2008-11-18.log

--- Day changed Tue Nov 18 2008
-!- nsh- is now known as nsh00:03
drazakhm01:59
drazakdoes one enzyme build the complemenatary strand of dna(polymerase?) or do 4?01:59
kanzureWhat do you mean, one per nucleotide? No.02:01
kanzureThere's a few enzymes involved in making the complementary strand of DNA, one being polymerase, yes.02:02
kanzureThere's also a few others involved at the replication fork, for instance.02:02
kanzureOkazake fragments are something else to consider.02:02
kanzureFor PCR, you just need DNA polymerase.02:03
drazaknot talking about for pcr02:03
drazakI'm talking about for sequencing02:03
drazakhm02:03
drazakPPi as a byproduct02:04
drazakneed to find some sort of flourescent/lumonescent dye that activated with PPi, and grabs it up before anythning else02:04
kanzure_http://video.google.com/videoplay?docid=-8640306924766056110 "Star Trek: New Voyages". I'd laugh if it wasn't so sad.02:15
ferrouswheeldrazak: "DNA polymerase epsilon  (Pol epsilon ) from Saccharomyces cerevisiae consists of four subunits (Pol2, Dpb2, Dpb3, and Dpb4) and is essential for chromosomal DNA replication."02:34
ferrouswheelis this what you were asking about?02:34
drazakto some degree02:34
drazak4 subunits huh02:35
ferrouswheelnot sure if all polymerase has a 4 subunit quaternary structure... but at least for S. cerevisiae it does02:35
kanzureIf you're interested in the subunit structure of polymerase, I have about 20 PDFs on that on the server:02:37
kanzurehttp://heybryan.org/~bbishop/docs/ellingtonia/polymerase/02:37
drazakhm02:42
drazakwell, I wonder how different the energies are released by the addition of different subunits02:42
kanzureHuh?02:43
kanzureSubunits are parts of the structure of polymerase. So what energy-releasal process are you talking about?02:43
-!- kanzure changed the topic of #hplusroadmap to: http://groups.google.com/group/openmanufacturing http://heybryan.org/02:44
drazakoh, not that one02:47
drazakwhen making a dna strand02:47
drazakthe breaking off of PPi from ATP/CTP/GTP/TTP02:47
drazakI wonder if it's different between them02:47
drazakI mean, they're ester linked diphosphate groups... butttt02:48
drazakwhm02:48
kanzureFor notes on the structure of DNA, I have a 20 MB HTML file over in http://heybryan.org/school/Physiology/02:49
drazakI'm just thinking alloud here02:50
kanzure_http://heybryan.org/school/Physiology/03-29-07,%20Digestive%20system.html <-- Not DNA, but still. Impressive, no?02:51
kanzure_http://heybryan.org/school/Biology/notes/01-24-07,%20Deoxyribonucleic%20acid.html02:52
kanzure_Ah, there we go.02:52
kanzureScroll down for the goods.02:52
drazakI dunno if what I'm thinking off would be there02:53
kanzureWorth a glance.02:53
kanzure_Ugh. This was 2005? http://heybryan.org/school/Biology/notes/11-11-05,%20The%20Cell%20Cycle.html 02:56
kanzure_I feel old.02:56
drazakkanzure_: nothing that I need02:58
drazakah well02:58
drazakI'll research it tomorrow02:58
drazakwrite what I'm looking for in my notes02:59
geneyou there kanzure?04:44
genecan you hear me now Kanzure?04:58
-!- fenn_ is now known as fenn05:50
fenngosh does this guy really thing going back to the moon will require training kindergartners in science and math?06:04
fennhaha they're talking about hardware based unit testing in emc (moving motors around and pressing switches n stuff)06:24
UtopiahGHMLhttp://markorodriguez.com/Research.html08:19
UtopiahGHMLSynthetic Cognition through Petascale Models of the Primate Visual 08:19
UtopiahGHMLCortex, Neno/Fhat: A Semantic Network Programming Language and Virtual Machine Architecture, CDMS: Collective Decision Making Systems, ...08:20
