--- Log opened Mon Aug 08 00:00:15 2011
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05:13 < delinquentme> so what are the difficulties associated with unwrapping DNA?
05:27 < foucist> delinquentme: well generally speaking, when a dna is duplicated, there's a pile of enzymes that unfold the dna, split it apart, and then others that copy each strand
05:27 < foucist> but i don't think the strands end up completely separate, it happens in multipe spots along the dna and moves along
05:27 < foucist> so as it finishes it gets wrapped up again
05:28 < foucist> or some shit
05:28 < delinquentme> lol
05:28 < delinquentme> comparatively... is DNA as a molecule .. fragile?
05:28 < foucist> i'm actualy mixing up the rna transcription and dna duplication parts in that explanation!
05:28 < foucist> kinda
05:29 < foucist> it's probably pretty stable in its folded up form
05:29 < foucist> there's like 3-levels of folding
05:29 < foucist> so it's basically tiny when folded
05:29 < foucist> but HUGE when unfolded
05:29 < foucist> long rather
05:29 < foucist> long as hell
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05:44 < delinquentme> yeah
05:44 < delinquentme> histones
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06:08 < delinquentme> hey so everyone else thinkgs im crazy ( whats new) .. i want to fit an electron microscope into a cm^3 .. where to start?
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07:05 < kanzure> "before you put him anywhere, i would recommend making him edit his "cover letter" for grammatical and spelling errors. it comes off very unprofessionally and that might rub a serious academic the wrong way"
07:05 < kanzure> " i'm not sure whether such a meandering, causal letter will get a reply from an excessively busy research professor, unless it is a simple: "thank you for your interest, maybe you should go get a degree.""
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07:48 < delinquentme> so is it possible that a lab who has sequencing equipment would want additional sequence alignment power?
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08:18 < drazak> who's in DIYBio Vancouver?
08:33 < archels> delinquentme: electron microscope into a cubic cm? The acceleration voltages involved would probably be quite high.
08:33 < delinquentme> archels, so one of the ideas i had on the matter was to "cascade" as much as possible across parallel sample scans
08:34 < delinquentme> IE if i want to scan 40 samples in parallel ... i could easily place all those samples within the same vacuum chamber .. and im wondering if the same could be done for the electron gum
08:34 < delinquentme> gun** IE one big one .. then just disperse the electrons and focus to individual samples
08:36 < archels> Oh so now you don't want just an electron microscope in 1 cm^3, but you also want to it image 40 samples in parallel?
08:37 < archels> Also, big is not that big given the size constraint. :)
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08:58 < delinquentme> kanzure, on aubreys reply  lol
08:59 < delinquentme> i thought that academics are all about the massive run ons and endless sentences?
09:04 < foucist> delinquentme: what was the email about
09:04 < delinquentme> foucist, my place within aging research
09:05 < foucist> at the forefront.. duh!
09:05 < foucist> jk
09:05 < foucist> hmm
09:06 < foucist> delinquentme: what are you studying in school?
09:06 < foucist> in uni
09:06 < foucist> delinquentme: i think nanotech & some combo of medical/bio is good
09:06 < foucist> go for a dual degree in MD/Phd in Biochemistry or some such
09:07 < foucist> so you get the medical and phd awesomenezz
09:07 < foucist> and go straight into rezearch
09:07 < delinquentme> did business marketing
09:07 < delinquentme> i dont like school
09:07 < delinquentme> i'm self taught basically from the ground up
09:07 < foucist> yeah skool sucks
09:07 < foucist> yeah
09:08 < foucist> so how do you want to contribute then? i.e. do you plan to study bio and sutff on your own?
09:08 < foucist> study research papers, do experiments? or what
09:08 < delinquentme> basically i want to look over biologists shoulders and take notes
09:08 < delinquentme> and then come up with ways to automate what they're doing
09:08 < delinquentme> in software or hardware
09:08 < foucist> ah
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10:28 < Tyrant> delinquentme, have you talked directly to SENS people? (not aubrey)
10:29 < delinquentme> Tyrant, nah cant say i have
10:29 < delinquentme> isnt he the main dude
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12:06 < Tyrant> delinquentme, he's the "main dude" in the sense that he's their figure head. if you want to do work in the labs though the best people to talk to are theo nes that work their, they have quite a bit autonamy about who they get as interns, etc.
