--- Day changed Sat Apr 18 2009
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00:02 < DrTread_> ok, this is fun. good night, world. we shall most likely conquer you in the morning. 
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00:10 < genehacker> fenn where can I download that sketchflat program?
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01:05 < genehacker> I don't believe it
01:05 < genehacker> I just do not believe it
01:15 < genehacker> http://groups.google.com/group/sci.nanotech/msg/96a67c84809c9a5d
01:15 < genehacker> kanzure, I do believe this belongs in your archives
01:16 < genehacker> I heard about fluidic replicators, but I never read the full proposal
01:16 < genehacker> and guess what?
01:20 < genehacker> a 8086 fluidic based processor with reasonably sized logic gates should be about a cubic foot
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02:12 < kanzure> uugghhh
02:12 < kanzure> this is terrible
02:17 < kanzure> okay, they just don't know how to turn off the building
02:17 < kanzure> genehacker: yeah, chris phoenix from CRN
02:18 < genehacker> what is?
02:19 < genehacker> turn off building?
02:19 < genehacker> turn off fluid flow
02:21 < kanzure> mitch porter. yeah, I've emailed mitch before.
02:21 < kanzure> the building is speaking to me
02:21 < kanzure> it thinks its on fire
02:21 < kanzure> it now has a thousand angry college-aged men and women very angry, and inside of it
02:21 < kanzure> ready to attack.
02:22 < genehacker> fuck?
02:22 < genehacker> the castillon is?
02:23 < genehacker> what the hell is going on there?
02:23 < genehacker> fire alarm going off?
02:23 < genehacker> if you smell smoke GTFO
02:24 < genehacker> well I hope you GTFO ok if everything is fine
02:25 < genehacker> would you like me to carry out visual aquisition of the building to guage the situation?
02:26 < kanzure> no, I confirmed that they are bullshitting by asking them.
02:27 < genehacker> what the hell is going on down there?
02:28 < kanzure> I think they have some newbies at the front desk
02:28 < kanzure> who don't know how to shut off the alarms
02:28 < kanzure> or, they possibly fell asleep
02:30 < genehacker> I heard that happens often down there is that true?
02:30 < kanzure> not really.
02:30 < kanzure> genehacker: will you post that link to OM?
02:30 < genehacker> sure just not right now
02:30 < kanzure> ok I will then
02:30 < genehacker> if you want to me to do so I will
02:31 < kanzure> yes
02:31 < kanzure> forget it
02:32 < kanzure> yay it stopped
02:32 < kanzure> >30 min. jeebus.
02:33 < genehacker> posted
02:34 < kanzure> "the building emergency condition has been cleared. you may return to your normal activity." <- x5.
02:34 < kanzure> now in spanish.
02:34 < kanzure> ugh
02:34 < genehacker> I had something like that happen in highschool
02:34  * kanzure stabs someone
02:34 < genehacker> during spainish class
02:35 < genehacker> damn
02:35 < genehacker> that was fast kanzure
02:36 < genehacker> so I did some oft napkin calculations
02:37 < genehacker> we could make a 8086 level processor with shrinky dink microfluidics
02:37 < genehacker> that would take up about a 2.5 cm cube
02:54 < fenn> that link is stupid
02:54 < fenn> he glosses over the whole materials problem with magic super UV-cure plastic
03:01 < kanzure> yes
03:01 < kanzure> drtread should be able to fix that
03:01 < kanzure> or at least yell at him about it
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03:14 < genehacker> wait a second
03:14 < genehacker> sounds like he's using arms
03:14 < genehacker> 7-dof arms
03:15 < genehacker> ugh
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12:16 < kanzure> fenn, what if a shape doesn't fall into a predefined category?
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14:04 < fenn> then approximate it
14:05 < fenn> or evaluate it exactly if you can figure out how
14:05 < kanzure> what do you mean by approximate
14:05 < fenn> like that catia gear example
14:05 < kanzure> right
14:05 < kanzure> so I was thinking of two types of shapes for this purpose
14:05 < kanzure> (1) tagged shape
14:05 < kanzure> (2) exact CAD data
14:05 < kanzure> if there's enough repeats of type #2s being used,
14:05 < kanzure> then it's time to write a quick script to replace all instances with a tag
14:05 < kanzure> so as to compress the information
14:06 < fenn> approximate like a bunch of line segments
14:06 < fenn> (not really, since you've got all sorts of curves at your perusal)
14:07 < fenn> and modeling something like cloth is always going to be hard, since it's stochastic
14:14 < kanzure> did you look at mtt yet?
14:17 < fenn> it's over my head
14:18 < kanzure> wonder how much of it is obfuscation because an academician wrote it, versus actually being complicated
14:18 < fenn> honestly it sounds like ADL bullshit
14:18 < fenn> look, a graph! your problems are solved.
14:19 < kanzure> it implements some sort of port/interface-based-physical-quantities-algebra-thingy
14:20 < kanzure> anywho. in python, I was going to make it so that the 'magnitude range' of physical quantities is defined by boolean algebraic expressions, i.e. typical if(condition1 && condition2 && (blah || blah2)) stuff
14:20 < kanzure> should I just store if(stuff) the stuff variable somewhere?
14:20 < kanzure> I mean, I want to define 'stuff' as a string
14:20 < kanzure> but it's equivalent to a conditional expression that needs to get evaluated at some point in the future
14:21 < kanzure> ideally I would like to avoid eval()
14:21 < fenn> yes, avoid eval() at all costs
14:21 < fenn> you shouldn't have to use it at all; if you are, you're coding perl or tcl or some other language
14:21 < kanzure> is it sick that I used to have a CMS project going where the pages were all eval()'d? :(
14:21 < fenn> put all the logic in an evaluation function
14:22 < kanzure> in a what?
14:22 < fenn> a function, that is called
14:22 < fenn> to evaluate the constraint
14:22 < kanzure> I guess I can have a class that represents a hierchical binary logic tree thingy
14:22 < kanzure> and evaluates the tree
14:22 < fenn> i still dont know how to make use of knowledge of the constraint
14:22 < kanzure> the operators are: less than, greater than, equal to, less than or equal to, greater than or equal to, plus or minus
14:23 < fenn> like, a human could look at the constraints and analytically determine some of the proper values
14:23 < fenn> but some iterative constraint solver is basically blind
14:23 < kanzure> this is not a constraint solver.
14:23 < kanzure> it's a thingy saying "hey look the ranges don't match up!"
14:23 < fenn> eh?
14:23 < fenn> oh, well, same thing
14:24 < kanzure> no?
14:24 < fenn> evaluator is part of the solver
14:24 < kanzure> a constraint solver takes on some form of a multivariable function optimization thingy
14:24 < kanzure> this is not what this is.
14:24 < fenn> while !solved(): fiddle_values()
14:25 < kanzure> what does that have to do with the evaluation of a boolean logic expression to represent an adequate 'range' of values
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14:25 < kanzure> thus my list of operators above
14:25 < fenn> you stuff the constraints in solved()
14:25 < kanzure> I think I've lost you.