* UtopiahGHML loves today Dilbert's cartoon :>09:56
drazakkanzure_: do you know if there are enzymes that add only one kind of dNTPs?12:24
kanzuredrazak: That's what those papers are about.12:37
kanzureSpecifically, not really. There are some polymerases that you can mutate a bit, but it's hard to do selection experiments on a "retarded polymerase".12:38
kanzurefrom Michel - 12:41
kanzurehttp://thingiverse.com/12:41
kanzureStupid. Click the 'upload' button .. they allow any file type. blah..12:42
nshARGHGHGHGHGH: http://www.nature.com/news/2008/081117/full/news.2008.1235.html12:47
nsh"The search for genome 'dark matter' moves closer"12:48
nsh*head against table, repeatedly*12:48
kanzurensh: Have you ever published?13:06
kanzurensh: The reason I ask is because I'd like you to go over a partial draft that I'm submitting to biomedcentral, the BMS Systems Biology journal.13:07
* nsh hasn't, but will read through anyway if you'd like13:07
kanzurehttp://heybryan.org/mediawiki/index.php/Towards_automatic_generation_of_linear_genetic_regulatory_networks_via_biobricks13:08
kanzureApparently a two-page technical "Towards blah blah blah" paper is acceptable and quite commonly appears in that journal.13:08
kanzuresecond page can very well just be screenshots of cool shit :)13:09
* kanzure goes down to eat.13:09
nshi'm not sure you can use the phrase "pathetic web interfaces" in a journal13:13
nshbut you should try anyway13:14
kanzureHeh.13:25
kanzureRawwrrr13:27
kanzureI hate these people.13:27
kanzureNew inbox email: "[agi] My prospective plan to neutralize AGI and other dangerous technologies..."13:28
UtopiahGHML??13:28
kanzurethat's like saying "my plan to neutralize bacteria"13:28
kanzureYeah, good luck there buddy!13:28
kanzure"my plan to neutralize electrons'13:28
UtopiahGHMLId like to read that actually, Dilbert's cartoon today was funny but I think I can laugh again 13:29
kanzure Wrong, wrong approach.13:29
kanzureUhm, it's on the AGI mailing list if you want.13:29
UtopiahGHMLpretty bold to post that on the official mailing list of the guys building the tool itself :P13:30
* UtopiahGHML reading http://www.mail-archive.com/agi@v2.listbox.com/msg15343.html13:31
UtopiahGHMLthis is definitely a former cracker with solid experience, his notions regarding security seem flawless...13:33
UtopiahGHML[I]13:33
UtopiahGHML(that's the Ironical [I] tag for those who wonder)13:33
UtopiahGHMLwtf is this a kind of joke or is the guy serious...13:35
UtopiahGHMLIm pretty sure the guy will lock himself out of this very website anyway, funny.13:38
kanzureThe problem though is that these people tend to be serious about this.13:54
kanzureNot his specific idea in this instance, but the subject of the thread itself plays on a long-deep fear in the AGI community.13:54
kanzure"Oh teh noes, AGI will rule the world wtf are we going to do? I know, I know! Let's have Eliezer Yudkowsky build an AI *first* that is **inherently NOT EVIL*** that will be a world dictator and stop all other AGI/AI projects from emerging!"13:55
UtopiahGHMLisn't it why most makes donations?13:57
kanzure_-Back.16:34
kanzure_-http://www.geocaching.com/ "find the money" game.17:03
nshdid i ever mention17:18
nshthat Eliezer is a fucking idiot?17:18
nshthat may not have come up before17:18
nshso, just putting it out there17:18
nshoh wow17:20
nshi feel so much stupider for reading that agi post17:20
nshthanks :-/17:20
kanzure_-fenn: http://code.google.com/p/pyglet/source/browse/trunk/experimental/glxgears.py <-- another reason not to use this is the giant gaping "TODO/FIXME" where the meat of the code would actually be ..17:41
