2009-04-20.log

--- Day changed Mon Apr 20 2009
kanzure-fenn: so one method that people have used is a silicon cantilever with a resistor built into it00:09
kanzure-as the cantilever bends, the resistivity changes00:09
kanzure-uh, resistance00:09
kanzure-did I just say resistivity? :(00:09
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genehackergoto ifpi.org right now00:15
genehackerERROR CONVERSATION LAPSE00:15
fennactually i think 'resistivity' is correct, in this case00:19
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genehackerhttp://www.wired.com/science/planetearth/magazine/16-06/mf_monkeybusiness00:31
genehackeryou can get in trouble for Biopiracy in Brazil00:31
genehackerheh00:32
genehackerI wonder what they'd do about a researcher going into a forest there, sequencing everything in sight and dumping all the data to the internet00:33
kanzure-what do you think prostitutes are doing?00:33
kanzure-"genetic sleuthing" or something.00:34
genehackerit's not piracy00:39
genehackerthough00:39
genehackerit's making copies00:39
kanzure-with a sufficiently long and sufficiently narrow nanochannel (picochannel?), would a fluidic scanning microscope device work? 00:41
kanzure-I don't think it would because of the force required to push liquid up such a small channel00:41
kanzure-but if it did you could just use light to detect whether or not the liquid is up to that particular point00:41
kanzure-which would tell you how far the liquid has been pushed00:41
fennprostitutes provide a service which interferes with the marriage racket.. it's more like online college degrees than piracy00:42
kanzure-ok ok, I'll just start stalking people and recovering DNA from their dirty dishes or something00:43
kanzure-wait, why am I doing this?00:43
fennwas that a barack obama reference?00:43
kanzure-not to my knowledge00:43
fennwow sounds like someone was really out to get that biologist01:00
fennsending assassins after him even01:00
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genehackerkanzure just mail them some junkmail01:27
genehackerthey pick it up01:27
genehackerbreath on it accidently01:27
genehackerand throw it away01:27
genehackerthen extract the DNA from the paper01:28
genehackerPCR is that sensitive01:28
genehackerand unfortunately the dude who wrote the anthrax letters knew about it01:28
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facefaceapparently someone said somethgin to me in the last 3 days... anyone got a history?03:11
facefaceI have it here somewhere...03:11
fenn12:32 #hplusroadmap: < kanzure> faceface: that's neat. why would it result in a publication though?03:27
fennin response to: " each buddy would result in a pub."03:27
fennstarting a new novel; which of these is best? left hand of darkness, the mote in god's eye, a fire upon the deep03:28
* fenn wonders how much a gold-plated, machined chunk of silver costs03:39
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facefacecheers fenn 07:47
facefacekanzure-: getting a bioinf person to solve a bio problem, and a bio person to use some bioinf, should be a (small) publication I guess... depending on the quality of the work.07:48
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kanzurehttp://www.opencircuits.com/Atomic_microscope10:58
kanzuregwyddion. hrm.10:58
kanzurehttp://www.nanosurf.com/ hrm. handheld AFM. "request a quote" blah11:06
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kanzureis my fluid-AFM idea any good? would you be able to move a dyed fluid in response to pico-levels of forces?11:19
kanzureor atto-levels, even? I don't think so. :-/ as you restrict the diameter of the channel, you increase the amount of force required to push liquid through, right?11:19
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kanzure-that sandstone bacteria (bacillus pasteurii) sounds pretty neat13:14
kanzure-"I researched different types of construction methods involving pile systems and realised that injection piles could probably be used to get the bacteria down into the sand – a procedure that would be analogous to using an oversized 3D printer, solidifying parts of the dune as needed."13:14
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kanzure-heh heh13:35
kanzure-3D selective laser sintering .. from orbit.13:36
kanzure-or er you don't need to be in orbit13:40
kanzure-just on a really tall mountain13:40
kanzure-you could print a city I think13:40
kanzure-am I going insane?13:40
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kanzure-Hey Eric13:45
kanzure-erm, junglistric 13:45
junglistrichello13:45
kanzure-did you see my diybio post on 3D printing of deserts (SLS) from orbit?13:45
junglistricno, i haven't, let me check the email digest13:46
kanzure-http://is.gd/tvV713:47
junglistrichm, pretty amazing13:50
kanzure-aren't there some serpinski triangle regulatory networks that we have engineered for bacteria?13:51
kanzure-I mean, that make serpenski triangles on a plate of agar?13:51
kanzure-I know we've done it with DNA (see Winfree/Rothemund, etc.), but I don't know about GRNs and multiple cells13:51
junglistrici had to look serpinski up.  what do you mean by GRN?13:53
kanzure-genetic regulatory network13:54
kanzure-there are ways to control the expression of genes that would be involved in shape or growth and so on13:54
kanzure-this is what is used in amorphous computation projects, for instance13:54
kanzurehttp://bytesizebio.net/wp-content/uploads/2009/04/iching-thealieness.jpg huh?13:58
junglistrica regulatory network that creates that type of structure, i'm not so sure.13:58
kanzureisn't that how gene expression re: HOX works?13:59
kanzurefor shape determination13:59
kanzureand destiny cells in embryo development14:00
junglistricsure, but the would have to be some collective regulation since we're talking about the shape of a colony14:02
