--- Day changed Tue Apr 21 2009
00:00 < DrTread> fenn, get open office!
00:00 < fenn> i usually dont bother looking at .ppt because it's either garbled or the content was worthless in the first place
00:00 < DrTread> LULZ True!
00:00 < fenn> and open office is a huge slow pig
00:00 < fenn> but now i have space to install it so i guess i might as well
00:01 < DrTread> i use NeoOffice
00:01 < kanzure-> fenn: liking your hdd?
00:01 < kanzure> pdf: http://heybryan.org/bioreactor/2008-10-28%20Algal%20biomass%20extraction%20presentation.pdf
00:01 < DrTread> slow pig? as opposed to MS Office?
00:02 < fenn> compared to any software i use regularly
00:02 < DrTread> kanzure, the .ppt opened just fine in NeoOffice :)
00:02 < DrTread> right.
00:02 < kanzure-> sorry, I don't understand pumpkin language
00:03 < DrTread> Love the picture of the ridiculously old ferrofilter
00:03 < kanzure-> :)
00:04 < fenn> 500 days to evaporate a liter of water? god i knew academics were slow but that's absurd
00:05 < DrTread> ok, i'm going this time, for sure. ni ni
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00:06 < fenn> by electromagnetic meant http://www.originoil.com/technology/low-cost-oil-extraction.html
00:07 < kanzure-> there's a group here at ut that we're working with that does electromagnetic disruption of algae
00:07 < kanzure-> they apparently did barrels of algae studies back in the day
00:07 < kanzure-> but we're not convinced.
00:07 < fenn> well it seems easy enough
00:08 < fenn> why not just try it
00:08 < kanzure-> truthfully? because the pi is scared of patents
00:08 < kanzure-> or scared of infringing on their patents or something
00:08 < fenn> do you guys actually have any algae to experiment on?
00:08 < kanzure-> yes
00:09 < kanzure-> this is mostly ran by biologists
00:09 < fenn> patents are no reason to not replicate an experiment
00:09 < kanzure-> algae we actually have down.
00:09 < kanzure-> we're also getting stuff from http://utex.org/
00:09 < kanzure-> I'm supposedly writing an interface to help automate the selection of strains from their database
00:09 < kanzure-> and then a custom database app for our lab to manage all of that information magical goodness
00:09 < kanzure-> such as the nile red fluoroscopy results, etc.
00:09 < kanzure-> and cell counting results and such
00:09 < kanzure-> we're currently working only with one or two strains at the moment though
00:10 < fenn> and if 'back in the day' is more than 20 years the patent is expired by now
00:10 < kanzure-> no, it's "recent"
00:10 < kanzure-> two years?
00:10 < fenn> oh, 'recent' back in the day
00:10 < fenn> really? radionics was hot shit in the 1970's
00:15 < fenn> i'm too lazy to find it, but hulda clarke's zapper is based on some other doctor who found resonant electrical frequencies of common parasites and pathogens; he'd put that electrical signal into the body to 'explode' the cells
00:16 < fenn> when you realize that the average bacterial cell is basically a capacitor it makes some sense
00:16 < fenn> charged up to something like 1.2V with proton gradient across the membrane
00:17 < kanzure-> I should have spent some more time on the math tonight instead of continuing to be feeling sick
00:17 < kanzure-> I wanted to figure out the maximum amount of energy that could be dispensed per cell
00:17 < kanzure-> without going under
00:18 < fenn> well what percentage of bacteria is oil?
00:18 < fenn> erm, algae
00:18 < kanzure-> of the mass?
00:18 < kanzure-> I don't quite know off the top of my head
00:18 < kanzure-> but we've been doing some quantifications of that
00:19 < kanzure-> at least in terms of cell counting
00:19 < fenn> something like 50% right? for GE strains
00:19 < kanzure-> our strains are non-GE and are doing 50%
00:19 < fenn> i dont know if that number is volume or mass
00:19 < kanzure-> 50% lipids :)
00:19 < fenn> or dry mass
00:19 < kanzure-> right. neither do I. but apparently we say that number a lot.
00:19 < fenn> 50% bullshit :P
00:20 < kanzure-> (why is this funded again?)
00:20 < fenn> because they have clout
00:20 < kanzure-> ?
00:21 < fenn> so if it's volume, then let's say the cell diameter is 20 microns
00:21 < kanzure-> 5 to 25 microns is what we're working with (at the moment)
00:21 < fenn> so that's 33 picoliters of volume
00:22 < fenn> so 16 pl of oil
00:22 < fenn> diesel is 39MJ/gal
00:23 < fenn> so you're getting 164 microjoules in oil per cell
00:23 < fenn> consider that to be equivalent to 30 microjoules of electricity after conversion losses
00:23 < fenn> which isnt much
00:24 < fenn> still with me?
00:24 < kanzure-> yes
00:24 < kanzure-> was away for a few moments
00:24 < kanzure-> I have no idea what the conversion efficiency is
00:24 < fenn> what is a typical cell count per liter of nutrient solution?
