2009-05-08.log

--- Day changed Fri May 08 2009
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kanzure-hm. I need a way to make a super-high velocity water drop. say, 300 m/sec.00:31
kanzure-converted air rifle?00:36
kanzure-12 drops of water per minute? wtf is this nonsense.00:37
kanzure-heh. it's just a rifle in a tetrahedral space frame.00:38
genehacker_why?00:48
kanzure-"Micromachining single crystal materials using a tetrahedral space frame machining centre00:48
kanzure-"00:48
genehacker_sauce?00:48
genehacker_perhaps you could build a water gun os some sorf00:50
genehacker_link?00:50
kanzure-don't have access.00:51
genehacker_yeah me neither01:05
genehacker_and I'm on the campus01:05
genehacker_mind explaining the droplets moving very fast part?01:08
kanzure-"I know, still a little slow, but wait until I put on the big blade"01:12
kanzure-is there any context in which that sentence makes sense?01:13
kanzure-because I'm fairly certain something would be slower with a larger blade01:13
kanzure-(the blades are circular)01:13
kanzure-genehacker_: it's just a pulsed water jet cutter01:13
genehacker_some anime?01:13
kanzure-by ridiculously high speed water drop impact01:14
genehacker_cool01:14
kanzure-nope, not anime :(01:14
genehacker_???01:14
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genehacker_http://science.slashdot.org/article.pl?sid=09/05/08/034424802:14
genehacker_look what made slashdot?02:15
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kanzure-cis-action: are you serious10:54
cis-action...10:55
kanzure-mindlessly chanting oaths is not what we need10:55
kanzure-we need real, effective safety protocols, not bullshit10:55
kanzure-"do not ingest hydrogen peroxide" > "do no harm"10:55
cis-actionyou think we have unsafe protocols right now?10:55
kanzure-we have no protocols :(10:55
kanzure-there's pcr.xml, but whatever10:56
cis-actionReality vs. perception of reality.  We need to be safe and seem safe.  pcr.xml is going to go way over most people's heads.  Besides, it has like 3 research topics rolled up into it as well.  We need dependable, demonstrable safety, as well as cutting-edge, early-adopter research-project safety.11:00
kanzure-what does that have to do with anything11:01
kanzure-have you already forgotten about the protocol-xml-to-english-readable-text translators?11:01
cis-actionha ha ha.11:01
cis-actionyou're talking to me.11:01
cis-actionI'm not the audience, you idiot.11:02
cis-action"no man is an island" etc. etc.11:02
kanzure-I just feel like nobody is listening or understanding11:02
kanzure-what?11:02
kanzure-you *are* the audience. you claim that Zach's essay was useful, or something11:02
kanzure-but it wasn't.. except for maybe the citations, but who cares? that could have been given as a bibliography without a crap waste of time essay attached11:02
cis-actionWe are going to get legislated out of existence by the rest of society if stuff like pcr.xml is our only response to the safety question.11:03
kanzure-would you say the same thing if pcr.xml is used to automatically generate instruction manuals11:03
cis-action"Oh yeah, we're safe.  We invented a whole new safety paradigm.  It's years ahead of the obsolete safety protocols used in traditional labs.  No need for you to worry, Mr. Citizen."11:04
kanzure-and an oath will make people feel better? now who's laughing11:04
cis-actionI'm not saying it's not a good idea.  I think it's a great idea.  But we need more.11:04
cis-actionyes!  you think it's stupid but it's true.11:04
kanzure-because it is stupid.11:04
kanzure-it has absolutely nothing to do with progress11:05
kanzure-and it has so far wasted a large portion of your time11:05
kanzure-ok, let's put it this way11:06
kanzure-you spend 2000 hours crafting an oath or something11:06
kanzure-versus spending 20 hours crafting safety protocols and ways to make sure people aren't going to do stupid things without knowing it11:06
kanzure-those 2000 hours might feel like they are being productive11:07
kanzure-but meanwhile people are dying because they are idiots11:07
kanzure-and because their software sucks or something11:07
kanzure-how "ethical" or "moral" is *that*11:07
cis-action1. Stop being so dramatic.  That's not a realistic description of the situation.  No one is dying, and the risk of serious injury seems really low right now.  11:08