junglistricmight be an undertaking for a bio-artist14:06
junglistricsome outside stimulus i.e. light14:06
kanzure-here at UT there was an igem project for that- bacterial patterning with a camera photograph14:08
kanzure-a mask of the PI was used and the bacteria then displayed that photo :)14:08
kanzure-it involved substantial genetic engineering of some signaling pathways apparently14:08
junglistricyeah perhaps to tune the bacteria to the desired stimulus14:10
junglistriceasier than it sounds14:11
junglistric*harder14:11
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bkerobkero@fir ~ $ uptime 20:06:38 up 916 days,  2:33, 33 users,  load average: 1.70, 1.50, 1.7015:10
kanzurehttp://www.acceleratingfuture.com/michael/blog/2009/04/interview-with-singularity-institute-president-michael-vassar/ <-- huh, Steve Rayhawk is now an employee of SIAI? good for him.15:11
kanzurebkero: we all hate you :)15:12
kanzurewhy can't *I* have an uptime of 916 days15:13
bkerokanzure: That's my 5-9's service.15:13
kanzure?15:13
bkerohttp://en.wikipedia.org/wiki/High_availability15:13
bkeroAvailability is measured in 9's.15:13
bkero2 9's is 99%.  5 9's is 99.999%15:14
kanzure-right.15:14
bkero5 9's is < 5 minutes of downtime/year.15:14
kanzure-oh. 15:14
kanzure-So you're cheating.15:14
bkero?15:14
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bkeroNo, it's been up the entire time15:14
bkeroI'm saying it's provided at LEAST five nines15:14
kanzure-hrm.15:15
kanzurewho introduced me to the concept of singing sand dunes in here?15:55
kanzurehttp://en.wikipedia.org/wiki/Singing_sand15:56
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kanzureI wonder if we could geoengineer sand dunes to produce ultrasonic booms16:12
kanzurehttp://www.singingbridges.net/about/16:14
kanzure"sonic sculpture"16:14
kanzurehttp://en.wikipedia.org/wiki/Sound_sculpture16:22
kanzurewhat neat sound devices have been built before? amplifiers, I guess16:24
kanzurepneumatic sand circuits?16:37
fennshape determination from hox etc is based on folding and other type of sheet deformation16:48
fennyou couldn't do that if locked in a matrix of sand particles16:49
fennand besides, bacteria don't grow in sheets16:49
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kanzuresee what you miss when you sleep?17:12
kanzurenot that anything has actually happened17:13
kanzureyou know what. nevermind.17:13
kanzureheh, thomas paviot adopted fernhout's quoting method (ok ok, maybe he just knows enough python)17:16
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kanzurehttp://hypography.com/forums/engineering-and-applied-science/18854-solar-desalinator-making-one-diy-serious.html17:19
kanzurehttp://heybryan.org/books/papers/solar%20still%20-%20diagram3%20-%20solar%20desalinator.jpg17:39
xp_prgwow brian cool idea!17:57
xp_prgbrian what about getting the salt too?17:57
kanzurewhat about it?18:04
kanzurehurt what?18:25
kanzureoh18:25
fennhttp://www.lowtechmagazine.com/2008/04/algae-fuel-biof.html18:31
kanzure-the first cantilever was hand-crafted 800 micrometer strip of gold foil glued to a diamond tip18:44
kanzure-for AFM.18:44
xp_prgkanzure harvest the salt from your desalinization18:59
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fenncost of sneakernet vs internet for large data transfers http://www.codinghorror.com/blog/archives/000783.html19:03
fennlinked from http://www.lowtechmagazine.com/2009/02/sneakernet-beats-internet.html19:03
fennenvelope full of microSD cards seems like a reasonable solution19:04
fennespecially with a lot of ISP's going with monthly bandwidth caps19:04
fenni think time warner was going to do a 5GB/mo cap (which frankly, is ridiculously small)19:05
fennmakes you wonder about space colonization; maybe data will be the most valuable transport cargo19:07
kanzure-glad somebody else is worrying about algae efficiency and of the processes19:10
kanzure-the problem is that we're not funded to examine efficiencies, we're funded to do something that might be impossible19:11
kanzure-so it's in our interest to not do those studies, or something19:11
kanzure-I don't know how this works.19:11
kanzure-but it's also because I don't entirely understand how to do the math I guess19:13
kanzure-for instance, killowatt hours have never ever made sense to me19:13
fennit's simple19:15
fennkilowatt is 1000 watts19:16
kanzure-even if I did the analysis, that doesn't mean it's fixed though- because the results will probably show us how much it sucks19:16
kanzure-yes, I know how much a kilo is :)19:16
fenn1000 watts for 1 hour is 1 kilowatt*hour19:16
kanzure-right, but they always relate this in some weird way to joules19:16
kanzure-that doesn't dimensionally make sense or something19:16
kanzure-but they use it for selling electricity19:16
fennjoule is a watt*second19:16
fennso a kilowatt hour is 3,600,000 joules19:17
kanzure-right19:17
kanzure-maybe there's something else that was supposedly confusing19:17
fenni think they should get rid of the "joule" unit and just call it W*s, "wuss" :P19:17
kanzure-or the fact that no device really tells you how many watts it takes to operate when it's operating in such and such mode?19:18
fennmanufacturers are getting better about that19:18
kanzure-I'm tempted to get Andrew Hessel to hire me on to an open source synthetic biology microalgae biofuel project19:18
kanzure-screw this closed/proprietary crap19:18
fennbut specmanship will never die, so there's still a need for independent testing19:18
fenngood luck finding one19:19
kanzure-finding what?19:19
fennopen source synthetic biology project with money19:19
kanzure-he has a source of funding for one.19:19
fennone that's not iGEM19:19
kanzure-right19:19
kanzure-that's him :)19:19
fennthe point of the article was that there are much more things going into algae biofuel production than just the algae19:22
kanzure-right19:22
