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| venturecommunist | kanzure: where i'm at right now is seeing a kind of incompatibility of the whole BioBricks concept (which is apparently where I got the term "assembly" from) with making fusion proteins. the molecular cloning manual you gave me is clearing that up to some extent | 02:06 |
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| venturecommunist | trying to zero in now on what are the most important additional concepts i need | 02:07 |
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| venturecommunist | okay i think gibson assembly? | 02:18 |
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| juri_ | you've got to know gibson assembly to really hack a gibson. | 02:38 |
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| venturecommunist | lol | 02:50 |
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| ParahSailin | yeah, no biobricks is pretty much crap | 06:50 |
| ParahSailin | i guess you could say they do the best they could given the current technological level | 06:52 |
| ParahSailin | but they dont even do that, its really hard to get access outisde of a .edu lab | 06:52 |
| venturecommunist | i think i've settled on gibson assembly | 06:54 |
| venturecommunist | it's quicker, doesn't make scars | 06:55 |
| venturecommunist | one thing i don't get is whether i have to synthesize HIV1 TAT or whether i can order it off the shelf | 06:56 |
| ParahSailin | yeah good luck actually with a more than 2 fragment ligation | 07:00 |
| ParahSailin | gibson will make a mess if you try to do something crazy like ligate backbone, tat, pkr and apaf1 in one pot | 07:00 |
| venturecommunist | i heard it could reliably do up to 6 things | 07:01 |
| venturecommunist | but in any event i could just do 2 at a time right? | 07:01 |
| ParahSailin | really the most reliable is clon-tech in-fusion | 07:01 |
| ParahSailin | venturecommunist: you heard liars | 07:02 |
| ParahSailin | in-fusion actually will do lots of things | 07:02 |
| gradstudentbot | Hey, let's write a paper about that. | 07:02 |
| venturecommunist | ParahSailin: you know a lot about this stuff? | 07:03 |
| ParahSailin | more than is of any actual value | 07:04 |
| ParahSailin | wetlab is a ghetto | 07:04 |
| venturecommunist | you mean a dead end for the people who get involved in it or? | 07:05 |
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| ParahSailin | i can tell you that in-fusion is likely to work without wasting more months of time than necessary | 07:11 |
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| venturecommunist | okay i have material on in-fusion | 07:15 |
| venturecommunist | i'm struggling with some basics i think though | 07:15 |
| venturecommunist | for one, is a promoter assumed to come with some canonical version of a gene? | 07:15 |
| venturecommunist | so you have to remove it to make it latent? | 07:15 |
| venturecommunist | do i have to worry about promoters for expression or is that mostly taken care of? | 07:16 |
| ParahSailin | you should start with plasmid that already has the promoter you want | 07:17 |
| venturecommunist | okay then i'll assume it comes like that | 07:18 |
| venturecommunist | ParahSailin: now tat for instance | 07:19 |
| venturecommunist | ParahSailin: i've found with the two human genes i think it was called cDNA ORF | 07:20 |
| venturecommunist | and that led to actual plasmids i could buy | 07:20 |
| ParahSailin | actually you should start with a plasmid that has promoter + his tag already | 07:20 |
| venturecommunist | but tat i'm not turning up something analogous, possibly because it's not human, it's hiv | 07:21 |
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| venturecommunist | ahh i get it now. cDNA means you don't need promoters | 07:33 |
| venturecommunist | since all the introns are excised | 07:33 |
| ParahSailin | dunno what you're asking | 07:36 |
| ParahSailin | stick your orf in line with the his tag | 07:37 |
| gradstudentbot | Cancer: still not cured. | 07:38 |
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| venturecommunist | it's gonna be His + tat + pkr + apaf1 | 07:42 |
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| nmz787 | kanzure: how do I get that npm package without npm? | 08:53 |
| nmz787 | this almost works registry.npmjs.org/inflate-stream | 08:55 |
| nmz787 | ahh, found it in there http://registry.npmjs.org/inflate-stream/-/inflate-stream-0.0.0.tgz | 08:55 |
