--- Log opened Sat Jan 19 00:00:34 2013 | ||
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@kanzure | GHill: why were you asking about papers ? | 00:45 |
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GHill | I'm just curious really. | 00:45 |
GHill | I 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 own | 00:46 |
@kanzure | fascinating concept | 00:47 |
GHill | But 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 |
GHill | Etc. etc. | 00:48 |
@kanzure | well, depends on your interestt | 00:48 |
@kanzure | -t | 00:48 |
@kanzure | i have everything from the mundane to the bizarre, | 00:49 |
@kanzure | http://diyhpl.us/~bryan/papers2/bio/The%20mammary%20gland%20-%20bioreactor%20for%20the%20production%20of%20recombinant%20proteins.pdf | 00:49 |
GHill | Pretty 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 |
GHill | Yeah, that's too technical. My chemistry/psychology background is too weak to get much out of that. | 00:50 |
@kanzure | well if you look at it that way, even microwaving some milk is too technical: | 00:51 |
@kanzure | http://diyhpl.us/~bryan/papers2/paperbot/Evidence%20for%20the%20absence%20of%20amino%20acid%20isomerization%20in%20microwave-heated%20milk%20and%20infant%20formulas.pdf | 00:51 |
GHill | According to a recent paper (Lubec et al., 1989) | 00:51 |
GHill | Hah | 00:51 |
@kanzure | time is relative in this channel | 00:52 |
GHill | Does seeing an older timestamp (let's say, pre-1990) make you more skeptical to what you're reading? | 00:52 |
@kanzure | no | 00:52 |
GHill | Is 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 |
@kanzure | i rarely look at the name of the journal unless by accident | 00:54 |
GHill | I ask because I recall seeing an article on HN recently that talked about this... the disappointingly rampant culture of fudging numbers in papers | 00:54 |
@kanzure | most papers are crap, but there are details that are worth learning about | 00:54 |
@kanzure | review articles tend to be less full of crap | 00:54 |
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 |
@kanzure | no i try to avoid ted.com crap | 00:55 |
@kanzure | yes, like here's a review exploring the ampa receptor in neurons: | 00:56 |
@kanzure | http://diyhpl.us/~bryan/papers2/neuro/Review%20-%202007%20-%20AMPA%20receptor%20trafficking.pdf | 00:56 |
@kanzure | or in particular their "trafficking" (expression and regulation of such) | 00:56 |
GHill | Huh? 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 science | 00:56 |
GHill | That ted.com video is very well worth watching, I promise | 00:57 |
@kanzure | ted.com takes an excruciatingly long time to deliver anything new to your eyeballs, most of the stuff they publish is old and trite | 00:57 |
@kanzure | i am offended that you would think i wouldn't know goldacre if it weren't for ted.com | 00:58 |
GHill | (Good thing Dr. Goldacre talks so fast! :)) | 00:58 |
@kanzure | ted.com is probably okay if you've been living under a rock for 20 years though | 00:58 |
GHill | What is your background? Did you do doctrate work in some psychology-related field? | 00:59 |
@kanzure | it 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 |
@kanzure | no, i dropped out of college to argue on irc | 00:59 |
GHill | Well, it's interesting you say that so bluntly | 01:00 |
GHill | Do you feel it was a beneficial and productive choice? | 01:00 |
@kanzure | ys | 01:00 |
@kanzure | yes | 01:00 |
GHill | Wow | 01:00 |
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GHill | To what end is it productive? | 01:01 |
brownies | he has an honorary masters degree from Freenode International University | 01:02 |
@kanzure | less of my time is spent working on classes | 01:02 |
@kanzure | in fact, zero of my time is spent on classes now | 01:03 |
brownies | and iirc he's also an ordained reverend | 01:03 |
nsh | topic? | 01:03 |
@kanzure | brownies: dude you don't have to tell my life story to everyone that you meet | 01:03 |
brownies | haha. you're right. i'm sorry. | 01:03 |
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GHill | I don't mind, I like getting to know people's back stories. :) | 01:03 |
@kanzure | you disgust me | 01:04 |
GHill | Really? Why? | 01:04 |
@kanzure | hahah | 01:04 |
brownies | too many emoticons | 01:04 |
brownies | shows weakness. | 01:04 |
GHill | Expressiveness improves communication | 01:04 |
@kanzure | are you just asking questions to ask questions | 01:04 |
GHill | Forgive 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 |
@kanzure | brownies: what are you doing awake? | 01:07 |
brownies | kanzure: coding | 01:09 |
@kanzure | brownies: i had another one of those "write some code for a few hours, but it runs perfectly the first time" moments | 01:10 |
@kanzure | i was expecting at least 30min of debugging on this one :\ | 01:10 |
brownies | kanzure: always nice when that happens | 01:16 |
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superkuh | paperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.3295.html | 11:15 |