fennso even if the algae is 'proprietary' it doesn't matter19:22
kanzure-no, I'm talking about the harvesting and lysis machinery19:22
kanzure-that's really the bottleneck19:22
kanzure-algae naturally grows- growth optimization only matters to some extent- it's *made* to grow19:23
fennthen why bring synthetic biology into it?19:23
kanzure-"ask it nicely to release its lipids"19:23
fenn'reusable' algae?19:23
kanzure-and less effort involved with lysing it or killing it or whatever19:23
fennbtw i linked to something about using diatomaceous earth for that, dunno if you ever saw that19:23
kanzure-no?19:24
fennwell i have no idea where it went19:24
kanzure-linkhunters19:24
fennmaybe it was on diybio?19:24
kanzure-what I want to do is come up with some theoretical curves and then some actual curves for testing different hardware for lysis and harvesting19:25
kanzure-for some reason we're now moving on to foam fractionation (or something similar to it)19:25
kanzure-with this giant machine with little to no specs 19:25
kanzurealso, adding in some natural flocculation protein would be neat19:27
kanzurethere's also some co-species methods where a bacteria or other plant thingy produces flocculants that will make the algae clump together19:28
kanzurewhich makes harvesting as easy as running a big giant stick through the pond.19:28
kanzurethesis on automated gear train design - (I guess that means I'm done with the visualizer??) 19:40
kanzurehttp://heybryan.org/books/papers/Automated%20Synthesis%20and%20Optimization%20of%20Gear%20Train%20Topologies%20-%20Albert%20Swantner%20-%202009.pdf19:40
kanzurehttp://code.google.com/p/sfepy/ simple finite elements for python20:04
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kanzurehey RandIter.20:04
RandIterhello20:05
RandIterjust came to see what you guys are up to20:05
kanzuretoday?20:11
kanzureDIY atom-scale resolution microscopy, algae farms, and I just learned about AHA! - the Austin Hackers Association20:12
fennhow do i get cp or tar to preserve everything? it always messes up the permissions and creation time (yes i've tried cp -a)20:32
fenngrr now it works of course, after i ask20:32
fenngremlins20:32
kanzurezip has always preserved creation times for me, fwiw20:35
fennoh i see.. cp -a changes the permissions back to original when it's done copying20:44
kanzurehrm. octave versus sympy for doing some mathematical modeling?20:44
fennwhat kind of modeling?20:45
kanzuremeh, just a basic multivariable model of how much algae you'd have to grow to get how much energy if some volume of algae has such and such growth phase curves and blah blah blah20:46
fennah20:46
kanzureplus maybe weather consideration stuff.20:46
fenni was just thinking about how to do differential equations the other day20:46
fenni guess maxima or some mathematica clone would be the standard solution20:46
kanzuresympy is a symbolic package, but I don't think I need to do symbolic stuff20:46
kanzureso octave would be it then. hm.20:46
fennhave you used octave/matlab before?20:47
kanzureI've used octave a bit20:49
fenn hm i thought it was a requirement that theses had pretty latex equations20:54
kanzurehe sent it to me in docx format20:57
kanzurewhich is Microsoft's latest way of raping the internet20:57
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kanzureHey genehacker.21:01
genehackeryes I know21:01
genehackerAHA21:01
genehackerdo they do software primarily or the other type?21:02
kanzureseems like "the other type"21:04
fenn"security professionals"21:06
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genehackersecurity21:06
kanzurehey DrTread21:07
DrTreadhey, bryan21:07
fennDrTread: i was supposed to ask you something but i forget what it was..21:08
fennsomething about fab lab21:09
fennperhaps you should just send an email to lfilip@mac.com instead of me acting as proxy messenger21:09
DrTreadooops... i didn't use your secret code name!21:09
DrTread:-x21:09
DrTreadanything to do with airspeed velocity of swallows?21:09
DrTreadah.21:09
DrTreadok.21:09
fenni hate not having a wiki or mailing list.. this is stupid21:10
DrTreadregarding fab stuff... one of my tweeple posted a link to a journal of interesting shapes...21:10
RandIterkanzure: considered numpy as an alternative to octave?21:10
DrTreadhttp://www.isama.org/hyperseeing/21:10
DrTreadmmmmm.... numpy21:11
DrTreadand scipy21:11
kanzurefenn: should we have a mailing list?21:11
fennguess i'm burned out on all that 'ooo math surfaces' stuff21:11
kanzurefenn: this is getting kind of ridiculous, with all of these mailing lists21:11
fennyes there should be a mailing list21:12
kanzurefor what now?21:12
kanzureshould I attempt to revive the old hplusroadmap mailing list?21:12
kanzureeven though it had no real purpose?21:12
DrTreadas i'll be the proud owner of a MakerBot by the end of this week, i'm getting a new interest in math surfaces21:12
fennnot for philisophy or whatever, just for basic announcements and so i'm not shuttling emails around between people21:12
kanzuremaybe we need a Bryan Bishop mailing list21:12
fenner, announcements is wrong21:12
fenni mean low level discussion that shouldn't be plastered all over the net21:12
DrTreadkanzure make it so. you're good at facilitating these things, right?21:13
fennlike 'what next?' or 'come help screw together some scaffolding tuesday at 6pm'21:13
kanzureah21:13
kanzurefor the fablab21:13
genehackerDR TREAD DON'T BUY A MAKERBOT21:14
DrTread2 late21:14
genehackerit's overpriced21:14
genehackeryou can get a CNC mill that can cut metal for about the same price21:14
genehackerbesides SKYNET designed some parts for makerbot21:14
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genehackerI don't trust skynet21:15
DrTreadhmmm... i have been lazy about building anything myself. buying a makerbot was a chance to jumpstart my own making things21:15
DrTreadah.21:16