bkerolol17:41
kanzure_-http://maven.smith.edu/~orourke/240/gears.py17:42
bkerouh17:43
bkerodoesn't exist17:43
bkeroGotta kill it17:43
kanzure_-does for me .. wtf? :)17:43
bkeroI hold cwn ctrl+c, and it gives me tracebacks, but that's it17:44
kanzure_-Ah, I see what you mean.17:45
kanzure_-apt-get install python-opengl17:45
-!- percent is now known as jihaad18:24
kanzure_-http://www.daniweb.com/forums/post701317-5.html drop-in compatible with import opengl stuffs? hrm..19:04
kanzure_-https://svn.zib.de/lenne3d/lib/pyopengl/3.0.0a5/OpenGL/Demo/NeHe/lesson42.py close enough.19:06
kanzure_-All hail NeHe.19:07
kanzure_-http://heybryan.org/shots/2008-11-18_glxgears.py.png <- Now accepts graphsynth output (well, not really. There's an intermediate CSV file.)19:52
kanzure_-http://heybryan.org/~bbishop/docs/repo/gears.py19:52
kanzure_-uh19:53
kanzure_-http://heybryan.org/~bbishop/docs/repo/gears/gears.py19:53
kanzure_-with other stuff in the dir.19:54
kanzure_-git clone git://repo.or.cz/pythoncad.git19:56
kanzure_-looks like I'll be using VTK http://www.nabble.com/CAD.py-td20270104.html19:57
kanzure_-http://www.vtk.org/Wiki/VTK/Writing_VTK_files_using_python19:57
kanzure_-http://cens.ioc.ee/projects/pyvtk/19:58
kanzure_-http://cens.ioc.ee/cgi-bin/cvsweb/python/pyvtk/examples/example1.py?rev=1.3 <--- not bad.19:59
kanzure_-http://rosettadesigngroup.com/blog/ Macromolecular Modeling Blog, by way of bbb@bioinformatics.org mailing list20:06
kanzure_-gene: Welch 2.224 from 630 to 745 is a viewing of the PBS docu "The Atom Smashers"20:07
ybithttp://nextbigfuture.com/2008/11/seaweed-fungus-and-algae-biofuel.html20:23
bkerokanzure_-: You said I needed to write you an email or something to get some algae samples?20:24
-!- Irssi: #hplusroadmap: Total of 16 nicks [0 ops, 0 halfops, 0 voices, 16 normal]20:25
bkeroMy digestor, growth tubes, and co2 supply are all ready. :)20:26
kanzure_-bkero: I was going to make a trip down to the lab today, so maybe I'll magically remember.20:29
bkeroHeh20:30
kanzure_-ybit: Apparently I'm attending a biofuel/algae conference tomorrow.20:30
kanzure_-http://en.wikipedia.org/wiki/List_of_Earth-crossing_asteroids <- So kind of Wikipedia/lazyweb to do our hard work for us.20:30
kanzure_-bkero: How do I go about mailing liquids?20:31
kanzure_-Uh.20:31
kanzure_-Hrm.20:31
bkeroGoto the mailing place on campus20:32
bkeroThey should know the procedure20:32
bkeroOr call them20:33
kanzure_-Uusally this requires MTAs, material transfer agreements.20:33
kanzure_-And usually this means that I have to have the professor's signature.20:33
bkeroWhich both our universities have :)20:33
bkeroo20:33
kanzure_-yeah ..20:33
bkeroI just have an on-campus job, so I use that to mail anything I need.20:33
kanzure_-so google me up a "guide to transferring biological agents"20:33
kanzure_-so do I of course :20:34
kanzure_-)20:34
kanzure_-multiple jobs it seems20:34
kanzure_-wtf am I doing here20:34
* kanzure_- goes20:34
geneso kanzure, what do you think largest feature size on a microchip should be21:36
genecould you get away with 4 micrometer feature sizes?21:39
kanzureWhy do you need it to fit within the category of micro-chip?21:41
genewould you 4 micrometer be ok if you wanted to make a microchip21:46
kanzureI don't know what you are asking.21:47
kanzureAre you asking about the ontological basis of calling something a microchip?21:47
geneno21:47
kanzurei.e., "if it has a 4 micrometer feature, is it still classified as a microchip?"21:48
geneOk21:48