14:26 < fenn> as pure code, not some kind of meta-code
14:26 < fenn> if(condition1 && condition2 && (blah || blah2))
14:26 < kanzure> I'm trying to come up with a way to express a 'range'
14:26 < fenn> not eval('if'('condition1' '&&' 'condition2'
14:26 < kanzure> so greater-than or less-than are important parts
14:26 < kanzure> right right
14:26 < kanzure> but those aren't really constraints
14:26 < kanzure> erm
14:27 < kanzure> I'm doing something a little different I think
14:27 < kanzure> you have an acceptable range for a physical quantity going in some direction
14:27 < kanzure> this 'acceptable range' is defined by some manipulation of the following operators: <, >, <=, >=, ==, +-
14:28 < kanzure> in some order possibly with &&, ||, etc.
14:28 < kanzure> do you know the typical newbie programming assignment? the one where you're asked to make a boolean algebra tree or something
14:28 < fenn> no
14:29 < kanzure> I don't recall how they go, but I'm fairly certain that's the same thing here.
14:29 < kanzure> hrm.
14:29 < kanzure> boolean expression tree
14:29 < fenn> it just does order of operations basically right?
14:29 < fenn> why reinvent the wheel
14:29 < fenn> any language already does that
14:30 < kanzure> so, isAcceptableRange() would be defined by each package maintainer?
14:30 < kanzure> for each interface definition
14:31 < fenn> no that's stupid
14:31 < kanzure> http://stackoverflow.com/questions/623413/expression-trees-for-dummies
14:31 < kanzure> then what are you suggesting
14:31 < fenn> build a list of requirements
14:31 < kanzure> (look for "Anyway, for an the expression"
14:31 < kanzure> )
14:31 < kanzure> except with logical operators too
14:31 < kanzure> or, erm, only logical operators
14:32 < fenn> no, you need physical quantities and references to code variables too
14:32 < kanzure> physical quantities is taken care of in my model.
14:33 < kanzure> oh, but I guess there's no cross-over
14:33 < kanzure> interdependent variables I mean..
14:33 < fenn> so there's two general ways to go about building this list, a bunch of functions, or a bunch of lambda's nested
14:33 < kanzure> crap.
14:33 < kanzure> I was assuming only independent variables
14:33 < fenn> note that functions/lambda's can contain any logic operator
14:34 < kanzure> what's a lambda?
14:34 < fenn> ... a function
14:34 < kanzure> ok
14:34 < fenn> mathy people like it for some reason
14:34 < fenn> probably because it's hard to read
14:35 < kanzure> so there are cases of interdependent variables?
14:35 < fenn> what does that mean
14:35 < kanzure> for instance, I was hoping to just say "range of N: 20 to 25 N" and then "range of kg: 5 to 9 kg"
14:35 < kanzure> and keep them separated
14:35 < kanzure> but it sounds like you want something more complicated?
14:36 < kanzure> so I was going to evaluate those in isolation of each other .. in other words, the range of one does not influence what possible range of the other could be
14:36 < fenn> if (N in range(20,25) and kg in range(5,9)): return true
14:36 < kanzure> right right
14:36 < kanzure> but it sounds like you want something more complicated than that
14:37 < kanzure> like "if N in range(20,25) but kg in range (6,7) out of the total range(5,9), then N has to be specifically something else"
14:37 < kanzure> or something.
14:37 < kanzure> erm.
14:37 < fenn> if (N in range(20,25) and kg in range(5,9) and kg = N*9.8) ?
14:37 < kanzure> I hope that's not the case
14:37 < kanzure> oh. um. 
14:37 < kanzure> whatever. it sounds like I just misinterpreted you
14:37 < kanzure> if that's as complicated as you can imagine getting it
14:37 < kanzure> then that's good.
14:37 < fenn> no, i can imagine it much more complicated
14:37 < kanzure> uh oh.
14:37 < fenn> but i think python syntax is capable of handling it
14:38 < fenn> i just dont feel like typing out pages of example code right now
14:38 < kanzure> ok
14:38 < kanzure> btw, the reason why it can't be written out like that- as python code- is because it doesn't .. erm.
14:38 < kanzure> so, if you have two interfaces, both have definitions like that
14:38 < kanzure> and you want to check if the ranges are compatible between the two
14:39 < kanzure> just having two if()'s or two evaluation-range-functions-dealies
14:39 < kanzure> is not going to be useful
14:39 < fenn> if a.satisfied() and b.satisfied() isnt good enough?
14:40 < kanzure> how do you know it's satisfied
14:40 < fenn> because you wrote the damn function
14:40 < kanzure> you can't compare overlapping ranges
14:40 < kanzure> if two sets of bounds are within each other, or whatever, then good
14:40 < kanzure> but you can't check that if it's written out in code.
14:40 < kanzure> because then you'd need to run some sort of continuum checker solver
14:41 < fenn> yes you can
14:41 < kanzure> which is going to be nasty
14:41 < kanzure> ?
14:41 < fenn> a = buggy; b = baby
14:41 < kanzure> ?
14:41 < fenn> a.baby = b
14:41 < kanzure> ?
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14:41 < fenn> and in the buggy code you have some expression that checks whether the baby will fit
14:41 < fenn> s/buggy/basket/
14:41 < kanzure> so it has to have its own checker?
14:42 < fenn> yes of course
14:42 < fenn> as part of the solver
14:42 < fenn> er, evaluator
14:42 < kanzure> who writes the code to check that a.baby fits?
14:42 < fenn> the buggy/basket maintainer
14:43 < fenn> or maybe it's just generic collision detection code stolen from elsewhere
14:46  * fenn runs some errands
14:47 < kanzure> errands.go()
15:00 < genehacker> got some errands to do too
15:04 < kanzure> argh the whole point of the internet is to get rid of geographic barriers
15:04 < kanzure> wtf is this..
15:21  * kanzure grins
15:22 < kanzure> "Single cell transfection using plasmid decorated AFM probes"
15:23 < genehacker> haha
15:24 < kanzure> 30% success rate
15:24 < kanzure> well that's not good..
15:25 < genehacker> 30%
15:25 < genehacker> ?
15:25 < genehacker> I 'd expect 100
15:25 < genehacker> if they're putting it RIGHT ON THE CELL
15:25 < kanzure> "how can you possibly fuck that up"
15:30 < kanzure> "Bacterial cell curvature through mechanical controll of cell grwoth"
15:31 < genehacker> ???
15:36 < kanzure> "Highly efficient molecular delivery into mammalian cells using CNT spearing". 
15:36 < kanzure> heh. spearing.
15:36  * kanzure feels like a caveman
15:37 < genehacker> I loled
15:38 < genehacker> this one company sells spear tipped micromanipulators for catch and release of microorganisms
15:40 < kanzure> "Light-induced gene transfer from packaged DNA enveloped in a dendrimeric photosensitizer"
15:52 < kanzure> heh heh
15:52 < kanzure> neat. photoporation with violet LEDs
15:52 < kanzure> sub-milliwatt power and an exposure time of tens of milliseconds
15:52 < kanzure> 405 nm
15:53 < genehacker> hey I had a laser that was 405 nm
15:57 < kanzure> hey, do you know Ben-Yakar or Frederic Bourgeois?
