2012-02-22.log

--- Log opened Wed Feb 22 00:00:21 2012
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kanzurebooop07:45
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kanzureboop09:48
Mokbortolan_Poop.09:52
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Mokbortolan_kanzure: is microwaved food safe, or is it a witch's brew of microwave-induced isomerized substances?09:53
Mokbortolan_err, a witch's brew of microwave-induced isomerizations?09:54
kanzurei don't know i'm not paranoid enough09:54
kanzuresomething something about not microwaving plastic09:54
Mokbortolan_I've read all these articles at "health" magazines, but I can't find any real research underlying the claims09:55
kanzurestop reading magazines :P09:55
Mokbortolan_they're the only ones with the chutzpah to challenege the microwave-manufacturer oligarchy! :p09:55
Mokbortolan_I've read about using microwaves in chemistry for a while09:56
Mokbortolan_so I know it does change food chemically...09:57
Mokbortolan_maybe I should do a mouse experiment with my daughter09:57
kanzureyou could also consider doing a water microbe project with her09:57
kanzurego to some local water bodies, lakes, streams, oceans and gather some critters09:58
kanzurebuy a nice microscope, take some videos09:58
Mokbortolan_yeah! I did that in school09:58
Mokbortolan_egg-yolk and paramecium09:58
kanzuresee if you can raise them09:58
kanzureetc. as a kid i would have loved that (i still do)09:58
kanzurei was more of a bug catcher; i didn't know things were that small :(09:58
Mokbortolan_I need to get a decent microscope09:58
Mokbortolan_I read about an adult wasp... smaller than a paramecium09:58
foucistsaw something about microwaves being less damaging on food than conventional means of heating, good for steaming veggies etc.. forget where though09:58
Mokbortolan_0.13mm09:59
Mokbortolan_they hatch (and mate!) inside insect eggs09:59
Mokbortolan_cant' remember what type of eggs, might be bees09:59
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kanzurewhy is dna-directed dna polymerase called "nucleotidyltransferase"10:14
kanzurewhat does -tidyl- have to do with it10:14
uniqanomalyhttp://img140.imageshack.us/img140/8797/33108908.jpg nanotech company name idea10:17
uniqanomalynot mine10:17
Mokbortolan_Nigerian Nanotech Inc.10:19
Mokbortolan_?10:19
rkosmaybe it could be used in the movie 2016 http://www.youtube.com/watch?v=iXYmFqEkCGQ10:19
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kanzurewhat about a series of switchable guanylyltransferases11:09
kanzurewe'd need 16 switchable enzymes11:10
kanzurepoly(n)-adenosine guanylyltransferases, poly(n)-guanine guanylyltransferases, poly(n)-thymine guanylyltransferases, poly(n)-cytosine guanylyltransferases11:11
kanzureunfortunately you would also have to wait for these to dissociate and for the next to attach when you switch your light over11:11
kanzurealso, they don't exist.11:12
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delinquentmeI might have to deploy this on amazon12:11
delinquentmehmmmm!12:11
delinquentmenot sure if heroku lets free customers run javer12:11
ParahSailinany way to have google alert for google scholar?12:16
kanzure"A chimeric construct in which loop1 from TdT was inserted in Pol mu displays terminal transferase activity, but a largely reduced DNA-dependent polymerization"12:18
ParahSailinwhat do you guys think about adhd12:18
kanzurei think adhd is great12:18
ParahSailinnot sure if i have it12:18
delinquentmeParahSailin, I think theres a big market for it12:19
delinquentmeand if you're a hammer every problem looks like a nail12:19
ParahSailinadderall makes me superman12:19
delinquentmeme too12:19
delinquentmebut then again any anphetamine does12:20
ParahSailini mean i can be lazy, and most of the stuff on dsm-iv would describe me12:20
ParahSailini guess there's just a continuum of "energy level" as a temperamental trait12:20
ParahSailinmotivation, akrasia, all that too12:20
delinquentmeParahSailin, i think ADHD is a combination of the fact we've got drugs for focus, parents with health insurance and college being shitty at engaging the students12:20