00:24 < fenn> i figured 20% conversion efficiency
00:24 < kanzure-> gah, I know this one
00:25 < fenn> you have to burn the oil, turn cranks, transform it to a useful voltage, etc
00:25 < fenn> honestly i think biofuel is a terrible waste
00:25 < kanzure-> I don't know what the cell counts are
00:25 < kanzure-> I want to say 1e5 per ml
00:25 < kanzure-> but I think this is wrong
00:26 < kanzure-> so anyway, 1e5 * 164 microjoules = microjoules per milliliter
00:26 < fenn> i hate how i always find these 'lab experiments' which are just a bunch of questions for students
00:27 < fenn> and the questions are what i want to know but i'd have to re-do the damn experiment to get the answer
00:27 < kanzure-> so for 10k gallons, that's about 605 MJ
00:27 < fenn> wait a minute, what number are you after? the amount of oil extracted? the amount of energy returned?
00:27 < kanzure-> um.
00:28 < kanzure-> well, I just want to see if the amount of energy returned is greater than the amount of energy put into the system for extraction/harvesting
00:28 < kanzure-> wait, shouldn't that be impossible?
00:28 < kanzure-> I should be looking at efficiency numbers
00:28 < fenn> ok then you want to consider the energy in a usable form
00:28 < fenn> since you won't be burning diesel directly in order to lyse cells
00:28 < kanzure-> what?
00:28 < kanzure-> I thought you said you already assumed 20% efficiency or something
00:28 < fenn> 605MJ chemical != 605MJ electrical
00:29 < kanzure-> blah, okay, so we magically come up with some microjoule content per each cell in terms of final product
00:29 < fenn> its simple, multiply chemical energy by conversion efficiency
00:29 < fenn> that's the amount of electrical energy available from the algae
00:29 < kanzure-> heh whereas you get 39 MJ/gal for diesel. neat. 
00:30 < kanzure-> I figure that it would then be significantly less than 605 MJ
00:30 < kanzure-> (due to non-perfect conversion efficiency)
00:30 < fenn> units '(1e5/ml)*10000gal*(20micron)^3*4pi/3' gal
00:30 < fenn> 33.5 gal of oil
00:31 < fenn> oops, divided by two
00:31 < kanzure-> what's all that about the volume and so on? 
00:31 < kanzure-> of the individual algae?
00:31 < fenn> total cell volume
00:32 < fenn> add up the volume of all the individual cells
00:32 < kanzure-> okay?
00:32 < kanzure-> what does that have to do with the 10,000 gal though?
00:32 < kanzure-> the algae is in the 10,000 gal at first
00:32 < fenn> dunno, you picked 10kgal
00:33 < fenn> i assume that's the size of some tank
00:33 < kanzure-> eh, right
00:33 < fenn> i wish units would make it easy to define arbitrary symbols/units like 'cell'
00:33 < kanzure-> I don't like doing math in irc. octave is way better.
00:33 < kanzure-> fenn: wonder if pq lets you define arbitrary units?
00:34 < kanzure-> erm, octave isn't way better
00:34 < kanzure-> I meant to say programming is way better
00:34 < fenn> units lets you define arbitrary units but not at the command line as far as i know
00:34 < fenn> isnt octave a programming language?
00:34 < kanzure-> everything is possible at the CLI with the proper usage of awk, sed and perl
00:34 < kanzure-> yes, but I'm not sure which one it is
00:34 < fenn> it's "not-matlab"
00:34 < kanzure-> ah right
00:35 < kanzure-> "definitely not matlab"
00:35 < fenn> is pq in debian?
00:35 < kanzure-> it's in pypi.python.org
00:35  * fenn pouts
00:36 < kanzure-> I'm sure python has a shell interface to pypi that we don't know about
00:36 < kanzure-> since perl has the cpan interface to cpan.org .. just figuring the python peeps would want a piece of that hot sexy action
00:37 < fenn> i'm so sick of incompatible package managers
00:37 < kanzure-> ok. I'm sick and have class tomorrow morning. I'm out. will act like I'm doing math later.
00:37 < fenn> gnite
00:37 < kanzure-> 'alien' is a good attempt.
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00:41 < fenn> d'eaux
00:41 < fenn> import quantities as pq
00:41 < fenn> it's not even called pq
00:44 < fenn> hm it has a stupid custom license, that's probably why it's not in debian
00:49 < kanzure-> "These facts show that protozoa are able to be used as a micro manipulator/actuator"
00:49 < kanzure-> ack, I'm "sleeping"
00:50 < genehacker> WTF?
00:50 < genehacker> how?
00:50 < genehacker> control em with light?
00:50 < genehacker> magnetic fields?
00:50 < kanzure-> close
00:51 < kanzure-> DC electric fields. so almost.
00:51 < genehacker> ah
00:51 < kanzure-> "electrical potential gradient"
00:51 < genehacker> oh I get it
00:51 < genehacker> mess with protons and stuff
00:51 < genehacker> seems I missed some interesting conversatiosn
00:52 < kanzure-> what's your favorite protozoan?
00:55 < genehacker> amoeba
00:55 < genehacker> cuz I can't think of anything else right now
00:55 < genehacker> anything that doe phototaxis is cool too
00:56 < kanzure-> wasn't there something that is attracted to high frequency strobe lights?