12:07 < Tyrant> also I know the sens lab in the bay area is using a tecan for which they could use quite a few modifications
12:31 < delinquentme> hmmm
12:31 < delinquentme> i think if i had my choice
12:31 < delinquentme> halcyon would be #1
12:31 < delinquentme> thoughts Tyrant ?
12:32 < Tyrant> I dont think theres much youd be able to do at halcyon
12:32 < delinquentme> specifics?
12:33 < Tyrant> well their current problem isn't throughput or automation
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12:33 < Tyrant> and working on their transmission electron microscope requires a very advanced understanding of its operation
12:34 < delinquentme> oh! there are public statements of the tech they're currently working on??
12:34 < Tyrant> their big problem right now is a lack of metalorganic chemists
12:34 < Tyrant> in the thiel network, yes
12:34 < delinquentme> thats one of the things i was looking for ... bc damn if all these biotech companies were like "This is what we are trying to solve"
12:34 < delinquentme> it would make it hella easy to be like " ok lets start here"
12:34 < delinquentme> thiel network O_o;;;
12:34 < delinquentme> ?
12:35 < Tyrant> the network surrounding sens, halcyon, etc. etc.
12:35 < delinquentme> i mean how'd you get access to this info
12:35 < Tyrant> im a thiel fellow
12:35 < delinquentme> @_@
12:35 < delinquentme> waiiit you're one of the 20 under 20??
12:35 < delinquentme> sorry wait
12:35 < Tyrant> yeah
12:36 < delinquentme> http://en.wikipedia.org/wiki/Organometallic_chemistry
12:36 < Tyrant> the info isnt very difficult to get from bryan anyway
12:36 < delinquentme> ^^ thats what they're after right
12:36 < Tyrant> yeah
12:36 < delinquentme> Tyrant, were you the guy building the HPLC machine?
12:36 < Tyrant> yea
12:36 < delinquentme> oh shit!
12:36 < delinquentme> hahah god IRC is so bad ass!!!!
12:37 < delinquentme> wow awesome to meet you
12:37 < Tyrant> where do you live?
12:37  * delinquentme shakes
12:37 < delinquentme> pittsburgh
12:37 < Tyrant> ah
12:37 < Tyrant> you need to go to the bay area for sens/halcyon/etc.
12:37 < delinquentme> frankly im interested in anyone who has stated purposes of human life extension
12:37 < delinquentme> anywhere
12:38 < Tyrant> I think what you're looking for is a startup that works on it
12:38 < Tyrant> and thats bay area
12:38 < delinquentme> yeah man i've been in a startup for a while now and startup is definitely what im after
12:38 < Tyrant> A startup in pittsburg? :P
12:38 < delinquentme> yeah haha
12:39 < delinquentme> they're here
12:39 < delinquentme> they're modest you know
12:39 < delinquentme> but im just
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12:39 < delinquentme> meh. like ive got this exhaulted image of what a startup founder should be
12:40 < Tyrant> theres no single image of a startup founder
12:40 < delinquentme> absolutely
12:40 < delinquentme> however theres passion
12:41 < Tyrant> generally that and hard work are the only global traits
12:42 < delinquentme> yah =] i wont say anymore
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16:21 < delinquentme> Collaborative Drug Discovery (CDD)  << thoughts anyone?
17:09 < klafka> hey
17:09 < klafka> in what sense?
17:15 < delinquentme> have you heard of em... and if you've got thoughts :D
17:16 < klafka> oh it's a thing
17:16 < klafka> no
17:19 < klafka> what is really collaborative about it
17:19 < klafka> it's like 'do your drug research in the CLOoooOOOooOOoooud
17:20 < delinquentme> lol are you sure?
17:20 < delinquentme> their website seems to be about collaborative drug discovery
17:26 < klafka> https://www.collaborativedrug.com/
17:26 < klafka> ?
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17:27 < delinquentme> yar!
17:28 < klafka> i guess the public part
17:28 < klafka> is open
17:29 < delinquentme> klafka, have you ever removed parts of DNA from an organism?
17:29 < klafka> sure
17:29 < delinquentme> oh
17:29 < delinquentme> bamf
17:29 < delinquentme> whats that process involve?
17:30 < klafka> um well i only did it from bacteria
17:30 < delinquentme> so yeah how would i do that with ecoli
17:30 < klafka> umm, i'm pretty sure I put a ligase in LB broth  + ecoli and spun them in a centrifuge
17:31 < delinquentme> LB ?
