2013-01-19.log

--- Log opened Sat Jan 19 00:00:34 2013
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@kanzureGHill: why were you asking about papers ?00:45
GHillI'm just curious really.00:45
GHillI have never read a paper before. I saw people ragging on news articles all the time that they're summarizing poorly... and recently I had the idea that I should consider reading them on my own00:46
@kanzurefascinating concept00:47
GHillBut I wouldn't know where to begin. I wouldn't know where to find one that I could really understand (my math background is weak :\).00:47
GHillEtc. etc.00:48
@kanzurewell, depends on your interestt00:48
@kanzure-t00:48
@kanzurei have everything from the mundane to the bizarre,00:49
@kanzurehttp://diyhpl.us/~bryan/papers2/bio/The%20mammary%20gland%20-%20bioreactor%20for%20the%20production%20of%20recombinant%20proteins.pdf00:49
GHillPretty broad! Not *too* deep in to biohacking, nootropics, etc. but something thought-provoking, interesting, and hopefully actually useful to me. Uhmm, something that would make the frontpage of HN and generate a lot of discussion? :)00:49
GHillYeah, that's too technical. My chemistry/psychology background is too weak to get much out of that.00:50
@kanzurewell if you look at it that way, even microwaving some milk is too technical:00:51
@kanzurehttp://diyhpl.us/~bryan/papers2/paperbot/Evidence%20for%20the%20absence%20of%20amino%20acid%20isomerization%20in%20microwave-heated%20milk%20and%20infant%20formulas.pdf00:51
GHillAccording  to a recent  paper (Lubec et al., 1989)00:51
GHillHah00:51
@kanzuretime is relative in this channel00:52
GHillDoes seeing an older timestamp (let's say, pre-1990) make you more skeptical to what you're reading?00:52
@kanzureno00:52
GHillIs your state of mind generally skeptical when you're reading these papers? If the paper has been published in a less-prestigious journal, does it make you more skeptical?00:53
@kanzurei rarely look at the name of the journal unless by accident00:54
GHillI ask because I recall seeing an article on HN recently that talked about this... the disappointingly rampant culture of fudging numbers in papers00:54
@kanzuremost papers are crap, but there are details that are worth learning about00:54
@kanzurereview articles tend to be less full of crap00:54
GHill'Review articles'?00:54
GHill(Btw, this is interseting: http://www.ted.com/talks/ben_goldacre_battling_bad_science.html -- you've probably seen it?)00:55
@kanzureno i try to avoid ted.com crap00:55
@kanzureyes, like here's a review exploring the ampa receptor in neurons:00:56
@kanzurehttp://diyhpl.us/~bryan/papers2/neuro/Review%20-%202007%20-%20AMPA%20receptor%20trafficking.pdf00:56
@kanzureor in particular their "trafficking" (expression and regulation of such)00:56
GHillHuh? Ted.com is crap? Dr. Goldacre is a highly reputed professor at Univ. of Oxford, and he caused quite a stir earlier last year for uncovering lots of messy details about bad science00:56
GHillThat ted.com video is very well worth watching, I promise00:57
@kanzureted.com takes an excruciatingly long time to deliver anything new to your eyeballs, most of the stuff they publish is old and trite00:57
@kanzurei am offended that you would think i wouldn't know goldacre if it weren't for ted.com00:58
GHill(Good thing Dr. Goldacre talks so fast! :))00:58
@kanzureted.com is probably okay if you've been living under a rock for 20 years though00:58
GHillWhat is your background? Did you do doctrate work in some psychology-related field?00:59
@kanzureit was always amusing how much they wanted to be "edge.org but with moving pictures" :p (guess brockman couldn't arrange that, huh)00:59
@kanzureno, i dropped out of college to argue on irc00:59
GHillWell, it's interesting you say that so bluntly01:00
GHillDo you feel it was a beneficial and productive choice?01:00
@kanzureys01:00
@kanzureyes01:00
GHillWow01:00
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GHillTo what end is it productive?01:01
brownieshe has an honorary masters degree from Freenode International University01:02
@kanzureless of my time is spent working on classes01:02
@kanzurein fact, zero of my time is spent on classes now01:03
browniesand iirc he's also an ordained reverend01:03
nshtopic?01:03
@kanzurebrownies: dude you don't have to tell my life story to everyone that you meet01:03
brownieshaha. you're right. i'm sorry.01:03
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GHillI don't mind, I like getting to know people's back stories. :)01:03
@kanzureyou disgust me01:04
GHillReally? Why?01:04
@kanzurehahah01:04
browniestoo many emoticons01:04
browniesshows weakness.01:04
GHillExpressiveness improves communication01:04
@kanzureare you just asking questions to ask questions01:04
GHillForgive me that I slided down to a path of asking useless questions, I'm too sleepy to get into reading research papers at this point, is the problem. :)01:05
@kanzurebrownies: what are you doing awake?01:07
brownieskanzure: coding01:09