00:56 < genehacker> http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=803138
00:56 < genehacker> dunno
00:56 < genehacker> can't get this page too load looks interesting
00:57 < genehacker> yeah it looks like it
00:58 < genehacker> my PDF reader is broken
00:58 < genehacker> damn
00:58 < fenn> python setup.py develop
00:58 < fenn> This uses setuptools to install a link in your site-packages directory which points to your source directory. This allows you to make changes in the source directory without having to reinstall
00:58 < kanzure-> I was working on a firefox extension earlier today where they force us to manually do that
00:58 < kanzure-> or something
01:09 < kanzure-> rectangular-shaped archae microorganisms http://microbewiki.kenyon.edu/index.php/Thermoproteus
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01:15 < kanzure-> protist information server http://protist.i.hosei.ac.jp/ with over 81,000 images
01:15 < kanzure-> time to crawl.
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04:12 < kanzure> gah, you guys are so boring.
04:13 < kanzure> can't a guy waking up in the middle of the night at least wake up to schemes for world domination? :/
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09:24 < kanzure-> hehe
09:24 < kanzure-> Print your AFM
09:25 < kanzure-> http://heybryan.org/books/papers/Print%20your%20atomic%20force%20microscope.pdf
09:25 < kanzure-> explores AFM via 3D goo squirtin'
09:25 < kanzure-> http://heybryan.org/books/papers/How%20to%20build%20a%20plastic%20AFM.html
09:26 < kanzure-> er, better link for that last one - http://web.archive.org/web/20080106164837/http://www.biophysik.physik.uni-muenchen.de/PlasticAFM/
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09:30 < kanzure-> oh my.
09:30 < kanzure-> http://heybryan.org/books/papers/AFM/
09:30 < kanzure-> STL and SLDPRT models of an AFM scope for SLS printing
09:31 < kanzure-> \o/
09:31 < kanzure-> I win teh internets
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12:53 < kanzure>  "History isn't a sine wave of endless ... patterns. It's ... a helix that brings similar events around in a different orbit."
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13:30 < kanzure> huh. the wall street journal just randomly called me up.
13:35 < kanzure> http://wsj.com/
13:35 < kanzure> is this prestigous?
13:44 < UtopiahGHML> yes
13:45 < UtopiahGHML> Im sure a full 1st page would bring exposure and potentially lot of money :-#
13:45 < kanzure> huh? why?
13:46 < UtopiahGHML> because people with money read it and they have money because they are used to invest in project that will work, they read it because they are eager to make even more so a well presented project... will tempt them
13:47 < kanzure> why don't I know about this?
13:47 < UtopiahGHML> (should look for a demographic study of the readers though)
13:49 < UtopiahGHML> http://weblogs.jomc.unc.edu/talkingbiznews/?p=3182
13:52 < kanzure> The Journal subsequently conducted a world-wide investigation of the causes and significance of 9/11, using contacts it had developed during its business coverage of the Arab world. In Kabul, Afghanistan, a Wall Street Journal reporter bought a pair of looted computers which had been used by leaders of Al Qaeda to plan assassinations, chemical and biological attacks, and mundane daily activities. The encrypted files were decrypted and translated.[40] It was during this coverage that Journal reporter Daniel Pearl was kidnapped and killed by terrorists.
13:52 < kanzure> The encrypted files were decrypted and translated.[40] It was during this coverage that Journal reporter Daniel Pearl was kidnapped and killed by terrorists.
13:53 < kanzure> http://en.wikipedia.org/wiki/The_Wall_Street_Journal
13:54 < UtopiahGHML> http://www.youtube.com/watch?v=CFdItYkCQ5U :\
13:54 < UtopiahGHML> Kevin Warwick quick talk, video posted 7 avril 2009
13:55 < kanzure> Captain Cyborg?
13:55  * kanzure salutes
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14:46 < kanzure-> hi fenn_ 
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16:01 < kanzure-> hey genehacker 
16:02 < kanzure-> did you see the AFM SLDPRT files?
16:02 < genehacker> no
16:02 < kanzure-> I posted it to diybio
16:03 < kanzure-> the parts are meant to be SLS'd
16:03 < kanzure-> and then there's a BOM of the screws required and so on
16:03 < genehacker> REALLY?
16:03 < kanzure-> the people that first made it, used it to study DNA
16:03 < kanzure-> yes
16:03 < genehacker> sequence it?
16:03 < kanzure-> well, no. but they were able to do 600 consecutive reads of the molecule.
16:03 < genehacker> how much does it cost?
16:03 < kanzure-> I don't know
16:03 < kanzure-> but there's a BOM
16:03 < kanzure-> and links to the parts on the web
16:03 < kanzure-> so conceivably it can be figured out
16:04 < genehacker> they have SLS machines downstairs
16:04 < kanzure-> http://heybryan.org/books/papers/AFM/
16:04 < kanzure-> the PDF is the paper
16:04 < nsh> kanzure, why did the WSJ call you?
16:04 < kanzure-> the HTML page is their BOM and such
16:04 < kanzure-> nsh: interview.
16:04 < nsh> re: diybio?
16:04 < kanzure-> http://heybryan.org/books/papers/AFM/How%20to%20build%20a%20plastic%20AFM.html
16:04 < kanzure-> diybio and such, yes
16:04 < nsh> ok
16:05 < genehacker> is that a hyperprecision hyperexpensive optical stage I see?
16:05 < genehacker> I think it is
16:05 < kanzure-> well, screw it
16:06 < kanzure-> just use a piezo tweet from the $100 STM design
16:08 < genehacker> no cool images?