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| nmz787 | if you want to express cDNA you should have promoters on it | 09:17 |
| nmz787 | cDNA is a DNA version of an mRNA, basically\ | 09:17 |
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| chris_99 | paperbot: http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4197360 | 10:08 |
| kanzure | hrmm | 10:09 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1109%2FMUE.2007.165 | 10:11 |
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| FourFire | have I been connecting and disconnecting frequently? | 12:20 |
| venturecommunist | FourFire: once 2 hours ago | 12:25 |
| FourFire | ok | 12:25 |
| FourFire | so, what's the most exciting thing you've learned in the past week venturecommunist ? | 12:25 |
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| venturecommunist | FourFire: that if you make a chimeric protein of his6 + tat + pkr + apaf1 that it will selectively induce apoptosis in virus infected cells | 12:27 |
| venturecommunist | for virtually all viruses | 12:27 |
| FourFire | wow | 12:27 |
| FourFire | source? | 12:27 |
| venturecommunist | http://www.plosone.org/article/info%253Adoi%252F10.1371%252Fjournal.pone.0022572 | 12:27 |
| FourFire | you know I wonder how valuable getting ten futurist or technologically engaged people to exchange their most exciting discovery with eachother would be on an idea networking utility basis | 12:29 |
| venturecommunist | i bet | 12:33 |
| venturecommunist | so what's the most exciting thing you learned in the last week | 12:33 |
| FourFire | oh, that this new diagnosis machine is being put on sale so now whole genome sequencing can be done for ~1000$ | 12:34 |
| FourFire | you bet, how much? | 12:35 |
| FourFire | 1000 satoshis? | 12:35 |
| venturecommunist | hmm | 12:37 |
| venturecommunist | wait is it 1000 dollars or satoshis | 12:37 |
| venturecommunist | what's a satoshi anyway? like .00001 cents? | 12:37 |
| venturecommunist | so like .01 cents i guess that would be? | 12:38 |
| ParahSailin | whole human genome sequencing already is <$1000 | 12:39 |
| venturecommunist | ParahSailin: sounds like what you're talking about | 12:39 |
| ParahSailin | one lane of hiseq will give you enough coverage to get what you need | 12:41 |
| FourFire | it's a 10 millionth of a BTC | 12:45 |
| FourFire | ParahSailin, is that redundant enough to cover for mistakes? | 12:45 |
| ParahSailin | one lane is only gonna be like 5-7x coverage on average so probably not good enough for all uses | 12:46 |
| FourFire | oh, right | 12:47 |
| FourFire | so it's redundant | 12:47 |
| FourFire | what sorts of uses require more redundancy? | 12:48 |
| FourFire | because I sort of want to buy my whole genome in one go and then use that data as advances allow more things to be figured out from it | 12:48 |
| ParahSailin | FourFire: de novo assembly | 12:49 |
| FourFire | eli5 ? | 12:49 |
| ParahSailin | 5-7x coverage means you're gonna have lots of gaps | 12:49 |
| ParahSailin | because its not uniform coverage | 12:49 |
| FourFire | oh, right | 12:49 |
| FourFire | I want every basepair that i have | 12:49 |
| ParahSailin | your coverage is gonna follow a gaussian distribution centered at 5-7x | 12:49 |
| ParahSailin | if you have 5-7x coverage on interesting snps, then you could be pretty certain of the genotype, because error rate is well below 1% | 12:50 |
| gradstudentbot | When is he back from sabbatical? | 12:50 |
| FourFire | yes, but you are talking about the sort og profiling 23andme does right? | 12:51 |
| ParahSailin | 23andme does microarray chips | 12:52 |
| FourFire | ok, so not like that | 12:52 |
| FourFire | when you said "what you need", what did you assume I needed? | 12:52 |
| ParahSailin | interesting snps | 12:53 |
| FourFire | but what I want is every basepair, or at least enough that it is easy to see exactly which genes and what metadata ("junk DNA") variants I have | 12:54 |
| ParahSailin | you could proabably get a decent idea from one lane of hiseq | 12:56 |
| FourFire | could I see what gives me my exact moles in the exact locations and pigments they are in? | 12:58 |
| FourFire | well how much does this one lane of hiseq cost to have done, on the inside? | 12:58 |
| ParahSailin | what | 12:59 |
| ParahSailin | https://dugsim.net/estimate_cost http://dnatech.genomecenter.ucdavis.edu/prices/ | 13:04 |
| Qfwfq | paperbot: http://muse.jhu.edu/login?auth=0&type=summary&url=/journals/mln/v119/119.5regier01.html | 13:47 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Cioran%27s%20Insomnia.pdf | 13:47 |