kanzurehrm, I might be able to get hessel in here21:16
genehackerwell have fun21:16
DrTreadinteresting discussion over coffee/adult beverage21:16
DrTreadok, genehacker, laser cutter: build one myself or buy an epilog or other unit?21:16
DrTread(with fab lab peeps help, of course)21:17
kanzuredid anyone else besides fenn see the SLS-3D-printing-of-the-desert-from-orbit thingy I posted?21:17
genehackerDrTread, are you on the campus?21:17
DrTreadnope.21:17
genehackeroh yeah21:17
genehackerdamn21:17
genehackerwell guess you can't use the laser cutter here then21:17
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DrTreadtrue enough.21:17
kanzureHey I}ruid.21:18
fenna haq'r!21:18
genehackersaw that SLS from space21:18
I}ruidoh noes! where???21:18
* I}ruid looks aroudn21:18
kanzureto your left21:18
kanzurehe's a hacker-ninja21:18
* fenn points at the wall behind I}ruid 21:18
DrTreadI}ruid, the hacker-ninja!21:18
genehackerit's already too late if you see the ninja21:18
kanzureI}ruid: we were just talking about SLS 3D printing of the deserts from orbit.21:18
DrTreadyes, i've googlestalked him since receiving email21:18
genehackerhow does the from orbit part work?21:19
kanzurewe all have :)21:19
I}ruid3D printing, as in object fabrication with those new-fangled printers?21:19
kanzuregenehacker: laser21:19
kanzureI}ruid: nope, there is a bacteria that turns sand into sandstone21:19
I}ruidahhh21:19
I}ruidneat.21:19
kanzureso if you gate that metabolic reaction with a laser-sensitive protein21:19
kanzureand then laser-activate the bacteria ..21:19
genehackerfusion powered laser?21:19
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kanzurewhy would it be fusion powered?21:19
kanzurehey ahessel.21:19
fenn<insert technobabble step here>21:19
ahesseljey21:19
ahesselhey21:19
I}ruidso the laser comes from orbit21:19
kanzureahessel: we're currently talking about 3D printing of deserts from orbit.21:19
I}ruidand you sandstone up some dope logos in the desert21:19
DrTreadfusion? i thought it was a Tc-99m gamma ray lazor?21:20
genehackeryou might be able to take advantage of barchans to spread your bacteria21:20
kanzurewell, you could also use a very tall tower21:20
fennDrTread: it's a neutron pumped lazor21:20
genehackersigh, if only we could get some Tc-9921:20
DrTreadah.21:20
kanzureso you don't have to be in orbit necessarily21:20
I}ruidhow would you spread the bacteria well enough to make that work?21:20
kanzurealthough it helps if you want to pattern a large area21:20
kanzureI}ruid: shhh!21:20
genehackertoo bad hafnium doesn't work21:20
kanzurethe wind?21:20
I}ruidcrop duster? (:21:20
DrTreadyes, i've been looking for Tc-99 for some time now. damned NRC!21:20
DrTreadfor purely safe, scientific purposes, of course.21:21
genehackerhttp://en.wikipedia.org/wiki/Barchan21:21
genehackerbarchans can self replicate21:21
kanzure" 21:21
kanzureA barchan dune is an arc-shaped sand ridge, comprising well-sorted sand. This type of dune possesses two "horns" that face downwind, with the slip face (the downwind slope) at the angle of repose, or approximately 32 degrees. The upwind side is packed by the wind, and stands at about 15 degrees. Simple barchan dunes may stretch from meters to a hundred meters or so between the tips of the horns."21:21
fennfire can also 'replicate'21:22
kanzureso can fairies21:22
fennand ewoks21:22
kanzurenah, they're just little infertile kids21:22
fennoh21:22
I}ruidin teddy bear suits21:22
I}ruidit's a furry convention up on Endor, y0.21:22
genehackerPURGE PURGE21:23
I}ruidhahah21:23
DrTread**shivers @ thought of Ewok sexxin**21:23
genehackerPURGE21:23
I}ruidgood thing I didn't follow that up suggesting that you contemplate the name of the planet in that context.21:23
I}ruidwhoops.21:23
DrTreadlet me run over to /b/ for a minute to get my sanity back.21:24
I}ruid(:21:24
* I}ruid behaves now21:24
genehackerI don't think /b/ is going to give it back21:24
kanzureI}ruid: yesterday I was going over some do-it-yourself atomic force microscopy stuff.21:24
kanzurehope you like what I forwarded to the list.21:24
DrTreadok, so we know solitons self-replicate. where are you headed with this, kanzure?21:25
kanzuresolitons? what?21:25
genehackerwe want to make a megastructure21:25
kanzuregenehacker was the one who said these "sand thingies" could self-replicate21:25
DrTreadsolitary waves, of which barchans are an example21:25
kanzurefenn and I disagree21:25
DrTreadoh. yes. sorry. :(21:25
I}ruidlooks interesting, I'll have to read it when I have more time and am not distracted by tha chatz21:25
fennit doesn't really matter if it 'replicates' since it's not useful for anything21:25
genehackerguess so21:26
DrTreadmegastructure, so we can take over the world?21:26
kanzurewell. no. not really. but we could fabricate a really really huge dog whistle I guess.21:26
fenni dont get how they are supposed to remove all the unbonded sand21:26
DrTreadand control all the dogs & use them to take over the world? ok... sanity has returned.21:26
I}ruidif you're creating sandstone from orbit by "painting" the desert, you could easily create building components, although sandstone is notoriously weak as a building material21:27
kanzureI}ruid: yes. that's where this started.21:27
I}ruidgotcha...21:27
DrTreadsandstone is as weak as its binder21:27
kanzureI}ruid: http://is.gd/tvV721:27
* I}ruid missed the beginning of the conversation (:21:27
kanzureI}ruid: that link will fill you in21:27
fennI}ruid: the original idea was to infuse sand with 'sandstone bacteria' by stabbing pipes into the sand and infusing the volume underground with bactera/nutrient solution21:27
genehackerperhaps we should make a giant wind powered machine that slowly goes across the desert squirting bacteria into the sand21:28
kanzureor just the surface for starters21:28
kanzuregenehacker: how would you make sure it covers a certain area21:28
