| --- Log opened Wed May 21 00:00:11 2014 | ||
| @fenn | markdown bullet points are so ugly | 00:08 |
|---|---|---|
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| @jrayhawk | Asterisks, or dashes? | 00:11 |
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| @fenn | asterisks. how do you do dashes? | 00:20 |
| jrayhawk | Same way. | 00:21 |
| @fenn | do they render differently? | 00:22 |
| jrayhawk | Nope. | 00:26 |
| jrayhawk | If it's the rendering you hate, you can feel free to throw css at either me or the repository. | 00:26 |
| jrayhawk | https://antportal.com/wiki/ has CSS I was reasonably impressed by. | 00:28 |
| @fenn | gah | 00:28 |
| @fenn | apparently paperbot is dumping its debug into my shell on gnusha :\ | 00:29 |
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| @fenn | i hate how it renders two bullet points for a double indent and three bullet points for a tripled indent | 00:29 |
| @fenn | in fact i hate bullet points | 00:29 |
| @fenn | fuck markdown | 00:30 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=154d7cd2 fenn: init >> http://diyhpl.us/diyhpluswiki/.gitignore | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=801ea910 fenn: scratchings >> http://diyhpl.us/diyhpluswiki/draft | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=035cccb5 fenn: preamble >> http://diyhpl.us/diyhpluswiki/draft | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=02919ed7 fenn: more sorting categories >> http://diyhpl.us/diyhpluswiki/draft | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b8282366 fenn: more words; increase verbiage! >> http://diyhpl.us/diyhpluswiki/draft | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=eddc7b86 fenn: effectiveness definition >> http://diyhpl.us/diyhpluswiki/draft | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=de833d64 fenn: %s/ \(\w\)/- \1/ and yamlify in general >> http://diyhpl.us/diyhpluswiki/draft | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=e44cc84f fenn: rename >> http://diyhpl.us/diyhpluswiki/goals.yaml | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=9235deb1 fenn: Revert "yank hplusroadmap.draft content" >> http://diyhpl.us/diyhpluswiki/declaration/ | 00:43 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=6b750cbb fenn: pull in goals.yaml >> http://diyhpl.us/diyhpluswiki/.gitignore | 00:43 |
| @fenn | oh, the magic "git filter-branch --subdirectory-filter" | 00:45 |
| @fenn | some day i'll remember how to do this stuff | 00:46 |
| @fenn | wtf markdown, _this_ is the same as *this*? | 00:49 |
| jrayhawk | http://wiki.freedesktop.org/testrepo/ https://secure.freedesktop.org/cgit/testrepo/tree/index.mdwn maybe this helps clarify the indenting situation? | 00:52 |
| jrayhawk | i am not really sure what you're complaining about where | 00:53 |
| @fenn | not really? what is doing on with 1. test translating to 1. 2. 3. 4.? | 00:53 |
| jrayhawk | that's really the browser's doing | 00:53 |
| jrayhawk | Just how numbered lists work. | 00:54 |
| jrayhawk | er, ordered lists. | 00:54 |
| @fenn | but a) there are 13 different levels of indentation, but it gets transformed into 5 because why? and b) they're all separate levels of indentation | 00:54 |
| @fenn | anyway the bullets are distracting | 00:55 |
| jrayhawk | Markdown has heuristics for what ranges of textual indentation apply to what sort of HTML sublisting. | 00:56 |
| jrayhawk | That page was to partially clarify the simple cases for me. | 00:56 |
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| @fenn | why doesnt ---- | 00:57 |
| @fenn | render as a horizontal rule? | 00:57 |
| jrayhawk | Hmm? | 00:57 |
| jrayhawk | says <hr /> right there | 00:57 |
| @fenn | oh it is invisible here nm | 00:57 |
| jrayhawk | oh, maybe I fucked up that bit of the CSS. | 00:58 |
| jrayhawk | Too lazy to look. Fuck CSS. | 00:58 |
| @fenn | CSS beats markdown | 00:58 |
| @fenn | at least i can override CSS if i want | 00:58 |
| jrayhawk | You know you can override markdown, right? | 00:58 |
| @fenn | er, no? | 00:58 |
| @fenn | there's the [!format] directive which i haven't looked at yet | 00:59 |
| jrayhawk | Support for HTML mixing is a required part of the markdown specification. | 00:59 |
| jrayhawk | Vitriolic attacks on how difficult it is to use are rather ironic when it is readily apparent you have never read the documentation for it. | 01:00 |
