| --- Log opened Tue Apr 16 00:00:59 2013 | ||
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| eleitl | paperbot: https://www.thieme-connect.com/ejournals/abstract/10.1055/s-0029-1241052?locale=de&LgSwitch=1 | 02:04 |
|---|---|---|
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/4ccedcae07582dec6309205affd7e388.txt | 02:04 |
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| superkuh | paperbot: http://www.nature.com/nphys/journal/v9/n4/full/nphys2560.html | 03:33 |
| paperbot | HTTP 401 unauthorized http://www.nature.com/nphys/journal/v9/n4/pdf/nphys2560.pdf | 03:33 |
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| eleitl | what are you doing with knotted vortices? | 04:00 |
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| chido | I need to order pipettes for my lab, has anyone a suggestion where to get them as cheap as possible? | 04:23 |
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| superkuh | Absolutely nothing. I thought it was an aesthetically interesting paper. | 04:32 |
| eleitl | Ah, thanks. | 04:38 |
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| eleitl | Anyone looked into new alternatives to Bitcoin? | 05:33 |
| chris_99 | the litecoin thing? | 05:34 |
| chris_99 | theres also zerocoin which sounds interesting, an add-on to bitcoin | 05:35 |
| eleitl | what do you think about PPCoin? | 05:36 |
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| eleitl | I'm looking for something with an improvement, or a different target. | 05:36 |
| eleitl | I'm not sure Litecoin is that different. | 05:36 |
| chris_99 | not heard PPCoin, the bitcoin price has dropped a lot lower now :( | 05:37 |
| eleitl | They claim their hash is ASIC-proof, but already you need a GPU to mine it | 05:37 |
| eleitl | yeah, I'm going to buy another couple BTC | 05:37 |
| chris_99 | ASIC-proof, that sounds a bit weird | 05:37 |
| eleitl | they try to level the playing field | 05:38 |
| eleitl | you can ASIC-proof e.g. by way of a large lookup-table | 05:38 |
| eleitl | or just a lot of evolving state, more than would fit on an ASIC | 05:38 |
| chris_99 | ah gotcha | 05:39 |
| eleitl | PPCoin claims it needs way less power, once it goes off mining mode to lottery mode | 05:39 |
| eleitl | I have no idea how true any of it is. | 05:39 |
| chris_99 | i'd be interested in knowing if any bitcoin alternatives would be adopted | 05:42 |
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| chris_99 | seen as bitcoin got in there first i guess | 05:42 |
| eleitl | in case I find enough time for research I'll let you know the result | 05:42 |
| chris_99 | cool | 05:43 |
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| @kanzure | "Youtube pre-Google was PHP" was it? | 09:21 |
| eudoxia | wasn't that like back in 2005 or something | 09:21 |
| Adifex | that's hard to imagine. | 09:21 |
| eudoxia | seems possible | 09:21 |
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| brownies | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/23579320 | 09:54 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/92891174b826ecf71b12bcbad4ae9090.txt | 09:54 |
| brownies | that... is not a PDF. | 09:54 |
| brownies | .meow | 09:57 |
| yoleaux | http://edgecats.net/cats/EYyO2.gif | 09:57 |
| brownies | at least 1 of the robots still has it together. | 09:57 |
| chris_99 | awh poor cat | 10:04 |
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| @kanzure | paperbot does not handle ncbi.nlm.nih.gov well at the moment | 10:39 |
| @kanzure | some pubmed papers have a link to the actual publisher's site which might have the pdf | 10:40 |
| @kanzure | also pubmedcentral.gov papers have a pdf but paperbot doesn't figure that out either i think | 10:40 |
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| ParahSailin | paperbot: http://www.bloomberg.com/quote/CXLX:SP | 11:57 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/896d267118bd63eea6e7a1a371222805.txt | 11:57 |
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| @kanzure | ParahSailin: how would you go about monitoring whether or not certain records have been removed/revoked from ncbi? | 12:18 |
| @kanzure | it turns out that not all of the data is public domain | 12:19 |
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| ParahSailin | redactions from genbank? | 12:32 |
| @kanzure | the data isn't public domain, i think it's possible for companies (perhaps those that have acquired patents from a bayh-dole compliance office) to cause information to be removed. | 12:33 |
| ParahSailin | i've experienced gi's being culled from genbank from one month to the next, but usually its because of redundancy | 12:37 |
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| @kanzure | "Celera initially announced that it would seek patent protection on "only 200–300" genes, but later amended this to seeking "intellectual property protection" on "fully-characterized important structures" amounting to 100–300 targets. The firm eventually filed preliminary ("place-holder") patent applications on 6,500 whole or partial genes. Celera also promised to publish their findings in accordance with the terms of the 1996 "Bermuda ... | 13:03 |