17:31 < klafka> the culture medium
17:31 < delinquentme> and spinning them in a centerfuge?
17:31 < klafka> yeah
17:31 < delinquentme> what does that contribute to the exchange / removal of genes?
17:31 < delinquentme> energy?
17:31 < klafka> it is used to separate DNA from the other crap in the cell
17:32 < delinquentme> OHHHhhhhhh
17:32 < delinquentme> so youre busting the organism open .. grabbing its DNA .. then you'd do the replacements
17:32 < delinquentme> derp this is actually miniprep stuff isnt it?
17:32 < klafka> yeah
17:32 < klafka> yup
17:32 < klafka> this is just standard dna purification + amplification proces
17:32 < klafka> s
17:33 < delinquentme> reading this article w church talking about creating an ecoli "chassis"
17:33 < delinquentme> IE removing as much of the DNA as possible to support a living ecoli organism
17:33 < evolv> I did it from birds and nonaviant reptiles
17:34 < delinquentme> and then using that guy to ker-chunk functional DNA snippets to do stuffs
17:34 < delinquentme> so then after you sub the plasmids in ... you just incubate
17:34 < delinquentme> and if stuff grows >> great success?
17:35 < delinquentme> i feel like im missing some part
17:36 < delinquentme> subbing in the plasmids >> electroporator :P
17:37 < klafka> sort of like what venter did
17:40 < delinquentme> yeah but theres complexity that im missing there
17:40 < delinquentme> is it the same process to get a organism to take up a new chunk of DNA as it is to get it to ditch some of its existing DNA?
17:41 < delinquentme> surely replacing ... would be different than " drop these basepairs and reconnect"
17:54 < klafka> no
17:55 < klafka> usually organisms only get rid of DNA if you lyse the cells
17:55 < klafka> you can get organisms to take up DNA much easier
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18:09 < delinquentme> http://benkrasnow.blogspot.com/2011/03/diy-scanning-electron-microscope.html
18:09 < delinquentme> check it!
18:09 < delinquentme> klafka, correct me if im wrong but after lysing a cell that organism is no more
18:09 < delinquentme> right?
18:10 < klafka> well if it's single celled
18:10 < delinquentme> you can selectively lyse cells?
18:10 < delinquentme> i assumed that when you lyse .. all the stuff pops
18:10 < QuantumG> presumably you could
18:11 < delinquentme> i guess i didnt follow klafka's statement on why multicellular wouldnt die from lysing?
18:12 < QuantumG> I expect he was presuming also :)
18:13 < klafka> haha well i mean you can lyse cells only locally
18:13 < klafka> for instance
18:13 < klafka> or you can remove the cells from a multi-celled organism then lyse them
18:14 < QuantumG> or just shoving a pin into your finger...
18:16 < klafka> right
18:16 < klafka> hence locally
18:20 < delinquentme> -_________-
18:23 < delinquentme> tagged my electron microscope post for relocation on stack over flowwww woot woot
18:28 < QuantumG> so what sort of resolution _do_ you get?
18:28 < delinquentme> QuantumG, on the DIY electron microscope?
18:28 < delinquentme> or?
18:28 < QuantumG> ya
18:29 < delinquentme> oh i didnt get all the way through the video
18:29 < delinquentme> this is strictly a concepting excercise
18:29 < QuantumG> oh, I thought this was you
18:29 < delinquentme> oh no
18:30 < delinquentme> its sweet that we'd expect that from this channel though huh :D
18:30 < delinquentme> QuantumG, what do you do on the daily?
18:30 < QuantumG> well, I was actually about to say that I'm thoroughly impressed. :)
18:30 < delinquentme> my heads abuzz with thoughts of venters work, with churches work, with left coast biotech startups .. man .. its wild right now
18:31 < klafka> hey so have we gotten any farther with the 5 man project?
18:31 < delinquentme> klafka, nope not that i know of .. i proposed we work on some of the life sciences challenges
18:31 < delinquentme> really I wish i had everyones resumes
18:31 < delinquentme> like i've got mine handy if youd like it
18:32 < delinquentme> .. wait are you part of the 5?
18:32 < klafka> kanzure said i can by
18:32 < klafka> be
18:32 < klafka> oh i can send you mine
18:32 < klafka> what's your email?
18:32 < delinquentme> carlcrott@gmail.com
18:32 < delinquentme> yeah ill shoot you  mine
18:33 < delinquentme> you guys have heard of the OpenPCR right?