| @fenn | i feel justified since it's supposed to be "intuitive" and "easy to use" | 01:01 |
| jrayhawk | Is it? | 01:01 |
| @fenn | "Markdown is intended to be as easy-to-read and easy-to-write as is feasible." | 01:01 |
| jrayhawk | "intuitive" | 01:02 |
| jrayhawk | is more what I am not finding. | 01:02 |
| jrayhawk | "easy" as a lot more potential connotations. | 01:02 |
| @fenn | there are so many wiki syntaxes and things like asciidoc and simpledoc that i've had to learn over the years and they all vary by tiny amounts in ways that are mutually incompatible some of the time | 01:03 |
| @fenn | see i cant even remember what they're called | 01:04 |
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| jrayhawk | s/ as a lot/ has a lot/ | 01:09 |
| jrayhawk | also if you're associating markdown with the concept of "wiki syntax" you're projecting motivations the authors never intended again | 01:14 |
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| @fenn | it's the same thing | 01:18 |
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| @fenn | they never would have used [] for links if it weren't descended from wiki syntax | 01:18 |
| jrayhawk | https://secure.piny.be/cgit/piny-hosting/tree/index.mdwn this is the primary intended link format. | 01:18 |
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| jrayhawk | If I were a better person, I would be doing 72 or 80 column linebreaking on those paragraphs. | 01:22 |
| jrayhawk | Reversed Mediawiki links do not make for smoothly readable READMEs. | 01:26 |
| @fenn | The bikeshed color should be ... | 01:29 |
| @fenn | ...blue of course | 01:29 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5c7ecb26 fenn: test inline declaration syntax >> http://diyhpl.us/diyhpluswiki/declaration/ | 01:58 |
| paperbot | ConnectionError: [Errno 111] Connection refused (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 625, in send) | 01:58 |
| @fenn | uh oh i broke everything | 01:58 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=efd6e249 fenn: index was included in the bullet point list, attempt to fix >> http://diyhpl.us/diyhpluswiki/index/ | 03:22 |
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| chris_99 | anyone done sequence mining out of interest | 06:00 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=da1b6677 fenn: fix broken include statement >> http://diyhpl.us/diyhpluswiki/declaration/ | 06:38 |
| eudoxia | i should move the cryopatients list from the transhumani wiki to a YAML file | 06:45 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b7e7f33d fenn: test format directive >> http://diyhpl.us/diyhpluswiki/goals.yaml | 06:49 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=8f9dda50 fenn: Merge branch 'master' of /srv/git/diyhpluswiki >> http://diyhpl.us/diyhpluswiki/ | 06:49 |
| @fenn | weird it deleted the link | 06:50 |
| @fenn | ikiwiki doesn't seem to like nesting directives inside other directives | 06:52 |
| @fenn | maybe i should be using templates instead? | 06:52 |
| @fenn | it seems like you should be able to inline a file (transclude it) but also get code highlighting | 06:53 |
| gradstudentbot | Where's my pellets? | 06:54 |
| @fenn | and then "toggle" collapse/expand it | 06:54 |
| @fenn | you can do all these things separately but not together | 06:54 |
| gradstudentbot | Did you do that pset? | 06:57 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=6981b70d fenn: try toggle >> http://diyhpl.us/diyhpluswiki/declaration/ | 07:04 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=5c2a2a92 fenn: This reverts commit 6981b70d8e39a1a406f95d3cd9aff911535b3869 >> http://diyhpl.us/diyhpluswiki/declaration/ | 07:04 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=74ca22ff fenn: eh good enough >> http://diyhpl.us/diyhpluswiki/declaration/ | 07:12 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=4c8b9204 fenn: remove non functioning directive code >> http://diyhpl.us/diyhpluswiki/goals.yaml | 07:12 |
| @fenn | what the bloody fuck | 07:13 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=8a7ed8fe fenn: attempt to appease our bullet-point gods >> http://diyhpl.us/diyhpluswiki/goals.yaml | 07:15 |
| @fenn | huh adding whitespace after the list worked | 07:16 |