15:57 < kanzure> they are working on this sort of thing apparently
15:57 < kanzure> here at UT
15:57 < genehacker> those names sound familiar
15:58 < kanzure> plus microfluidic integration
15:58 < genehacker> photoporation?
15:58 < genehacker> using light
15:58 < kanzure> well, no, they call it "laser nanosurgery"
15:58 < kanzure> but that's the same damn thing
15:58 < genehacker> what cells did they transfer genes to?
15:58  * kanzure reads
15:59 < kanzure> C. elegans
15:59 < kanzure> I don't think they actually did it, they were just thinking about it
15:59 < kanzure> oh, nevermind
15:59 < kanzure> they did.
16:00 < genehacker> oh that paper5
16:00 < kanzure> serial trapping of worms in channels, etc.
16:02 < kanzure> hrm. so immobilize cells in a gel. transfect with LED photoporation. not bad.
16:07 < genehacker> animal cells
16:07 < genehacker> photoporation
16:07 < genehacker> hmmm
16:09 < kanzure> what was the name of that paper that used LEDs to produce millions of degrees of heat in a bubble?
16:10 < kanzure> ah, "Whole Blood Pumped by Laser Driven Micropump"
16:12 < kanzure> oh. makes sense. I was looking that up for "cell lysis".
16:12 < kanzure> so of course it should work for transfection..
16:13 < genehacker> kanzure do me a favor and find me a micropump that is 90% efficient
16:33 < kanzure> hm. weird. DNA synthesis with only three LEDs and a capillary tube?
16:34 < kanzure> http://heybryan.org/books/papers/A%20scalable%20method%20for%20multiplex%20LED-controlled%20synthesis%20of%20DNA%20in%20capillaries.pdf
16:36 < kanzure> ack.
16:36 < kanzure> 180 s for photodeprotection and 60 sec for coupling of the base
16:36 < kanzure> 360 seconds per base
16:37 < kanzure> 160 nt in 16 hours.
16:37 < kanzure> I guess that's not too terrible :-/
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17:26 < kanzure> hey cis-action.
17:26 < kanzure> I just sent out a list of really neat papers to diybio
17:26 < kanzure> including transfection of cells via LEDs
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18:01 < fenn> the LED thing is totally obvious but still really cool
18:02 < kanzure> neat image: http://heybryan.org/books/papers/Nanoscale%20Operation%20of%20a%20Living%20Cell%20Using%20an%20Atomic%20Force%20Microscope%20with%20a%20Nanoneedle-fig4.png
18:02 < fenn> you could make your own PCR primers
18:02 < kanzure> hm?
18:02 < kanzure> oh, with the synthesizer
18:02 < kanzure> yes
18:03 < fenn> poor cells
18:03 < kanzure> RAPE
18:03 < fenn> heh that'd be fun to heckle people with at a biotech conference
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18:04 < kanzure> fenn: now we just need to get a fundie to believe it.
18:05 < fenn> huh. you know, those capillary tubes are the same as i used in the PCR machine at IU
18:05 < kanzure> instead of me spitting out tons of links, here's some latest papers: http://heybryan.org/books/papers/?C=M;O=D
18:05 < fenn> so you could feasibly put the PCR mix, nucleotides, synthesis, and amplification sequence all in the same tube/machine
18:06 < kanzure> hum.
18:06 < kanzure> sounds like it.
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18:06 < fenn> well, not really
18:06 < kanzure> it would be staged operation
18:06 < fenn> they have to wash the tube between steps right?
18:06 < kanzure> have to inject the strand you want to amplify later
18:06 < kanzure> um
18:06 < kanzure> I didn't see anything about that
18:06 < kanzure> I'm still kind of confused by it
18:06 < kanzure> why do they have multiple LEDs? is there diffusion going on here?
18:07 < fenn> no, the synthesized oligo is bound to the capillary wall
18:07 < kanzure> how would the light reach the strands being built way the hell on the other side of the tube
18:07 < kanzure> oh
18:07 < fenn> th idea is you have multiple synthesis sites along the tube (one per LED)
18:07 < kanzure> right
18:07 < fenn> with as sharp a cutoff as possible to reduce half-formed strands
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18:08 < kanzure> so you wash it in between steps or not?
18:08 < kanzure> how do you change the nucleotide out? and what's the point of having 3 LEDs? why not just one
18:09 < fenn> dunno
18:10 < kanzure> it's neat to find these papers hidden in the literature
18:10 < fenn> since you can't have a perfect sphere (no way to wash it out) i guess you're stuck with half-formed product anyway
18:10 < kanzure> nobody noticed them before as being all too important because, honestly, the performance /does/ suck
18:10 < kanzure> but it's better than nothing
18:10 < fenn> yeah certainly, good enough for pcr primers
18:10 < fenn> once you have a bottle of the right chemicals you get essentially as many pcr primers as you want
18:11 < fenn> which is way better than $20/pop
18:12 < kanzure> did you see the LED-based photoporation paper?
18:13 < kanzure> or the plasmid-covered AFM probe transfection method?
18:23 < fenn> 'this method is comparable or surpasses the quality of published commercial oligonucleotides'
18:26 < fenn> so i suggested meeting somewhere at 4, the guy replied 'ok' so i assumed he'd show up
18:26 < fenn> but then the next day at 11 am he wanted a confirmation, but i was asleep, so he never showed up!
18:26 < kanzure> hm.
18:27 < fenn> is it standard protocol to respond 'ok' to 'ok'?
18:27 < kanzure> not to my knowledge
18:31 < kanzure> another neat image: http://heybryan.org/books/papers/Direct%20observation%20of%20DNA%20translocation%20and%20cleavage%20by%20the%20EcoKI%20endonuclease%20using%20AFM.pdf.1.png
18:31 < kanzure> an endonuclease in action
18:38  * fenn mumbles something about .jpg's
18:38 < kanzure> wha?
18:38 < kanzure> they were png files
18:38 < kanzure> I don't like jpegs because then I have to decide on compression
18:39 < fenn> oh boo hoo
18:39 < fenn> so no compression at all is better?
18:39 < kanzure> I'm an idiot, aren't I?
18:39 < kanzure> :/
18:39 < genehacker> yeah
18:39 < genehacker> JPEG sux
18:39 < fenn> it's better than PNG for photographs
18:39 < genehacker> especially for things with big borders
18:40 < genehacker> like webcomics
18:40 < fenn> borders?
18:40 < fenn> like a demotivational poster?
18:40 < genehacker> ie MSpaint type drawings
18:40 < genehacker> exactly
18:41 < genehacker> http://images.google.com/images?q=compression&oe=utf-8&rls=org.mozilla:en-US:official&client=firefox-a&um=1&ie=UTF-8&sa=N&hl=en&tab=wi
18:41 < genehacker> see the compression poster
18:41 < fenn> eh, what?
18:41 < genehacker> http://emmastott.me/blog/tag/comrpession/
18:41 < genehacker> to get the full effect, you have to see the poster downsized first
18:42 < fenn> whatever.. those should be .svg anyway
18:43 < kanzure> another neat image: RNA polymerase doing its thing: http://heybryan.org/books/papers/Direct%20observation%20of%20one-dimensional%20diffusion%20and%20transcription%20by%20Escherichia%20coli%20RNA%20polymerase.pdf.1.jpeg
18:44 < fenn> how do they get these pictures?
