--- Log opened Sat Feb 25 00:00:25 2012
00:01 < utopiah> Monday http://www.media.mit.edu/events/2012/02/27/jennifer-lewis-printing-functional-materials
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08:20 < kanzure> boop
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08:27 < chris_99> yoho
08:29 < kanzure> a pirate's life for someone
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08:37 < bkero> yo ho ho
08:37  * bkero thought for a second that was Juliette Lewis
08:38 < bkero> wtf?  scientologists?  printing?
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09:14 < rkos> http://www.youtube.com/watch?v=AKxmqMH4w_A finally bbc gets its hands on biology
09:15 < rkos> or synthetic biology to be more accurate
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09:22 < chris_99> oh i think i saw that, is that the one with the 'spider goat' rkos?
09:22 < kanzure> roar i demand better protein engineering material
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09:40 < rkos> yeah chris_99
09:54 < kanzure> "During protein synthesis, tRNAs are delivered to the ribosome by proteins called elongation factors (EF-Tu in bacteria, eEF-1 in eukaryotes), which aid in decoding the mRNA codon sequence. Once delivered, a tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to ...."
09:54 < kanzure> "This complex transiently enters the ribosome, with the tRNA anticodon domain associating with the mRNA codon in the ribosomal A site. If the codon-anticodon pairing is correct, EF-Tu hydrolyzes guanosine triphosphate (GTP) into guanosine diphosphate (GDP) and inorganic phosphate, and changes in conformation to dissociate from the tRNA molecule."
09:54 < kanzure> we need something like that to make juul's method work
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09:54 < kanzure> except for handing off a nucleotide to a polymerase, instead of handing off tRNA to a ribosome
09:56 < kanzure> i guess it makes the tRNA bind to the ribosome immediately
09:56 < kanzure> but how does it dissociate the tRNA if it's incorrect?
09:56 < kanzure> "EF-Tu contributes to translational accuracy in three ways. It delays GTP hydrolysis if the tRNA in the ribosome’s A site does not match the mRNA codon, thus preferentially increasing the likelihood for the incorrect tRNA to leave the ribosome. It also adds a second delay (regardless of tRNA matching) after freeing itself from tRNA, before the aminoacyl-tRNA fully enters the A site."
09:57 < kanzure> "This delay period is a second opportunity for incorrectly paired tRNA (and their bound amino acids) to move out of the A site before the incorrect amino acid is irreversibly added to the polypeptidic chain."
09:57 < kanzure> "A third mechanism is the less well understood function of EF-Tu to crudely check aminoacyl-tRNA associations and reject complexes where the amino acid is not bound to the correct tRNA coding for it."
09:57 < kanzure> uhuh..
09:57 < kanzure> maybe the ribosome has some ability to determie whether or not it wants that particular tRNA to bind
09:57 < kanzure> *determine
09:59 < kanzure> so the hand-off function here seems to be "well, the tRNA is placed inside this little pocket, and the ribosome might choose to do some chemical wizardry, otherwise it's free to float away"
09:59 < kanzure> and i guess the elongation factor stays there blocking the pocket for just long enough for that reaction to be catalyzed
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11:34 < kanzure> wtf
11:34 < kanzure> http://www.deepdyve.com/
11:34 < kanzure> "DeepDyve is the largest online rental service for professional and scholarly research articles"
11:34 < kanzure> "With DeepDyve, you can "rent" an article which allows you to view-only the full article from the DeepDyve site for 24 hours (or more), but you cannot print or download the document. With DeepDyve, you get reduced access in exchange for a massively reduced price — up to 90% off the cost of purchasing the document."
11:35 < kanzure> uhuh...
11:35 < kanzure> "With DeepDyve, our users can "rent" and read-only the full article for as little as $0.99. Rented articles cannot be downloaded or printed."
11:35 < kanzure> how the fuck do they get the data to my computer then?
11:35 < kanzure> what the hell are they smoking
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11:37 < ParahSailin__> i think if someone were to make a pirate .onion service for article retrieval then they ought to charge some nominal btc fee
11:37 < chris_99> thats ridiculous kanzure
11:38 < kanzure> http://docs.deepdyve.com:80/doc_repo_server/get-image/KrZVM2CFO1/1/1?t=1330202517&p=1&a=preview&key=teeQiJ2CSm0xaT3gpS57A01rxeY.
11:38 < chris_99> i'm guessing they never heard of google scholar
11:38 < kanzure> images :(
11:40 < kanzure> so how is an image "read-only"?
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11:49 < chris_99> they expect you can't edit the text i guess
11:51 < kanzure> people don't read papers to edit the text
11:51 < kanzure> i mean,
11:51 < kanzure> people don't download papers to edit the text anyway, i don't see how this is different
11:52 < chris_99> copying the text is handy though
11:52 < chris_99> for quotes
11:53 < chris_99> sounds a useless service though anyhow
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12:53 < delinquentme> whats the european version of the NCBI?
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12:54 < kanzure> delinquentme: http://www.ebi.ac.uk/ ?