fenni mean if you have huge machinery available to move sand around, why not just build walls out of cement or something?21:28
genehackerwhat do you mean?21:28
kanzuregenehacker: your machine would be subject to the direction of the wind21:28
kanzureso you would only get some weird pattern of bacterially-active sand21:29
genehackerturbine powered21:29
kanzurewhich isn't very useful for laser patterning21:29
kanzureturbine powered?21:29
genehackerwind turbine powered21:29
genehackerkite powered21:29
fenni'm picturing something like a strandbeest21:29
kanzureooh.21:30
genehackeryeah sorta like that21:30
genehackerkites are better21:30
genehackerget more wind21:30
fennof course21:30
ybit<random_tweet_of_the_day> http://www.q-linkproducts.com/h_our_technology.shtml :: when i have my open eeg setup, i may test this </random_tweet_of_the_day>21:31
genehackermore POWER21:31
fennso, you're saying 'move all that sand with wind powered shovels' basically, right?21:31
kanzureybit: am I following you? http://twitter.com/kanzure21:31
ybitkanzure, i dunno21:32
ybithttp://twitter.com/heathmatlock21:32
fennybit: qlink, although it sounds good, is a total scam. the circuit isn't actually even a circuit21:32
ybiti don't tweet much, just on this channel ;)21:32
fennit's a resistor with pads that go nowhere, and a coil that goes nowhere21:32
kanzureok. now I am.21:32
fennsee http://www.badscience.net/wp-content/qlink.JPG21:32
ybitthanks fenn, i was looking for specs21:33
genehackerhttp://www.darkroastedblend.com/2006/11/even-bigger-machines-dig-bigger-holes.html21:33
genehackeri'm thinking something like this21:33
fennfor $100 or so they could at least try to do what they claim21:33
kanzuredo we have sand submarines yet?21:33
genehackerno21:33
ybitoh, guess i'm still looking for specs :)21:33
kanzurewhy haven't you made one yet? get on with it.21:33
fenni mean it wouldn't be hard to make an active damping antenna21:33
I}ruidreference for qlink? what is this device intended to do?21:34
kanzureI}ruid: it's the one that ybit linked to21:34
I}ruidoh, there it is (:21:35
I}ruidthe faux HTML threw me off (:21:35
genehackerHAHHAHAHHAHAA21:35
genehackerqlink21:35
genehacker"My intuition and logic suggest that Clarus type products will be an important part of humanity’s future."21:36
genehackerO'RLY?21:36
DrTread**incredulous glare**21:36
kanzurefenn: this might have backfired on me. this is becoming wrongplanet.21:36
DrTreadi do know a yoga instructor who wears a qlink. she's not dead yet.21:37
I}ruidwell, as long as there's intuition and logic involved...21:37
kanzurewhy not just build one of the openEEG systems?21:37
kanzureor better yet, the open-rTMS system?21:37
genehackerthe heavily regulated underground rogue chemistry sets of the 21st century will instead synthesize new terrestrial compounds, counter-earths and other illegal geosimulants, rare earth anti-elements that might then catalyze a wholesale resurfacing of the world through radical landscape architecture.21:38
genehackerhuh?21:38
DrTreadintuition & logic alone produced Aristotle, & science suffered for 2000 years. :(21:38
kanzureDrTread: there's actually a mechanism in the brain responsible for intuition and insight, and I was intent on harvesting it21:39
genehackerDAMN YOU ARISTOTLE!21:39
kanzurehttp://heybryan.org/thinking.html are my notes on it21:39
DrTreadjust don't use Protomatter!21:39
kanzured-cycloserine is an interesting chemical for those purposes.21:39
fennphilosophy suffered for 2000 years because there was 1500 years of dark ages in between21:39
I}ruidthis site is way too new-agey... where's the science?  where's the whitepaper? (:21:39
I}ruidpeer review anyone?21:39
fennI}ruid: please don't waste your time on q-link21:39
genehackerok well I have to go study for a test AFK21:39
fennthanks for nothing genehacker 21:39
genehackerthanks for feedback21:40
fennwhat people don't realize is that there was only like 200 years of philosophy before all development ceased21:40
fennthen it started back up again in the 18th century21:40
I}ruidonce it becomes no longer amusing then I'm wasting my time (:21:40
I}ruidat least right now it's providing the lols21:40
fennwell, western philosophy at least21:42
I}ruidfenn: you talking western philosophy?  cuz I'm pretty sure eastern dominates in longevity21:42
I}ruidhah, beat me to my own comment21:42
I}ruidgg21:42
kanzureholy shit. somebody who uses "gg" still.21:42
fennis that some kind of usenet thing?21:42
kanzureI heard of it in subnet, so no.21:42
kanzuresubspace, I mean21:42
I}ruidno, it's a gamer thing.21:43
ybitgood game*21:43
kanzurehttp://en.wikipedia.org/wiki/SubSpace_(computer_game)21:43
ybityeah, it's used often21:43
I}ruidit's used almost unconciously by FPS players21:43
DrTreadwow. kanzure, for a youngun, you've got quite a memory21:44
ybit:P21:44
kanzureDrTread: I was playing Continuum, the free version of Subspace 21:44
I}ruidas soon as a match ends there's an obligitory flood of "gg"'s in the in-game-chat21:44
kanzureyep.21:44
I}ruidI blame little-league baseball coaches.21:44
DrTreadkanzure, you're responsible for my returning to IRC for the first time in 12 years. thx.21:45
kanzureDrTread: sorry :(21:45
kanzureDrTread: but we're sufficiently worthwhile I think21:45
kanzureunless you need me to throw harder problems at you?21:45
DrTreadyes, you are, and i'll eventually recover my self-esteem.21:45
DrTread;)21:45
kanzurenope, all of the self-esteem is for me me me21:45
ybitI}ruid: if it's baseball coacheswh to blame, i ask: where's the "potb"? (pat on the butt)21:46
* fenn mumbles something about self-esteem punks21:46
kanzure?21:46
DrTreadit's my dinner time... bbl21:46
kanzurehm. me too.21:47
I}ruidI still think you should all move to SILC21:47
I}ruidit's far superior to IRC>21:47
I}ruids/>/./21:47
kanzureyou fail at regular expressions21:47
I}ruidhahah yea, I do.21:47