18:33 < delinquentme> i was wondering what it would cost to make their heating block 96 well
18:33 < delinquentme> any ideas?
18:33 < delinquentme> i feel kind of rude asking tito outright
18:33 < klafka> not offhand
18:34 < klafka> i guess the one thing my resume doesn't show that is relevant to this channel is i have quite a bit of bio experience
18:34 < klafka> i'm 6 classes shy of a bs in bioinformatics (6 classes that are like 40,000 total though :()
18:35 < delinquentme> klafka, ignore that chat invite.. was getting punchy
18:35 < klafka> ah
18:35 < delinquentme> 40 grand?
18:35 < klafka> eh no maybe 25k
18:35 < delinquentme> feck
18:35 < delinquentme> dude seriously
18:35 < delinquentme> simplifying bio education
18:35 < klafka> i think i t's like 2500 or 4k a class
18:36 < delinquentme> esp on the high end
18:36 < delinquentme> fuck everything about those college courses
18:36 < klafka> heh
18:36 < klafka> that was when my father decided to no longer pay for my education
18:36 < delinquentme> ... PS are you guys enrolled in the free stanford AI class?
18:36 < klafka> so i got my one bs
18:36 < klafka> no
18:36 < klafka> i've watched most of andrew ng's ml class, and i've taken a bunch of ML / pattern recognition classes
18:37 < klafka> maybe i should watch it though, it's like peter norvig
18:37 < klafka> he's kind of awesome
18:37 < delinquentme> http://www.ai-class.com/
18:38 < delinquentme> klafka, have you dont any bayesian implementations in ruby?
18:38 < delinquentme> done**
18:38 < klafka> aah no, i've thought about it
18:39 < klafka> i've done stuff that is not really Bayesian but not really frequentist either
18:39 < klafka> although i'm fairly familiar w/ Bayesian learning
18:39 < delinquentme> i read a bit about it
18:39 < delinquentme> its just probabalistic models right?
18:40 < delinquentme> ba ba ba balistic
18:40 < delinquentme> lulz
18:41 < klafka> um Bayesian learning? well it does imply a probabilistic model, but it's a specific type of one
18:41 < delinquentme> dude turns out i derped on sending this one girl my resume
18:41 < klafka> it's one where you integrate over all possible priors
18:41 < klafka> er
18:41 < klafka> not priors
18:41 < delinquentme> assumptions
18:41 < klafka> but over the entire space
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18:45 < delinquentme> damnnnn some reason my resume it taking forever to send
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19:07 < kanzure> sup
19:07 < klafka> oh deli oh you left
19:07 < klafka> hey kanzur
19:07 < klafka> e
19:09 < kanzure> reading backlog..
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19:27 < kanzure> klafka: hey, how about a lego design sharing site
19:27 < kanzure> delinquentme: do you like that project idea?
19:27 < kanzure> ybit: you?
19:27 < kanzure> Nam-Ereh-Won: would you be ok with that?
19:27 < kanzure> foucist: or you?
19:28 < klafka> hmm lego sharing could be cool
19:28 < kanzure> like for leocad designs
19:28 < kanzure> there's no modern site for doing this, last i checked
19:28 < kanzure> also a plugin to leocad to download it, or an iphone/android client to view designs
19:29 < klafka> i see
19:30 < klafka> can we interface it with a social network and then develop algorithms to recommend you other leocad designs?
19:30 < klafka> :P
19:30 < kanzure> sure why not
19:30 < klafka> heh
19:30 < kanzure> we can also do GAs on designs
19:30 < kanzure> and other wacky shit..
19:30 < klafka> oh fun
19:30 < kanzure> fenn wrote a lot of lego-related code for skdb "back in the day"
19:31 < kanzure> http://diyhpl.us/cgit/lego/
19:31 < kanzure> we can also enlist mike rayhawk for some graphic design http://mikerayhawk.com/
19:38 < Nam-Ereh-Won> oooh
19:38 < Nam-Ereh-Won> and the projects could generate bricklink shopping lists
19:47 < delinquentme> lego sharing
19:48 < kanzure> yeah there's some pretty good individual-lego-buying sites out there
19:48 < delinquentme> ahah well i dig legos .. examples?