12:55 < delinquentme> yeahh just got it :D
12:55 < delinquentme> 10q
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13:06 < yashgaroth> re: deepdyve, I tried it out for a while but their selection is beyond terrible
13:06 < yashgaroth> if you want to print it can you presumably printscreen and do that, idk whether you can haxor it to get the pdf that they display
13:07 < delinquentme> awesome example of locating pathways within the metabolic system of ecoli http://www.youtube.com/watch?v=F8qcDQaY8Mw
13:07 < kanzure> yashgaroth: you can get a raw link to each image if you go looking
13:07 < yashgaroth> haha it's easier than I thought then
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14:41 < kanzure> yashgaroth: i need a nucleotide-binding enzyme that can dump a nucleotide to polymerase
14:41 < kanzure> i was thinking the elongation factors that plug into ribosomes look interesting
14:44 < yashgaroth> they do, but I doubt we could modify one to bind pol/nucleotides instead of ribosomes/tRNAs
14:45 < yashgaroth> EFs are a good metaphor for what we're trying to do though
14:58 < kanzure> EF backbones might be reusable, maybe
14:58 < kanzure> i haven't seen yet how much EFs vary between species
15:09 < yashgaroth> far less than most proteins
15:13 < kanzure> yashgaroth: http://groups.google.com/group/enzymaticsynthesis/msg/ce426232cb5f1373?hl=en_US&
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16:46 < kanzure> "vitamin c is a bug that needs to be patched" http://news.ycombinator.com/item?id=3633993
16:47 < kanzure> http://bbot.org/blog/archives/2012/02/24/the_pinnacle_of_evolution/
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17:48 < delinquentme> git config --global --add color.ui true
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17:49 < delinquentme> ^^ kanzure
17:49 < delinquentme> awesome
17:49 < kanzure> heh
17:50 < delinquentme> im playing around w themes in ubuntu for the first time
17:50 < delinquentme> SO PRETTY
17:50 < delinquentme> they've got surprisingly amazing designers
17:50 < delinquentme> GUH!
17:50 < delinquentme> GEEKING OUT
17:52 < sylph_mako> Last I looked they only had like 3 ok themes. How many are there now?
17:52 < delinquentme> theres the base themes but also the customized ones
17:53 < jrayhawk> Typically if you want crazily overworked themes, e17 is the ecosystem to look for them in
17:54 < delinquentme> e17?
17:55 < jrayhawk> http://www.youtube.com/watch?v=IKXXVZs9Hgg for example
17:57 < delinquentme> unnecessary transion effects
17:57 < delinquentme> thats just sucking performance .. b ut its cool ish
18:01 < jrayhawk> They're using a compositing window manager, so it's probably actually more efficient than what you've got.
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18:03 < delinquentme> derp
18:03 < delinquentme> lol
18:04 < jrayhawk> In computational terms, that is. Obviously it's the overlapping window model, so interactive efficiency is disgustingly low.
18:04 < sylph_mako> I once designed a window manager. Step one was throwing out the idea that anything should overlap ever.
18:05 < sylph_mako> I will never be able to code this window manager. By the time I put down the design I was wondering how to add 3d graphs.
18:06 < sylph_mako> Every window was to dynamically maintain a planar graph representing how useful it would find each possible allocation of dimensions at that time.
18:06 < sylph_mako> It was perfect. Too perfect to exist.
18:06 < jrayhawk> Haha
18:08 < sylph_mako> not planar. IDK if there's a word for it.
18:08 < jrayhawk> multivariate
18:10 < sylph_mako> for every x,y: x,y>0,  f(x,y) must be defined. And it only increases or stays the same as the variables increase.
18:11 < jrayhawk> Um, why must it only increase or stay the same as the variables increase?
18:12 < jrayhawk> oh i guess "heat map" is probably specifically what you want
18:13 < sylph_mako> because a window can never express less to a user given more screen space. The utility only increases.
18:13 < jrayhawk> Pixel art becomes inaccurate if scaled by a non-integer value.
18:13 < jrayhawk> That is less desirable.
18:13 < sylph_mako> But the utility of surrounding windows would decrease as it's alocated more space. So it's just about balancing that.
18:14 < sylph_mako> But the window doesn't have to scale up the pixel art, it can just center it at a reasonable resolution.
18:14 < kanzure> delinquentme: i'm able to help with phantomjs.. it's basically just javascript like jquery
18:15 < jrayhawk> If it's just centering it, then you've just defeated the point of your scoring system.
18:15 < jrayhawk> A window next to it could clearly utilize that space better, and *can't*
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18:17 < sylph_mako> No see, that's where the utility of the size just stays the same. It would be like stairs. The window manager would look at its graph and see; there's no point in giving it more than this unless I can get it up to the next step.
18:18 < jrayhawk> Ah.
18:25 < jrayhawk> That sort of paradigm would work well for irregular windows and displays, so long as you can enumerate the variables determining the size of the shapes involved.
18:25 < sylph_mako> enumerating configurations is a bit of a holy grail of mine.
18:26 < jrayhawk> Something like a car dashboard, which is typically L-shaped and unpleasantly rounded, for instance.
18:26 < sylph_mako> I would have no idea where to start in trying to adapt this for irregular shapes like that.