I}ruids/\>/\./21:47
I}ruidwhich is funny, since that's all I did for nearly 2 years at TippingPoint21:48
I}ruidwell, when I wasn't doing VoIP security research... that was the busywork.21:48
fennthe first one was fine?21:48
I}ruid. is a special character, should be escaped21:49
fennnot in sed21:49
fennat least not in the second half of substitution21:49
I}ruidahh true21:49
I}ruidtime to make something to eat, bbl21:51
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* kanzure goes back to modeling an algae growth biofuel thingy21:57
I}ruidI saw a biofuel article today22:00
I}ruidwas pairing modified yeast with something, one sec22:00
DrTreadback.22:00
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I}ruidhttp://www.newscientist.com/article/dn16989-yeast-and-bacterium-turned-into-gasoline-factory.html22:01
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DrTreadbeware of anything that says "cheaper than oil"22:10
DrTreadoil is pretty darned cheap (right now, anyway)22:11
kanzureyep, saw it22:12
fennvegetable oil is cheaper than gasoline22:25
fennat least when you buy soybean oil at the asian market in 5 gallon jugs22:25
fennalso the street price of gasoline in USA is way lower than it ought to be due to subsidies22:27
fennlook at prices in any other country for more realistic cost22:27
DrTreadsubsidies, or lack of taxes = lack of internalization of external costs22:28
DrTreadif you want subsidies, buy vegetable oil.22:29
DrTreadany decisions on the heater material choice? gallium, aluminum, glycerol, etc?22:31
fennheater? the PCR block?22:35
fennkanzure: could you snag me some microcentrifuge tubes some time? like 30 of each size (should be two sizes, small and regular)22:37
fenn4mm and 8mm diameter i think22:37
kanzure-okay.22:37
kanzure-does anyone have some suggestions for interesting things to look at under an AFM scope?22:37
DrTreadi have a thousand ideas for an AFM22:38
fenngraphene, liquid zeolite, umm.. yeah just about anything22:38
DrTreadin situ tribology22:39
kanzure-I've been looking for some good papers of interesting images22:39
kanzure-but it's not like anybody publishes anything interesting22:39
DrTreadpffft22:39
kanzure-because it costs to print even black and white photos22:39
DrTreaddefine interesting22:39
kanzure-not a grid of atoms22:39
fenni bet a lot of biological materials would be very interesting22:41
DrTreadelectrically conductivity of DNA strands22:41
DrTreadwait... that would require STM22:42
kanzure-well, not necessarily22:42
kanzure-I have a bibliography of papers of AFM DNA sequencing22:42
kanzure-want?22:42
kanzure-or a photo gallery of bacteria would be nice.22:44
kanzure-I was trying to search for bacteriophage morphological diversity the other day22:44
kanzure-but there's only like five shapes that viruses follow22:44
fennyou can do afm over larger areas than usual right? so you could use it in place of a regular light microscope for some things22:44
kanzure-even though there's something like 1E30 viruses on the planet. shouldn't there be more shapes than just a bunch of spheres and rods? damn.22:45
fennself assembly lends itself to simple shapes22:45
kanzure-tell that to Paul Rothemund.22:45
kanzure-because he's been breaking that particular law.22:45
fennwell, there's no particular reason for evolution to favor more complex shapes22:45
fennthey have to do basically one thing: protect the DNA22:46
kanzure-true, but when using search terms regarding novelty, morphotypes, diversity, etc. etc., something should pop up22:46
kanzure-even just an oddball that somebody found somewhere22:46
fenni doubt there have even been a large number of viruses and phages studies22:46
fennstudied*22:46
kanzure-thought virology was a huge field?22:46
fennthey only study the interesting ones22:47
fenni forget the numbers but there's like a gazillion viruses per ml of antarctic sea water22:48
fennwhere they come from, nobody knows22:48
DrTreada gazzilion is like a lot, right?22:48
fennit's less than a quintrillion22:48
fennbut more than a jillion22:48
kanzure-I saw that paper, actually22:49
kanzure-wikipedia references it22:49
fennon the panspermia page?22:49
kanzure-no22:49
kanzure-the paper on viruses per volume of sea water22:49
ybitwhat is superkuh's blog url?22:50
fennthere should be a requirement to include scientific mysteries in educational curricula22:50
kanzure-ybit: http://superkuh.ath.cx/22:50
fennright now it's like nobody even knows what the big problems are in science22:50
fennunless you are a specialist in the field22:51
kanzure-that's because everybody has been bullshitted by strings and multiple dimensions22:51
fennthose are just explanations22:52
DrTreadin texas, the important mystery is how creation happened so fast, and why there are fossils.22:52
kanzure-well, they are obsessed with it.22:52
fenngiven any set of observations, there are a number of ways to explain it22:53
DrTreadand why Forrest Mimms III is  such an avid creationist.22:53
fenneh, i forget where i was going with this22:53
fennDrTread: you'd never know from looking at his webpage22:53
DrTreadhe doesn't advertise22:53
fennthen he isn't 'avid'22:54
DrTreadand he's not a "young earther"22:54
DrTreadtouche22:54
fennah well, if he's not a 'young earther' then it's just semantics22:54
fenn'did god create the universe? or was it a mysterious point source of near-infinite energy?'22:54
fennpersonally i don't care, since it doesn't influence the results22:55
kanzure-gasp, you're ranting just to rant?22:55
DrTreadThe wingnut echo chamber has recently gone insane over the idea that Eric Pianka, an distinguished and much-loved ecologist at UT, advocates mass genocide by ebola in order to bring down world population. The allegation was leveled by disgruntled creationist Forrest Mims, and rapidly spread to the blogosphere via places like Dembski’s blog (three posts!) and Telic Thoughts, and then went to...22:55