18:45 < kanzure> AFM
18:45 < kanzure> hrm.. single-plasmid PCR with an AFM tip made of mica. hrm. and a mildly acidic solution. silicon nitride tip.
18:46 < genehacker> mica?
18:46 < genehacker> I think I found some of that once
18:46 < genehacker> interesting stuff
18:49 < kanzure> single plasmid PCR with AFM tip: http://heybryan.org/books/papers/Recovery%20and%20amplification%20of%20plasmid%20DNA%20with%20AFM%20and%20PCR%20-%20single-plasmid%20PCR.pdf
18:49 < fenn> http://www.youtube.com/watch?v=V1qWmrp6GAs  Carbon atoms moving at the edge of a hole in graphene0:16
18:49 < fenn> Carbon atoms moving at the edge of a hole in graphene  been directly observed in real time. With a transmission electron
18:49 < kanzure> heh. so couple that with the AFM-based plasmid delivery system.
18:49 < fenn> blarg
18:49 < kanzure> you fail at copy-paste
18:49  * fenn blames youtube
18:50 < fenn> i thought afm needed vacuum, not warm sticky cell gloop
18:50 < kanzure> so, if you can use an AFM tip to deliver plasmids into a cell, and amplify a single plasmid on a tip, .. 
18:50 < kanzure> apparently not?
18:51 < kanzure> I've been seeing some room-temperature stuff
18:52 < kanzure> it would be fun to grow a collection of microbes and randomly pit them against each other and take AFM imaging videos of the results
18:52 < kanzure> since there's such a ridiculously large diversity of them, you'll never grow bored
18:52 < fenn> except 99% of them will just ignore each other
18:53 < kanzure> then poke a hole in one of them and place the other in it
18:53 < kanzure> the survivor, wins!
18:53 < kanzure> heh' single-cell directed evolution
18:53 < kanzure> uh oh, transcellularism?
18:53 < fenn> in high school we had an 'ant gladiator arena'
18:54 < fenn> my ants always lost
18:54 < kanzure> :(
18:55 < fenn> i went to fry's electronics today, way the hell out there
18:55 < kanzure> yep.
18:55 < fenn> they actually have real electronics tools and components and stuff
18:55 < kanzure> the home I was going to be put into is right around the corner
18:55 < kanzure> convenient, but not.
18:56 < fenn> not
18:57 < kanzure> so I'm not sure now whether to keep reading maniacally or not, 
18:57 < kanzure> photoporation + dna synthesis + afm stuff kind of completes the chain
19:03 < fenn> why is photoporation better than other stuff? dont you need (yet more expensive) chemicals?
19:04 < kanzure> huh? it looked like you just shine a focused LED at a cell
19:04 < kanzure> and the plasmids go in.
19:04 < kanzure> kind of like the cell lysis method with LEDs except less intense
19:05 < fenn> pew pew
19:05 < kanzure> transfection by impingement?
19:05 < kanzure> or is that the sound of a laser?
19:05 < fenn> don't you need a microscope?
19:06 < kanzure> not if you know where the cells are
19:06 < kanzure> or, erm, maybe for the lense
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19:07 < kanzure> (I sent the link in the recent diybio email)
19:07 < kanzure> ah: http://heybryan.org/books/papers/Violet%20diode-assisted%20photoporation%20and%20transfection%20of%20cells.pdf
19:08 < fenn> der.. 'focused at a spot 1mm in diameter'
19:08 < fenn> is that right?
19:08 < fenn> no, it's 1um
19:09 < fenn> wtf is she using a camera shutter
19:09 < kanzure> yes
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19:11 < fenn> have you found any references of photoporation with bacteria?
19:12 < kanzure> haven't looked
19:14 < kanzure> doesn't look like there's anything.
19:14 < fenn> i bet they are too small for it to work
19:15 < fenn> did ultrasound work with bacteria?
19:15 < fenn> yes, looks like it
19:15 < kanzure> ultrasound work with bacteria for what?
19:16 < kanzure> also, there was another paper- "Sonoporation of suspended cells with a single cavitation bubble in microfluidic confinement"
19:16 < kanzure> http://heybryan.org/books/papers/Sonoporation%20of%20suspension%20cells%20with%20a%20single%20cavitation%20bubble%20in%20a%20microfludici%20confinement.pdf
19:16 < kanzure> but that was for hman HL60 cells
19:17 < kanzure> "cavitation bubbles can induce membrane poration of cells located in their close vicinity"
19:17 < fenn> The mixture was subjected to 1-MHz US treatment under 0.5 MPa for 90 seconds, with a duty cycle of 50%
19:17 < fenn> that sounds doable
19:18 < fenn> hard to imagine it being any cheaper than electroporation though
19:18 < fenn> looks like it's much more efficient and higher cell survival rate
19:19 < fenn> not like that really matters with bacteria
19:19 < kanzure> "We demonstrate the ability to accurately position up to 34 micrometer sized bubbles using laser energies of 56 microjoules" using a spatial light modulator (SLM) (a.k.a, LCD hacks here we come) <- generation of laser-induced cavitation bubbles with a digital hologram (so, not ultrasound)
19:19 < kanzure> this is getting a bit too complicated for me to remember all at once
19:20 < kanzure> neat, they write stuff out of bubbles
19:20 < fenn> interesting "Sonoporation may activate the stress response genes, including RecA, thus increasing the frequency of double-crossover homologous recombination."
19:21 < kanzure> Generation of laser-induced cavitation bubbles with a digital hologram http://heybryan.org/books/papers/Generation%20of%20laser-induced%20cavitation%20bubbles%20with%20a%20digital%20hologram%20-%20LCD%20-%20spatial%20light%20modulator.pdf
19:22 < fenn> i'm surprised you can't buy a real holographic display yet
19:22 < fenn> with some of this GPGPU stuff it should be easy
19:22 < kanzure> ever hear of sonoluminescence?
19:22 < fenn> yes
19:22 < fenn> only at high power levels
19:24 < genehacker> sonolumination is weird
19:24 < genehacker> some people think it might be fusion
19:25 < fenn> genehacker: other way around
19:25 < fenn> fusion might be caused by sonoluminescence
19:26 < genehacker> yeah
19:27 < fenn> wow 1024x768 LCD in a 20mm package
19:29 < genehacker> WHERE!
19:30 < genehacker> OH GOD I CAN SEE FOREVER
19:30 < genehacker> I am not talking about the LCD
19:30 < fenn> are you all right?
19:34 < genehacker> not really
19:34 < genehacker> mental stability is ok
19:34 < genehacker> it's just slightly disturbing
19:34 < genehacker> a movie called moonwalker
19:35 < genehacker> exists
19:35 < genehacker> let's see that LCD screen now shall we?