kanzureThen what are you asking?21:49
geneI could conceivably make a micropositioner accurate to 4 micrometers21:49
kanzuregene: Remember, the original microprocessor people were drawing circuits in wax with sharp sticks from trees.21:50
kanzure(Actually, with forks or the opposite ends of pens, probably.)21:50
geneand I could conceivably use this micropositioner to do electrochemical  etching21:51
genedag21:51
genedang21:51
genedid I mention I could conceivably make this micropositioner with legos21:53
kanzureI think you should start by trying to make the original setups that the Intel guys were using in the 50s?21:54
drazaktubes?!21:55
geneno21:55
geneno21:55
geneSo anyway21:55
genewhat do I need to do to do electrochemical etchingn21:55
kanzureNo, not tubes.21:56
kanzureThey weren't using micropositioners and were still able to make circuits.21:56
kanzurePretty small circuits too.21:56
kanzureAnd without ridiculously expensive masks.21:56
fennjust so you know, VTK is really hard to understand21:56
fenn(supposedly it would be easier if you buy the book)21:56
kanzureI don't know. It will require some searching.21:57
kanzureI might have some information here:21:57
kanzurehttp://heybryan.org/semiconductor.html21:57
kanzurehttp://heybryan.org/semiconductors.html (one of those)21:57
kanzurefenn: robogami2007 is pretty neat21:57
kanzureyay psychic powers21:57
kanzureyay budgets..21:57
kanzure_http://www.youtube.com/watch?v=fIFA_PiDn7k robogami21:58
kanzureI wonder about grammar rules for origami.22:00
fennlet's see it do a crane22:01
kanzurehttp://heybryan.org/books/Manufacturing/origami/ <- check the Introducing robotic origami folding paper22:04
genecan't find the intel thing22:07
kanzureooh.22:09
kanzurefenn: see also the 'Constituting' paper in that dir.22:10
kanzureit has a data struct for origami22:10
genedoes anyone know of any cheap, highly accurate linear actuators?22:13
genedon't CD players use linear actuators to move the laser pickup?22:14
fenndefine cheap and accurate in quantitative values22:39
genecheap as in preferably under $2022:41
fennin qty 1?22:42
fennbacklash or no backlash22:43
genewhat's backlash?22:43
fennsomething you need to be aware of if you're using a linear actuator22:43
geneoh yeah22:45
geneno backlash22:45
fennnot gonna happen unless you DIY22:46
fennhttp://www.dumpstercnc.com/22:46
fennyou mind telling me what this is for? i dont like doing engineering in the dark22:47
geneelectrochemical machining mill22:48
fennwell, all the standard CNC stuff applies then, so off to CNCzone you go22:49
geneindeed22:50
fennyou forgot to mention the corrosive resistance requirement22:50
kanzure_http://www.langorigami.com/art/monumental/monumental.php4 monumental origami22:50
kanzure_webEOS22:50
* kanzure_ can't find webEOS22:50
genethe actuator doesn't need to work in a corrosive environment 22:50
kanzure_hah, second to last image22:50
genejust the toolhead22:50
kanzure_guy pulling giant sheet of paper22:50
kanzure_hehe22:50
genenow if we could only make a paper folding machine that folds paper we'd be set22:51
fennis that an ice skating rink?22:52
fennoh nm it's just a regular floor22:53
genefenn22:53
fenngene22:53
geneI am trying to make a small mill22:53
genea very small mill22:53
fennso is 90% of the rest of the geek populace22:53
fennwith varying degrees of seriousness22:53
kanzureManual folding is a good start.. then a machine.22:54
fenni dont know where people get the idea that making stuff is cheap and easy even if you dont know what you're doing22:54
genehttp://electronics.howstuffworks.com/cd4.htm22:55