DrTread...the Drudge Report and caused a national media firestorm appearing in my local paper by Monday morning. I smelled a rat from the beginning, and now I have been proved right. KXAN News36 in Austin, TX, has just debunked the whole thing, and for good measure has posted a 20-minute unedited interview with Pianka which everyone must watch to realize the full depravity of what the wingnuts have...22:55
kanzure-isn't that violating some sort of law22:55
DrTread...done here. Pianka says several times that Mims is a “crazy kook” that “distorted and changed everything I said.” The death threats that have flooded Pianka and the Texas Academy of Sciences are also a nice touch.22:55
DrTreadnope. doesn't influence the results.22:55
fenn'disgrunted creationist' is just poor reporting22:56
fenngiven all the possible descriptions of forrest mims22:56
DrTreadyep.22:56
DrTreadsorry i brought it up. :(22:56
fennwell i have yet to see any first-hand info on his supposed creationist stance22:56
DrTreadfwiw, i still LIKE Mr. Mimms, and he does good science.22:57
kanzure-hm22:57
kanzure-"Self-repair Of Bacterial Cell Wall Against Multiple Puncturings By An AFM Tip"22:57
kanzure-"We report, for the first time, that bacteria survive multiple stabbings by an atomic force microscopy (AFM) tip under physiological conditions"22:58
kanzure-"This experiment, which generated a characteristic puncture curve, was repeated more than 50 times at different locations on the same bacterium."22:58
kanzure-hahah22:58
kanzure-god I love science22:58
kanzure-"MatLab® code was written to analyze the puncture curves, which carry an abundance of information on such characteristics of the bacterium as the surface elasticity, the critical pressure needed to puncture the bacterial cell wall, the interaction of the AFM tip with the interior of the bacterium and the precise width of the bacterium in the physiological environment."22:59
DrTreadyes. pitty you can't puncture monkeys like they used to. :(22:59
DrTreadbacteria don't have a fan club yet.22:59
fenni'm a big fan of bacteria22:59
fennthing is, a monkey isnt much different from a human22:59
fennso it makes sense to feel sorry for a monkey being stabbed23:00
kanzure-uh?23:00
kanzure-are we trying to rationalize?23:00
fennrationalize what?23:00
kanzure-feeling sorry for certain things rather than other things?23:00
fennyes23:00
kanzure-what, wouldn't you uplift all of the bacteria if you could?23:00
fennthere's a logic to it23:00
DrTreadyes, yes we are. we are only a few decades post-Tuskegee experiment. 23:01
fennbacteria are already so far above us it would be poor form to try to improve them23:01
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fenni don't mean individual cells, i mean the network23:03
kanzure-"regardless of tip geometry and puncturing density varying between 20 and 40 puncturing events per square micrometer. "23:04
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DrTreadoh snap! kitty on keyboard23:05
DrTreadlost thread.23:05
kanzure-DrTread: we're puncturing bacteria with AFM tips with 20 to 40 puncturing events per square micrometer23:05
DrTreadok.23:05
kanzure-heh23:06
DrTreadshall we make our own AFM?23:06
DrTreadi've always wanted to.23:06
kanzure-yes.23:06
kanzure-I was surprised the other day with how simple they are23:06
DrTreadindeed.23:06
kanzure-fenn suggested using capacitance to detect the bend/deflection in the cantilever tip instead of a laser+photodiode method23:06
kanzure-and I have an old collection of papers on diy-ways to make sharp cantilever probe tip thingies23:07
kanzure-and then the $100 STM guy's "cut a piezo tweet into four sections and wire them up separately" method (just using a pocket knife + solder + wires)23:07
kanzure-and "z-xis approach mechanism consisting entirely of a screw" method.23:08
fenncapacitance makes sense for a lot of reasons: it's cheap, easy to build, doesn't require any added weight to the cantilever, and gives you an analog value (instead of digital like a photodiode strip would)23:08
DrTreadok.23:08
kanzure-the problem is that I'm rusty with my electronics.23:08
fennyou never learned electronics23:08
DrTreadbut capacitance requires AC to measure, doesn't it?23:08
kanzure-not true23:08
DrTreadPffft23:08
kanzure-well, I took classes, but I didn't learn much from them23:09
DrTreadread Forrest Mimms' books. :)23:09
DrTreadthey're great!23:09
fennDrTread: you set up a resonant circuit, (LCR circuit)23:09
kanzure-I used to be an electronics kid, but..23:09
* kanzure- still hasn't got through "The Art of Electronics" entirely23:09
fennthen measure the frequency somehow23:09
fennthe 'somehow' is where there are a lot of options23:09
DrTreadright. so you have to pick a frequency that will make the tip resonate at a useful frequency23:09
fennno23:09
fennit doesn't move the tip23:09
DrTreador not at all?23:10
fennelectrical resonance not mechanical23:10
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kanzure-the tip is stationary23:10
kanzure-the sample is attached to a piezo23:10
DrTreadand just how does a capacitor plate (the tip) not experience a mechanical force from the electrostatic charge?23:10
kanzure-the piezo moves the sample.23:10
DrTreadyes, that's correct, but so does every other force field.23:11
fennDrTread: it's a tiny amount charge23:11
DrTreadand a tiny tip :)23:11
DrTreadmost AFMs are run in an oscillatory mode, anyway23:11
DrTreadunless you are measuring a very hard surface (array of atoms = boring)23:11
DrTreadthe z-axis moves in and out of contact with the surface23:12
kanzure-AFM bacteria puncturing diagram: http://heybryan.org/books/papers/puncturing_bacteria_AFM_probe.gif23:12
DrTreadas the x- and y- are scanned23:12
kanzure-RAPE23:12
fenni thought they used PID to keep the 'altitude' constant23:12