19:36 < fenn> http://www.holoeye.com/lcos_microdisplay_color_sequential.html
19:36 < genehacker> oh that one
19:37 < fenn> it's very similar to the spatial light modulator they're using in that last paper
19:37 < genehacker> we need one that is black and white
19:37 < genehacker> and that we can put light through
19:37 < genehacker> we can't use an LCD in it's reflective mode
19:37 < fenn> http://www.holoeye.com/spatial_light_modulator_lc_r_2500.html
19:37 < fenn> it's not reflective, it's transmissive
19:38 < fenn> er. i think it is at least
19:38 < genehacker> not the LCD display
19:38 < genehacker> or at least one of them is
19:38 < genehacker> that SLM is cool
19:38 < fenn> ok i'm wrong, they're both reflective
19:39 < fenn> in which case, why is it special for sequential color
19:39 < fenn> *drool*
19:46 < kanzure> so uhh
19:46 < kanzure> if you can do single plasmid AFM tip stuff, 
19:47 < kanzure> why not single DNA strand AFM tip stuff
19:47 < kanzure> and then why not ligate strands of DNA together by pick and place?
19:48 < fenn> to do what?
19:49 < kanzure> very large genome synthesis
19:50 < fenn> why is that better than sticky end ligation
19:50 < fenn> (self assembly)
19:51 < kanzure> you could have many, many strands of DNA on a surface
19:51 < kanzure> and then you assemble them in order by picking them up
19:51 < kanzure> and then doing some facy ligation only once at the assembly site for attaching each strand
19:51 < kanzure> (maybe some of that fancy ultrasound-picoliter-stuff)
19:51 < fenn> picoliter is way huge compared to a dna strand
19:52 < kanzure> eh? 
19:52 < kanzure> crap crap crap.
19:52 < fenn> you could probably fit a human genome in a picoliter
19:53 < fenn> cube 10 microns on a side
19:53 < genehacker> kanzure, just be cause we can doesn't mean we should
19:53 < genehacker> just because we can doesn't mean it's efficient
19:54 < kanzure> speak for yourself mr. fluidic replicator
19:55 < kanzure> just trying to find a way to avoid chemicals.
19:55 < kanzure> which is awkward since it's all chemistry
19:55 < genehacker> i don't have to, exponential growth
19:56 < fenn> just jamming dna together with a stick isn't going to covalently bond it
19:56 < fenn> at least not the way you want it to
19:56 < fenn> so you're going to need ligase anyway
19:56 < kanzure> right
19:56 < kanzure> I'm ok with having to use ligase
19:57 < kanzure> can you ligate two nucleotides together? <- there you go..
19:57 < fenn> you could synthesize both strands of a short sequence (100bp or whatever) but leave overlapping sticky ends
19:58 < kanzure> right. traditionally you just attach that with a ligase step to the bigger piece that you're currently synthesizing
19:58 < fenn> then when you anneal, the matching oligos will pair up first, then the matching sticky ends will pair up
19:58 < fenn> oh, i'd do it all at once
19:58 < kanzure> I thought sticky ends would ..
19:58 < kanzure> erm. how are sticky ends addressed together?
19:59 < fenn> complementary base pairing
19:59 < genehacker> mechanosynthesis
19:59 < kanzure> there's only so many base pairs, so you can only ligate two strands together at once
19:59 < kanzure> two different strands I mean
19:59 < genehacker> you're doing it wrong
19:59 < fenn> hang on lemme draw a pic
19:59 < fenn> genehacker: shut up
19:59 < genehacker> ok
19:59 < fenn> thanks :)
20:01 < fenn> http://imagebin.org/46044
20:02 < fenn> each sticky sequence would be different
20:02 < fenn> there would be a maximum number of oligos you could anneal at the same time before you start getting mismatches
20:03 < kanzure> what is blue, what is red?
20:03 < kanzure> complementary strands?
20:03 < fenn> you pick the ligation sites for maximum selectivity
20:03 < fenn> yes
20:03 < fenn> synthesized in different spots on the light directed synthesis
20:04 < kanzure> I still don't see why annealed oligos would necessarily form in some order for the final strand..
20:04 < fenn> it's a grammar
20:05 < fenn> a sticks to ~a, b sticks to ~b
20:05 < kanzure> so then how do you get a to stick to b?
20:05 < fenn> you don't
20:05 < kanzure> then how do you get an assembled molecule
20:05 < fenn> you put a and ~b on one strand, b and ~a on the other ( that would form a ring)
20:06 < fenn> a and b are the sticky sequence
20:06 < fenn> you leave that part out of the complementary strand so it's exposed as single strand DNA
20:07 < kanzure> so you're using complementary strands of ssDNA tails or something?
20:07 < kanzure> and these tails (ideally) match up more often than errors? to be ligated together
20:07 < fenn> yes, this is basic recombinant DNA stuff
20:07 < kanzure> blah, didn't know it was watson-crick base pairing crap
20:08 < fenn> in old fashioned techniques they use restriction enzymes to cut a genome or plasmid at the sticky sequence
20:08 < fenn> but restriction enzymes only recognize like 5-15bp
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20:08 < fenn> whereas i think you'd want a longer sequence so you could have more oligo's in the same annealing step
20:10 < fenn> so at the end you will have a sequence of a certain length, run it on a gel to remove all the mismatched sequences (should be able to discriminate by the number of bp in your oligo)
20:10 < kanzure> Mechanical separation of the complementary strands of DNA. "the typical forces along the opening are in the range of 10-15 pN. The separation force signal is shown to be related to the local GC vs. AT content along the molecule."
20:10 < kanzure> "variations of this content on a typical scale of 100-500 bases are presently detected." (1997)
20:15 < fenn> did you ever compile pythonocc "--with-doc"?
20:15 < kanzure> no
20:15 < kanzure> have you?
20:15 < fenn> i'm wondering if it's simple (and why isnt it on by default??)
20:15 < kanzure> it might be the doxygen stuff
20:16 < fenn> no
20:16 < fenn> it adds docstrings
20:16 < kanzure> gasp
20:16 < kanzure> docstrings? is that the stuff before a function that describes it?
20:16 < fenn> then you can just do help(foo) or pydoc foo
20:16 < fenn> yes
20:16 < kanzure> because I get popups in InteractiveVeiwer that tells me about the functions, in terms of parameters
20:16 < kanzure> oh
20:16 < kanzure> but not full text
20:16 < kanzure> okay, guess it's different
20:16 < fenn> it's supposed to be helpful natural language text
20:17 < fenn> somehow i doubt OCC is going to be helpful though :P
20:23 < drazak> kanzure: 
20:23 < drazak> I haven't read any of the openthermocycler thread
20:23 < drazak> but
20:23 < drazak> have peltier devices been suggested?
20:24 < drazak> along with adding drops of mineral oil to the microcuvettes?
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20:27 < kanzure> drazak: not anything about mineral oil, IIRC
20:28 < drazak> it will prevent condensation from building on the top of the device from uneven heating, you have to make sure to pipette from underneath the layer of oil when removing samples
20:28 < drazak> peltier devices are simple DC heaters/coolers that could be efficiently used
20:29 -!- DrTread [n=irchon@166.133.152.12] has joined #hplusroadmap
20:30 < kanzure> Hey DrTread.