16:09 < kanzure-> it's in the paper
16:09 < kanzure-> http://heybryan.org/books/papers/Single-molecule%20cut-and-paste%20surface%20assembly.pdf
16:09 < kanzure-> http://heybryan.org/books/papers/Print%20your%20atomic%20force%20microscope.pdf
16:09 < genehacker> of molecules?
16:09 < kanzure-> right, they do single molecule shit
16:09 < genehacker> I'm looking at the paper
16:09 < kanzure-> and I don't know why, why not just do big stuff at first?
16:10 < genehacker> could they detect if a molecule is present in air?
16:10 < kanzure-> well, it's air-exposed if that's what you mean
16:10 < genehacker> IE could I detect if lead is present in tuna
16:11 < kanzure-> in the other paper they were assembling structures made out of DNA
16:11 < genehacker> or something like that
16:11 < kanzure-> by hybridizing strands attached to the probe tip
16:11 < kanzure-> which, as it happens, is a good way to transfect cells too
16:11 < genehacker> hmmm...
16:11 < kanzure-> there were some recent studies about stabbing bacteria 50 or 60 times with an AFM tip
16:11 < kanzure-> and it survives
16:12 < kanzure-> yeah, in that cut-and-paste paper they have a 10x10 micrometer letter "M" made out of oligos
16:12 < genehacker> oh yeah I found a perfect method for mounting a head mounted display
16:12 < kanzure-> ?
16:13 < genehacker> http://www.metalgearsolid.cz/images/games/mgs4/stroje/solid_eye2.png
16:13 < genehacker> this
16:13 < genehacker> strap to head
16:14 < kanzure-> eh, only if you don't have to adjust its distance in front of your eye
16:14 < kanzure-> also, that's not good for flip-displays where you want to be able to recover the use of your eye rapidly by a hand flipping motion
16:14 < genehacker> make it clear
16:15 < genehacker> ideally you'd have some augmented reality set up
16:15 < kanzure-> "analysis of potential mating trajectories and grasp .."
16:16 < kanzure-> did you see the paper about moving stem cells around in the human body by using magnets?
16:16 < genehacker> read article
16:16 < kanzure-> the paper is from 2005
16:16 < genehacker> didn't read paper
16:16 < genehacker> no
16:16 < kanzure-> but they are only now getting a business out of it
16:17 < kanzure-> so it's something relatively straightforward
16:17 < kanzure-> you just need to make sure the organism has mechanoreceptors
16:17 < genehacker> huh
16:17 < kanzure-> and then go find yourself the metal microbeads
16:17 < ybit> haven't read it yet: http://www.philosophy.ox.ac.uk/__data/assets/pdf_file/0019/3853/brain-emulation-roadmap-report.pdf
16:17 < kanzure-> and then make sure your magnetic field looks right
16:17 < ybit> it's from bostrom
16:17 < kanzure-> hrm
16:17 < kanzure-> I'm not sure how I feel about bostrom writing a brain emulation roadmap
16:18 < kanzure-> he'll probably just rant about philosophy :/
16:18 < kanzure-> and then cite dennet and call it quits
16:18 < ybit> :P
16:18 < genehacker> you know I was disappointed to learn that the robotic graspers they're using with the robotics lab just use force feedback to pick stuff up 
16:19 < genehacker> I want a robot that can assemble anything from parts
16:20 < kanzure-> what?
16:20 < kanzure-> force feedback is useful though
16:20 < genehacker> analysis of mating trajectories?
16:20 < kanzure-> right
16:20 < kanzure-> I was making a joke
16:20 < kanzure-> it was a paper about robotic grasping and such
16:20 < genehacker> oh
16:20 < kanzure-> it was something I was reading for skdb
16:21 < kanzure-> but you laughed when you first heard the title
16:21 < kanzure-> so I thought you were thinking about human mating or something
16:21 < kanzure-> so when you mentioned a HUD, I figured it was an appropriate time to cite that joke
16:21 < genehacker> it does sound funny
16:21 < kanzure-> you know what, nevermind
16:21 < kanzure-> <-- is a terrible comedian
16:21 < genehacker> ah well
16:21 < kanzure-> now then
16:22 < genehacker> hey, are you going to go print that AFM?
16:22 < genehacker> or at least get a quote on it
16:22 < kanzure-> I'll definitely look into getting a quote
16:22 < genehacker> I'd like to figure out how much it cost to 3d print things down there
16:22 < kanzure-> and if they won't do it
16:22 < genehacker> I'm still waiting on my reprap parts
16:22 < kanzure-> then ponoko and shapeways will be happy to
16:23 < kanzure-> there are also a few machined parts involved
16:23 < genehacker> they might be free
16:23 < kanzure-> maybe I can get diybio to give me money for the project?
16:24 < genehacker> anyway, we need to find a tiny cheap bw lcd screen
16:24 < genehacker> to see if we can't make a gene synth
16:24 < kanzure-> what's wrong with the LED capillary gene synthesizer approach?
16:24 < genehacker> show me
16:25 < kanzure-> http://heybryan.org/books/papers/A%20scalable%20method%20for%20multiplex%20LED-controlled%20synthesis%20of%20DNA%20in%20capillaries.pdf
16:25 < genehacker> could we do 600,000 mer with it? 
