--- Day changed Sat Nov 01 2008
00:37 < xp_prg> kanzure_ do you understand the output of synbioss?
00:38 < kanzure_> I haven't finished converting it to run on linux yet.
00:44 < xp_prg> converting it?
00:45 < kanzure_> It includes various windows-only libs.
00:45 < kanzure_> imports.
00:46 < xp_prg> pyGTK is cross platform, I am confused what you mean
00:47 < kanzure_> Why would they look in C:\GTK for my GTK installation then?
00:47 < kanzure_> That's clearly a Windows directory.
00:47 < drazak> you did it wrong
00:54 < ybit> it says that its available for linux
00:54 < ybit> btw, who did what in flash?
00:54 < ybit> i went to some link which had flash.
00:55 < ybit> why? you will have to answer to the semantic web gods later
00:55 < ybit> + open source gods = not good for you
00:56 < drazak> http://downloads.sourceforge.net/synbioss/synbioss-1.0.1-src.zip?modtime=1221064192&big_mirror=0
00:56 < drazak> download that
00:56 < drazak> unzip it
00:56 < drazak> and compile
00:56 < drazak> and it will work in linux
00:56 < drazak> the .exe is windows i386 specific
00:59 < kanzure_> drazak: Look at setup.py
01:01 < drazak> I'm decently certain that the os module converts c:/ to ~
01:02 < kanzure_> I wonder why it failed on my system.
01:02 < drazak> what was the error?
01:03 < kanzure_> It's been a while. I probably ranted about it in here, though.
01:16 < xp_prg> hi drazak I am using flash because it is more robust for what I need to do
01:16 < drazak> why are you telling me?
01:16 < xp_prg> the back end will be python with django though
01:16 < xp_prg> you asked
01:16 < kanzure_> Why django?
01:16 < kanzure_> Who the fuck said anything about django?
01:16 < drazak> no, ybit asked
01:17 < xp_prg> its the best web framework for python
01:17 < xp_prg> do you know a better one?
01:17 < kanzure_> That doesn't answer my question.
01:17 < xp_prg> kanzure_ what would you have me use?
01:18 < kanzure_> I'd have you write the dman script you should have written months ago.
01:18 < kanzure_> *damn
01:18 < xp_prg> I want to use google engine but python needs to use libsbml which is a shared library, google engine can't handle that
01:18 < kanzure_> Not a web service thing. Not a flash app. Just the script.
01:18 < kanzure_> I don't care about the google engine.
01:18 < xp_prg> kanzure_ you agreed  this would be an ajax app
01:18 < xp_prg> I made my libsbml script
01:18 < xp_prg> what is missing that you want?
01:18 < kanzure_> No you didn't.
01:18 < kanzure_> The sbml script is incomplete and doesn't reconstruct the same data.
01:19 < kanzure_> though it is a step in the right direction
01:19 < xp_prg> I asked you what the next step was and you told me you didn't want my help
01:19 < xp_prg> I would love to know what the next step you want me to do is with that python script
01:19 < kanzure_> Yeah, I don't need that flash bullshit.
01:19 < kanzure_> I just told you. 
01:19 < kanzure_> Also, I told you a few days ago as well.
01:20 < xp_prg> kanzure_ please help me to understand what "same" data your referring to, I need an example to attempt to recreate manually, can you supply one please?
01:20 < xp_prg> or is it just reverse engineer the entire functionality of the synbioss designer by myself?
01:21 < kanzure_> I gave you over 50 MB of examples. What the hell man.
01:21 < xp_prg> just raw xml?
01:21 < kanzure_> Yep, entire functionality.
01:21 < kanzure_> Yes, that was the output of the designer-website-thingy on the neptune servers.
01:21 < kanzure_> http://heybryan.org/graph/synbioss/tmp/
01:21 < xp_prg> yes, I see that, well I am working on it, I just made one that worked with synbioss, now I have to reverse engineer it
01:22 < kanzure_> http://neptune.cems.umn.edu/designer/interface1.php
01:22 < kanzure_> http://neptune.cems.umn.edu/designer/interface2.php
01:22 < xp_prg> yes I know where it is
01:22 < kanzure_> http://neptune.cems.umn.edu/designer/interface3.php
01:22 < xp_prg> the truth is you don't really need those, you can use the modeler directly in synbioss
01:22 < xp_prg> it is probably more robust anyway
01:22 < kanzure_> Fuck GUIs.
01:23 < kanzure_> I just want that script.
01:23 < xp_prg> kanzure_ may I ask how you will supply the inputs to the script?
01:23 < kanzure_> Do you have a memory problem?