19:49 < kanzure> uh.. i don't remember any of them off the top o my head
19:49 < kanzure> fenn might
19:55 < klafka> i am not really too familiar with legos
19:56 < klafka> well
19:56 < klafka> i assume you're talking about not the normal legos
19:57 < foucist> kanzure: limited market..
19:58 < kanzure> there's no market whatsoever
19:58 < kanzure> but the market isn't the oint
19:58 < kanzure> klafka: mostly the normal legos
19:58 < klafka> oooh ok
19:58 < kanzure> foucist: it's just a project to get on the ol' resume
19:59 < foucist> kanzure: there's a lot of other moer useful things you could do tho perhaps
20:00 < kanzure> like what
20:16 < delinquentme> now cant you just make these on the lego website?
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20:30 < kanzure> delinquentme: what?
20:30 < kanzure> i said a lego sharing site
20:32 < klafka1> kanzure
20:32 < klafka1> you know what would be cool
20:32 < klafka1> 'how well will my laptop run linux'
20:32 < klafka1> you give the website specs/model name/number
20:32 < klafka1> it (if given a model name/number) crawls for specs, asks for confirmation, and returns any potential driver issues
20:35 < delinquentme> i say we start a website that lets people run genetics expiriments that look cool in test tubes
20:35 < delinquentme> it would be like DIY bio lab decorative expiriments
20:36 < klafka1> man installing scipy on this linux vbox
20:36 < klafka1> fuun
20:36 < klafka1> building atlas atm
20:37 < kanzure> delinquentme: that makes no sense
20:37 < kanzure> "that letsp eople run genetic experiments".. they are already able to do that
20:37 < kanzure> what are you talking about, specifically?
20:41 < delinquentme> http://dbprng00ikc2j.cloudfront.net/work/image/323776/mf2ji7/testtube_plants.jpg
20:42 < kanzure> delinquentme: are you the type of person that doesn't tend to think in complete thoughts or sentences?
20:43 < delinquentme> lol
20:43 < QuantumG> this _is_ the ADHD channel
20:43 < delinquentme> im tracking down images
20:43 < delinquentme> and i just helped my little bro make his PS3 gamertag ... pedobear
20:43 < delinquentme> =/
20:43 < delinquentme> my name is on the account
20:44 < uniqanomaly> pedolicious
20:44 < uniqanomaly> haha
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20:47 < delinquentme> test tube bonsais >_<
20:47 < delinquentme> http://static3.depositphotos.com/1000708/115/i/950/depositphotos_1157988-Leaf-buds-in-test-tube.jpg
20:47 < delinquentme> we could make hippy fodder
20:48 < delinquentme> embed plant seeds into tapioca balls
20:48 < delinquentme> they could throw it and greenify the world
20:48 < delinquentme> http://lh4.ggpht.com/-9C9XBxNXuUc/STGNmfsxyTI/AAAAAAAATmo/JzqJTGLTFQY/IMG_3578.JPG
20:49 < delinquentme> how hard is it to engineer flourescent algae
20:49 < delinquentme> i know other groups have done it
20:49 < kanzure> in a month?
20:49 < delinquentme> get test tubes with a few shades of glowing algae?
20:49 < kanzure> what the hell man
20:49 < kanzure> :(
20:49 < kanzure> you guys don't even live together
20:49 < delinquentme> out source that shit!
20:50 < delinquentme> infact there was a kickstarter with GFP
20:50 < delinquentme> that'd be hot :D
20:56 < delinquentme> umm derp?
20:56 < delinquentme> The rationales behind the comparison of sequences may be manifold.
21:12 < kanzure> are you a hidden markov model bot
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21:13 < delinquentme> bayesian
21:13 < delinquentme> noper!
21:14 < delinquentme> lol im reading the bioinformatics tut on the max planck society website and that "manifold" was on there
21:17 < delinquentme> http://www.wired.com/dangerroom/2011/06/pentagons-new-factory-your-dna/  << darpa grants?
21:17 < delinquentme> i think they've got a few bucks
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23:53 < ybit> current project is to make a site for a local jewelry store, i think $2000 is a good asking price. they don't want to pay by the hour
23:54 < ybit> a friend of mine is giving me a template he used when freelancing, i think he got it from legalzoom.com
23:54 < ybit> that should give me enough money to get in school
23:55 < ybit> i've got enough now, but that will pay for me to actually live
23:56 < ybit> ..so no lego repo for now
--- Log closed Tue Aug 09 00:00:16 2011