18:26 < jrayhawk> "unpleasantly" from an engineering persepctive
18:27 < jrayhawk> Well, you have the heat maps, so it would just be matter of iterating out the forces being exerted by the windows on eachother.
18:27 < delinquentme> kanzure, so its just "where does that code go" assuming that the headless webkit can download things
18:27 < delinquentme> whats the name of that portion of the setup?
18:28 < jrayhawk> You can even have concepts of "inertia" and "dampening" to make the resizing seem fluid enough to be aesthetically pleasing
18:29 < delinquentme> if i want to extend my 2 free hours of wireless .. thats probably just changing my mac adress right?
18:29 < kanzure> delinquentme: haha i don't know what to call it either
18:29 < kanzure> delinquentme: http://code.google.com/p/phantomjs/wiki/QuickStart
18:30 < sylph_mako> I guess I could do an L shaped display by cutting out a section of a rectangular display with a window with infinite utility at the size of the notch..
18:31 < sylph_mako> But if windows wern't rectangular their heat maps wouldn't be two dimensional?
18:32 < jrayhawk> Depends on the shape; circles are defined by one variable, ovals are defined by two.
18:33 < jrayhawk> You can make more complex shapes with higher numbers of variables. You'd need to define a function rather than a static map at some point, of course.
18:33 < sylph_mako> shit. 4d graphs made of Hyperplanes.
18:34 < sylph_mako> and so on.
18:37  * delinquentme has < 25% ideas of whats going on .. but he likes dis convo
18:38 < delinquentme> i need dis
18:38 < delinquentme> http://imgur.com/gallery/5Fjfx
18:38 < jrayhawk> hee hee, now i want to combine this system with a car and an accelerometer, and have all the instrumentation dynamicly pack itself to one side when you take a corner
18:40 < kanzure> what was that python ide that mark sims kept on using?
18:43 < sylph_mako> Heheh.
18:44 < jrayhawk> oh, ovals are merely "rounded shapes", ellipses are the simple one
18:45 < jrayhawk> geometry is hard
18:45 < jrayhawk> and ellipses and rectangles are rotatable, which i suppose would be a third variable
18:46 < sylph_mako> I think you'd have trouble extrapolating how eliptical windows would impinge on the utility of other windows.
18:47 < jrayhawk> Assuming you want to fully determine the closest metastable solution with every frame, yes.
18:47 < jrayhawk> I don't see why that would be necessary, though.
18:47 < jrayhawk> s/every frame/every render/
18:48 < sylph_mako> Perhaps I should learn more about these heat maps?
18:49 < sylph_mako> Since seeing the code bubbles thing I know I need to consider things more like, rough and iterative. That kind of modeling of intersection is useful.
18:49 < jrayhawk> Or, I guess, if you want to fully solve perfect stability, you're pretty screwed, but assuming you don't mind slowly iterating on a per-frame basis, you can find metastability *eventually*
18:57 < jrayhawk> assuming some jerk didn't add an accelerometer to the mix, anyway.
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19:09 < sylph_mako> Another problem is apps misrepresenting their utility graphs in order to get more screen space. Presumably the only solution to that is to castrate every developer except the queen so that the only viable evolutionary strategy is to selflessly act in the interest of the hive.
19:10 < jrayhawk> that seems like a problem to be solved by distributions
19:11 < sylph_mako> distributions?
19:11 < sylph_mako> Like having an external party provide apps' utility graphs?
19:11 < jrayhawk> If an application has a utility graph that doesn't interoperate well with an existing ecosystem, it is a bug to be fixed.
19:11 < sylph_mako> Ah.
19:12 < jrayhawk> If the originator doesn't fix it, a downstream distributor can do so instead.
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19:13 < jrayhawk> See: Joerg Schilling vs. every Linux distribution
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19:26 < sylph_mako> I don't really see a limiting criterion on distribution as a solution. Distros that don't get apps in the repos until like a year after they're ready are just.. not really doing it...
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19:26 < sylph_mako> There have to be open repos.
19:26 < sylph_mako> Is what I mean to say.
19:26 < sylph_mako> [While we're talking about impossibly correct solutions ;]
20:05 < delinquentme> UN BELIEVEABLE
20:05 < delinquentme> un effing believeable
20:05 < delinquentme> i *THINK*
20:05 < delinquentme> i just deployed this sucker to heroku
20:06  * delinquentme shit eating grin
20:12 < delinquentme> kanzure,
20:12 < delinquentme> i dont know what to do men
20:12 < delinquentme> man** this is AWESOME
20:13 < delinquentme> like all I have left is to insert some entries and build the frontend
20:25 < foucist> delinquentme: happy with heroku eh? :P
20:26 < delinquentme> foucist, so heroku is cool
20:26 < delinquentme> but whats cooler is that I've THUSFAR got this brilliantly complex tech stack working
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21:07  * ThomasEgi hates noisy magnetometer data for beeing ways too noisy
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23:32 < kanzure> http://www.gwern.net/Death%20Note%20Anonymity
23:35 < Steel_ZZZ> is this an example of a waste of time?
--- Log closed Sun Feb 26 00:00:26 2012