20:30 < kanzure> DrTread: Creative uses of LEDs for diybio: http://groups.google.com/group/diybio/t/ba6de9183f9ba83e
20:31 < drazak> led's are good for RTPCR too
20:31 < DrTread> hello. I'm @ friend's house, bored
20:31 < DrTread> saw that on your twitted. :-)
20:31 < kanzure> drazak: feel free to reply to that thread on diybio
20:32 < kanzure> DrTread: woah, you actually read my twitter feed? :)
20:32 < drazak> kanzure: I will soon
20:32 < kanzure> drazak: I mean the one about LEDs :)
20:32 < DrTread> I hang on every word!
20:33 < drazak> I'll post them both
20:36 < drazak> I'm thinking about other things too :)
20:36 < drazak> the people who are doing the open thermocycler should include a buffer
20:36 < drazak> that you cna buy more of
20:36 < DrTread> kanzure, you mentioned the collyer brothers. I'm watching a movie about other famous recluses
20:36 < kanzure> DrTread: Is it a good movie?
20:37 < DrTread> the Edies Bouvier
20:37 < DrTread> documentary. weird. 
20:37 < DrTread> see link to them @ end of collyer's wikipedia
20:38 < DrTread> tonight there's a movie on HBO about them. 
20:39 < DrTread> these people male me want to give away all of my junk
20:39 < kanzure> turn it off.
20:39 < kanzure> before damage occurs
20:40 < DrTread> Pffft. I'm at a friend's house. I can't turn of off. :-(
20:40 < DrTread> I don't watch any TV. I don't know what to do. :(
20:42 < genehacker> DrTread just don't watch moonwalker and you'll be alright
20:42 < DrTread> no problem. ;)
20:44 < drazak> kanzure: If I send an email to the email I get digests from, will it post to the board?
20:44 < fenn> genehacker: there was a 'moonwalker' video game, where you were michael jackson, and the goal was to collect blonde children :)
20:45 < fenn> and avoid ninjas with machine guns
20:45 < genehacker> oh god
20:45 < fenn> there was even a sequel
20:45 < genehacker> I just know that in the movie michael jackson morphs into a jet, then a flying car, then a jack rabbit
20:45 < genehacker> yes there were children
20:46 < fenn> drazak: you can avoid having to use mineral oil with a heated lid
20:46 < DrTread> MJ is unfettered by good taste. 
20:46 < drazak> fenn: right
20:47 < drazak> fenn: but if we're making this the cheapest thermocycler out there, why have a heated lid?
20:47 < drazak> not that a second peltier device/water chamber will cost much, but...
20:47 < fenn> because a heated lid is so ridiculously easy it'd be stupid not to
20:47 < fenn> you dont even need a peltier, just some power resistors
20:48 < DrTread> yes, heat is easy. 
20:48 < fenn> i'm really wondering why you need a peltier at all
20:48 < drazak> peltier is 1000x more efficient, you can cool with it, and it has more surface area
20:48 < fenn> wouldnt a simple heatsink+fan work better?
20:48 < drazak> you can cool with a peltier
20:48 < drazak> flip the current
20:48 < fenn> but PCR is 50-95C most of the time
20:48 < drazak> right
20:48 < fenn> who gives a flying fuck about cooling
20:48 < drazak> but you have to go from 95C to 50C at one step
20:49 -!- DrTread [n=irchon@166.133.152.12] has quit [Remote closed the connection]
20:49 < drazak> if you're doing 20 or 30 cycles
20:49 < fenn> and that's when you turn the fan on
20:49 < drazak> and it takes 5 minutes to cool by hair
20:49 < fenn> bah
20:49 < drazak> that's an extra 90 minutes or so
20:49 -!- DrTread [n=irchon@166.133.152.12] has joined #hplusroadmap
20:49 < fenn> you have to get rid of that heat somehow
20:49 < drazak> and then the time spent /at/ the temperatures
20:50 < drazak> which is why you have an upper and lower water bath
20:50 < fenn> water bath???
20:50 < drazak> yup
20:50 < fenn> GTFO
20:50 < drazak> to keep consistant temperature over each microcuvette
20:50 < drazak> submerse the bottoms of each in a water bath
20:50 < drazak> hey, this is my idea
20:50 < drazak> I haven't read the thread :P
20:50 < DrTread> big blocks of aluminum work great. 
20:51 < drazak> DrTread: sure, if you want some cuvettes to work and some not to
20:51 < drazak> which means more reagent
20:51 < drazak> which is the expensive part, in the end
20:51 < fenn> drazak: almost all commercial PCR machines use big blocks of aluminum
20:51 < drazak> huh
20:51 < drazak> it's prone to uneven heating, imo
20:51 < fenn> not water baths
20:51 < fenn> you're wrong, sorry
20:51 < drazak> well what do I know? :P
20:51 < drazak> but they are prone to uneven heating, aluminium blocks
20:52 < drazak> you don't have to be an ass about my being wrong
20:52 < fenn> aluminum is the third most conductive element
20:52 < fenn> sorry if i'm being an ass
20:52 < drazak> well then
20:52 < fenn> but water bath is just so wrong..
20:52 < drazak> your heater has to have enough surface area to evenly heat it
20:52 < drazak> also
20:53 < drazak> power resistors are slow, no?
20:53 < DrTread> single xtal diamond is great, but expensive
20:53 < fenn> sorry, gold is third, aluminum is fourth
20:53 < fenn> by area
20:53 < DrTread> best way is to pump temp controlled water thru alum block. 
20:54 < drazak> mhm
20:55 < DrTread> of
20:55 < DrTread> course, conduction to cuvettes is an issue
20:56 < fenn> hey i know let's submerse them in a pool of mercury
20:56  * drazak eyerolls
20:57 < DrTread> LOL! no, Na-K
20:57 < fenn> you could dispense with the heating element altogether and resistively heat the molten metal
20:57  * drazak eyerolls
20:57 < fenn> ok ok how about field's metal
20:57 < fenn> it's "non-toxic"
20:57 < drazak> galium?
20:58 < fenn> (note the quotes)
20:58 < drazak> we could use gallium resistively heated
20:58 < drazak> :D
20:58 < DrTread> yeah. that, too. buy it sticks to everything. 
20:59 < fenn> i'm from the light bulb + capillary tube school of PCR
20:59 < drazak> that's slow though
20:59 < fenn> so worrying about heat conduction to plastic tubes seems silly when you can get a 10-fold improvement by switching to capillary tubes
20:59 < fenn> drazak: cycle time under a minute, usually
20:59 < drazak> :o
20:59 < drazak> how do the capillary tubes work then?
20:59 < drazak> also brb
21:01 < fenn> there's a glass tube, about a mm.. you stick it into your eppendorf (for large arrays of reactions i just dotted things out on parafilm) and it sucks the mix up into the tube.. then you seal the ends with a bunsen burner and stick it in a hole poked through a piece of rubber
21:01 < fenn> tube = 1mm OD
21:01 < fenn> inside the machine there's a light bulb, a fan, and a temperature sensor with the same thermal characteristics as the glass tubes
21:01 < fenn> all the tubes are the same distance from the bulb
21:01 < kanzure> hrm. comB2 and comB3 genes look interesting.