| @kanzure | ... Statement", by releasing new data annually (the HGP released its new data daily), although, unlike the publicly funded project, they would not permit free redistribution or scientific use of the data." | 13:03 |
| @kanzure | "In March 2000, President Clinton announced that the genome sequence could not be patented, and should be made freely available to all researchers. The statement sent Celera's stock plummeting and dragged down the biotechnology-heavy Nasdaq. The biotechnology sector lost about $50 billion in market capitalization in two days." | 13:03 |
| @kanzure | haha clinton made a statement? i wonder if scotus is going to agree or not. | 13:04 |
| Adifex | capitalization that was all fluff anyway. | 13:04 |
| @kanzure | "But it has emerged that Celera may in fact be running behind its competitors. Human Genome Sciences, Maryland and Incyte, California, have each filed at least 6,300 full patent applications. Incyte have been granted 173." | 13:07 |
| @kanzure | ParahSailin: do you guys just use data straight from genbank and whatever? | 13:09 |
| @kanzure | ParahSailin: or do you audit your data's license? | 13:10 |
| @kanzure | paperbot: http://papers.ssrn.com/sol3/Delivery.cfm?abstractid=1411328 | 13:22 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/6d2622ea15d9de2c9543ea88cc95cb17.txt | 13:22 |
| @kanzure | paperbot: http://papers.ssrn.com/sol3/Delivery.cfm/SSRN_ID1411328_code857510.pdf?abstractid=1411328&mirid=5 | 13:22 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/d02e5c640682f111df7d975f8c5e3b3b.txt | 13:22 |
| @kanzure | haha that's a user-agent xss hole | 13:23 |
| @kanzure | wow even worse | 13:23 |
| @kanzure | var sQuery = "abstract_id=1411328"; | 13:23 |
| @kanzure | var sBrowser = "pdf-defense-force"; | 13:23 |
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| @kanzure | hm they seem to be filtering it pretty well | 13:34 |
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| Adifex | hey kanzure, I saw you're in #neuroscience as well - what other good rooms are there with reasonable activity? | 13:51 |
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| @kanzure | uh.. can you be more specific? what do you need? | 14:03 |
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| @kanzure | sciencedirect is using optimizely http://cdn.optimizely.com/js/180772688.js | 14:04 |
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| Adifex | anything with good science discussion. Any favorites? | 14:06 |
| @kanzure | woot deepdyve xss found. | 14:13 |
| @kanzure | Adifex: no, they are all terrible at science. | 14:15 |
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| @kanzure | diybio-eu is crazy | 14:35 |
| @kanzure | the london group apparently migrated their communications to use lhs-biohacking@lists.kentgeek.org a few months ago | 14:36 |
| @kanzure | this fragmentation is really annoying | 14:36 |
| @kanzure | https://lists.kentgeek.org/mailman/listinfo/lhs-biohacking | 14:36 |
| @kanzure | https://lists.kentgeek.org/pipermail/lhs-biohacking/ | 14:36 |
| @kanzure | gah since june 2011 | 14:36 |
| @kanzure | wtf.. | 14:37 |
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| Adifex | http://trubrain.com | 14:57 |
| Adifex | real or bunk? | 14:57 |
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| @kanzure | probably just random supplements. | 14:58 |
| @kanzure | may or may not make you feel better about yourself. | 14:58 |
| @kanzure | some of them might be something you are missing in your system, but then again your daily intake might cover the basics already. | 14:59 |
| Adifex | I imagine if you take Piracetam over a long period of time, your brain would simply acclimate to it, and any benefits would be wiped out. | 15:00 |
| @kanzure | that sounds like something you would have to support with evidence dude | 15:01 |
| ParahSailin | kanzure: ftp://ftp.ncbi.nlm.nih.gov/pub/ | 15:03 |
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| ParahSailin | havent ever paid attention to license | 15:03 |
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| @kanzure | ParahSailin: i've been pondering that doing gene data licensing audits for biotech companies might be viable, but it's sorta scaremongery ("companies are going to sue you for using their data when you assemble genomes! of course, they don't actually have relevant evidence that you used their sequenced data, but who the hell knows until discovery.") | 15:06 |
| @kanzure | esp. if your data is from ncbi, the likelihood of using someone else's data is increased dramatically since it's all license-unknown. | 15:07 |
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| @kanzure | ParahSailin: what is your company doing? just hoping? | 15:13 |
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| ParahSailin | kanzure: i dont foresee an instance in which the license on ncbi data could get my employer in trouble | 15:19 |
| ParahSailin | kanzure: main thing we're doing right now is trying to do genotyping cheaper than microarray | 15:20 |