16:25 < kanzure-> no
16:25 < kanzure-> think 40mer
16:25 < kanzure-> in 16 hours
16:27 < genehacker> boooooooooooooooooooooooooooooooooooriiiiiiiiiiiiiiiiiiiiiiiiiiinnnnnnng
16:27 < kanzure-> how long did it take you to type that
16:27  * nsh smiles
16:27 < genehacker> around 5.4 seconds
16:28 < kanzure-> nsh: check this out :)
16:28 < kanzure-> http://heybryan.org/books/papers/Direct%20observation%20of%20one-dimensional%20diffusion%20and%20transcription%20by%20Escherichia%20coli%20RNA%20polymerase.pdf.1.jpeg
16:28 < genehacker> any way the deal with maskless array synthesis, is that we can make DNA microarrays for testing if  we have cancer or what not
16:29 < kanzure-> what, genetic markers of cancer?
16:29 < kanzure-> have I told you about pinkarmy yet?
16:29 < genehacker> yeah, but I don't recall what they're trying to do
16:29 < kanzure-> we're doing oncolytic viruses to selectively infect cancer cells in the human body
16:30 < kanzure-> (and kill those cells, in particular)
16:30 < genehacker> well the thing is we can put a whole bunch of 80 mer sequences on a chip
16:31 < genehacker> I'm wondering how big an image we want on that chip
16:31 < kanzure-> too bad the pixel density sucks for the 50 inch LCDs
16:31 < genehacker> how big do we want the image on the chip?
16:32 < kanzure-> ok, suppose you have some error rate that you are going to get
16:32 < kanzure-> big enough to make the error rate inconsequential
16:32 < genehacker> I need to know this so I can use some optic formulas to calculate what lenses we'd need and if this is feasible
16:32 < genehacker> ah well I have to go
16:49 < fenn_> wow this toy is $94 http://linuxdevices.com/news/NS7591575275.html
16:49 -!- fenn_ is now known as fenn
16:50 < fenn> that's a lot of hardware
16:51 < fenn> 17 servos, a gyro, and a tiny linux SBC
16:52 < fenn> i can't even get a gyro for under $40
17:21 < kanzure-> http://www.scienceblog.com/cms/ultrasound-imaging-now-possible-smartphone-20461.html
17:22 < kanzure-> oh god it runs windows :(
17:25 < kanzure-> laser lipolysis
17:25 < kanzure-> huh
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17:45 < kanzure-> this is a neat organism: http://protist.i.hosei.ac.jp/PDB2/PCD4710/htmls/09.html
17:45 < kanzure-> or this: http://protist.i.hosei.ac.jp/PDB2/PCD4709/htmls/81.html
17:47 < kanzure-> Micrasterias thomasiana
17:47 < kanzure-> http://protist.i.hosei.ac.jp/PDB/Images/Chlorophyta/Micrasterias/thomasiana/sp_03.html
17:48 < kanzure-> http://protist.i.hosei.ac.jp/PDB2/PCD4710/htmls/28.html
17:48  * fenn wonders if kanzure has found a new hobby
17:50 < kanzure-> shape :)
17:52 < fenn> pokemon
17:52 < kanzure-> yeah :(
17:55  * kanzure- has been coughing up a lung. it's painful.
17:58 < xp_prg> what is that Kanzure?
18:00 < kanzure-> what is what?
18:00 < ybit> a lung, duh!
18:00 < xp_prg> that picutre 28.html
18:00 < kanzure-> I think it's Micrasteri thomasiana
18:01 < xp_prg> it makes a shape, I wish I understood how it knew what shape to make
18:01 < kanzure-> crescentin
18:01 < kanzure-> it's a protein 
18:01 < kanzure-> look it up
18:01 < kanzure-> what's electrowetting? is it really just the change in contact angle due to an electric potential?
18:02 < kanzure-> xp_prg: see this. http://heybryan.org/books/papers/Bacterial%20cell%20curvature%20through%20mechanical%20control%20of%20cell%20growth.pdf
18:02 < xp_prg> crescentin causes shape to occur?
18:03 < ybit> project polymath? funny that their first course is on web design
18:03 < ybit> good idea, needs a little tuning though
18:03 < kanzure-> project polymath hasn't done anything
18:03 < kanzure-> I contacted them and stalked them down, but nothing happened
18:03 < kanzure-> xp_prg: not really
18:04 < xp_prg> kanzure well what does?
18:04 < kanzure-> but it's a way to force them to change shape
18:04 < fenn> huh. there's youre AFM photodiode strip http://www.taosinc.com/productdetail.aspx?product=18
18:04 < fenn> for $10
18:04 < fenn> supposedly
18:11 < kanzure-> 34 pixel zones? not ba
18:12 < kanzure-> *ad
18:12 < kanzure-> *bad
18:12 < kanzure-> I don't think that means what I think it means though
18:12 < ybit> i am failing to see how we will ever transfer our gray matter to another substrate or at even create onto and retreive memory from bmi. help me please.
18:12  * ybit blushes
18:13 < kanzure-> http://microfluidics.ee.duke.edu/
18:13 < ybit> -at
18:13 < kanzure-> ybit: bmi would be a way to interface with computers
18:13 < kanzure-> not necessarily have correlates of 'memory'
18:13 < kanzure-> I don't know what 'memory' is
18:13 < kanzure-> however, if you want to be occupied for a while, look up the artificial hippocampus brain implants
18:15 < ybit> i kind of have this feeling my brain is trapped until cloned, at which point it isn't even 'mine'
18:15 < kanzure-> hrm. so droplets can be controlled under direct electric control?
