--- Log opened Thu Jan 16 00:00:25 2014
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02:06 < 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
02:07 < venturecommunist> trying to zero in now on what are the most important additional concepts i need
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02:18 < venturecommunist> okay i think gibson assembly?
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02:38 < juri_> you've got to know gibson assembly to really hack a gibson.
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02:50 < venturecommunist> lol
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06:50 < ParahSailin> yeah, no biobricks is pretty much crap
06:52 < 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
06:54 < venturecommunist> i think i've settled on gibson assembly
06:55 < venturecommunist> it's quicker, doesn't make scars
06:56 < venturecommunist> one thing i don't get is whether i have to synthesize HIV1 TAT or whether i can order it off the shelf
07:00 < 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
07:01 < 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
07:02 < 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.
07:03 < venturecommunist> ParahSailin: you know a lot about this stuff?
07:04 < ParahSailin> more than is of any actual value
07:04 < ParahSailin> wetlab is a ghetto
07:05 < venturecommunist> you mean a dead end for the people who get involved in it or?
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07:11 < ParahSailin> i can tell you that in-fusion is likely to work without wasting more months of time than necessary
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07:15 < 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?
07:16 < venturecommunist> do i have to worry about promoters for expression or is that mostly taken care of?
07:17 < ParahSailin> you should start with plasmid that already has the promoter you want
07:18 < venturecommunist> okay then i'll assume it comes like that
07:19 < venturecommunist> ParahSailin: now tat for instance
07:20 < 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
07:21 < venturecommunist> but tat i'm not turning up something analogous, possibly because it's not human, it's hiv
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07:33 < venturecommunist> ahh i get it now. cDNA means you don't need promoters
07:33 < venturecommunist> since all the introns are excised
07:36 < ParahSailin> dunno what you're asking
07:37 < ParahSailin> stick your orf in line with the his tag
07:38 < gradstudentbot> Cancer: still not cured.
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07:42 < venturecommunist> it's gonna be His + tat + pkr + apaf1
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08:53 < nmz787> kanzure: how do I get that npm package without npm?
08:55 < 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
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09:17 < 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\
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10:08 < chris_99> paperbot: http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4197360
10:09 < kanzure> hrmm
10:11 < paperbot> http://libgen.org/scimag/get.php?doi=10.1109%2FMUE.2007.165
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12:20 < FourFire> have I been connecting and disconnecting frequently?
12:25 < 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 ?
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12:27 < 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
12:29 < 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
12:33 < venturecommunist> i bet
12:33 < venturecommunist> so what's the most exciting thing you learned in the last week
12:34 < FourFire> oh, that this new diagnosis machine is being put on sale so now whole genome sequencing can be done for ~1000$
12:35 < FourFire> you bet, how much?
12:35 < FourFire> 1000 satoshis?
12:37 < venturecommunist> hmm
12:37 < venturecommunist> wait is it 1000 dollars or satoshis
12:37 < venturecommunist> what's a satoshi anyway? like .00001 cents?
12:38 < venturecommunist> so like .01 cents i guess that would be?
12:39 < ParahSailin> whole human genome sequencing already is <$1000
12:39 < venturecommunist> ParahSailin: sounds like what you're talking about
12:41 < ParahSailin> one lane of hiseq will give you enough coverage to get what you need
12:45 < FourFire> it's a 10 millionth of a BTC
12:45 < FourFire> ParahSailin, is that redundant enough to cover for mistakes?
12:46 < ParahSailin> one lane is only gonna be like 5-7x coverage on average so probably not good enough for all uses
12:47 < FourFire> oh, right
12:47 < FourFire> so it's redundant
12:48 < 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
12:49 < 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
12:50 < 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?
12:51 < FourFire> yes, but you are talking about the sort og profiling 23andme does right?
12:52 < 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?
12:53 < ParahSailin> interesting snps
12:54 < 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
12:56 < ParahSailin> you could proabably get a decent idea from one lane of hiseq
12:58 < 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?
12:59 < ParahSailin> what
13:04 < ParahSailin> https://dugsim.net/estimate_cost http://dnatech.genomecenter.ucdavis.edu/prices/
13:47 < 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
13:48 < Qfwfq> paperbot: I love you.
13:49 < 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
13:50 < 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
13:51 < 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)
13:52 < FourFire> ParahSailin, one great use of General AI: tirelessly increasing scientific literacy in the general population
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14:21 < nmz787> ParahSailin: what would the best service today be for metagenomic sequencing, one of the microbiome projects maybe?