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| kanzure | what was wrong with bullets? | 08:28 |
| kanzure | or the way the file was | 08:28 |
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| nmz787_i | in case my post is censored (because who knows).... re diybio blogs.... A bunch of those sites haven't published a new post in more than 6 | 09:38 |
| nmz787_i | months... what is your limit for considering a blog active? | 09:38 |
| nmz787_i | (amplino, openpcr) | 09:38 |
| nmz787_i | How about non-self-published blog noise (most posts on glowingplant | 09:38 |
| nmz787_i | aren't actually about their own project)? | 09:38 |
| @fenn | when you expect flutes it's whistles | 09:38 |
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| kanzure | i dunno if it matters if they are active or not, the internet does not discriminate the age of your content | 09:57 |
| kanzure | it's unfortunate that mac has hired a blogger for diybio.org | 09:59 |
| kanzure | why not hire someone to, i dunno, build things | 09:59 |
| kanzure | instead of reading rss feeds and an inbox | 09:59 |
| kanzure | it's not like labor is dramatically more expensive than rss labor | 10:00 |
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| chris_99 | am i right/wrong in thinking scientists 100 yrs or so ago, had a broader range of interests than those now | 10:28 |
| chris_99 | *scientific interests | 10:28 |
| ParahSailin | probably right | 10:28 |
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| FourFire | chris_99, there's much more specialization, sure | 10:29 |
| FourFire | There's more things to learn about a given field and more fields, period | 10:29 |
| chris_99 | i quite like the idea of having a broader range of knowledge, as you could maybe find connections between different areas, that you wouldn't if you specialized very deply | 10:30 |
| chris_99 | *deeply | 10:30 |
| kanzure | having a broader range of knowledge these days is harder to demonstrate because it sounds like you're just regurgitating content | 10:31 |
| chris_99 | hmm, not if you actually practice in those areas too though | 10:32 |
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| chris_99 | i would like to become a gentleman scientist ;) if i could just win the lottery... | 10:43 |
| kanzure | why would you need to win the lottery? | 10:43 |
| chris_99 | just for the funding, then one could do it full-time, without needing to worry about subsidising it | 10:44 |
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| kanzure | there are other ways of accumulating piles of money besides lotteries.. entirely more efficient methods too. | 10:44 |
| eudoxia | yeah like kanzure's script that mines new cryptocoins | 10:45 |
| chris_99 | hmm i wonder if you can apply to funding bodies like the EPRSC without belonging to a uni | 10:46 |
| kanzure | eudoxia, all my other income comes from software consulting and software contracting | 10:48 |
| eudoxia | kanzure: i noticed there isn't a link to heybryan.org/resume.pdf on your page, is that intentional? | 10:49 |
| kanzure | it's because of this epic struggle between (1) the fact that i am bombarded with more offers than i can deal with and (2) my interest in being paid large amounts of money and (3) how much i dislike working | 10:50 |
| kanzure | i'm afraid that if i actually put effort into marketing my work, i might have to do even more work | 10:50 |
| kanzure | and who the fuck wants that? | 10:51 |
| eudoxia | i assumed (1) | 10:51 |
| juri_ | :) | 10:51 |
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| kanzure | world's pretty crazy out there at the moment | 10:54 |
| kanzure | degree holders with 4 years of education and 0 years of experience getting $100k offers.. so what do you think people with 3, 5, 10 years of experience can nail? etc | 10:54 |
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| heath | contacts in phoenix? | 11:46 |
| heath | does anyone have contacts in phoenix?* | 11:46 |
| heath | it's strange when you're talking to a higher up in government | 11:47 |
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| heath | ~2 contacts away from the president of the US | 11:47 |
| heath | well..1 | 11:48 |
| heath | pres -> advisor -> person i talk with | 11:48 |
| kanzure | heatsync is in phoenix i think? | 11:48 |