18:15 < ybit> anywho, off to read
18:16 < ybit> (cloned in the sense of being emulated)
18:16 < kanzure-> lots of neat videos
18:17 < fenn> ybit: kurzweil gets around this with the concept of 'prosthetics'
18:18 < fenn> where more and more of you gets vested in the prosthetics as a gradual process until the brain itself no longer matters
18:18 < kanzure-> so, I've been lowering my expectations or something
18:19 < kanzure-> I mean, not in a degrading way, but in the sense that it'd be cool to just be able to somehow get something similar to me spawned
18:19 < kanzure-> even in the sense of genetic cloning
18:19 < kanzure-> now, the brain would be nice to be able to copy 
18:19 < fenn> ybit: typical example is a nanobot that attaches itself to a neuron and takes over its function
18:19 < kanzure-> but I don't think I'm going to become depressed if I can't figure it out ..
18:19 < ybit> fenn: right, gradual replacement. i'll have to look into this, but i'm failing to see how exactly parts are going to be replaced
18:19 < kanzure-> as long as my toolchain keeps me in the loop
18:19 < ybit> fenn: oh.
18:20 < kanzure-> ybit: this is also what the "godseed" is about
18:20 < ybit> fenn: i forgot about that.
18:20 < fenn> kanzure-: you're too young to be thinking about having kids
18:21 < ybit> :P
18:22 < ybit> i seem to recall a problem whereby the nanobot has a difficult time copying the exact state of the neuron
18:22 < kanzure-> what information is worth copying?
18:22 < kanzure-> this is kind of why you should be around to fine tune the systems
18:23 < ybit> how philisophical is that question?
18:23 < kanzure-> hrm
18:23 < kanzure-> state = information
18:23 < kanzure-> that's what I meant
18:23 < kanzure-> what states are worth copying? I mean, what variables are you talking about?
18:23 < fenn> won't linking to http://heybryan.org/books/papers/AFM/ in an email cause google to spider your paper collection?
18:23 < kanzure-> the fact that there's some random protein attached to some random neuronal membrane somewhere in your prefrontal cortex?
18:23 < kanzure-> yes
18:23 < kanzure-> fenn: but actually I'm more worried about /books/ more than /books/papers/
18:24 < ybit> i seem to recall a lot of information concerning connections are stored in each neuron
18:24 < kanzure-> and I figure that /books/ won't be indexed because of how slowly it loads
18:24 < fenn> kanzure-: but it's all the same tree
18:24 < ybit> are/being
18:24 < kanzure-> fenn: I know :(
18:24 < fenn> then why did you do that?
18:24 < kanzure-> maybe this is bad, I don't know
18:24 < kanzure-> because because
18:24 < kanzure-> blah
18:24 < kanzure-> I don't want to set up robots.txt
18:24  * kanzure- goes to fix
18:25  * ybit is off to read
18:26 < kanzure-> okay. fixed.
18:27 < kanzure-> hm
18:28 < kanzure-> http://www.google.com/search?q=heybryan.org+books+papers&ie=utf-8&oe=utf-8&aq=t&rls=com.ubuntu:en-US:unofficial&client=firefox-a
18:28 < kanzure-> or more appropriately I guess: http://www.google.com/search?hl=en&client=firefox-a&rls=com.ubuntu%3Aen-US%3Aunofficial&hs=SiP&num=100&q=site%3Aheybryan.org+inurl%3Apapers&btnG=Search
18:38 < kanzure-> http://heybryan.org/books/papers/?C=M;O=D
18:38 < kanzure-> added two papers on the brainbow mice
18:38 < kanzure-> the recombinant gfp stuff
18:41  * fenn mumbles something about selling USB AFM's on ebay
18:42 < kanzure-> interesting idea
18:42 < kanzure-> I searched ebay the other day and didn't see anything re: AFMs
18:42 < kanzure-> how much do you think they would go for?
18:43 < kanzure-> http://shop.ebay.com/items/?_nkw=scanning+electron+microscope&_sacat=0&_trksid=p3286.m270.l1313&_odkw=atomic+force+AFM&_osacat=0
18:43 < kanzure-> oh fuck
18:43 < kanzure-> $110k for a SEM
18:50 < genehacker> hahaha bacterial pokemon
18:50 < genehacker> oh wait protist
18:50 < genehacker> oh yeah, my favorite protist is slime mold
18:51 < genehacker> they swarm
18:51 < ybit> what to focus on: aubrey's 7 deadly things or gradual uploading, hmm...
18:52 < genehacker> well let's make a nanobot first
18:52 < genehacker> also what freaks me out is memory loss
18:54 < ybit> i don't mind losing some memory if i'm going to be able to store a lot more than i currently can. i'm not fine with meory loss now, but it occurs often
18:54 < genehacker> no I mean in the long run
18:54 < genehacker> the LONG run
18:54 < ybit> explain please
18:54 < kanzure-> ybit: first step is figuring out what memory is
18:54 < genehacker> thousands of years
18:54 < kanzure-> or if you're just bullshitting yourself :/
18:55 < ybit> genehacker: i'm not asking about the how long 'long' is :P
18:55 < ybit> kanzure, true, hmm
18:55 < genehacker> ah well
18:56 < genehacker> you know what would be great?