rkosi don't think you're ever going to get to the end of it if you try to think about whether someone really has a syndrome from the dsm or not12:21
ParahSailinbut man the people in #/r/ADHD are pretty hostile to that idea12:21
ParahSailinthe raging victimhood12:21
kanzureadhd+adderall is very different from not-adhd+adderall, from what i can tell12:21
ParahSailin"we are different in kind from you, not in degree"12:21
delinquentmeParahSailin, victimhood is awesome12:21
delinquentmeits like an extension of religion!12:21
delinquentmeim lazy!12:21
delinquentmebut its not my FAULT12:21
kanzureParahSailin: solution, stop reading reddit12:21
delinquentmeYESSS12:21
rkosi tend to think that if someone can get some use out of CBT/drugs for their life then thats the only justification you need12:21
delinquentmedont reddit unless r/boobies12:22
delinquentme:P12:22
Mokbortolan_yeah, there are very definite differences in the brains of people diagnosed with adhd and those who do not meet those criteria12:22
delinquentmekanzure, any idea if I can get java on heroku for a rails application?12:22
rkosno need to try to appeal to some god given normal state which you need medical assistance to reach12:22
delinquentmebut i mean my life is so much better when things arent my fault12:23
kanzuredelinquentme: no i think you have to choose a particular stack on heroku12:23
kanzuredelinquentme: stop channeling redditisms in to here.. they aren't useful12:23
Mokbortolan_and the characteristics for ADHD start in childhood and are a common thread throughout a sufferer's life12:24
Mokbortolan_it's basically a developmental disorder12:24
Mokbortolan_AFAIK12:24
delinquentmekanzure, motivation :P12:24
delinquentmebut it doesnt work for everyone12:25
ParahSailini guess "doesn't like to do things that are not very rewarding" is a disease now12:25
kanzureParahSailin: i think you're talking about different things12:25
delinquentmeParahSailin, so when parents were taught12:25
delinquentme*NOSE TO THE GRINDSTONE*12:25
delinquentmeeat shit till it tastes good!12:25
ParahSailinthats pretty much the conclusion i came to on my own, but i went to #/r/ADHD to get the contrary view12:25
delinquentmeaka the military model12:25
delinquentmewell yeah!12:25
kanzureadhd is presumably caused by some particularly different receptors on neuronal membranes12:25
kanzureany of the psychological explanations of adhd are bullshit12:26
delinquentmewho wants to be emotionally raptured when you can just eat shit day in and day out12:26
kanzureit's like trying to explain schizophrenia with psychology12:26
rkoswell illness has never been an absolute12:26
Mokbortolan_http://www.citeulike.org/user/xinian/article/178726212:26
kanzurei think you two are just being drawn into the reddit hype12:26
kanzureso i suggest you stop that..12:26
* delinquentme humps Mokbortolan_ 's leg12:27
* delinquentme mantra: composure12:27
delinquentmeJuul, you didnt host your RJB on heroku did you?12:27
rkosbut there is no real test for ADHD kanzure12:28
kanzurerkos: you can do sequencing to determine what sort of mutations on receptors you have12:28
rkosso when you talk about ADHD you talk about a very large group of people that aren't defined by something concrete like different receptors12:28
kanzureare you talking about misdiagnosing people?12:29
kanzureor the disorder itsel12:29
kanzure*itself12:29
rkoswell sequencing is not used in clinics and certainly not in psychiatry here at least12:29
* delinquentme sings ke$sha at the top of his lungs12:29
delinquentme^^^ ADHD12:29
ParahSailinwell a video i just watched gave fmri stuff about areas of the brain that dont light up for adhd12:30
rkosisn't ADHD defined by some list of symptoms instead of some concrete feature like the receptor thing?12:30
kanzurerkos: ok so how is that not a real test12:30
kanzureyes it's true that people make mistakes when diagnosing patients.. is that what you want to talk about ??12:31
rkosi didn't even know there was any test for ADHD12:31
ParahSailinif its a receptor thing, then the only solution is chemical dependency?12:31