@kanzurebrownies: i had another one of those "write some code for a few hours, but it runs perfectly the first time" moments01:10
@kanzurei was expecting at least 30min of debugging on this one :\01:10
brownieskanzure: always nice when that happens01:16
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superkuhpaperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.3295.html11:15
paperbotHTTP 401 unauthorized http://www.nature.com/neuro/journal/vaop/ncurrent/pdf/nn.3295.pdf11:15
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@kanzurewhat how is that unauthorized11:21
@kanzurepaperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/pdf/nn.3295.pdf11:22
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/6c2cf946039e318af63ff057f7ed92bb.txt11:22
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@kanzure.. oh.11:22
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@kanzuregene_hacker: sup?11:59
gene_hackersup11:59
@kanzurek11:59
@kanzurenmz787: we should probably update the diybio faq with the new suppliers (like openbiotech)12:16
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gene_hackerwhat are you working on?12:23
@kanzuretop secret stuff12:24
gene_hackerit can't be anymore topsecret than what I'm working on12:25
gene_hackerdid I tell you about the aliens we got yesterday12:25
gene_hackerWOOPS12:25
gene_hackeroh shit, you aren't supposed to know about that12:25
gene_hackeractually, the stuff I'm working on, will hopefully be opensource someday12:26
gene_hackerif you haven't already, I highly encourage you to sign up for the DARPA FANG challenge12:26
gene_hackerthey12:26
gene_hackerhave some pretty interesting software up for download12:27
@kanzureare you still at ut austin?12:27
gene_hackeryeah12:29
gene_hackeranyway check out the software I mentioned, supposed to make it easy enough for your average joe to design a tank12:33
gene_hackerbut, it could probably be used for other stuff to, like other really complicated mechanical systems and whatnot12:34
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nmz787kanzure: do you know of any open calls for synBio related grants?12:52
nmz787or gene therapy?12:52
@kanzureno. ask john cumbers.12:52
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@kanzurehmm so it looks like i neglected to make a backup of QuteMol 0.5.1 for nanoengineer,14:12
@kanzurei don't see it in http://diyhpl.us/~bryan/irc/nanoengineer/dependencies/14:13
balrog0.5.1?14:20
balroglatest I see is 0.4.114:20
@kanzureyeah i'm checking some .tar.gz archives14:20
@kanzurei only have this: http://diyhpl.us/~bryan/irc/nanoengineer/qutemole-stuff.txt14:21
balrog40414:21
@kanzureeh once more14:22
balrogqutemol-stuff.txt is blank14:22
@kanzurewtf14:23
@kanzurehttp://diyhpl.us/~bryan/irc/nanoengineer/qutemol-stuff.txt14:23
@kanzureso now it works? am i making a typo somewhere?14:23
@kanzureoh i forgot the e. i see.14:24
@kanzureright, so, qutemol != qutemole14:24
@kanzureah.. here we go:14:28
@kanzurehttp://diyhpl.us/~bryan/irc/nanoengineer/snapshots/QuteMolX_0.5.1_20080512.tar.gz14:29
@kanzureok posted: https://groups.google.com/group/nanoengineer-dev/t/fa63ab1e2a75724114:30
nmz787paperbot: http://www.cabdirect.org/abstracts/19551404514.html;jsessionid=66169BB54AF0849AF73D79547BA8CB4B?gitCommit=4.13.16-2-g77374b314:48
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/d18b139a3583e8c14ff6eb7615f8bb03.txt14:48
nmz787hmm14:49
nmz787i don't even know how to get this14:49
nmz787paperbot:14:51
nmz787paperbot: http://pubs.acs.org/doi/abs/10.1021/ja01551a07014:51
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/A%20Manual%20of%20Paper%20Chromatography%20and%20Paper%20Electrophoresis.pdf14:51
nmz787paperbot: http://pubs.acs.org/doi/abs/10.1021/ja01624a09414:54
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/A%20Manual%20of%20Paper%20Chromatography%20and%20Paper%20Electrophoresis..pdf14:54
nmz787kanzure: see the above double period in the file_ext (link works when i remove one)14:55
nmz787also works with 214:55
nmz787oh14:55
@kanzurethe link works when you remove one because the previous attempt created the file name with only one period14:55
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nmz787well they're two different articles14:56
@kanzurethere's a period in the title of the second one, which is why the filename ends up with two periods.14:57
@kanzureyes, paperbot doesn't check for previously existing files in my ~/public_html/papers2/paperbot/14:57
nmz787paperbot: http://onlinelibrary.wiley.com/doi/10.1002/ange.19550671421/abstract14:57
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/364967132746e5062defd26ee3724547.txt14:57
nmz787cool well it seems to have worked fine, adding a period is as good as adding (1) or (2) at the end14:58
@kanzuregene_hacker: how is matt campbell?14:58
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nmz787paperbot: http://link.springer.com/article/10.1007%2FBF01858742?LI=true15:42
paperboterror: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/17dfdee14222ffa2871a1874900c0aff.txt15:42