18:56 < ybit> (^ rhetorical i'm guessing)
18:56 < genehacker> if matter was infinitely divisible
18:56 < fenn> ybit: gradual uploading has a higher overal redundancy in the end.. with 'ageless pseudo-immortality' you can still get run over by a truck
18:56 < kanzure-> unfortunately not
18:56 < kanzure-> gene doesn't ask rhetorical questions
18:56 < kanzure-> even though they are supposed to be rhetorical
18:57 < fenn> genehacker: but it is, i swear!
18:57 < genehacker> if matter was infinitely divisible, you could make a smaller and smaller computer that was more power yet takes less energy
18:57 < kanzure-> hm. so brainbow was done in 2007?
18:57 < kanzure-> time flies.
18:58 < kanzure-> why hasn't anyway copied brainbow yet?
18:58 < ybit> fenn: it would only be done to 'stay alive' until this 'upload' is complete..
18:58 < fenn> wow that's cool
18:58 < kanzure-> I want more pretty pictures
18:58 < kanzure-> fenn: did you see the paper?
18:58 < fenn> no
18:58 < kanzure-> http://heybryan.org/books/papers//Transgenic%20strategies%20for%20combinatorial%20expression%20of%20fluorescent%20proteins%20in%20the%20nervous%20system.pdf
18:59 < kanzure-> followup / related paper-  http://heybryan.org/books/papers//A%20technicolour%20approach%20to%20the%20connectome.pdf
18:59 < genehacker> eventually the energy needed for computation approaches zero...
18:59 < kanzure-> really beautiful. I read it a few years ago, but didn't have it on the server
18:59 < kanzure-> genehacker: you saw brainbow too, right?
18:59 < genehacker> I believe so
18:59 < fenn> can they do micro MRI yet? i'm sure i've heard about it but i forget
19:00 < kanzure-> erm, something about enhanced imaging by sticking in metal electrodes
19:00 < fenn> genehacker: you're wrong about that.. there's a minimum 'bit erasure energy'
19:00 < kanzure-> but really, that paper has the most beautiful images I've ever seen in a paper
19:00 < genehacker> hmmm...
19:00 < kanzure-> fenn: didn't anders come up with a number for that?
19:00 < genehacker> interesting
19:00 < kanzure-> genehacker: it's in his paper about supercomputing superobjects
19:00 < kanzure-> maximum computation per some space volume or something
19:00 < fenn> i dont think anders came up with it, he just examined the consequences
19:00 < kanzure-> written by Anders Sandberg
19:00 < genehacker> I'm saying if matter was infinitely divisible
19:00 < kanzure-> oh.
19:00 < genehacker> but it isn't
19:00 < kanzure-> yay for images: http://images.google.com/images?q=brainbow&oe=utf-8&rls=com.ubuntu:en-US:unofficial&client=firefox-a&um=1&ie=UTF-8&sa=N&hl=en&tab=wi
19:01 < genehacker> micro mri as in about millimeter features
19:01 < fenn> no as in micro meter features
19:01 < genehacker> MRI sux :(
19:01 < fenn> you're just jealous
19:02 < genehacker> MRI really only looks at blood vessels from what I hear
19:02 < genehacker> we really need a doping agent that hooks up to neurons to see them
19:03 < fenn> there's plenty of protons in a neuron
19:03 < genehacker> or something like that
19:03 < kanzure-> blah. firefox crashed. now I remember why I don't use firefox.
19:05 < genehacker> yeah there's plenty of protons in everything else too
19:07 < fenn> i think what you'd really want to see is sodium or calcium
19:07 < fenn> but i dont think those have a nuclear magnetic field
19:09 < genehacker> yup
19:09 < genehacker> you do that with a laser unfortunately
19:09 < fenn> do what
19:10 < fenn> why are all these brainbow images so low rez
19:12 < kanzure-> hrm.
19:13 < fenn> a protein called aequorin releases blue light upon binding with calcium.
19:13 < kanzure-> images: http://heybryan.org/books/papers/brainbow/
19:16 < kanzure-> I like this one: http://heybryan.org/books/papers/brainbow/brainbow2.jpg
19:16 < fenn> i want a gigapan :(
19:16 < kanzure-> mouse brain atlas is kinda like that
19:16 < kanzure-> although the images don't overlap because they are individual slices
19:33 < kanzure-> so I've been working on a firefox extension while I've been sick
19:33 < kanzure-> to help me search google scholar
19:33 < kanzure-> basically it keeps track of search queries that have been sent to google scholar
19:33 < kanzure-> it's kinda my magical device thingy to keep track of query permutations that you've already exhausted
19:33 < kanzure-> just need an annoying way to notify you that you're running the same search again. hrm.
19:33 < kanzure-> I'm thinking of a sidebar that just lists similar queries that you've run.
19:33 < fenn> does google alerts cover google scholar?
19:34 < kanzure-> not to my knowledge
19:34 < kanzure-> also, how does one set up google alerts for 35,000 previously executed queries?
19:34 < fenn> with a bot
19:34 < fenn> do you have those 35k queries?
19:34 < kanzure-> google doesn't like bots (ironically).
19:34 < kanzure-> no :(
19:34 < kanzure-> it's stored on their servers
19:35 < kanzure-> I have access to the pages, but they don't like me going through the list
19:35 < fenn> how do you access that?