| heath | right | 11:48 |
| * heath is idling in the room | 11:48 | |
| kanzure | their resident transhumanist is Jacob Rosenthal <jakerosenthal@gmail.com> | 11:48 |
| heath | not as much activity as the hackerspace in hsv (huntsville) or even bna (nashville) | 11:48 |
| kanzure | why do you only have villages | 11:49 |
| gradstudentbot | Who the hell stole my pipette? | 11:50 |
| Mokstar | yay, my 23andme results are back | 11:57 |
| chris_99 | do they give you raw DNA data now, i forget | 11:57 |
| Mokstar | oh neat, I'm related to jimmy buffet | 11:57 |
| Mokstar | chris_99, yes, but no health analysis | 12:00 |
| chris_99 | how much does that cost ye | 12:01 |
| Mokstar | ooh, I've got 3.1% Neanderthal | 12:01 |
| Mokstar | 23andme doesn't sell that anymore | 12:01 |
| Mokstar | I'll have to get it done on my own | 12:01 |
| chris_99 | i think i'd rather not know if i've got disease X though | 12:03 |
| Mokstar | what's a good service to analyze this data? | 12:03 |
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| kanzure | just run it against snpedia | 12:19 |
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| kanzure | opencascade has a custom garbage collector? | 13:11 |
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| jrayhawk | chris_99: genetic diseases aren't usually deterministic | 13:21 |
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| kanzure | .title http://mikejmoffitt.com/wp/?p=270 | 14:00 |
| yoleaux | Michael J Moffitt's Project Log » Blog Archive » NeoVGA: Neo Geo Line Doubler in VHDL | 14:00 |
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| kanzure_ | iiiiiiiii | 15:43 |
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| eudoxia | i sure hope that wasn't some kind of irssi exploit | 15:44 |
| kanzure_ | just ssh lag | 15:45 |
| kanzure_ | it's impressive that irssi is okay with a lag of 159 | 15:46 |
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| kanzure_ | huh | 15:49 |
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| kanzure_ | Join to ##hplusroadmap was synced in 422 secs | 15:50 |
| kanzure_ | there we go | 15:50 |
| justanotheruser | Time for another freenode DoS? | 15:51 |
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| kanzure_ | presidential bioethics committee complaining about neuroscience: http://www.bioethics.gov/sites/default/files/Gray%20Matters%20Vol%201.pdf | 18:30 |
| kanzure_ | "However, beyond the distinction between treatment and enhancement, cognitive enhancement raises pressing ethical issues concerning equitable access to enhancements and their benefits, appropriate management of risks, and obligations and freedoms to enhance or not.26" | 18:32 |
| kanzure_ | "recommendation 1: stop paying us and allow the committee to disband" | 18:33 |
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| catern | if only | 18:36 |
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| QuantumG | so, have ya read beggars in Spain? | 19:35 |
| kanzure_ | no | 19:38 |
| QuantumG | it's not bad | 19:38 |
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| kanzure_ | if you wanted an efficient government system of granting time-limited commerce-limited monopolies, why should it have anything to do with "technology disclosure"? | 19:49 |
| QuantumG | you shouldn't :) | 19:50 |
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| kanzure_ | i'm just contemplating ideas about abolishing the patent system; really i seem to care more about the patent system leaving technology alone more than anything | 19:51 |
| kanzure_ | you will not be able to convince everyone to give up their patents because "you will be destroying trillions of dollars" | 19:51 |
| kanzure_ | but you could possibly convince them to get rid of the technology component to patents | 19:52 |
| kanzure_ | (disclosure of technical machines can happen some other way, like through the public domain or something) | 19:52 |
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| QuantumG | so, do you agree with me that trade secrets are better than patents? | 19:52 |
| QuantumG | (because at least trade secrets can be busted by interested reverse engineers) | 19:52 |
| kanzure_ | i'm not sure, what are the trade secrets keeping secret? | 19:52 |
| QuantumG | how to make stuff, probably | 19:53 |