fennso PID would keep it from oscillating23:12
DrTreadthere are a number of ways of doing it, but constant altitude is difficult for soft objects23:13
DrTreadbacteria squish23:13
DrTreadI love the picture... there are visible molecules in the membrane, but the AFM tip is a perfectly smooth elipsoid23:14
kanzure-hah23:14
DrTreadsome time back, i bought a bag of 100 bare piezo discs from Goldmine for just this purpose.23:15
DrTreadnow where did i put them...23:15
fennin a ziploc bag23:15
DrTreadgood. good. now, where's that bag?23:16
fenni sense that .. the bag may be.. located in ... a cardboard box23:16
kanzure-your jedi powers are weak, old man23:16
DrTreadooooh, you're on to something!23:16
kanzure-heh.23:16
kanzure-DrTread: you don't have an inventory system?23:16
DrTreadnow all i have to do is look in every cardboard box23:16
kanzure-inventory. system.23:16
DrTreadHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAHHAHAHAHAHAHAH23:17
DrTreadha23:17
kanzure-:(23:17
DrTreadha23:17
fennwe can help23:17
kanzure-that's kinda what we're here for23:17
DrTread:D23:17
DrTreadcool!23:17
fennbut first you need to realize that there's a problem23:17
kanzure-hah23:17
DrTreadcome on over! take my stuff!!!23:17
kanzure-really?23:17
kanzure-may I?23:17
DrTreadi need to get rid of lots of it!23:17
DrTreadyes23:17
DrTreadplease23:17
fenn^-^23:17
kanzure-I can have a guy at your door in 15 minutes.23:18
DrTreadyou're on :)23:18
kanzure-ppst, fenn..23:18
kanzure-heh'23:18
fennam i "the guy"?23:18
kanzure-pretty much.23:18
fennwell, all right i guess23:19
DrTreadsqueee23:19
fennwhat i really meant was making an inventory system for him23:19
DrTreadoh.23:19
kanzure-right right23:19
DrTreadmy garage, library, dining room & one bedroom are jammed with stuff. most of it was acquired with intentions of hacking23:20
fennnot consumer junk i hope23:20
kanzure-hm. you haven't met david yet have you, fenn?23:20
DrTreadoh, no! University of Michigan property disposition junk!23:20
fennno23:20
fennkanzure-: some people *cough ahem hrm* save stuff like vacuum cleaners or inkjet printers with the intent of making something useful out of them23:22
kanzure-right.23:22
DrTreadhave those, too. :(23:23
kanzure-I'm still confused about how to get everything organized here in austin23:23
kanzure-hell, jonathan cline still hasn't even met with you yet.23:24
kanzure-and then I get into thinking about combinatorial meetups and such23:24
kanzure-and it's just hard to get everything happening23:24
fennthat's what this fab lab is suposed to be for right?23:24
kanzure-but then I don't want to bother with a new mailing list either really23:24
kanzure-hrm23:24
kanzure-but then it's just yet another new mailing list or something obscure23:24
fennno, it's not a mailing list at all23:24
DrTreadif it's a real fab lab, then it won't be obscure.23:25
fennit's a physical space23:25
kanzure-i'm talking about a way to organize things23:25
DrTreadjust create a Twitter hashtag23:25
DrTreadproblem solved.23:25
kanzure-urhm.23:25
fennugh please not twitter23:25
kanzure-no.23:25
DrTreadwhy not? it's good enough for Oprah23:25
fenni'd learn how to use RSS if there was sufficient motive23:25
kanzure-I don't know if RSS is sufficient- don't we want more than announce capabilities?23:26
kanzure-maybe I just need to be better at keeping up with the austin peoples23:26
kanzure-going through the whole fablab spiell over and over again can get, painful23:26
kanzure-because I have to remember where each person is coming from23:26
kanzure-for instance, cline was actually somewhat clueless23:27
kanzure-since he's coming from a very "purely" diybio/synbio perspective23:27
kanzure-even though he more or less fits the bill..23:27
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kanzure-and the austin geek website thingy hasn't been very helpful in organizing things either23:28
kanzure-jon lebkowsky must not be moving quickly enough, or something23:28
kanzure-or too focused on 'social media' crap23:28
DrTreadi need to step away from the computer for a bit. i'll keep it open...23:31
kanzure-there is no away. only the silicon way.23:38
kanzure-http://en.wikipedia.org/wiki/Category:Electron_microscope_images23:39
fennadd "pressure cell" to your algae lysis method list23:53
DrTreadback, but for how long?23:54
fennyou pump water at high pressure through a tiny hole, and the pressure change as they exit the hole causes cells to explode23:54
DrTreadfenn, that's my favorite method.23:54
fennit's so elegant :P23:54
DrTreadyes, in a medieval torture chamber sort of elegance way23:54
kanzure-fenn: but I was the one who told you about that method23:55
kanzure-in the literature it's called fluid shear force lysis or something23:55
kanzure-(minus "lysis" in the name of the method)23:55
kanzure-we (by that I mean, not me) are also building an osmotic pressure chamber too.23:56
DrTreadpouring salt on wounds?23:56
kanzure-(not the same thing though)23:56
kanzure-what?23:56
DrTreadosmotic pressure23:56
fennit's usually fresh water, if you want them to lyse23:57
DrTreadtrue.23:57
fennnot that i know why they would call it a chamber23:57
DrTreadyou want them to blow up, not shrivel23:57
fennthe electromagnetic method is interesting23:58
fennreminds me of doctor hulda clark quackery23:58
DrTreadsorry kids, but this old man needs to go to bed now. he turns into a pumpkin in 45 seconds23:58
kanzure-fenn, did you not see the powerpoint presentation?23:58
fenntell the fairy i miss her23:58
kanzure-presentation: http://heybryan.org/bioreactor/2008-10-21%20Algal%20biomass%20extraction%20presentation.ppt23:58
DrTreadwill do. **poof**23:59
fennkanzure-: could you pdf-ify that?23:59
* kanzure- grumbles something about having to move chairs because he doesn't remember how to force soffice to do that remotely23:59

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