cis-action2. you lead the crusade to get your machine-readable safety ontology used in 10 labs and then I think you have the beginnings of a point11:09
kanzure-people aren't dying because they aren't doing stupid things11:09
kanzure-but once you have a million different protocols online11:09
cis-action3. I'm not planning on writing a creed.  Hopefully someone else will.  I just am trying to defend the general idea because I believe it's important to our relationship with the rest of society.11:10
kanzure-*you* try implementing effective safety measures into them "after the fact"11:10
cis-actionyes, well, as you said already, we have 0 protocols.  Let's work hand-in-hand doing the safety markup on the first one.11:10
cis-actionI'm actually excited about that.11:11
kanzure-yeah, instead of wasting time on writing lengthy essays11:11
cis-actionbah, it was shorter than most of your emails.11:11
kanzure-most of my emails are not about ethics/morals ;-)11:11
cis-actionYou are acting like the stereotypical autistic engineer, hackles raised by talk of humanities students.11:12
kanzure-that was a freaking *engineer* who wrote the essay :(11:13
kanzure-I don't know what it would take to convince you people that humanities is not the way to do engineering11:15
kanzure-ok. I'm done ranting.11:26
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kanzure-has anyone seen a MEMS rocket yet? either an array of micropropulsion thruster thingies. just wondering why these aren't more popular for rocket enthusiasts.12:25
kanzure-there are some for nanosatellites, but I was hoping for something in the atmosphere12:25
kanzure-there are micro aerial vehicles, but they have flapping wings (wtf)12:25
xp_prgwhat is a MEMS rocket?12:30
kanzure-cis-action: have you joined the papers mailing list yet?12:33
cis-actionHmm, I don't think I have.12:34
kanzure-cis-action: it's like getarticles except for discussing papers that you happen to be reading12:34
cis-actionoh neat12:34
cis-actionI'm interested.12:35
kanzure-I posted a link to diybio and getarticles btw.12:35
kanzure-cis-action: http://postbiota.org/mailman/listinfo/papers12:35
fenni was always skeptical of tiny arrays of rockets12:36
fennit just doesnt seem like it could possibly be as efficient as one big rocket12:37
fenner, arrays of tiny rockets12:37
cis-actionhey wait a second, this mailing list is just messages from you, bryan.12:38
kanzure-eugen leitl posts sometimes.12:39
kanzure-there are also a few other subscribers12:39
kanzure-fenn: I should just go do the math, but really I think the ratios should still work12:40
cis-actionok12:40
kanzure-for a liquid propellant, it should still be able to have a giant tank on board12:40
kanzure-(relatively giant)12:40
kanzure-cis-action: still need the pyrosequencing paper?12:41
cis-actionwhy another mailing list and not a group on citeulike or mendeley?12:41
cis-actionyeah12:41
kanzure-mendeley crashes when you import more than 10,000 papers12:41
cis-actionoh12:42
cis-actionYeah I haven't been that impressed12:42
kanzure-as for citeulike, I actually recently registered12:42
kanzure-and have put some references on there.12:42
kanzure-not too impressed with the groups already there though12:42
kanzure-seems underused or something?12:42
cis-actionha ha so does the Papers mailing list12:42
kanzure-well, that's certainly true12:42
kanzure-metagenomics pyrosequencing: http://heybryan.org/books/papers/Metagenomic%20pyrosequencing%20and%20microbial%20identification.pdf12:43
cis-actionok, I will try posting the next couple of papers I read to both Papers and to a citeulike group12:43
cis-actionthanks12:43
kanzure-feel free to invite me on citeulike to a group or whatever12:43
kanzure-or send me a link.12:43
cis-actionwill do.12:43
cis-actionbtw the Urine DNA sequencing paper is fascinating 12:43
cis-actionI want a sequencer in my toilet.12:44
kanzure-heh12:44
kanzure-did you read it?12:44
kanzure-they injected DNA into blood and some mice pissed it out12:44
cis-actionjust the first page, including abstract12:44
kanzure-there was another paper from a while back12:44
cis-action0.06%12:44
kanzure-where they used a bladder as a bioreactor12:44
cis-actionSo, about the sequencing paper... I am interested in just bootstrapping Jason's BioWeatherMap project and trying to do direct sequencing off of some sample I grab12:46
kanzure-have you considered direct electronic identification of nucleotides?12:46