| kanzure_ | i don't think that trade secrets are better or worse than patents for disclosing technology | 19:53 |
| kanzure_ | at least with a trade secret you can choose whatever representation of the data you want | 19:53 |
| kanzure_ | so it's probably better | 19:53 |
| kanzure_ | (rather than "serialize to legalese" as the de facto mandatorial standardo) | 19:55 |
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| kanzure_ | and if patents lose their technology component, you could possibly shift them to be more about dividing up legal protection regarding commerce revenue or something for different industries... it sounds preposterous, but it's just a more efficient way of saying what the current system is trying to say anyway. | 19:58 |
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| kanzure_ | not sure how to make that seem less ominous. the current situation has a bunch of advantage by way of obfuscation and indirection. | 20:03 |
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| QuantumG | then you'll get secrecy and protectionism | 20:07 |
| QuantumG | current situation: I won't bother reverse engineering this because I could just go read the patent, and even when I know how, the government will stop me from using that knowledge | 20:07 |
| QuantumG | your situation: I won't bother reverse engineering this because even if I succeed the government will stop me from using that knowledge. | 20:07 |
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| QuantumG | my situation: the government protects no-one, there's a lot more secrecy, but also a lot more reverse engineering. | 20:07 |
| kanzure_ | no, in "your situation", the government would not stop you from using the knowledge | 20:07 |
| QuantumG | apparently this is bad because only big companies can do reverse engineering.. little companies need to be protected. I've never seen any proof of this assertion. | 20:08 |
| kanzure_ | (or could you explain how/why it would? remember, in "your situation", patents have lost their technology component) | 20:08 |
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| QuantumG | yeah, so instead they're carving out markets | 20:08 |
| QuantumG | right? | 20:09 |
| kanzure_ | yes, probably some additional tax revenue or some shit, i have no idea | 20:09 |
| kanzure_ | "participatory patent tax" | 20:09 |
| QuantumG | Microsoft gets the software market (or some bit of it), so what's the point of trying to make a better word processor now? | 20:09 |
| kanzure_ | rate-adjusted by industry or some crap haha | 20:09 |
| kanzure_ | that "the point" was never the point | 20:10 |
| kanzure_ | there was a fairly fascinating empirical study that shows that patents actually reduce innovation | 20:11 |
| kanzure_ | the study was done by someone who was pro-patents, and then he looked at his data and frowned | 20:11 |
| kanzure_ | *innovation and related incentives | 20:11 |
| QuantumG | compared to what? | 20:11 |
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| kanzure_ | http://archive.mises.org/18812/andrew-torrance-patents-and-the-regress-of-useful-arts/ | 20:11 |
| QuantumG | I remember reading this a while ago.. but I'm not reading it again, so help me out | 20:12 |
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| kanzure_ | yeah i don't remember that detail, sorry | 20:12 |
| kanzure_ | at the moment if you have a word processor patent, you can reasonably get it in front of a judge and extract some revenue | 20:13 |
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| kanzure_ | (patent licensing revenue is the name of this particular game) | 20:14 |
| QuantumG | .. and? | 20:20 |
| kanzure_ | huh? i was responding to your microsoft point | 20:20 |
| kanzure_ | heh what if it was a guessing game, where you had to come up with some n-digit number, and the closest guesses get the patents/markets awarded to them, based on some distance or something | 20:21 |
| kanzure_ | and then it's some weirdo "monopoly lottery" | 20:21 |
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| kanzure_ | hrm i suppose that's more random than "have a bunch of wizards show up in court and say things about magic that nobody understands" | 20:26 |
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| QuantumG | that's gunna be around no matter what you do | 20:28 |
