's a cool approach to dna synthesis | 21:21 |
| kanzure | two streams. one stream is just a cleaning solution. the other one has your reagents | 21:21 |
| kanzure | then you move the bead between one stream and the other | 21:21 |
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| yashgaroth | so what types of sequences do you want that can't come from an existing genome? | 21:31 |
| kanzure | there are many existing genomes that i don't have access to. | 21:32 |
| yashgaroth | such as | 21:32 |
| kanzure | yours | 21:32 |
| kanzure | stuff listed on ncbi | 21:32 |
| yashgaroth | pretty much all the important bits in my genome are the same as yours | 21:33 |
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| Mariu | hey guys | 21:36 |
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| delinquentme | Mariu, howwwday! | 21:42 |
| delinquentme | word to the christ child bio_boris | 21:43 |
| delinquentme | ololol | 21:43 |
| delinquentme | sorry im now subscribed to r/ratheism | 21:43 |
| Mariu | hey delinquentme | 21:43 |
| delinquentme | watching afro samurai | 21:51 |
| delinquentme | am i settling? | 21:51 |
| kanzure | can i convince you to work on things possibly | 21:56 |
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| sylph_mako | fyi I just checked and /r/ratheism isn't a thing. | 22:34 |
| yashgaroth | that place is nearly as much a circlejerk as /r/politics | 22:35 |
| sylph_mako | I unsubscribed twice. | 22:36 |
| yashgaroth | you're sure you don't want to see a jpeg of a famous atheist with one of their quotes overlaid? | 22:37 |
| yashgaroth | perhaps a fictional facebook conversation or two? | 22:37 |
| sylph_mako | It was the straw-manning that got to me. | 22:38 |
| sylph_mako | At least with facebook conversations the subject is a real person. | 22:38 |
| sylph_mako | http://www.reddit.com/r/RepublicOfAtheism/ this place is probably never going to be as bad. | 22:38 |
| sylph_mako | Not much gets posted there. | 22:38 |
| sylph_mako | It is as it should be.' | 22:38 |
| kanzure | why are you people using reddit? | 22:43 |
| kanzure | stop that. that's how bad things like reddit happen. | 22:43 |
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| yashgaroth | but it's like watching a friend slowly succumb to crack addiction while simultaneously being run over by a car | 22:44 |
| yashgaroth | and then making a shitty rage comic about it | 22:45 |
| yashgaroth | as a thousand other people cheer him on | 22:47 |
| sylph_mako | There are plenty of uninfected subreddits where you can avoid all of that shite. | 22:49 |
| yashgaroth | okay I'm no good at similes but you get the idea | 22:49 |
| yashgaroth | yes but the default frontpage makes me want to claw my eyes out | 22:49 |
| klafka | hahaha | 22:56 |
| klafka | ssssh kanzure | 22:56 |
| kanzure | deliquentme: you should do a video of LH001 actually doing something | 23:05 |
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