| Qfwfq | paperbot: I love you. | 13:48 |
| kanzure | ParahSailin: i need some way to make sure that this doesn't become bio 101 again | 13:49 |
| kanzure | ParahSailin: or the "glowing gel electrophoresis fanclub" | 13:49 |
| wallmani | gradstudentbot: does anyone love you? | 13:49 |
| gradstudentbot | The lab meeting was cancelled. | 13:49 |
| ParahSailin | kanzure: hm... first ban delinquentme | 13:49 |
| kanzure | that's not bio 101 that's remedial boi | 13:49 |
| delinquentme | DNA modifications?? | 13:50 |
| kanzure | *bio | 13:50 |
| delinquentme | whats the topic heeere? | 13:50 |
| ParahSailin | i think fourfire's questions are fair though, im giving fairly insider knowledge on current state of affairs | 13:50 |
| kanzure | insider info is the best kind of info | 13:50 |
| FourFire | thanks | 13:50 |
| kanzure | yeah no specific complaints | 13:50 |
| kanzure | it was just a general statement | 13:50 |
| ParahSailin | kanzure: i think as long as the people who know and do stuff are grumpy about textbook questions it wont become that | 13:51 |
| FourFire | ParahSailin, I don't feel like paying up just yet, so I'll let you know when I want to purchase that sort of service (I am assuming you are somehow involved in the process) | 13:51 |
| FourFire | ParahSailin, one great use of General AI: tirelessly increasing scientific literacy in the general population | 13:52 |
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| nmz787 | ParahSailin: what would the best service today be for metagenomic sequencing, one of the microbiome projects maybe? | 14:21 |
| ParahSailin | be more specific | 14:22 |
| nmz787 | ParahSailin: I would think the procedure would be extract eDNA, PCR with 16S and 18S primer sets, then ... | 14:22 |
| ParahSailin | you want to do metagenomic sequencing of some flora? | 14:22 |
| nmz787 | yeah | 14:22 |
| nmz787 | well not gut or anytrhing | 14:22 |
| nmz787 | soil, kombucha, beer | 14:22 |
| nmz787 | wine | 14:22 |
| ParahSailin | you'd send it into ucdavis or something for library prep and sequencing and then do bioinformatics on it | 14:23 |
| ParahSailin | if you wanted to actually pay for all of that at one time i know that these guys will do that http://eurekagenomics.com/ | 14:25 |
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| nmz787 | well all but the informatics | 14:46 |
| nmz787 | says here $89 for 1 sample, but only does 16S http://ubiome.com/pages/faq | 14:49 |
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| kanzure | http://www.justice.gov/usao/nys/pressreleases/January14/SilkRoadForfeiture.php | 16:17 |
| venturecommunist | kanzure: no attempted murder? was that all trump up? | 16:24 |
| kanzure | i imagine that they are not legally obligated to list all of the charges in this announcement | 16:25 |
| venturecommunist | so you think that charge is still being prosecuted? | 16:26 |
| kanzure | no idea | 16:28 |
| chris_99 | paperbot: http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1714203 | 16:49 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1109%2FWCICA.2006.1714203 | 16:49 |
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| kanzure | http://www.matasano.com/matasano-square-microcontroller-ctf/ | 18:27 |
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| kanzure | huh it has an html/js debugger | 18:30 |
| venturecommunist | kanzure: i'm stuck at "sign up" or "forgot your password" | 18:39 |
| kanzure | it seemed to let me in.. | 18:39 |
| venturecommunist | oh you probably signed up then | 18:39 |
| venturecommunist | i was trying to guess a password :P | 18:39 |
| kanzure | this hwole thing seems like cheating | 18:40 |
| kanzure | they give you a working debugger | 18:40 |
| kanzure | with the op codes already translated into asm text | 18:40 |
| kanzure | and there are also labels for addresses/functions | 18:40 |
| venturecommunist | i think they want to ease you into it, onboard more competitor | 18:40 |
| kanzure | and a full memory dump after every step | 18:40 |
| kanzure | this is an unreasonable amount of information | 18:40 |
| kanzure | most of the time you'd be lucky to know whether the device is receiving your signals at all | 18:41 |
| venturecommunist | so is the game tutorial / walkthrough but it onboards more people | 18:41 |
| venturecommunist | kanzure: do you think a beer keg is reasonable for a diy bioreactor? | 18:43 |
| venturecommunist | for a giant e coli colony | 18:43 |
| venturecommunist | what would that need? air stones? | 18:43 |