21:02 < drazak> fenn: seems tedious to setup
21:02 < fenn> drazak: this is the idaho scientific thermocycler, btw
21:03 < kanzure> five proteins in Heliobacter pylori form a transmembrane channel that induces natural competence.
21:03 < kanzure> hellooo
21:03 < fenn> http://www.idahotech.com/RapidCycler2/index.html
21:04 < DrTread> well,
21:04 < DrTread> let's give ourselves ulcers 
21:05 < kanzure> doesn't matter, we just want the genes
21:05 < kanzure> does anyone here have ulcers and not mind gi surgery by an amateur?
21:06 < DrTread> you???
21:06 < kanzure> in particular: VirB7, VirB8, VirB9, VirB10
21:06 < fenn> i suggest not culturing human pathogens
21:07 < kanzure> oh ok
21:07 < fenn> i'm sure there are plenty of other naturally competent cells
21:08 < DrTread> heliobacter is hard to culture
21:08 < DrTread> anthrax is easy :-D
21:08 < kanzure> yay, these genes are sequenced and in NCBI
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21:09 < kanzure> cis-action: hey
21:09 < kanzure> cis-action: you remember ADP1?
21:09 < cis-action> hi yep
21:09 < cis-action> just talking about it actually
21:09 < cis-action> ....why?
21:09 < kanzure> cis-action: natural competence is caused by a transmembrane channel protein complex (thingy) which happens to be sequenced and in NCBI
21:10 < kanzure> which potentially means us transplanting it to other organisms
21:10 < drazak> that thingy sounds like a connexin
21:10 < drazak> :D
21:10 < cis-action> ... suggesting we should just biobrick that up
21:10 < kanzure> hell yeah
21:10 < cis-action> how long is the gene(s)
21:10 < fenn> kanzure: "five proteins" meaning five different proteins or a 5-mer?
21:10 < kanzure> haven't counted :p but I'm looking at one that has a ~30 AA sequence 
21:10 < kanzure> fenn: I think it's five different proteins, yes
21:10 < fenn> oh. that sucks
21:11 < kanzure> why?
21:11 < fenn> i bet there's something with just one gene product
21:11 < kanzure> they are on agrobacterium tumefaciens plasmid pTil5955
21:11 < genehacker> ahem
21:11 < genehacker> I think we are forgetting the lightbulb thermocycler
21:11 < drazak> eh oh well
21:11 < fenn> nopaline?
21:11 < kanzure> VirB7, VirB8, VirB9, and VirB10. eh, which is only four. wait a moment.
21:11 < genehacker> aluminum isn't that expensive
21:12 < kanzure> okay. the paper says four.
21:12 < fenn> genehacker: it's not the expense, it's about the mess and inconvenience of a water bath
21:12 < genehacker> aluminum is hard to drill
21:12 < fenn> oh come on
21:12 < genehacker> if you won't have a drill press
21:12 < genehacker> like me
21:13 < fenn> i will drill some holes in a block for you
21:13 < DrTread> I have all tools
21:13 < drazak> that sounds so naughty
21:13 < genehacker> you have a drill press?
21:13 < DrTread> dirty minds think alike
21:13 < fenn> there are like 7 drill presses in the shop
21:13 < kanzure> this would make quite the hell of an igem project. hrm..
21:13 < genehacker> then drill me some extruder barrels
21:14 < drazak> you know
21:14 < DrTread> I have a lathe, mill, too
21:14 < drazak> drill press seems like the wrong way to get holes in the aluminium for a cuvette
21:14 < drazak> you'd want something that pretty much exactly fit it
21:14 < fenn> drazak: yes, a reamer is probably better
21:14 < drazak> yeah
21:14 < fenn> i'd like to do some experimenting to see if it really matters
21:15 < genehacker> a liquid galium bath would be interesting
21:15 < genehacker> i have some liquid gallium
21:15 < fenn> step-drilling can get pretty good fits (makes a pop noise when you pull it out)
21:15 < DrTread> remember differential expansion
21:15 < fenn> DrTread: which expands more, LDPE or aluminum?
21:16 < genehacker> ah yes thermal expansion
21:16 < genehacker> aluminum
21:16 < fenn> or whatever eppendorf tubes are made of
21:16 < genehacker> aluminum
21:16 < drazak> make it a micron bigger than!
21:16 < DrTread> oh, I thought glass. n/m
21:16 < genehacker> well let me check thermal expansion coefficients
21:16 < drazak> I can't imagine going from ~298K-373K is a lot of expansion for Al
21:17 < fenn> microcentrifuge tubes are made of polypropylene
21:17 < fenn> or polycarbonate
21:17 < DrTread> ldpe is much bigger
21:17 < genehacker> how big are EP tubes drazak?
21:18 < drazak> not big
21:18 < DrTread> 7-8 mm od, iirc
21:18 < drazak> yeah
21:18 < drazak> but they come to a tip
21:18 < fenn> there are smaller, thin-wall tubes for PCR
21:18 < genehacker> http://en.wikipedia.org/wiki/Coefficient_of_thermal_expansion#Thermal_expansion_coefficients_for_some_common_materials
21:18 < genehacker> all be
21:18 < fenn> thanks lazyweb
21:19 < genehacker> look at the thermal expansion coefficient of PVC and look at aluminum
21:19 < drazak> yeah, those are the ones I was thinking of
21:19 < drazak> I think they're called microcuvettes
21:19 < drazak> they usually come in sheets, in real lab ones
21:19 < genehacker> yeah I know what you're talking about
21:20 < DrTread> ok, the main feature us starting. I'll sign off. 
21:21 < genehacker> so what are EP tubes made of?
21:21 < fenn> PE+PP have huge thermal expansion, which means they'll swell up and get stuck in the holes at high temp (which is a good thing)
21:21 < drazak> PE?
21:21 < fenn> genehacker: polypropylene
21:21 < fenn> for the 'living hinge'
21:21 < genehacker> ok
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21:22 < genehacker> so we want them to stay in the hole?
21:22 < fenn> when the tube expands, that pushes it against the walls
21:22 < fenn> which makes for good thermal contact
21:23 < fenn> also the lid will be pushing it down, so if the hole has a matching conical bottom it will push along the taper too
21:23 < fenn> i dont think most diy people will be up for making conical drill bits though
21:23 < genehacker> yeah me too
21:23 < fenn> (even though it's not really that hard)
21:26 < genehacker> we could just use gallium 
21:26 < genehacker> though gallium likes to form alloys with other metals
21:26 < genehacker> as I learned
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21:52 < kanzure> so I find a high quality paper (you can actually read it) and it's going over the genes necessary for natural competence
21:52 < kanzure> and the one diagram that I actually need to see, where the nucleotide sequence is given,
21:52 < kanzure> is static/noise. :(
21:54 < genehacker> damn college parties
21:54 < fenn> damn rogue CIA programs
21:55 < genehacker> I go to a college party, I think I am going to have a good time but no
21:55 < genehacker> they have REDACTED}
21:56 < genehacker> hmmm...