kanzureParahSailin: not necessarily of course12:31
Mokbortolan_"ADHD" will likely be split up into separate disorders in time12:32
rkosbut i have a friend who has ADHD and he was just given meds after a few vists and no test12:32
kanzurerkos: to be fair, it's more like "here's a lot of shit that we observe in adhd versus controls"12:32
Mokbortolan_mine is "ADHD - Predominantly Inattentive".  I don't have any hyperactivity symptoms, for example12:32
ParahSailinbecause i'd like to solve my problems, but i dont trust the integrity of most docs12:32
kanzureMokbortolan_: mine is adhd-hyperactive12:32
ParahSailinor the state of medical science for that matter12:32
kanzureParahSailin: nor should you12:33
Mokbortolan_you CAN use them to inform your own search for increased performance12:33
ParahSailini dont know where to look for better info12:33
ParahSailinyah i guess i would be adhd-i as well12:34
ParahSailinwhat they used to call ADD12:34
Mokbortolan_but I don't buy this whole transfer of responsibility to physicians12:34
kanzurehow do you know that's not ADD12:34
kanzureADD and ADHD definitely have differences12:34
ParahSailindsm-iv calls add adhd-i12:34
kanzurehmmm is that so12:35
ParahSailinproblem with adderall is that it makes me completely emotionally cold12:35
Mokbortolan_the wiki on ADHD-PI is very good12:35
kanzureParahSailin: that's odd, i'm sorry to hear that12:35
Mokbortolan_adderall kills my creativity12:35
Mokbortolan_and makes me socially weird12:35
kanzurekills your creativity?12:35
kanzureman i must have hit the jackpot12:35
Mokbortolan_yep12:35
ParahSailini wish i could turn on and off adderall mode for just when i needed it12:36
Mokbortolan_I think (conceptually) it focuses activity, whereas normally I'm calling on regions spread throughout my brain12:36
kanzurealso i tend to ignore anything that talks about adhd in terms of dopamine.. dopamine is such a cop-out answer12:36
ParahSailini dont need to stay awake in the 2s and 3s am12:36
kanzurealthough talking about particular dopamine receptors might be ok12:36
ParahSailini just need four hours of high focus work12:36
Mokbortolan_so I can get better at the task at hand, but I can't reference other data useful in  conceptual leaps12:36
kanzureParahSailin: then use the smaller dosages?12:36
kanzureParahSailin: i really like the enzyme engineering that went into this12:38
rkosor methylphenidate instead of adderall12:38
kanzureParahSailin: http://diyhpl.us/~bryan/papers2/polymerase/A%20specific%20loop%20in%20human%20DNA%20polymerase%20mu%20allows%20switching%20between%20creative%20and%20DNA-instructed%20synthesis.pdf12:38
kanzure"Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region"12:40
kanzurethat's also cool^12:41
kanzure"Class II enzymes (found in bacteria and eukaryotes) carry a flexible loop in their catalytic core required for switching the specificity of the nucleotide binding pocket from CTP- to ATP-recognition."12:43
kanzurestalk: Tom Hargreaves <hex@freezone.co.uk>12:51
kanzurehttp://sphere.chronosempire.org.uk/~HEx/tmp/prop.pdf12:51
kanzure"Light-dependent RNA polymerase: a research proposal"12:51
kanzurehttp://sphere.chronosempire.org.uk/~HEx/12:53
kanzurealso he makes sonic music :3 http://sphere.chronosempire.org.uk/~HEx/sonic/12:54
kanzurelooks like he's an ok programmer https://www.google.com/search?num=100&hl=en&q="hex%40freezone.co.uk"12:55
ParahSailinredox might be best way to control an enzyme13:01
kanzuredelinquentme: i sent you a rails job email13:02
delinquentmeoh hot!13:02
Mokbortolan_http://www.popsci.com/technology/article/2012-02/new-disposable-dna-sequencer-runs-molecular-analysis-powered-usb13:02
kanzureMokbortolan_: not released yet ;)13:03
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archels<span class="hideMe">13:43
archels<strong>Guardian Angels</strong>13:43
archels<em>for a smarter life</em>13:43
archelsWhat is this doing behind the logo of the Human Brain Project (www.humanbrainproject.eu)?13:44
kanzure*shrug* lots of insecure servers out there13:46
kanzurepage.onLoadFinished = handle_checkout_page_reloading;13:46
kanzureerm.. ignore that13:46