kanzure-i.e., building the AFM machine and sequencing DNA by detecting the force of different nucleotides12:46
cis-actionI'm trying to figure out how I need to prepare a sample and what I should be sequencing.  Everyone says 16s ribosomal dna and I have no idea there are better options.12:47
kanzure-no idea there are12:47
kanzure-what?12:47
kanzure-45 MB file of DNA sequencing papers & bibtex: http://heybryan.org/books/papers/bibliographies/DNA%20sequencing.tar.gz12:47
cis-action...no idea *if* there are better options (genomically).12:47
cis-actionwe should collaborate.  I'll get and prepare the samples, and you build an AFM and do the single-molecule sequencing12:47
kanzure-haha12:48
kanzure-would you pay for it?12:48
cis-actionthanks12:48
cis-actionhmmm12:48
kanzure-STM DNA sequencing bibliography: http://heybryan.org/books/papers/bibliographies/STM-DNA-sequencing.bib12:48
cis-actionit depends on the budget, really, and if you would document the construction instructions at the same time12:48
kanzure-STM DNA IETS sequencing bibliography: http://heybryan.org/books/papers/bibliographies/STM-DNA-sequencing-IETS.bib12:48
kanzure-I don't have a full estimate of how much it would cost, but if you think there's a chance that we could drum up some funding to build a diy afm, that would be great12:48
kanzure-the big price factor is going to be the plastic parts12:49
kanzure-which can be uploaded to ponoko and we can check how much they would cost to be built12:49
kanzure-or I might be able to print them for free at school here 12:49
cis-actionfor sure12:49
cis-actionI bet as a community we could raise $1k12:49
cis-actionyeah I have access to a fablab here and I could laser cut stuff there12:50
kanzure-the trick is figuring out if AFM can do DNA sequencing. STM can, but AFM hasn't been used extensively for these purposes in the literature.12:50
kanzure-Progress in sequencing DNA with AFM http://heybryan.org/books/papers/Progress%20in%20sequencing%20DNA%20with%20an%20AFM.pdf12:51
kanzure-that was from 1990 though12:51
kanzure-almost as old as I am ..12:51
wrldpcwhat's up with broderick on GRG?12:54
wrldpcsheesh12:54
kanzure-damien?12:55
wrldpcaye12:55
kanzure-I haven't been reading his emails, what's up?12:55
fenn'big price factor is going to be the plastic parts' you gotta be kidding12:57
cis-actionkanzure: http://diybio.chipin.com/diy-afm-dna-sequencer12:57
kanzure-the rest was like nuts and bolts12:57
wrldpcHe brought up this point that I thought had died ages ago regarding Aubrey and Cambridge.  Just creating more bullshit chatter and distracting people away from discussing the science.12:57
cis-actionof course... we could just put the money towards a commercial sequencing budget.12:58
wrldpcIt's like when no one has something substantive to contribute they resort to some kind of trite philosophical or political point.12:58
kanzure-cis-action: yes. that's why I suggested the community nominations for sequencing or something. or even just SNP stuff via 23andme.12:58
wrldpcReally annoying.  Then when I call him on it the moderator of the group sides with him exhibiting the same "institutional bias" that got Aubrey fired in the fucking first place.12:58
kanzure-wrldpc: damien doesn't seem to be too important. ignore him.12:58
wrldpck12:59
kanzure-GRG is very academic-oriented. they all secretly hate Aubrey or something.12:59
wrldpcaye12:59
kanzure-cis-action: but really, what about the 23andme community nominations idea?13:10
cis-actionhow would it work?  I mean, what does it have to do with 23andMe?13:10
kanzure-it was suggested in the thread where somebody mentioned a company was going to do free sequencing of a whole genome13:11
kanzure-and instead, we were thinking of doing SNP analysis for some member of the diybio community13:11
kanzure-by pooling together 'lottery money'13:12
kanzure-even though it's not very DIY :(13:12
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kanzure-eh?13:20
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kanzure-not that anybody cares, but13:48
kanzure-http://heybryan.org/books/papers/AFM-DNA-sequencing/13:48
kanzure-sequencing by hybridization. hrm.13:51
kanzure-wasn't there some paper about using an AFM tip to pop off a nucleotide from the DNA stack or something? mechanical separation, or some such14:09