19:36 < kanzure-> I enabled a "track my searches" button somewhere
19:37 < fenn> this cnc design looks eminently replicable with raw materials input http://joescnc.com/themachines-06.php
19:39 < genehacker> damn fenn
19:39 < genehacker> that looks pretty nice
19:39 < fenn> "Plans for the Joe's 06 CNC Router have and always will be open source and FREE."
19:42 < fenn> bah
19:42 < fenn> "By downloading these plans you are agreeing to use them for personal use ONLY! not to be used in any reproduction of the machine or parts other than personal use without my expressed permission."
19:43 < fenn> makes me want to call up shonen bat
19:43 < kanzure-> "
19:43 < kanzure-> "
19:43 < kanzure-> Genetically encoded fluorescent sensors of membrane potential
19:44 < kanzure-> ah, voltage-sensitive dyes
19:44 < kanzure-> neat.
19:52 < kanzure-> so, it would be neat to infect yourself with a bacteriophage that adds in that fluorescent probe
19:52 < kanzure-> you'd be the "glowing brain" superhero guy
19:59 < fenn> you mean supervillain guy
20:01 < genehacker> indeed
20:05 < kanzure-> just because I have a beard doesn't make me a supervillain
20:05 < fenn> yes it does
20:05 < fenn> well, a villain at least
20:06 < fenn> certainly not a superhero - how many superheroes have beards? none
20:07 < kanzure-> vegeta?
20:07 < fenn> you mean prince vegeta, intergalactic supervillain?
20:07 < fenn> he has a beard?
20:08 < fenn> i never got that far
20:09 < kanzure-> really?
20:09 < kanzure-> do you want to watch it with me sometime? i'm only slightly joking
20:09 < kanzure-> I guess I mean do you want the download links
20:09 < fenn> "How does Superman shave? Surely he has a beard of steel?"
20:09 < fenn> no, i think i've seen enough dragonball
20:10 < fenn> green arrow had a beard, though he always struck me as somewhat 'on the edge'
20:25 < kanzure-> tony stark
20:25 < fenn> villain
20:26 < kanzure-> wtf?
20:26 < fenn> superheroes are imbued with their powers by god
20:26 < fenn> tony stark was a violent capitalist oppressor
20:30 < kanzure-> you're not being fun.
20:32 < kanzure-> "Where's the fire! I always found that expression interesting especially since my lab assistant was killed in a fire."
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20:41 < kanzure-> all of these papers suck. I want to find fancy images of in vivo stuff.
20:42 -!- fenn_ is now known as fenn
20:42 < kanzure-> but nobody publishes images because it costs an arm and a leg
20:51 < kanzure-> http://www.stemcellschina.com/
21:00 < fenn> hm. i dd'd a 1GB image to my 512MB SD card and now linux swears it's a 1GB disk
21:06 < wrldpc> lol@$110K SEM
21:06 < wrldpc> as soon as I get a lot of money I'll buy you all a bunch of stuff.
21:06 < wrldpc> including the sem.   
21:06 < wrldpc> something better.
21:06 < wrldpc> bbiab
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21:07 -!- xp_prg [n=xp_prg3@99.2.31.217] has quit ["This computer has gone to sleep"]
21:08 < kanzure-> "Regulating gene expression with light-activated oligonucleotides." bwahah
21:11 < kanzure-> oh. azobenzene.
21:18 -!- DrTread [n=irchon@71.145.142.46] has joined #hplusroadmap
21:18 < DrTread> evening. 
21:18 < kanzure-> Good evening.
21:18 < kanzure-> DrTread, did you see the AFM CAD files I posted?
21:19 < DrTread> no. on heybeiab?
21:19 < kanzure-> http://heybryan.org/books/papers/AFM/
21:19 < DrTread> make that heybrian
21:19 < kanzure-> also, I was surprised to learn today that fenn had never seen brainbow- so just in case you've been missing out-
21:19 < kanzure-> http://heybryan.org/books/papers/brainbow/
21:20 < DrTread> out of the loop, eh?
21:20 < fenn> neurology's not my thing
21:20 < kanzure-> wait, what?
21:21 < kanzure-> brains?
21:22 < DrTread> I am greedily reading Theodore Gray's new book
21:25 < kanzure-> ooh. "Gene silencing in mammalian cells using light-activated antisense agents"
21:25 < DrTread> Oooh cool! is there a gene for stupidity?
21:25 < kanzure-> "
21:25 < kanzure-> "
21:25 < kanzure-> Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization
21:26 < kanzure-> they must be tapping into our brains again
21:30 < kanzure-> light-activation of gene function in mammalian cells via ribozymes
21:30 < kanzure-> neat too
21:31 < DrTread> I received a reply from lfilip. 
21:32 < DrTread> I'll go for a tour on thurs or Fri. 
21:33 < kanzure-> you sent email? tis good
21:34 < DrTread> yes. you told me to, Brain. 
21:34 < DrTread> I mean Bryan. :-)
21:35 < kanzure-> wonder if photolabile DNA synthesis is capable of adding a photocaging group on to the oligos
21:42 < kanzure-> http://angosypublishing.com/ supposedly a free 3D body thingy
21:42 < kanzure-> ah, http://visiblebody.com/
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23:31 < kanzure-> infrasound?
23:34 < kanzure-> "Mental abilities of male relatives of psychotic patients"
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23:41 < kanzure-> "Relation of mathematical ability to psychosis"