paperbot | HTTP 401 unauthorized http://www.nature.com/neuro/journal/vaop/ncurrent/pdf/nn.3295.pdf | 11:15 |
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@kanzure | what how is that unauthorized | 11:21 |
@kanzure | paperbot: http://www.nature.com/neuro/journal/vaop/ncurrent/pdf/nn.3295.pdf | 11:22 |
paperbot | http://diyhpl.us/~bryan/papers2/paperbot/6c2cf946039e318af63ff057f7ed92bb.txt | 11:22 |
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@kanzure | .. oh. | 11:22 |
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@kanzure | gene_hacker: sup? | 11:59 |
gene_hacker | sup | 11:59 |
@kanzure | k | 11:59 |
@kanzure | nmz787: we should probably update the diybio faq with the new suppliers (like openbiotech) | 12:16 |
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gene_hacker | what are you working on? | 12:23 |
@kanzure | top secret stuff | 12:24 |
gene_hacker | it can't be anymore topsecret than what I'm working on | 12:25 |
gene_hacker | did I tell you about the aliens we got yesterday | 12:25 |
gene_hacker | WOOPS | 12:25 |
gene_hacker | oh shit, you aren't supposed to know about that | 12:25 |
gene_hacker | actually, the stuff I'm working on, will hopefully be opensource someday | 12:26 |
gene_hacker | if you haven't already, I highly encourage you to sign up for the DARPA FANG challenge | 12:26 |
gene_hacker | they | 12:26 |
gene_hacker | have some pretty interesting software up for download | 12:27 |
@kanzure | are you still at ut austin? | 12:27 |
gene_hacker | yeah | 12:29 |
gene_hacker | anyway check out the software I mentioned, supposed to make it easy enough for your average joe to design a tank | 12:33 |
gene_hacker | but, it could probably be used for other stuff to, like other really complicated mechanical systems and whatnot | 12:34 |
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nmz787 | kanzure: do you know of any open calls for synBio related grants? | 12:52 |
nmz787 | or gene therapy? | 12:52 |
@kanzure | no. ask john cumbers. | 12:52 |
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@kanzure | hmm so it looks like i neglected to make a backup of QuteMol 0.5.1 for nanoengineer, | 14:12 |
@kanzure | i don't see it in http://diyhpl.us/~bryan/irc/nanoengineer/dependencies/ | 14:13 |
balrog | 0.5.1? | 14:20 |
balrog | latest I see is 0.4.1 | 14:20 |
@kanzure | yeah i'm checking some .tar.gz archives | 14:20 |
@kanzure | i only have this: http://diyhpl.us/~bryan/irc/nanoengineer/qutemole-stuff.txt | 14:21 |
balrog | 404 | 14:21 |
@kanzure | eh once more | 14:22 |
balrog | qutemol-stuff.txt is blank | 14:22 |
@kanzure | wtf | 14:23 |
@kanzure | http://diyhpl.us/~bryan/irc/nanoengineer/qutemol-stuff.txt | 14:23 |
@kanzure | so now it works? am i making a typo somewhere? | 14:23 |
@kanzure | oh i forgot the e. i see. | 14:24 |
@kanzure | right, so, qutemol != qutemole | 14:24 |
@kanzure | ah.. here we go: | 14:28 |
@kanzure | http://diyhpl.us/~bryan/irc/nanoengineer/snapshots/QuteMolX_0.5.1_20080512.tar.gz | 14:29 |
@kanzure | ok posted: https://groups.google.com/group/nanoengineer-dev/t/fa63ab1e2a757241 | 14:30 |
nmz787 | paperbot: http://www.cabdirect.org/abstracts/19551404514.html;jsessionid=66169BB54AF0849AF73D79547BA8CB4B?gitCommit=4.13.16-2-g77374b3 | 14:48 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/d18b139a3583e8c14ff6eb7615f8bb03.txt | 14:48 |
nmz787 | hmm | 14:49 |
nmz787 | i don't even know how to get this | 14:49 |
nmz787 | paperbot: | 14:51 |
nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/ja01551a070 | 14:51 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/A%20Manual%20of%20Paper%20Chromatography%20and%20Paper%20Electrophoresis.pdf | 14:51 |
nmz787 | paperbot: http://pubs.acs.org/doi/abs/10.1021/ja01624a094 | 14:54 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/A%20Manual%20of%20Paper%20Chromatography%20and%20Paper%20Electrophoresis..pdf | 14:54 |
nmz787 | kanzure: see the above double period in the file_ext (link works when i remove one) | 14:55 |
nmz787 | also works with 2 | 14:55 |
nmz787 | oh | 14:55 |
@kanzure | the link works when you remove one because the previous attempt created the file name with only one period | 14:55 |
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nmz787 | well they're two different articles | 14:56 |
@kanzure | there's a period in the title of the second one, which is why the filename ends up with two periods. | 14:57 |
@kanzure | yes, paperbot doesn't check for previously existing files in my ~/public_html/papers2/paperbot/ | 14:57 |
nmz787 | paperbot: http://onlinelibrary.wiley.com/doi/10.1002/ange.19550671421/abstract | 14:57 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/364967132746e5062defd26ee3724547.txt | 14:57 |
nmz787 | cool well it seems to have worked fine, adding a period is as good as adding (1) or (2) at the end | 14:58 |
@kanzure | gene_hacker: how is matt campbell? | 14:58 |