| kanzure | i have never grown ecoli in a beer keg | 18:43 |
| kanzure | you would be better off growing yeasts or algae in a beer keg | 18:43 |
| venturecommunist | no i wouldn't think many had but there are large bioreactors for ecoli right? | 18:44 |
| kanzure | well at least they don't like you modify the ROM... although, flashing the ROM seems like the most practical way to break the device. | 18:44 |
| venturecommunist | the scientist made an off hand comment in an interview when asked if he'd ever been tempted to try the DRACO potion that there's barely enoug for the rats as it is | 18:44 |
| venturecommunist | so i was thinking how WOULD you scale production? | 18:45 |
| kanzure | algae production can be scaled by building more tanks | 18:45 |
| venturecommunist | so you're saying express in algae | 18:46 |
| kanzure | no i am saying beer kegs are good with algae | 18:47 |
| kanzure | your query was about a keg not about how to culture ecoli | 18:48 |
| kanzure | nobody told you to culture ecoli in a keg... | 18:48 |
| venturecommunist | why, what do you culture e coli in | 18:49 |
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| kanzure | usually petri dishes | 18:54 |
| kanzure | sometimes packed columns of beads with agar everywhere but i've never seen one working | 18:54 |
| venturecommunist | i've heard of liquid cultures for e coli | 18:55 |
| venturecommunist | i assumed there's glass and stainless steel bioreactors | 18:55 |
| venturecommunist | http://www.ebay.com/itm/PRECISION-400-LITER-JACKETED-BIO-REACTOR-316-STAINLESS-STEEL-TANK-/171066511377 | 18:57 |
| venturecommunist | a used beer keg on ebay is probably $100 or $150 | 18:59 |
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| heath | paperbot: http://www.ncbi.nlm.nih.gov/pubmed/24256506 | 19:52 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1021%2Fja4062294 | 19:52 |
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| ParahSailin | haha yeah get it working at flask scale first | 20:14 |
| ParahSailin | a liter of culture is about as much protein as a normal nickel column will handle | 20:15 |
| ParahSailin | the utility of a beer keg is mainly in being able to be pressurized so that you have beer on tap | 20:16 |
| ParahSailin | if you want to grow lots of bugs, a simple barrel would be cheaper | 20:17 |
| kanzure | for my ultraplan i will start with 1 billion liters of culture | 20:18 |
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| ParahSailin | what's sad is that in my old lab i had some dna fragments for purification methods other than nickel column, like that ice nucleation protein display one and the elastin-like peptide tag one | 20:23 |
| ParahSailin | i could not give those things away to any other so-called practitioners like cathal at the time | 20:23 |
| ParahSailin | ohnoes patents i could not! | 20:23 |
| ParahSailin | if i were to do something now, it would be really hard to get my hands on those again | 20:24 |
| ParahSailin | in hindsight, i should have gone to schloendorn | 20:25 |
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| ParahSailin | but he was doing a thiel for-profit at the time | 20:25 |
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| kanzure | yeah i should have recommended avery | 20:28 |
| kanzure | or cory, although cory is now neck-deep in being an academic.. | 20:28 |
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| ParahSailin | jesus christ, idt "gblocks" are cheap now | 20:28 |
| ParahSailin | used to be 250 for 450nt, now 129 for 750nt | 20:29 |
| augur | oh hai | 20:30 |
| ParahSailin | not to mention the aav vector i got access to-- pretty doubtful i'd ever get my hands on that again | 20:31 |
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| klafka | hi | 20:45 |
| kanzure | hello | 20:46 |
| klafka | so i'm excitedly working on something cool now | 20:47 |
| klafka | a decentralized machine learning system | 20:48 |
| kanzure | pasky: ping | 20:48 |
| kanzure | pasky would probably enjoy talking about that. | 20:48 |
| klafka | sweet | 20:48 |
| klafka | i got laid off so i'm going to work on a thing i actually care about | 20:48 |
| kanzure | no way you got laid off | 20:48 |
| kanzure | "sorry, we've decided that hiring programmers isn't hard enough, so we're going to axe our team and make it even harder.." | 20:49 |
| klafka | lol | 20:49 |
| klafka | merger + redundancy | 20:49 |
| klafka | or whatever | 20:49 |