genecd players22:55
fenngood luck22:55
fennhave you ever actually taken apart a cd player?22:56
fennthere's no "sweet delectable linear actuator module" that you can just pluck out22:57
genewell22:57
kanzurefenn: it's annoying, isn't it.22:57
fennkanzure: i intend to change this22:57
geneit looks like cd players also have some strange stabilizing mechanism22:58
fennit's to make up for the inadequacies of the cheap rack and pinion drive22:58
genewell they do22:58
geneusing magnets22:59
fennand notice that it moves a tiny lens on a tiny lever arm22:59
fenn1 micron accuracy over 1mm travel isnt that difficult23:00
kanzuredo tell?23:00
fennof course they calibrate the shit out of them at the factory with expensive equipment23:00
genewell23:01
genecd's can also self calibrate I believe23:01
kanzureyou speak in tongues. 23:01
kanzurethe intention to change this makes up for inadequacies in evolutionary behavior to jump on magic bullets and bandwagons?23:01
kanzurewhat?23:02
fenna cd is basically a giant pseudorandom linear encoder23:02
fennwrapped in a spiral23:02
genewell23:02
geneI'm not an expert23:02
genebut CD laser pickups have more than one pixel23:03
kanzure_eric hunting just posted to om about the 'unimat' in germany: http://www.thecooltool.com/produktgruppe.php?language=e&status=20&sh_id=15&ptitel=Unimat+Classic23:03
geneand might be able to track the pixels23:04
fennugh23:04
fennunimat just won't die23:04
genewhat?23:05
genewhat's so bad about unimat?23:05
geneit's small right?23:05
fennit's sloppily constructed23:05
fennit's also a lot smaller than it looks23:06
geneok23:06
geneyou just got me very interested23:06
fennit's woodworking crap23:06
geneis it a mill?23:07
fennno23:07
genecan it be?23:07
fenni'm just going to say no23:08
fenni like the 'reconfigurable machine tool' idea, but they just haven't done it23:09
kanzurehuh, robotorigami got to slashdot.23:10
genehave you heard about kulibin?23:11
genesome russian milling machine that can be reconfigured into anything23:11
kanzure_http://www.origamiboulder.com/23:11
fenni only see stuff about the watch maker23:12
genehuh?23:12
fennivan kulibin 176723:12
geneno23:13
kanzure_bioknoppix - for the molecular biologist in you. hm.23:15
genehttp://translate.google.com/translate?u=http%3A%2F%2Fwww.mntc.ru%2F&hl=en&ie=UTF-8&sl=ru&tl=en23:16
geneso how do you get sub micron accuracy on a cnc machine?23:17
fennuh, glass scales i guess23:18
fennand preloaded ballscrews23:18
genewhat are preloaded ball screws?23:18
fennthe balls push on both sides of the screw thread with a certain amount of "preload" force23:19
fennone way to do this is to use oversize balls23:19
fennanother way is to use two nuts pushing against each other 23:19
kanzure_http:/www.score.cs.tsukuba.ac.jp/webeos .. This is why you go open source. Your server dies and everybody mutters your name to damn it.23:22
kanzurehm23:22
kanzureinteresting23:22
kanzureSo there's a big thing going on about the whole cutting-off-analog-television broadcasting.23:23
kanzure"We urge you to convert ASAP .. do not wait until you get static."23:23
kanzurebecause then they can't reach them :)23:23
fennwebeos is some kind of origami thing?23:23
kanzureThey don't want to lose viewers.23:23
kanzure<quick link to Paul's link to the 10,000 hours link re: TV>23:24
kanzureyes23:24
fennyeah yeah 2000 wikipedias a yaear23:24
kanzureAJAX crap, so say the papers23:24
kanzurebackend is some stupid mathematica notebook file23:24
kanzurebut they have an api for folding and so on23:24
kanzurewhich now that I think about it is probably kind of obvious23:24