fennthat sounds highly unlikely to work even if someone wrote a paper about it14:17
kanzure-ah, it was just denaturation via mechanical force :(14:18
kanzure-er, separating of complementary strands14:18
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kanzure-http://en.wikipedia.org/wiki/Microfluidic_Sanger_Sequencing15:13
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kanzure-http://heybryan.org/books/papers/Microfabricated%20bioprocessor%20for%20integrated%20nanoliter-scale%20Sanger%20DNA%20sequencing.pdf15:16
kanzure-microfluidic system for Sanger-method DNA sequencing15:17
kanzure-includes some nice diagrams of their design15:17
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kanzure-Eco International E-Recycling Drive tomorrow at 2 pm - 6 pm here in Austin. might want to go by to pick up some junk.17:34
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fennyou sure that wasn't last saturday?17:47
kanzure-was announced on television, so maybe there will be people hanging around the spot with stuff to drop off17:49
fennwhere?17:50
fennthis monitor can't decide if it's broken or not17:53
kanzure-can't find it.17:56
fennsweet campbell hired me18:14
fennjune 1 to august 1718:14
fenngreat time to be in texas eh :P18:15
kanzure-your whole migration thing is kind of fucked up18:16
kanzure-you're like a bird with brain damage18:16
kanzure-anyway, congratulations18:16
fennheh18:17
kanzure-will he pay you18:17
fenn$13/hr18:17
kanzure-so if you want to cover a portion of rent or something, that would be neat18:18
fennyeah18:18
kanzure-hm. bacteriophages have an internal pressure of 50 atm.18:55
fennwow18:59
kanzure-the addition of a sequence of nine arginine residues to a protein makes it bind to silicon surfaces. O.o19:11
kanzure-or just use the bacteria ribosomal protein L2. hm.19:11
kanzure-I wonder if that works for sand too.19:12
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kanzure-fenn: hm. the hours he's offering me during the summer is somewhat lower than what I was anticipating. my funds are going to be a little tight. (sata gave me some weird hours too, so not everything is quite matching up)19:25
kanzure-posted some abstracts: http://heybryan.org/mediawiki/index.php/Virus19:27
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kanzure-er, this is kind of hard to search for19:43
kanzure-what does the 'position' function in lisp do?19:44
fennIf the sequence contains an element satisfying the test, then the index within the sequence of the leftmost such element is returned as a non-negative integer; otherwise nil is returned.20:02
kanzure-any thoughts on making clisp tell me the line number of an error? -v doesn't do the trick.20:06
drazakno offense20:56
drazakbut do any of you have girlfriends?20:56
kanzure-not anymore.20:57
drazakmhm20:58
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jm|spacei have robots, if that counts21:06
jm|spacewhy do you ask? do you need one?21:07
kanzure-mom wants to buy me this: http://austin.craigslist.org/fuo/1140266244.html21:07
drazakjm|space: no, I have one21:08
kanzure-so certain are you.21:08
kanzure-these clisp restarts are useless. they don't tell you context.21:11
kanzure-"oops, the value you entered for that variable was of the wrong type but I didn't tell you what type of the variable was to begin with, so ha ha!"21:11
kanzure-"(and you can't go back because that's not an option)"21:11
fennum isnt the point of the restart that you can go back?21:19
kanzure-there's an ABORT.21:21
kanzure-hm. sbcl has much more detailed output about what's going wrong with the script. lots of undefined variables floating around.21:22
kanzure-fenn: did albert ever send you the source yet21:37
kanzure-why can't we do this with our fablab? http://dsc.discovery.com/tv/doing-davinci/doing-davinci.html21:38
kanzure-getting funding for making all of davinci's inventions? please please please21:38
kanzure-"I AM SICKENED BY YOUR WEAKNESS" is one of the t-shirts the guys wear. heh.21:42
drazakkanzure-: have you thought much about H1N1?21:54
kanzure-no. but I have been feasting off of Superkuh's previous work being anxious about H1N1.21:59
drazakwell22:00
drazakI'm thinking of working out how well tamiflu will work on it22:01
drazakas my project for tonight22:01
kanzure-did you see my post to diybio about the synthesis of oseltamivir?22:02
drazakmissed it22:02
drazakI've been busy22:02