| klafka | but i have low minimum cost of living so i can funemploy it up for a bit and work on my own shit | 20:50 |
| klafka | i've been thinking about this for awhile | 20:50 |
| klafka | basically it'd be cool so you don't have a centralized data store for people | 20:50 |
| klafka | but instead learn small models in a p2p fashion and then combine those weak models into a strong classifier | 20:50 |
| klafka | at least that's my thought | 20:51 |
| kanzure | this sounds like one of those problem solvers that is really good on a very specific class of problems | 20:51 |
| klafka | possibly | 20:52 |
| klafka | depends | 20:52 |
| kanzure | gradstudentbot: it depends | 20:52 |
| gradstudentbot | I think our octopus might be smarter than me. | 20:52 |
| klafka | it's a situation that is amenable to a small subset of learning algorithms | 20:52 |
| kanzure | hm maybe the lookup feature doesn't work | 20:52 |
| klafka | right now i'm playing with the idea w/ random forests | 20:52 |
| kanzure | gradstudentbot: IT DEPENDS | 20:52 |
| gradstudentbot | If I was your endoplasmic reticulum, would you want me smooth or would you want me rough? | 20:52 |
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| @archels | A so-called “technological singularity” identifiable with hyperalgorithmic super-consciousness (as distinguished from algorithmic super-computation) may be in our future. As Penrose puts it (p. 178), “it might be possible to have a conscious entity that is not biological at all, in the sense that we use the term ‘biology’ at the present time; but it would not be possible for an entity be conscious if it did not incorporate the part | 23:29 |
| @archels | dualism anno 2014 | 23:29 |
| @archels | this is re Penrose's quantum conscioussness theory http://www.sciencedirect.com/science/article/pii/S1571064513001188 | 23:30 |
| @archels | The blind faith that Hodgkin–Huxley type neuron bursts explain neural information processing completely will collapse soon, and then brain building projects [16] all over the world will face the danger of banking on an incomplete picture of a neuron. | 23:30 |
| @archels | no one believes that HH neurons explain neural information processing completely, guys. come on | 23:31 |
| kanzure | blah blah blah consciousness blah blah blah mind-body duality bullshit | 23:31 |
| @archels | yessss | 23:32 |
| kanzure | it is very interesting how believers in consciousness think they are not talking about mind-body duality | 23:32 |
| kanzure | archels: surely nobody in your profession is worried about this topic | 23:35 |
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| @archels | nobody in my profession seems to worry about anything outside their microscopic scientific subdomain, which is worrying in and of itself | 23:47 |
| kanzure | i imagine this is an accurate characterization of your profession: | 23:48 |
| kanzure | http://static.guim.co.uk/sys-images/Technology/Pix/pictures/2008/06/20/marvin.article.jpg | 23:48 |
| @archels | which is me and which is my PI? :) | 23:49 |
| kanzure | gradstudentbot: which one are you? | 23:49 |
| gradstudentbot | That's definitely a Nature paper. | 23:49 |
| @archels | hrrm I still haven't read Koch's book on consciousness | 23:50 |
| @archels | I don't think his stance is very much less fuzzy than Penrose's | 23:50 |
| @archels | the reason I bring it up is because he is generally seen as a respectable neuroscientist (I think) | 23:53 |
| kanzure | penrose?? | 23:54 |
| kanzure | `. | 23:54 |
| kanzure | stupid ssh escape sequence | 23:54 |
| entelechios | archels a book for you | 23:56 |
| entelechios | "the emerging physics of consciousness", j.a. tuczynski et al | 23:56 |
| entelechios | you know how to look for it | 23:57 |
| kanzure | ugh | 23:57 |
| kanzure | fuck off | 23:57 |
| entelechios | who, me? | 23:57 |
| kanzure | yes | 23:57 |
| entelechios | how come though | 23:57 |
| entelechios | are you just going to be a dick or do you have a point | 23:57 |
| kanzure | your theories of consicousness are boring and unoriginal and wrong | 23:57 |
| entelechios | i don't have any you asshole | 23:58 |
| kanzure | you might as well be telling me to read a book about souls | 23:58 |
| kanzure | which is a decidedly unfriendly thing to do | 23:58 |
| kanzure | okay, maybe it's not as extreme as a book about soul theory or something | 23:59 |
| kanzure | but it's pretty bad :) | 23:59 |
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| --- Log closed Fri Jan 17 00:00:35 2014 | ||
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