kanzureuhm.. cathal just posted an email: " - To further explore the DIY aspect of eating in the future, the13:47
kanzurebutcher Ed Hick will give a live demonstration on how to skin and13:47
kanzureprepare a whole rabbit. www.hicks.ie"13:47
roksprokdoes that mean all cooking is diybio?13:55
roksproki guess home brewing is pretty similar anyway13:55
Mokbortolan_if by "diybio" you mean "struggling to survive", then yes!13:56
Mokbortolan_Now who's up for a game of Centrifugal Bumblepuppy?!?!14:01
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archelsGuardian Angels, a project to develop nanoscale sensors and interfaces for detecting and responding to environmental danger.14:10
kanzureis that a lifeboat foundation thing14:14
kanzurearchels: how's your protein engineering / rational desig14:14
kanzuredesign14:14
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archelskanzure: practially zero, I'm trying to engineer neural networks instead.14:21
ParahSailinwhats your protein engineering thing14:31
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kanzurehrmm short-patch compartmentalized self-replication14:41
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foucistanyone here into evolutionary computation ?16:03
kanzurei've dabbled a bit with GAs and evolutionary search16:04
foucistcool16:07
foucistkanzure: btw, you know of a rails job?16:07
kanzureyeah a few..16:07
kanzureneed something?16:08
kanzure*need one?16:08
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kanzurehttp://news.diybio.org/17:01
kanzurewelp there goes http://bit.ly/diybionews217:01
n_benthahey kanzure17:02
n_benthais that group about sequencing dna using enzymes instead of chemical anaylsis?17:03
kanzureit's not sequencing. synthesis.17:04
kanzureand yes.. using an enzyme17:04
n_benthaoh. ribosomes have u beat17:05
kanzureno ribosomes do their own thing17:06
n_benthaoh dna synthesis17:06
n_benthai know ribosomes are different, sorry17:06
n_benthadna pol 3, right?17:06
kanzureribosomes aren't under direct human control17:06
kanzurepolymerase isn't either17:06
kanzurethere is no particular polymerase picked out yet17:06
kanzurebut there are many candidates (about 3000)17:06
n_benthaso u want to be able to synthesize dna de-novo?17:07
kanzurei want to control dna polymerase's activity with either light, electricity or mechanical mechanisms17:07
n_benthainstead of making oligio's?17:07
kanzure*optical17:07
n_benthaah cool17:07
kanzure*electrial17:08
kanzure*electrical17:08
n_benthaso flash one wave length and have it add some A's, and another wavelength and have it at some T's?17:08
kanzureit doesn't have to be light, but yes.17:08
n_benthaah that would be cool. but wouldn't rearrangement of existing sequences combined w/ oligios work better?17:09
kanzurewhat?17:09
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kanzureare you a biologist?17:09
n_benthayes17:09
kanzureok so you're talking about ligating things together?17:09
n_benthaof course17:09
kanzureok yes i agree ligation is a useful mechanism17:10
kanzurewe've developed a ligation scheme that we want to test (in this channel)17:10
kanzurebut it's unrelated to the enzymatic synthesis roadmap17:10
n_benthaoooh cool17:10
n_benthai guess i just don't stand the purpose of the enzymatic synth17:10
kanzuredna polymerase is many thousands of times more efficient than chemical oligo synthesis17:11
n_benthatrue17:11
kanzureand in the time that it takes you to access your oligo library for ligation, it will have already synthesized whatever it was from your library that you were trying to fetch ;)17:11
n_benthaah ok i see what you're saying.17:12
n_bentha it seems like a space-pen situation to me (so much effort to make a pen that writes in space when the russians just used pencils), but i'm a conscientious objector so don't let me discourage the endeavor17:13
kanzurethis enzyme already exists17:14
kanzureit's just doing its own thing.17:14
n_benthaoh u want to modify it17:14
n_benthacool17:14
kanzureare you sure you're a biologist :x17:14
kanzurei mean, polymerase definitely exists17:15
n_benthayes17:15
n_benthabut haven't many complex sequences arisen from errors in replication?17:17