| ParahSailin | the rest is projects for clients, and i assume any liabilities are passed along to them | 15:21 |
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| ParahSailin | clients are mostly universities anyway | 15:21 |
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| ParahSailin | when's cory gonna gimme reads to assemble :( | 15:22 |
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| Adifex | Which company, ParahSailin? | 15:27 |
| ParahSailin | eurekagenomics | 15:28 |
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| @kanzure | ParahSailin: he claims his harvard collaborators haven't put them online yet. | 16:17 |
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| @kanzure | yashgaroth: sup | 19:31 |
| yashgaroth | not much | 19:32 |
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| Lemminkainen | hey yashgaroth how's the muscle research coming? | 20:39 |
| yashgaroth | eh pretty good, I guess | 20:39 |
| Lemminkainen | how're your targets coming? | 20:40 |
| yashgaroth | targets remain unchanged | 20:40 |
| Lemminkainen | I forget, were you doing an siRNA knockdown approach or a transfection approach? | 20:40 |
| yashgaroth | transfection, siRNA knockdown is short-lasting and siRNA is annoyingly difficult to produce | 20:41 |
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| Lemminkainen | were you targeting satellite cells or muscle synctycia? | 20:42 |
| yashgaroth | both, I suppose; the protein is secreted so you shouldn't need to target satellite cells specifically | 20:42 |
| Lemminkainen | so when will it be ready to experiment on cpopell with? | 20:43 |
| yashgaroth | once/if it works on myself | 20:44 |
| yashgaroth | if it doesn't have any obvious effect for me I'm gonna try fusing it to an Fc fragment, boost the half-life | 20:44 |
| yashgaroth | which will also make it possibly immunogenic, which is why I'm not trying that from the get-go | 20:45 |
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| Lemminkainen | aye aye; gonna make it a liposomal transfection protocol so users of it can sensually rub it on themselves in the shower? | 20:46 |
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| yashgaroth | as adjective as that would be, that would only transfect dead surface skin cells | 20:47 |
| yashgaroth | also liposomes are expensive, toxic, and less efficient than electroporation | 20:47 |
| Lemminkainen | waitaminute, how're you electroporating yourself? | 20:48 |
| yashgaroth | power supply and controller, hooked up to the two syringe needles that will be located in my arm | 20:49 |
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| Lemminkainen | sufficiently kinky | 20:50 |
| yashgaroth | probably won't be too painful, but then I don't even have any tattoos | 20:51 |
| Lemminkainen | you including a reporter fusion to track successful transfection, right? | 20:53 |
| yashgaroth | nah fuck no that'd be super immunogenic | 20:54 |
| yashgaroth | maybe a serum assay for follistatin | 20:54 |
| Lemminkainen | could do a localized assay for IGF-1 | 20:55 |
| Lemminkainen | I keep forgetting that you cant just stick GFP into people | 20:55 |
| yashgaroth | true, but follistatin acts on several pathways for muscle growth, igf-1 being a major one admittedly | 20:55 |
| yashgaroth | if you could stick any protein you wanted into people, we'd have cured a lot more diseases by now | 20:55 |
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| ParahSail1n | why not just shoot up some aav vector | 20:56 |
| yashgaroth | what did I just say about immunogenicity | 20:56 |
| ParahSail1n | aav is non immunogenic | 20:56 |
| Lemminkainen | and no guarantee that wouldn't hit his sphincter muscles | 20:57 |
| yashgaroth | in lab animals living in controlled environments their entire lives | 20:57 |
| yashgaroth | no protein or virus is 'non immunogenic' | 20:57 |
| yashgaroth | especially after the first exposure to a massive dose | 20:57 |
| yashgaroth | it's fine for people with Serious Diseases who can go into a hospital and take a heavy course of immunosuppressants | 20:58 |
| yashgaroth | which is an assumed OK for clinical gene therapies, but not me | 20:58 |
| Lemminkainen | seems that we'd ideally move to a multilayered nanoparticle approach for in vivo transfection, then | 20:59 |
| ParahSail1n | eh, you should be fine, immunogenicity only reduces efficacy | 20:59 |
| ParahSail1n | not gonna hurt you more than non-treatment | 20:59 |
| yashgaroth | and then the immune system attacks the transduced cells | 21:00 |
| ParahSail1n | if you're naive, the first dose should work good enough | 21:00 |
| ParahSail1n | thats not how magic works | 21:00 |
| ParahSail1n | immunogenicity is to capsid | 21:00 |
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| yashgaroth | yep, capsid gets enveloped and digested by the host cell, and some of that's gonna get displayed | 21:00 |
| yashgaroth | sure if you're naive the first dose will probably go fine, but good luck figuring out dosage levels and repeat administration | 21:01 |
| ParahSail1n | im not sure that display of capsid proteins is a frequent enough of an event to be concerned about | 21:02 |