| QuantumG | if there's no patent system, the court cases will be about whether or not Bob violated his employment contract when he left to go work for a competitor | 20:28 |
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| kanzure_ | yeah but if the courts are just going to end up in a wishy-washy interpretation battle (like the same one that happens over the constitution), you might as well have the USPTO settle the argument ahead of time by doing its job (granting monopolies, definitively or something) | 20:29 |
| QuantumG | see, for example, John Carmack and the Occulus Rift. | 20:29 |
| kanzure_ | if you're not going to write down what you're actually granting the patenteeor, then you're really just deferring it to the court case, and for sufficiently magical things, it's more or less random either way too | 20:29 |
| kanzure_ | because often legalese is either too specific or overly general | 20:29 |
| kanzure_ | and you can't figure out what parts the uspto was really intending to grant | 20:29 |
| kanzure_ | QuantumG: is there a court case about that particular one? | 20:30 |
| QuantumG | http://popcultureblog.dallasnews.com/2014/05/zenimax-and-id-software-have-filed-a-lawsuit-against-oculus-vr-and-dallas-based-john-carmack-is-in-the-middle.html/ | 20:30 |
| QuantumG | .title | 20:30 |
| yoleaux | Zenimax and Id Software have filed a lawsuit against Oculus VR, and Dallas-based John Carmack is in the middle | 20:30 |
| kanzure_ | i knew there was something problematic about his job switch, didn't know it was a lawsuit yet | 20:31 |
| QuantumG | almost every announcement of a company with deep pockets acquiring a smaller outfit is accompanied by them. | 20:32 |
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| QuantumG | http://quantumg.net/aprt-short.gif because animation | 21:15 |
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| kanzure_ | QuantumG: can you render that using electrostatic potential maps instead? kthx | 21:16 |
| kanzure_ | and if transparency is an option then enable that | 21:17 |
| kanzure_ | mayavi2 might have this | 21:17 |
| QuantumG | doing that now (no transparency) | 21:17 |
| kanzure_ | it's pre-computed, so rendering is fast, right? | 21:18 |
| QuantumG | it's reasonably fast, yeah | 21:18 |
| QuantumG | ~15 sec per frame | 21:18 |
| QuantumG | http://quantumg.net/aprt-short-surface.gif | 21:22 |
| kanzure_ | hrm | 21:22 |
| kanzure_ | cool | 21:22 |
| QuantumG | purple = PRPP binding site, blue = adenine binding site .. this is 7 different homologs | 21:23 |
| QuantumG | I have two more, but I dropped them cause they're long form, not short form, so they look too out of place | 21:23 |
| QuantumG | http://quantumg.net/both.html | 21:25 |
| kanzure_ | do you have any good papers on rational protein design? | 21:26 |
| QuantumG | Beyond directed evolution—semi-rational protein engineering and design, Directed evolution made easy, Microfluidic Compartmentalized Directed Evolution, Protein Design by Directed Evolution, Recent trends in biocatalysis engineering | 21:28 |
| kanzure_ | yes microfluidic compartmentalized emulsion stuff is fun | 21:29 |
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| kanzure_ | but iirc there are some people that know how to get specific holes and arms on proteins these days? | 21:29 |
| -!- justanotheruser1 is now known as justanotheruser | 21:29 | |
| QuantumG | so that first paper tells me | 21:30 |
| kanzure_ | paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982887/pdf/nihms235064.pdf | 21:31 |
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| kanzure_ | paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982887/pdf/nihms235064.pdf | 21:31 |
| paperbot | ConnectionError: [Errno 111] Connection refused (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 625, in send) | 21:31 |
| kanzure_ | o_____o | 21:31 |
| kanzure_ | paperbot: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982887/pdf/nihms235064.pdf | 21:32 |
| paperbot | TypeError: unicode() argument 2 must be string, not None (file "/usr/local/lib/python2.7/dist-packages/requests/models.py", line 825, in text) | 21:32 |
| kanzure_ | back to the drawing board.. | 21:32 |
| kanzure_ | did people used to have drawing boards to go to? | 21:32 |