n_bentharesulting in rearrangements of sequences17:18
kanzuresome polymerases have better fidelity and error correction than others. for instance, some have a 1-in-10,000 error rate.17:19
n_benthaof course17:21
n_benthai wasn't necessarily talking about those kinds of errors, but was just saying that new sequences have come about through errors17:22
n_benthaso it's unlikely that there's an enzyme that'll be able to link specific amino acids together17:23
kanzurewe're not linking amino acids17:23
n_benthanucleotides*17:24
kanzurewell, what about CCA-adding enzyme.. seems like that exists to me..17:24
n_benthamaybe...17:29
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delinquentmelawl18:31
delinquentmethank god for headphones18:31
delinquentmemusic. it makes you soar18:31
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delinquentmeand it also makes you want to rip faces18:31
delinquentmethank god im not ripping faces w this terribul coffee shop muzak18:32
mag1stra1edelinquentme: How did the interviews go?18:39
delinquentmemag1stra1e, not bad! but I want everything to happen faster18:39
delinquentmegot 2 more tomorrow18:40
delinquentmemaybe 3 so well see18:40
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mag1stra1ethats great man!18:41
mag1stra1eHow was the one job you really wanted to do?18:42
mag1stra1eDid they give you a pay scale for it yet?18:42
kanzureyashgaroth: so i was reading something today about chimeric polymerases18:46
yashgarothlike those modified high-fidelity/temp ones?18:47
kanzurenope18:47
kanzurehttp://diyhpl.us/~bryan/papers2/polymerase/A%20specific%20loop%20in%20human%20DNA%20polymerase%20mu%20allows%20switching%20between%20creative%20and%20DNA-instructed%20synthesis.pdf18:48
delinquentmemag1stra1e, nahh man! no payscales yet18:50
yashgarothit seems like if you can decouple the processivity of the pol from the phosphate being released, you could add one at a time, if you then allow it to proceed with an external signal18:51
kanzurethe polymerase motor is sorta well studied, but yeah that's still an unknown18:51
yashgarothbut like with all of this, you'll need to be significantly more reliable than chemical synthesis18:51
kanzurei'm more worried about switching nucleotide selectivity18:51
mag1stra1edelinquentme: have you interviewed with that company yet?18:52
yashgarothare we still focused on washing in the nucleotide for each step, or using transfer-RNA-like adaptors that can be activated at will18:52
kanzurei don't think i've seen any engineered protein with 4+ chromophores or other light/mechanical/electrical inducable confomational change18:52
kanzurewashing is not ok in my opinion18:52
kanzurewashing significantly defeats the purpose18:52
yashgarothokay good cuz that'll be unreliable18:53
delinquentmemag1stra1e, yeahh the LBL one phone interview .. the dude said he was impressed but whoknows18:53
delinquentmepayrate could go either way as they're closely coupled bc being a *HUGE* lab << lots of gov funding18:53
delinquentmebut they're also .. gov funded18:53
yashgarothbut yeah if you're trying to get one molecule with four light-selectable motifs to add each base, and only doing one at a time, you might as well just design one from scratch18:54
mag1stra1edelinquentme: I really hope it works out for you!18:54
kanzureyashgaroth: i don't even know how that would look.18:54
yashgaroththe elongation is pretty energetically favorable, and all pol does is make sure it matches the template, which we're not doing anyway18:54
mag1stra1eit could be promising if he really likes you18:54
mag1stra1eJust got to keep your hopes up I guess lol18:54
delinquentmemag1stra1e, keep applying is what it is :D18:55
yashgarothoh man I have no idea how it'd look either, but we're modifying pol so heavily that it'll be a totally new structure anyway18:55
kanzurewell no i mean.. if you have 4 nucleotide binding pockets, where do they go18:55
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yashgarothoh, I was hoping one carrier protein for each nucleotide18:56
kanzurei'd rather only interface with 1 giant enzyme18:56