kanzurefold(a,b) where there's an arc splitting sides A and B23:25
genewhat if I used air bearings?23:25
kanzurehm, maybe each fold() call adds a new surface to the stack 23:25
kanzurethis isn't quite the same thing with origami that we were playing around with in blender of course23:25
fennheh i like their crane animation with the flapping wings: http://www2.score.cs.tsukuba.ac.jp/score-group-homepage/view?set_language=en23:25
kanzurethat was 3D object -> mesh it -> to origami diagram23:25
fennthat was papercraft, not origami23:26
kanzureoh right23:27
kanzuretape edges here, or something23:27
fennyes lots of taping and lots of cutting23:27
genehey why not make a paper cutting machine out of paper?23:29
genefor printing out papercraft23:29
kanzuregene: just out of curiosity, did you see the news blitz about launching origami planes from space shuttles?23:30
geneyes23:30
geneyes I did23:30
fennyay space pollution!23:30
kanzurewell, in all fairness, it was supposedly towards earth23:30
geneyou know I once contemplated making a  paper airplane with a jato on it23:30
fenni wonder, did the astronauts bring them up folded or did they have to fold in space?23:30
kanzurehm.23:31
geneI believe they brought it up folded23:31
kanzureisn't that kind of redundant?23:31
fennwhich, the astronauts or the cranes? :)23:32
genethe plane to be launched from space23:32
fenna paper plane full of paper cranes23:33
kanzureoooh, astronauts lose a bag of tools in space .. I'm amazed this made the news, but glad I guess. (television news)23:33
genethe cool thing is is that it is so light it will withstand reentry23:33
kanzurewhat's the glide ratio?23:33
fennhow do you lose a bag of tools? arent they tethered on at all times?23:33
genedunno23:33
geneno23:34
geneAFK23:34
kanzureyeah .. 23:34
kanzuregene: glide ratio is just how many feet horizontal per vertical lost.23:34
fennno mention of what will happen to the bag of tools..23:36
kanzurehm, so I might as well just make up my own API for origami folding.23:39
kanzureit looks like the SCORE guys were doing what I was doing with supermetal, with specific 'points of interest' on the shapes (or in this case, the 2D surfaces)23:39
kanzureso given a square piece of paper, the four corners are given labels, and then you say fold(A,B) where A and B are opposite corners perhaps23:39
kanzureI guess there's also half-folds, blah23:40
fennyou could fold at any arbitrary location23:40
kanzurebut anyway, given a full fold(A,B) where A and B are opposite to each other, plus a crease, 23:40
kanzurewell23:40
kanzureI think what I'm trying to do is come up with a correlation of what each function adds to the list of possible places to fold at23:40
kanzurebut you're right, you could just randomly fold anywhere.23:41
kanzureI'm also wondering about mechanical contraptions made from origami23:43
kanzurehopping frogs are boring.23:43
fenntheo janssen mechanism?23:43
* kanzure googles23:44
kanzureoh23:44
kanzurethat too23:44
kanzurehm. this looks like it's straight out of hod's videos.23:44
fennthere was a papercraft version23:44
geneI don't know what the glide ratio is kanzure23:46
genebut I heard it is fairly high23:46
kanzureIt would be fun to see what other mechanical motions are possible.23:46
geneI think theo jansen used a GA to optimize that mechanism23:47
genewhich explain's its similarity to hod's videos23:47
geneoh23:55
genethe magnets in the CD player might not be for stabilization23:55
genehttp://www.physics.udel.edu/~watson/scen103/cd-focusing.html23:55

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