| QuantumG | yeah, gimme 3 minutes | 21:33 |
| kanzure_ | nah, ncbi has it | 21:33 |
| kanzure_ | i just wanted paperbot to archive it | 21:33 |
| kanzure_ | it is usually capable of archiving a public access pdf | 21:33 |
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| QuantumG | http://quantumg.net/both.html added links | 21:36 |
| kanzure_ | in the ncbi-hosted pdf, there's a reference to a study where tunnels in proteins were improved by a handful of different amino acid residues | 21:39 |
| kanzure_ | prolly applies to every protein-with-a-hole in that protein family | 21:40 |
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| QuantumG | "Directed evolution made easy" is about PACE. You've heard of that? | 21:46 |
| kanzure_ | yes | 21:46 |
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| kanzure_ | wait.. acronym overload. | 21:47 |
| kanzure_ | is it this one? http://diyhpl.us/~bryan/papers2/bio/A%20system%20for%20the%20continuous%20directed%20evolution%20of%20biomolecules.pdf | 21:47 |
| QuantumG | yup | 21:47 |
| kanzure_ | the t7 rna pol one | 21:48 |
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| kanzure_ | i don't remember the details of this method. did they have a library of different phages? | 21:49 |
| kanzure_ | aha, accessory plasmid and mutagenesis plasmid | 21:51 |
| QuantumG | "First, a crucial gene for phage replication is removed from the phage’s genome and placed in an ‘accessory plasmid’ in E. coli. Expression of this gene can then be tied to a wide range of biological activities," | 21:52 |
| -!- Qfwfq_ is now known as Qfwfq | 21:53 | |
| QuantumG | "Engineered bacteria and phage are then placed in vessels called lagoons, such that a continuous stream of E. coli move in and out of the vessel. The E. coli only stay in the lagoon for about 20 or 30 minutes, just long enough for phage infection and replication to occur. Only phage that activate | 21:54 |
| QuantumG | the essential gene in the E. coli plasmid can reproduce and infect incoming bacteria. The better the phage is at inducing gene expression in the accessory plasmid, the more phage are produced." | 21:54 |
| QuantumG | .. and, ya know, it's all glassware. | 21:57 |
| kanzure_ | their transfection method doesn't seem to require calcium chloride what's going on | 21:57 |
| kanzure_ | is that legal | 21:57 |
| QuantumG | (if that's a joke, I missed it) | 21:58 |
| kanzure_ | "by heat shock" | 21:58 |
| kanzure_ | "NEB Turbo competent cells" | 21:58 |
| kanzure_ | oh, electroporation too | 21:59 |
| kanzure_ | electroporation sort of counts as glassware | 21:59 |
| sheena | someone is putting new DNA markers in Ecoli? | 22:00 |
| sheena | i heard it on the radiooo | 22:00 |
| nmz787 | hi didly ho | 22:00 |
| kanzure_ | nucleotides | 22:00 |
| nmz787 | nuculartides | 22:00 |
| nmz787 | its pronouced nucular | 22:00 |
| gradstudentbot | I am busy researching. | 22:01 |
| Mokstarboush | New cule-air, Ms. Aisles. | 22:04 |
| kanzure_ | .ety nuclear | 22:04 |
| yoleaux | nuclear (adj.): "1846, "of or like the nucleus of a cell," from nucleus + -ar, probably by influence of French nucléaire. Use in atomic physics is from 1914; of weapons, from 1945. Hence nuclear physics (1933), nuclear energy (1941), nuclear war (1954)." — http://etymonline.com/index.php?term=nuclear | 22:04 |
| kanzure_ | .ety nucléaire | 22:04 |
| yoleaux | Sorry, I couldn't find the etymology of that. | 22:04 |
| Mokstarboush | .ety jazz hands | 22:05 |
| yoleaux | Sorry, I couldn't find the etymology of that. | 22:05 |
| kanzure_ | .ety nucleus | 22:05 |
| yoleaux | nucleus (n.): "1704, "kernel of a nut," 1708, "head of a comet," from Latin nucleus "kernel," from nucula "little nut," diminutive of nux (genitive nucis) "nut," from PIE *kneu- "nut" (cognates: Middle Irish cnu, Welsh cneuen, Middle Breton knoen "nut," …" — http://etymonline.com/index.php?term=nucleus | 22:05 |
| kanzure_ | "little nut" :) | 22:05 |
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| Mokstarboush | yay! I don't have MTHFR mutations! http://imgur.com/NAfQlFe | 22:09 |
| kanzure_ | .title http://www.bbc.com/news/blogs-magazine-monitor-23178484 | 22:09 |
| yoleaux | Egypt crisis: Why are Cairo protesters using laser pens? | 22:09 |
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