kanzure-you might want to look at it :)22:02
drazakI need to get my moleskin notebook in a sec22:02
drazakto quote 'stuff white people like' "it's where we write all of our really great ideas"22:02
drazakwe need more neuraminidase inhibitor class drugs22:04
drazakhaving only two makes the ability for the virus to mutate to immunity very likely, espescially if we have pandemonic panic and start injecting people with drugs22:06
drazakI also need to find out how the flu virus is fought off by the immune system22:08
drazakkanzure-: do you have books on immunology?22:08
kanzure-antibodies22:08
kanzure-on the server22:08
drazakwell no shit sherlock22:08
kanzure-heybryan.org/books/Medical/22:09
kanzure-http://heybryan.org/books/Medical/22:09
drazakyah already there22:09
kanzure-http://heybryan.org/books/Medical/Medicine%20-%20Fundamental%20Immunology%205th%20Edition%20-%20William%20E.%20Paul%20-%202003.pdf22:10
kanzure-http://heybryan.org/books/Medical/Medicine%20-%20Microbiology%20Immunology%202005.pdf22:10
drazakalready downloading the first one22:10
kanzure-http://heybryan.org/books/Medical/Medicine%20-%20%5bIsilo%20Book%20-%20Medicine%5d%20Adelman%20-%20Manual%20of%20Allergy%20and%20Immunology%20Diagnosis%20and%20Therapy%204th%20ed.rar22:10
kanzure-http://heybryan.org/books/Medical/USMLE%20-%20Biochemistry,%20Immunology,%20Microbiology%20-%20USMLE%20Lecture%20Notes%20%5bKaplan%5d.pdf22:10
kanzure-http://heybryan.org/books/Medical/Medicine%20-%20Pathology%20-%20Robbins%20Pathologic%20Basis%20Of%20Disease%207ed%20(eBook).pdf22:11
kanzure-ack, firefox crashed. why am I using firefox.22:11
drazakis all good22:11
drazakI have the pathology one on my other laptop22:11
drazakthere's chemical synthesis of oseltamivir on wikipedia now22:12
kanzure-http://en.wikipedia.org/wiki/Oseltamivir_total_synthesis22:16
kanzure-nice.22:16
drazakyup22:17
katsmeow-afkomd, it's 56megabytes22:59
drazakmhm22:59
katsmeow-afkkanzure, are you on dialup?!23:01
drazakkatsmeow-afk: he's not23:01
katsmeow-afkhmm, i am getting only 22ks from him23:02
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kanzure-katsmeow: what do you want?23:18
kanzure-er, or if you know of a good proxy for me to install on a faster server, ..23:18
drazakkanzure-: I have a faster server if you need it 23:19
kanzure-I do too.. 23:19
kanzure-my outgoing connection sucks, but not if I am out going to the university23:19
kanzure-so I just need to install a good proxy server on one of my machines23:19
kanzure-unfortunately there are no proxypass tutorials left on the web anymore (wtf)23:19
katsmeowa proxy on a faster server wouldn't help you unless it cached for a long while23:19
kanzure-yes it would23:20
kanzure-I have 10 MB/sec back and forth to that server23:20
kanzure-(to multiple servers actually)23:20
katsmeowthen why do you need the proxy?23:20
kanzure-because you're getting dialup speeds23:21
kanzure-and I'm a nice guy?23:21
katsmeowoh23:21
katsmeowwell, i won't be pushy, i can throttle back my fetch rate if it helps23:22
kanzure-it doesn't23:22
katsmeowk23:22
katsmeowi was interested in just the one book23:23
kanzure-http://httpd.apache.org/docs/2.2/mod/mod_proxy.html23:26
kanzure-ok23:28
kanzure-http://adl.serveftp.org/heybryan/papers/23:28
-!- kanzure- changed the topic of #hplusroadmap to: taking over world, etc. etc. fast download of paper dump: http://adl.serveftp.org/heybryan/papers/23:28
kanzure-can someone tell me how that is? please?23:29
katsmeowgimme to min to finsh the dl still going23:31
katsmeowwoo, bloody well faster23:35
katsmeow9x faster23:35
kanzure-have fun.23:36
katsmeow /books/ is there?23:36
kanzure- yes. /heybryan/ is /books/ basically.23:37
katsmeowah23:37
kanzure-heh that's right I have all of these aptamer protocols I took from ellington23:45
kanzure-I should probably make some sort of use of this ..23:45
kanzure-http://heybryan.org/books/ellingtonlab/A_E-Lab_Stuff/Lab%20Talks/Tech%20Talks/23:47
kanzure-http://heybryan.org/books/ellingtonlab/Lord_Vader_stuff/grades.txt23:52
kanzure-Levy, Matthew \t 10323:52
kanzure-bah23:52
kanzure-(Levy was his favorite phd postdoc guy)23:52
kanzure-artificial self-replicating system? http://heybryan.org/books/ellingtonlab/Lord_Vader_stuff/puppy3.jpg23:55
kanzure-self-replication by condensation http://heybryan.org/books/ellingtonlab/Lord_Vader_stuff/puppy4.jpg23:56

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