01:23 < kanzure_> We've gone over this many times before.
01:23 < xp_prg> like how will you supply promoters, effectors, biobricks?
01:23 < kanzure_> I keep telling you CLI, but maybe you don't understand what a script is?
01:23 < kanzure_> What a cli-only script is, I mean.
01:24 < xp_prg> you have not gone over the CLI input specification
01:24 < kanzure_> Same input as on the HTML document.
01:24 < kanzure_> pages.
01:24 < kanzure_> *HTML pages.
01:24 < kanzure_> And yes, I did go over that.
01:24 < xp_prg> kanzure_ that is what goes in, not how, like for example lets say the script is kanzurehy3s.py
01:24 < kanzure_> What?
01:25 < xp_prg> you would invoke it on the cli with ./kanzurehy3s.py input1 input2 input3
01:25 < kanzure_> You could. Another option would be to ask for user input via STDIN.
01:25 < kanzure_> Either way.
01:25 < xp_prg> oh ok, I didn't know how you wanted that done, that is all I am asking
01:25 < kanzure_> What?
01:25 < kanzure_> Parameters are fine.
01:25 < xp_prg> well it would help me to understand the parameters you want it to accept and how you will specify them
01:26 < kanzure_> The same parameters as on the HTML pages .. I just said this two minutes ago.
01:26 < xp_prg> for example:  find . -name "*.py"
01:26 < xp_prg> kanzure_ yes man, but a cli program takes arguments in a certain way, what is that way you want me to use?
01:27 < xp_prg> like -name specifies the name of the files to search for
01:27 < kanzure_> HTML form elements have a 'name' variable that specifies its name.
01:27 < kanzure_> *it's
01:27 < kanzure_> hrm, *their
01:29 < xp_prg> kanzure_ I am not asking what needs to go into the script but how it will be supplied on the command line
01:29 < kanzure_> You were asking about the name of the parameters. You might as well preserve the same naming scheme of the parameters.
01:30 < kanzure_> I don't know why you would change it at this point.
01:30 < xp_prg> ok lets try with an example:
01:30 < xp_prg> ./kanzurehy3s.py -biobricks b123, b234, b456
01:30 < xp_prg> is that how you want to do it?
01:30 < kanzure_> <input name="thingy" value="user supplied variable">
01:30 < xp_prg> or like this:
01:30 < kanzure_> ./program --thingy="user supplied variable"
01:31 < xp_prg> ok
01:31 < xp_prg> that is all I was asking
01:41 < kanzure_> You can also do STDIN.
01:42 < xp_prg> so prompt the user for input like enter the bio brick:>
01:42 < xp_prg> is that what you mean?
01:44 < kanzure_> Yes, that's "standard input".
02:27 < kanzure_> http://heybryan.org/~bbishop/docs/Voltage-controlled_ring_oscillator_for_13_Hz_to_407_MHz.pdf 
02:35 < kanzure_> Ultrasound stimulation of the heart.
03:53 < kanzure_> fenn: So I was doing a phone conference today with the VOICED people.
03:54 < kanzure_> It's interesting how literally equivalent their problems are to the ones we were thinking about months ago.
03:54 < kanzure_> Basically they want better formats and more detail to be packed into it, but everyone is generally clueless.
03:55 < kanzure_> One character associated with this crowd is apparently surprised how "little detail" all of this work involves, apparently he does finite element analysis and so on, and thus would obviously think much of this 'design' work is pathetic, though I don't see him going through a few million designs with his partial differentials.
03:56 < kanzure_> +-
04:01 < kanzure_> For solid (metal) mechanical systems, an algebraic language allowing for 3D geometric primitive subtraction and addition can be used, plus part mating algorithms to make 3D model files for those FEM simulations, I guess.
04:03  * kanzure_ needs to remember to see if the coffee filters capture the algae. 
04:07 < kanzure_> I wonder why there's no library for doing that, even in OpenGL or Blender. "Make giant sphere. Take out a triangle on the surface at the pi/2-th coord." <- Isn't subtractive modeling obvious?
04:07 < kanzure_> or additive.
04:08 < kanzure_> I suppose it's because it's annoying to have to recalculate the mesh, and calculating collisions between objects given a mesh.
04:11 < kanzure_> Set of operators (add/del), set of primitives, some way of specifying where on the so-far-constructed-object to perform the action (other than pre-defined based off of the nature of each of the primitives in use)
04:11 < kanzure_> perhaps also parameters to each of the individual primitive generators
04:18 < kanzure_> I'm not sure how to relate 'functions' to which primitives to involve. I suppose certain shapes are better/worse for different situations (preferentialism). Hexapods for some scenarios, triangles for ribs/ribbing, ..