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nmz787 | paperbot: http://link.springer.com/article/10.1007%2FBF01858742?LI=true | 15:42 |
paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/17dfdee14222ffa2871a1874900c0aff.txt | 15:42 |
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cathalgarvey | paperbot: https://www.sciencedirect.com/science/article/pii/S1369526600001631 | 17:24 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3ea5b3a8e6204a797b8a76f7929a61cb.txt | 17:24 |
cathalgarvey | <- Is shameless at this hour of the night | 17:24 |
cathalgarvey | paperbot: http://www.sciencedirect.com/science/article/pii/S1369526600001631 | 17:25 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9d5742b3263a1b3c7e97fc874a9e3e85.txt | 17:25 |
cathalgarvey | Nuts, ah well | 17:25 |
cathalgarvey | Sorry to pollute the channel there! ;) | 17:25 |
yashgaroth | I can DCC the article to you or something | 17:26 |
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cathalgarvey | Hey Yashgaroth, not that big a deal | 17:27 |
cathalgarvey | I was just curious to see the biosynthetic pathway graph in the article, to compare to the shortcut used in golden rice | 17:27 |
cathalgarvey | Thanks though! :) | 17:27 |
yashgaroth | paperbot: 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.pdf | 17:29 |
paperbot | SSLError: [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 |
yashgaroth | wha | 17:29 |
cathalgarvey | Lol | 17:29 |
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@kanzure | yashgaroth: that had proxy.lib.pdx.edu in it | 17:30 |
@kanzure | paperbot: 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.pdf | 17:30 |
paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/bb504dd855f95c94b67523aa7de3e253.pdf | 17:30 |
yashgaroth | oh uh right how did that happen | 17:30 |
@kanzure | there you go | 17:30 |
@kanzure | "Carotenoid biosynthesis in flowering plants" | 17:31 |
@kanzure | science! | 17:31 |
@kanzure | cathalgarvey: are you gunning to be the martha stewart of potted biology | 17:31 |
@kanzure | don't answer that | 17:33 |
cathalgarvey | :D | 17:33 |
cathalgarvey | Thanks! | 17:33 |
cathalgarvey | Nah, have a lecture to give on Monday as a guest, at a design/synbio module in Dublin | 17:33 |
cathalgarvey | part 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 features | 17:34 |
cathalgarvey | golden rice is a nice example, using ctrl as a shortcut to the end of a biosynthetic chain that takes plants much longer to accomplish | 17:34 |
cathalgarvey | ..so I just wanted to see how many steps it skips! :) | 17:34 |
gnusha | https://secure.diyhpl.us/cgit/paperbot/commit/?id=cf7c1b78 Bryan Bishop: auto-remove proxy.lib.pdx.edu from urls | 17:35 |
gnusha | paperbot: reload papers | 17:35 |
paperbot | gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-01-20 01:35:27) | 17:35 |
cathalgarvey | Bo-ring, it only skips one step via Zeta-Carotene. Still, nice example of adaptation and crossover in genetics | 17:36 |
cathalgarvey | Thanks! :) | 17:36 |
cathalgarvey | Gotta run, it's hella late and I gotta get slides made. You guys rock! | 17:36 |
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@kanzure | publishers have terrible url structures | 17:38 |
@kanzure | someone should sell schools a publisher url shortener "BUT WITH SCIENCE STATS THAT YOU CAN INCLUDE IN GRANT APPLICATIONS" | 17:38 |
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rigel | hey | 17:45 |
@kanzure | hello | 17:45 |
rigel | so there are some folks working on redrafting the computer fraud and abuse act | 17:45 |
rigel | http://ie1.shell.thequux.com/wiki/start | 17:46 |
rigel | if yall are interested in that at all | 17:46 |
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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 |
rigel | juri_: this is the law that aaron swartz was charged under | 18:35 |
rigel | as well as people like aurenheimer (who is a colossal ass, but all he did was increment some urls) | 18:36 |
@kanzure | url guessing is illegal too? | 18:53 |
@kanzure | doesn't that make the lottery illegal? | 18:53 |
juri_ | doesn't that make web-crawlers illegal? ;) | 19:06 |
@kanzure | why is that surprising? i thought they always claimed that. | 19:08 |
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strangewarp | Talking with normal people about thorium reactors makes me want to live in a cave | 19:33 |
@kanzure | a batcave? | 19:34 |
juri_ | s/about thorium reactors// | 19:34 |
strangewarp | hermit cave, or possibly caveman cave | 19:34 |
@kanzure | because hermit caves have thorium reactors ? | 19:36 |
nmz787 | a wind cave? | 19:36 |
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JayDugger | Good morning, everyone. | 22:08 |
@kanzure | https://github.com/kanzure/pokemon-prism | 22:13 |
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rigel | what "normal person" talks about thorium reactors? | 23:28 |
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