| yashgaroth | when you're injecting 10 billion viral particles, it might be | 21:02 |
| yashgaroth | lemminkainen nanoparticles are fine but the advantage of viruses is their ability to transit to the nucleus and then enter it, which occurs from specific protein-protein binding; and those proteins will be immunogenic | 21:03 |
| Lemminkainen | there's still a distinction to be made between capsid vector and its payload; may develop immune reaction against the capsid, but not its contents | 21:03 |
| yashgaroth | sure, and immune response to the contents is more a problem for people missing the delivered gene, which admittedly is 99% of clinical gene therapy | 21:04 |
| Lemminkainen | if the contents are genetic, there is no immune response to it | 21:05 |
| @kanzure | heh EFF wants source code submissions to be mandatory for software patents | 21:05 |
| yashgaroth | there is an immune response to the protein that is produced | 21:05 |
| @kanzure | https://www.eff.org/sites/default/files/eff_comments_on_enhancement_of_quality_of_software-related_patents.pdf | 21:05 |
| Lemminkainen | proteins like Cleaver and Artemis deal with dsRNA and weird naked cytosolic DNA | 21:05 |
| yashgaroth | and a reaction to the capsid will destroy all the transduced cells, probably not on the first dose in a naive target, but likely on any subsequent dose | 21:05 |
| yashgaroth | if some cells of a person with MD start producing dystrophin, eventually the immune system will notice and steamroll them | 21:07 |
| Lemminkainen | you're overthinking it dude there are lots of viruses, e.g. cytomegalovirus, that subvert cytosolic digestion and MHC-I display of their capsids by fucking with rough ER trafficking | 21:07 |
| yashgaroth | mhm and they either go latent without producing any protein, or use those MHC-disrupting genes while they're doing a full-scale invasion anyway | 21:08 |
| Lemminkainen | yep they do, but why do you suppose our genomes are littered with the remains of ancient viruses? | 21:08 |
| yashgaroth | because some of them snuck into germ cells and became latent | 21:08 |
| yashgaroth | if it was easy to sneak foreign protein production into cells, gene therapy would have >1 clinical trial successes | 21:09 |
| Lemminkainen | sure, some did, but also consider tumor immunology; MHC-I presentation during cancer growth becomes deranged and NK CD8+ T-cells are supposed to nip them in the bud before they get too big | 21:09 |
| Lemminkainen | often they do, but when a tumor gets too big, IL-10 kicks in to knock down the CD8+ rager and the tumor survives | 21:09 |
| Lemminkainen | if you're doing body-wide transfection, the immune system would have to go into sepsis death mode to deal with it and it has very specific regulatory mechanisms against it | 21:10 |
| yashgaroth | which may not kick in until after multiple organ failure | 21:10 |
| @kanzure | hrmm https://defendinnovation.org/ this breaks text selection. eff is now officially evil. | 21:11 |
| Lemminkainen | true enough, but we're smarter than allowing sepsis to spiral in controlled cases if we have an inkling it may happen | 21:11 |
| yashgaroth | and those controlled cases are why people with serious diseases will be under heavy immunosuppression when they get the gene therapy | 21:12 |
| Lemminkainen | yashgaroth I get the impression you're laying failure of genetic engineering clinical trials at immunology's feet when I'd suggest there's a lot to do with bad targeting going on | 21:12 |
| Lemminkainen | we still really suck at getting anything into a nucleus in vivo | 21:12 |
| yashgaroth | nah, viruses are awesome at that shit | 21:12 |
| yashgaroth | finding a synthetic or other non-immunogenic molecule that will bind & activate importin, that's a problem | 21:13 |
| yashgaroth | using plasmids and other non-viral methods, you're stuck hoping really hard that a plasmid ends up in the nucleus | 21:15 |
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| Swordsman | guys | 22:23 |
| Swordsman | Did you see this? http://donottouch.org/ | 22:24 |
| Swordsman | someone just linked it in #chemistry a little while ago, I was thinking that it seemed interesting in regards to AI research and the like | 22:24 |
| Swordsman | I'm guessing it might be old news to you, but I got pretty excited when I saw it | 22:25 |
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| @fenn | "50 years of pointing and clicking".. can you get any more depressing than that | 22:41 |
| @kanzure | sure, how about this: englebart is proud of the mouse. | 22:42 |
| @kanzure | engelbart | 22:42 |
| @fenn | engelbart's mouse was mostly a selector; the commands were actually performed by the chording keyboard | 22:48 |
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| @kanzure | this is really rudimentary but it covers the basics https://www.coursera.org/course/compneuro | 23:41 |
| @kanzure | on computational neuroscience. | 23:41 |
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| --- Log closed Wed Apr 17 00:00:00 2013 | ||
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