04:18 < kanzure_> bleh
04:18  * kanzure_ goes off to write about the 'superneuron' simulator
04:34 < gene_> kanzure, we have a problem
04:35 < gene_> a big one
04:41 < kanzure_>  What?
04:44 -!- Nofairs is now known as SurpriseAbortion
04:44 < SurpriseAbortion> Me.
04:44 < kanzure_> Not much of one.
04:47  * SurpriseAbortion goes back to his corner
04:47  * SurpriseAbortion sobs
04:47 -!- SurpriseAbortion is now known as Nofaris
04:47 < kanzure_> There, there, I'm sure some infertile couple might want you.
04:47 < Nofaris> I'm sorry, I'm in a really silly mood right now
04:48 < Nofaris> More like a pregnant teenager in a religious household
04:49 < kanzure_> Backstory?
04:49 < Nofaris> More like back alley
04:56 < gene_> it's with the bioreactor
04:56 < kanzure_> What?
04:57 < gene_> the place we have to put the scaled up reactor is near
04:57 < gene_> a major river
04:57 < kanzure_> ?
04:57 < gene_> not only that, but the river is downhill from the bioreactor
04:57 < gene_> the species we are growing is not native
04:58 < kanzure_> ?
04:58 < gene_> we don't want to introduce an invasive species
04:59 < gene_> especially not into a major river
05:01 < kanzure_> http://heybryan.org/bioreactor/media/
05:03 < gene_> is that a cell
05:03 < gene_> a lysed cell?
05:03 < kanzure_> No.
05:04 < gene_> flocculated cells?
05:04 < kanzure_> Centrifuged.
05:04 < kanzure_> I told you, I centrifuged today.
05:04 < gene_> that's centrifuged
05:04 < gene_> whoa
05:05 < gene_> that's really clumpped up
05:05 < kanzure_> 1.2 to 1.5 mm diameter splotch on the side.
05:05 < kanzure_> You kidding me?
05:05 < gene_> that is VERY clumped up
05:05 < kanzure_> It worked great.
05:05 < gene_> did you see the sonicator we got?
05:05 < gene_> when did you show up?
05:06 < kanzure_> I didn't see.
05:06 < kanzure_> I was in the lab at 11 and 3.
05:06 < gene_> I left at 2:30
05:06 < gene_> when did you do the centrifuging?
05:06 < kanzure_> 11 and 3.
05:06 < gene_> dang
05:06 < gene_> you know
05:07 < gene_> I think the centrifuges work in a vacuum
05:07 < gene_> on 190?
05:08 < gene_> did you push the coverslip down?
05:08 < gene_> it looks like cells got flattened
05:09 < kanzure_> The second batch was a centrifuge->microwave and then another one for microwaving->centrifuging.
05:09 < kanzure_> The microwaving didn't help.
05:09 < gene_> you microwaved it?
05:09 < kanzure_> Got bored.
05:10 < gene_> hahahahaha
05:10 < kanzure_> But yeah, the algae clumps up and can be tapped off the side of the tubes.
05:10 < gene_> it looks like you lysed the cells
05:11 < kanzure_> Where's me liquid, and why did it still clump?
05:11 < kanzure_> Or, even, why did the chlorophyll stay?
05:11 < gene_> what do you mean?
05:11 < gene_> why wouldn't chrollyphyll say
05:11 < gene_> stay anyway
05:12 < kanzure_> No cell walls, so I'd imagine there to be more diffusion instead of uniforn chlorophyll (like with cellular membranes in tact).
05:12 < gene_> so those flattened cells are the microwaved ones right?
05:12 < kanzure_> Anyway, on the microwaved algae slides, I noticed rainbow-like colorings, like oil in a parking lot.
05:12 < kanzure_> Yes.
05:14 < gene_> YOU DID!
05:14 < gene_> SWEET
05:15 < kanzure_> Might have been oils from my fingerprint.
05:15 < gene_> I think you sintered them bryan
05:15 < gene_> they melted
05:16 < gene_> and fused together or something
05:18 < gene_> what was it like after you microwaved them?
05:18 < gene_> brittle?
05:18 < kanzure_> Macroscopically the same.
05:18 < gene_> huh
05:18 < kanzure_> No, it was also brittle before. 
05:18 < gene_> weird
05:18 < gene_> did it look different?
05:18 < kanzure_> Under the scope, yes.
05:19 < kanzure_> The first few pictures are the ones that I didn't microwave. The rest is. That's why you don't see distinct cell bodies.