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cathalgarveypaperbot: https://www.sciencedirect.com/science/article/pii/S136952660000163117:24
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3ea5b3a8e6204a797b8a76f7929a61cb.txt17:24
cathalgarvey<- Is shameless at this hour of the night17:24
cathalgarveypaperbot: http://www.sciencedirect.com/science/article/pii/S136952660000163117:25
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9d5742b3263a1b3c7e97fc874a9e3e85.txt17:25
cathalgarveyNuts, ah well17:25
cathalgarveySorry to pollute the channel there! ;)17:25
yashgarothI can DCC the article to you or something17:26
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cathalgarveyHey Yashgaroth, not that big a deal17:27
cathalgarveyI was just curious to see the biosynthetic pathway graph in the article, to compare to the shortcut used in golden rice17:27
cathalgarveyThanks though! :)17:27
yashgarothpaperbot: http://pdn.sciencedirect.com.proxy.lib.pdx.edu/science?_ob=MiamiImageURL&_cid=272018&_user=1694017&_pii=S1369526600001631&_check=y&_origin=article&_zone=toolbar&_coverDate=2001--01&view=c&originContentFamily=serial&wchp=dGLzVBA-zSkzV&md5=f79967701419d948f8f1a1a9ca87b105&pid=1-s2.0-S1369526600001631-main.pdf17:29
paperbotSSLError: [Errno 1] _ssl.c:504: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 632, in send)17:29
yashgarothwha17:29
cathalgarveyLol17:29
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@kanzureyashgaroth: that had proxy.lib.pdx.edu in it17:30
@kanzurepaperbot: http://pdn.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272018&_user=1694017&_pii=S1369526600001631&_check=y&_origin=article&_zone=toolbar&_coverDate=2001--01&view=c&originContentFamily=serial&wchp=dGLzVBA-zSkzV&md5=f79967701419d948f8f1a1a9ca87b105&pid=1-s2.0-S1369526600001631-main.pdf17:30
paperbotno translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/bb504dd855f95c94b67523aa7de3e253.pdf17:30
yashgarothoh uh right how did that happen17:30
@kanzurethere you go17:30
@kanzure"Carotenoid biosynthesis in flowering plants"17:31
@kanzurescience!17:31
@kanzurecathalgarvey: are you gunning to be the martha stewart of potted biology17:31
@kanzuredon't answer that17:33
cathalgarvey:D17:33
cathalgarveyThanks!17:33
cathalgarveyNah, have a lecture to give on Monday as a guest, at a design/synbio module in Dublin17:33
cathalgarveypart of the stuff I'd like to cover is a recap of the synbio "thing", and adaptation of genetic systems is one of the core features17:34
cathalgarveygolden rice is a nice example, using ctrl as a shortcut to the end of a biosynthetic chain that takes plants much longer to accomplish17:34
cathalgarvey..so I just wanted to see how many steps it skips! :)17:34
gnushahttps://secure.diyhpl.us/cgit/paperbot/commit/?id=cf7c1b78 Bryan Bishop: auto-remove proxy.lib.pdx.edu from urls17:35
gnushapaperbot: reload papers17:35
paperbotgnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-20 01:35:27)17:35
cathalgarveyBo-ring, it only skips one step via Zeta-Carotene. Still, nice example of adaptation and crossover in genetics17:36
cathalgarveyThanks! :)17:36
cathalgarveyGotta run, it's hella late and I gotta get slides made. You guys rock!17:36
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@kanzurepublishers have terrible url structures17:38
@kanzuresomeone should sell schools a publisher url shortener "BUT WITH SCIENCE STATS THAT YOU CAN INCLUDE IN GRANT APPLICATIONS"17:38
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rigelhey17:45
@kanzurehello17:45
rigelso there are some folks working on redrafting the computer fraud and abuse act17:45
rigelhttp://ie1.shell.thequux.com/wiki/start17:46
rigelif yall are interested in that at all17:46
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juri_computer fraud and abuse? sounds like one hell of a party.18:24
juri_i'll bet they party harder than the bureau of tobacco and fire arms.18:24
rigeljuri_: this is the law that aaron swartz was charged under18:35
rigelas well as people like aurenheimer (who is a colossal ass, but all he did was increment some urls)18:36
@kanzureurl guessing is illegal too?18:53
@kanzuredoesn't that make the lottery illegal?18:53
juri_doesn't that make web-crawlers illegal? ;)19:06
@kanzurewhy is that surprising? i thought they always claimed that.19:08
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strangewarpTalking with normal people about thorium reactors makes me want to live in a cave19:33
@kanzurea batcave?19:34
juri_s/about thorium reactors//19:34
strangewarphermit cave, or possibly caveman cave19:34
@kanzurebecause hermit caves have thorium reactors ?19:36
nmz787a wind cave?19:36
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JayDuggerGood morning, everyone.22:08
@kanzurehttps://github.com/kanzure/pokemon-prism22:13
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rigelwhat "normal person" talks about thorium reactors?23:28
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--- Log closed Sun Jan 20 00:00:35 2013

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