14:22 < 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
14:23 < ParahSailin> you'd send it into ucdavis or something for library prep and sequencing and then do bioinformatics on it
14:25 < 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/
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14:46 < nmz787> well all but the informatics
14:49 < nmz787> says here $89 for 1 sample, but only does 16S http://ubiome.com/pages/faq
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16:17 < kanzure> http://www.justice.gov/usao/nys/pressreleases/January14/SilkRoadForfeiture.php
16:24 < venturecommunist> kanzure: no attempted murder? was that all trump up?
16:25 < kanzure> i imagine that they are not legally obligated to list all of the charges in this announcement
16:26 < venturecommunist> so you think that charge is still being prosecuted?
16:28 < kanzure> no idea
16:49 < 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
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18:27 < kanzure> http://www.matasano.com/matasano-square-microcontroller-ctf/
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18:30 < kanzure> huh it has an html/js debugger
18:39 < 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
18:40 < 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
18:41 < 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
18:43 < 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
18:44 < 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
18:45 < venturecommunist> so i was thinking how WOULD you scale production?
18:45 < kanzure> algae production can be scaled by building more tanks
18:46 < venturecommunist> so you're saying express in algae
18:47 < kanzure> no i am saying beer kegs are good with algae
18:48 < 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...
18:49 < venturecommunist> why, what do you culture e coli in
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18:54 < kanzure> usually petri dishes
18:54 < kanzure> sometimes packed columns of beads with agar everywhere but i've never seen one working
18:55 < venturecommunist> i've heard of liquid cultures for e coli
18:55 < venturecommunist> i assumed there's glass and stainless steel bioreactors
18:57 < venturecommunist> http://www.ebay.com/itm/PRECISION-400-LITER-JACKETED-BIO-REACTOR-316-STAINLESS-STEEL-TANK-/171066511377
18:59 < venturecommunist> a used beer keg on ebay is probably $100 or $150
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19:52 < heath> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/24256506
19:52 < paperbot> http://libgen.org/scimag/get.php?doi=10.1021%2Fja4062294
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20:14 < ParahSailin> haha yeah get it working at flask scale first
20:15 < ParahSailin> a liter of culture is about as much protein as a normal nickel column will handle
20:16 < ParahSailin> the utility of a beer keg is mainly in being able to be pressurized so that you have beer on tap
20:17 < ParahSailin> if you want to grow lots of bugs, a simple barrel would be cheaper
20:18 < kanzure> for my ultraplan i will start with 1 billion liters of culture
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20:23 < 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!
20:24 < ParahSailin> if i were to do something now, it would be really hard to get my hands on those again
20:25 < ParahSailin> in hindsight, i should have gone to schloendorn
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20:25 < ParahSailin> but he was doing a thiel for-profit at the time
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20:28 < kanzure> yeah i should have recommended avery
20:28 < kanzure> or cory, although cory is now neck-deep in being an academic..
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20:28 < ParahSailin> jesus christ, idt "gblocks" are cheap now
20:29 < ParahSailin> used to be 250 for 450nt, now 129 for 750nt
20:30 < augur> oh hai
20:31 < ParahSailin> not to mention the aav vector i got access to-- pretty doubtful i'd ever get my hands on that again
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20:45 < klafka> hi
20:46 < kanzure> hello
20:47 < klafka> so i'm excitedly working on something cool now
20:48 < 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
20:49 < 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
20:50 < 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
20:51 < 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
20:52 < 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?
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23:29 <@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
23:30 <@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.
23:31 <@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
23:32 <@archels> yessss
23:32 < kanzure> it is very interesting how believers in consciousness think they are not talking about mind-body duality
23:35 < kanzure> archels: surely nobody in your profession is worried about this topic
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23:47 <@archels> nobody in my profession seems to worry about anything outside their microscopic scientific subdomain, which is worrying in and of itself
23:48 < 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
23:49 <@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.
23:50 <@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
23:53 <@archels> the reason I bring it up is because he is generally seen as a respectable neuroscientist (I think)
23:54 < kanzure> penrose??
23:54 < kanzure> `.
23:54 < kanzure> stupid ssh escape sequence
23:56 < entelechios> archels a book for you
23:56 < entelechios> "the emerging physics of consciousness", j.a. tuczynski et al
23:57 < 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
23:58 < 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
23:59 < kanzure> okay, maybe it's not as extreme as a book about soul theory or something
23:59 < kanzure> but it's pretty bad :)
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--- Log closed Fri Jan 17 00:00:35 2014