mag1stra1e:)18:56
yashgarothcomplexes, man, nature loves a good complex18:56
kanzurewhat are you going to do, wait for your laser to transfer enough energy to all the nucleotide-protein complexes?18:57
yashgarothwhere did laser come in18:57
kanzurehuh?18:57
kanzurewhat mechanism are you talking about?18:57
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yashgarotha laser works, but I was thinking more diffuse light, unless you're doing a thousand different reactions in a small area, which I guess you plan to18:58
kanzurethere's a lot of ADP/GTP/CTP-binding enzymes that have pretty good selectivity19:00
kanzurewe could just steal binding pockets from them19:00
delinquentme2012-02-23T03:01:31+00:00 heroku[web.1]: State changed from starting to crashed19:02
kanzurecongratulations you probably have a syntax error19:02
kanzuredid you run it locally first19:02
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delinquentmekanzure, thats..19:03
delinquentmenot a bad idea19:03
delinquentme2012-02-23T03:01:26+00:00 app[web.1]: Exception in thread "main" java.lang.NoClassDefFoundError: org/jruby/Main19:05
delinquentmedis19:05
delinquentmeok so I've verified that it downloaded that file correctly...19:08
delinquentmekanzure, is this if  fi stuff shell scripts19:18
delinquentme?19:18
kanzurewhere are you looking19:20
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delinquentmesometimes I feel like I pitch some heavy shit in my emails hahah20:28
delinquentmekanzure, the email attached to that position you forwarded is busted20:29
kanzurejust email whoever sent it20:30
delinquentmejring@sharedhr.com is in the from field20:31
kanzureyeah just email that person20:33
delinquentmegot it sorted20:36
delinquentmethanks for the heads up20:36
delinquentmeNAO20:38
delinquentmewe interface w the heorku20:38
delinquentmeNO!20:38
delinquentmet3h sinatra20:38
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sylph_makoSo, how about that google HUD thing.22:07
sylph_makoPersonally I'm underwhelmed but I still desperately need an optical uplink and I'll take what I can get.22:08
zacharycohn_sylph_mako: it's an early look at the v1.22:10
zacharycohn_I'm pretty excited, I will probably get one22:10
sylph_makoIt is very exciting. To see something like that finally being pushed mainstream.22:10
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Stee|sylph_mako, link?22:24
sylph_makoStee|, http://bits.blogs.nytimes.com/2012/02/21/google-to-sell-terminator-style-glasses-by-years-end/22:26
Stee|good22:38
Stee|that'll help development efforts22:39
kanzurehelp what?22:39
Stee|we're working with some sixthsense stuff on my site22:40
Stee|this makes a nice neat package for that22:40
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sylph_makoCould I get a link to that stuff Stee|?23:07
* kanzure sleeps23:11
Stee|sylph, the convo?23:13
Stee|we're just getting started now23:13
* Mokbortolan_1 designs a brain input system.23:15
Stee|Mokbortolan_1, go post it!23:15
Mokbortolan_1post what?23:15
Mokbortolan_1I'll post the kickstarter link when it's ready :p23:15
Stee|your dev efforts23:16
Mokbortolan_1oh23:16
Mokbortolan_1well, it'll be proprietary23:16
Stee|bah, fair23:16
Stee|talked to rdb?23:16
Mokbortolan_1at least, the hardware stuff23:16
Mokbortolan_1there'll be an open source SDK23:16
Stee|how much cash are you going to need?23:16
Mokbortolan_1I have no idea23:17
Stee|any idea when you're going live with this?23:17
Mokbortolan_1could be $20,000, could be $2,000,00023:17
Mokbortolan_1it'll take 1-2 years minimum23:17
Mokbortolan_1the goal is to give my friend some new eyes23:17
Mokbortolan_1he's going blind23:17
Mokbortolan_1and he's too cool to let him wander around with a cane23:18
sylph_makoStee|, the sixthsense stuff? I thought sixthsense was the lanyard projector thing, not really designed for a HUD.23:21
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sylph_makoErm. The chest projector.23:25
Stee|sylph: just imagine instead of it projecting out on something, it instead simply puts that video output onto the hud23:25
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