05:19 < gene_> yeah
05:19 < gene_> that's very odd
05:19 < gene_> let's try repeating it?
05:20 < gene_> anyway what's are the cell walls made out of anyway?
05:20 < kanzure_> I spent three hours on it.
05:20 < gene_> on what?
05:20 < kanzure_> Membranes are lipid bilayers with integral-proteins embedded throughout with a distribution.
05:20 < gene_> huh
05:21 < gene_> not silicon dioxide or anything?
05:21 < kanzure_> You haven't taken a bio class?
05:21 < kanzure_> But yeah, silicon isn't popular in cells.
05:22 < gene_> diatoms have SiO2 cell walls
05:22 < kanzure_> There's no 'cell wall' here. Not plants.
05:22 < gene_> ok
05:23 < gene_> congrats bryan
05:23 < gene_> I believe you've discovered a new lysis method
05:24 < gene_> microwave disruption
05:25 < kanzure_> No, it's been in the literature.
05:25 < gene_> how long did you microwave it for
05:25 < gene_> damn
05:26 < kanzure_> A minute. I don't have the wattage rating of the microwave.
05:26 < gene_> good enough
05:26 < kanzure_> But it's one of those ancient microwaves with a wood case.
05:26 < kanzure_> Looks like it belongs in a station wagon.
05:26 < gene_> so we can't patent it?
05:26 < kanzure_> What the fuck?
05:26 < kanzure_> Get out.
05:26 < gene_> I want to fucking patent it
05:27 < kanzure_> ?
05:27 < gene_> so microwave disruption isn't anything new?
05:28 < kanzure_> Correct.
05:28 < kanzure_> Studies on microwave disruptions, that lay out specific numbers, would be somewhat new though.
05:29 < gene_> microwave disruption on a massive massive  scale would be new too
05:30 < kanzure_> How do you know?
05:30 < gene_> what?
05:30 < gene_> I guess it's not new
05:31 < gene_> if you consider certain 'cases'
05:34 < gene_> microwave cell lysis is patented
05:34 < gene_> did you add salt to it?
05:34 < kanzure_> What's with you and patents?
05:34 < gene_> I need some money
05:35 < kanzure_> Go get a job?
05:36 < gene_> why get a job when you can live off patent money
05:36 < kanzure_> Are you a patent troll?
05:37 < gene_> or product you sell money
05:37 < gene_> no
05:37 < kanzure_> I think you are.
05:37 < gene_> don't believe in that kind of think
05:37 < kanzure_> You're the one looking to patent stuff.
05:37 < gene_> if you patent something you have to sell it
05:38 < gene_> not leave it patented and not develop it
05:38 < kanzure_> So what?
05:39  * kanzure_ is guessing gene_ hasn't read the algamics papers etc.
05:39 < gene_> algamics
05:39 < gene_> never heard of it
05:39 < gene_> anyway have my own ideas to patent
05:40 < kanzure_> If you patent and try to sell shit, I'll build it for free. Screw selling.
05:40 < gene_> heh
05:40 < gene_> I don't think you'll be able to build it
05:42 < gene_> I don't think you'd even buy it either
05:42 < kanzure_> I don't buy much.
05:43 < gene_> I doubt my product market would even try to build it for free
05:44 < gene_> so what's algamics?
05:45 < gene_> how would you build something for free?
05:45 < kanzure_> Free as in, for no money. Not free energy.
05:46 < gene_> how?
05:46 < kanzure_> Money is just icing on a cake, it's not the foundations of physics and reality.
05:46 < gene_> how
05:46 < gene_> I know that
05:46 < kanzure_> The forming of materials into the result.
05:46 < gene_> how
05:47 < gene_> so I want to own the Mona Lisa
05:47 < gene_> what then?
05:47 < kanzure_> What the hell is ownership?
05:47 < gene_> the mona lisa
05:47 < kanzure_> That's a painting.
05:47 < kanzure_> Not ownership.
05:48 < gene_> I want to own it
05:48 < gene_> have ownership of it
05:48 < kanzure_> What the hell is ownership?
05:50 < gene_> Ownership is the state or fact of exclusive rights and control over property, which may be an object, land/real estate, intellectual property (arguably) or some other kind of property. It is embodied in an ownership right also referred to as title.
05:50 < gene_> sauce: wikipedia
05:50 < kanzure_> "Control is an illusion; order our comforting lie. Through chaos, from chaos, into chaos we fly."
05:51 < gene_> so
05:51 < Nofaris> lol
05:51 < gene_> I own this laptop
05:52 < kanzure_> That was all just a bunch of crap to me. "Rights" are sociology-crap.