21:57 < genehacker> I wonder how hard it would be to make  an IR spectroscopy unit
21:58 < kanzure> infrared LED + something something something
21:58 < kanzure> or see the cereal box + CD methods
21:58 < genehacker> I want to detect a certain chemical that isn't very complex in small concentrations in the air
21:59 < genehacker> so I can put it on a robot
22:00 < fenn> you want a mass spectrometer
22:00 < genehacker> yeah, like I can get a cheap one of those
22:00 < fenn> spectroscopy only works in high concentrations
22:00 < genehacker> sure they have some the size of game boys
22:01 < genehacker> I want to detect alcohol
22:01 < genehacker> ok?
22:01 < drazak> I can have things mass spec'd by the lady upstairs
22:01 < drazak> for probably free
22:02 < genehacker> I want to make a robot that goes around the the dorms automatically sampling the air and seeing if there is alcohol present
22:02 < genehacker> so that way people don't have parties with alcohol
22:02 < genehacker> and I can to parties without getting arrested
22:06 < nsh> wtf
22:06 < fenn> genehacker: that's the dumbest idea i've ever heard
22:07 < genehacker> of course, but people would still buy it
22:07 < fenn> hmm. an alcohol-sniffing robot could be useful, but not for your intended scenario
22:07 < nsh> have you been arrested for being at a college party with alcohol, genehacker?
22:07 < genehacker> DVD rewinders exist, and people buy them too
22:07 < genehacker> no
22:08 < nsh> then what's your point?
22:08 < fenn> actually it would probably sell better as a cellphone attachment
22:08 < genehacker> hmmm...
22:08 < genehacker> now all we have to do is figure out how to constuct a really really tiny alcohol sensor
22:10 < genehacker> detecting alcohol at low concentrations might cause some problesm
22:11 < genehacker> alcohol present in mouthwash or hand santizing wipes could set it off
22:12 < kanzure> ok. mission accomplished.
22:12 < genehacker> kanzure, could you tell me what parameters I need to feed that gear generator program of yours?
22:12 < genehacker> I know the gear needs to be able to withstand 500 oz/in of torque for sure
22:13 < kanzure> genehacker: unfortunately it's not my program. I don't actually have the source code laying around here. But IIRC it wants you to set some initial variables like xyz input location, and torque
22:13 < genehacker> it's a gear in a gear
22:15  * fenn suspects someone is going to be disappointed
22:16 < genehacker> I don't think that program can generate weird internal gears so
22:16 < genehacker> I'll just do it my self
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23:25 < kanzure> so, sata wants me to design some sort of photovoltaic solar powered floatation device that flaps large-surface-area arms around wildly
23:26 < genehacker> hey I got a 10v solar cell you want it?
23:26 < genehacker> btw I'm taking dynamics I could do this
23:27 < kanzure> what does taking dynamics have to do with it
23:27 < genehacker> sounds like to me you want some sort of crank mechanism
23:27 < kanzure> well, for one, a mechanical system like this might not even be a good idea.
23:27 < kanzure> what happened to us thinking about jets? etc.?
23:27 < genehacker> heh
23:28 < genehacker> you should see what they use to aerate fish farms
23:28 < genehacker> they use paddle wheels that spin REALLY REALLY FAST
23:28 < fenn> what's wrong with a bubbler?
23:29 < fenn> super low power, high surface area, stirs the water around
23:29 < fenn> impossible to break
23:29 < genehacker> http://www.youtube.com/watch?v=meDcNK0-tio&feature=related
23:29  * kanzure nods
23:29 < fenn> if it does break, they cost so little as to be disposable
23:29 < kanzure> fenn: I am not convinced that this is going well at all
23:30 < kanzure> I've been in the group for how many months now? and have seen no efficiency charts, no nothin'
23:30 < kanzure> nor have I been able to create them for that matter
23:30 < kanzure> but that's another problem
23:30 < kanzure> I don't think 'efficiency' is a big issue there :/
23:30 < kanzure> just throw money at it, that'll git'r'done!
23:30 < genehacker> http://www.youtube.com/watch?v=vDUyNom6hZ4&feature=PlayList&p=C1F9C0526125C311&index=0&playnext=1
23:31 < genehacker> if it's solar-powered
23:31 < kanzure> where is boise?
23:31 < kanzure> hm, idaho.
23:31 < kanzure> is there some third world country named boise? because that's more likely to be what this person means
23:31 < kanzure> http://en.wikipedia.org/wiki/Boise_(disambiguation)
23:32 < kanzure> http://heybryan.org/~bbishop/docs/gears/CADgears2/modclasscorrect.bmp (just generated a few minutes ago)
23:33 < genehacker> I think something might be wrong
23:33 < genehacker> uhm seriously
23:33 < genehacker> did you look at the matlab script I gave you?
23:33 < fenn> why are you making .bmp files?
23:34 < genehacker> I mean it makes 3d models of gears
23:34 < kanzure> fenn: that's what pythonocc exports
23:34 < genehacker> sure, it's in easy matlab format
23:34 < kanzure> I would convert them, but that would be an extra step
23:34 < fenn> jesus that thing looks dangerous
23:34 < kanzure> ?>
23:35 < fenn> 'hey bubba lets weld some rotating spikes onto yet tractor'
23:35 < kanzure> heh
23:35 < genehacker> well, at least they thought to do aerating in the first place
23:35 < fenn> seriously, bubblers rock
23:36 < kanzure> fenn: if you want, you could come to the next lab meeting and knock some sense into everyone
23:36 < genehacker> hmmmm....
23:36 < genehacker> so we need a solar powered air compressor?
23:36 < fenn> my fees are very reasonable
23:36 < kanzure> fenn: oh?
23:37 < genehacker> kanzure if you're gonna make it solar powered
23:37 < genehacker> look into making something beam style
23:37 < genehacker> BEAM style
23:37 < kanzure> beam robotics, or beam beams
23:37 < kanzure> okay
23:37 < fenn> beam is lame
23:37 < fenn> just charge a battery
23:38 < genehacker> do you call a giant walking robot with metal detectors on it that seeks out metallic objects lame?
23:38 < genehacker> (metallic objects largely being unexploded munitions)
23:40 < genehacker> the guy who built this giant robot once sent it on a path down a hall way to terrorize his secretary
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23:51 < fenn> hmm calculus.
23:53 < fenn> given a heatsink at 90C, mass 30g, heat capacity 0.9J/gK, and junction to ambient of 0.5 degree per watt, how long will it take to cool off to 40C, given an ambient temperature of 25C
23:54 < genehacker> oh god, not heat transfer
23:54 < genehacker> that class is hard
23:54  * fenn looks at http://books.google.com/books?id=lIBCltUml6oC&pg=PA91&lpg=PA91&dq="long+will+it+take+to+cool+off"&source=bl&ots=RPhthHS2QE&sig=oyI3Rgj4V5elPbliUD6pShGKgtI&hl=en&ei=kK7qSaqdDOWwtgf1m4yXBg&sa=X&oi=book_result&ct=result&resnum=4
23:55 < fenn> i hate when a problem seems so simple but i can't figure out how to put it into equation form
23:56 < fenn> all these textbook problems are exactly the same