05:52 < kanzure_> According to who?
05:52 < gene_> ok
05:53 < gene_> I am going to have your  computer ok?
05:53 < kanzure_> What?
05:53 < gene_> I am going to have it
05:53 < kanzure_> It's over here, and it's behind the lock.
05:54 < gene_> guess I'll have to bring my thermite then
05:55 < gene_> ok
05:55 < gene_> I see what you mean by ownership
05:55 < gene_> now
05:57 < gene_> so I can have your computer if I can get it?
05:57 < kanzure_> You basically just asked "if I can get it did I in fact get it" and by the nature of the scenario you're just repeating yourself.
05:58 < Nofaris> lol...
05:59 < gene_> So I can have your computer in my room and use it if I can move it out of your room without your consent
06:00 < kanzure_> What does my consent have to do with anything?
06:00 < Nofaris> It removes a possible threat
06:00 < Nofaris> to his plan
06:00 < Nofaris> Silly
06:01 < kanzure_> Maybe his plan shouldn't be considering stupid threats like that.
06:01 < kanzure_> I mean to say that perhaps you should be able to plan so that threats aren't even possible within the framework.
06:02 < gene_> heh
06:02 < gene_> I can get that tombstone out of your room
06:02 < Nofaris> Some threats cannot be completely eliminated
06:02 < kanzure_> Nofaris: Fuck death.
06:02 < kanzure_> http://fuckdeath.org/
06:03 < Nofaris> LOL
06:03 < Nofaris> BEST WEBSITE EVER
06:03 < Nofaris> <3
06:03 < kanzure_> http://sens.org/
06:03 < kanzure_> http://mprize.org/
06:04 < gene_> no Kanzure I would not like to have sex with death
06:04 < Nofaris> Good websites
06:04 < Nofaris> Already know of them
06:04 < Nofaris> What are you up to kanzure?
06:04 < gene_> just kidding fuck death
06:04 < kanzure_> Nofaris: Hm?
06:04 < kanzure_> Nofaris: Right now?
06:04 < gene_> world domination
06:04 < gene_> that's what we're up to
06:04 < Nofaris> Yes
06:04 < kanzure_> Nofaris: I'm writing up some notes on the superneuron simulator.
06:05 < Nofaris> What is that?
06:05 < kanzure_> A neuron simulator.
06:05 < Nofaris> that is super
06:05 < kanzure_> Meh, I got pretentious when I named it.
06:05 < Nofaris> You named it eh?
06:06 < gene_> you're writing documentation?
06:06 < kanzure_> 'Superneuron'.
06:06 < kanzure_> gene_: Not really.
06:06 < gene_> or code?
06:06 < kanzure_> gene_: It's just some explanation as to why it's a multicompartment differential-equation-like model rather than a simple array-based ANN.
06:06 < kanzure_> Nah, it's not code. Just some pseudocode. For the class.
06:06 < gene_> do you understand diff eq?
06:07 < kanzure_> I'm rusty on partials.
06:07 < gene_> damn
06:07 < gene_> do you dare explain your differential equation
06:09 < kanzure_> It's just some stuff about rates of change of membrane potentials in relation to ion concentrations etc.
06:09 < gene_> damn
06:09 < kanzure_> brb
06:10 < gene_> I've been thinking about writing something like that for e.coli
06:10 < gene_> for simulating chemotaxis
06:11 < gene_> can I see that pseudocode? I am sorta having trouble applying differential equations
06:13 < xp_prg4> kanzure based on what I can tell, building hy3s takes the intel fortran compiler that costs money, is that what your finding?
06:15 < kanzure_> xp_prg4: I haven't looked into compiling hy3s yet.
06:15 < kanzure_> Mostly because I'm still waiting on ahem, a few other things.
06:15 < kanzure_> Like, uh, that script.
06:16 < xp_prg4> well I can't even test the script without hy3s
06:16 < kanzure_> Tell me how you think that's true.
06:16 < kanzure_> What's the goal of the script?
06:16 < kanzure_> What's the output of the script?
06:16 < xp_prg4> because that is the end result, we make a script that makes an sbml file and then it converts to netcdf which then goes to hy3s
06:16 < kanzure_> Uh, so why does that require hy3s?
06:17 < xp_prg4> to make sure it will work
06:17 < kanzure_> Wrong.
06:17 < gene_> can I see that pseudo code?
06:17 < kanzure_> You have the examples in http://heybryan.org/graph/synbioss/tmp/
06:17 < kanzure_> Remember?
06:17 < kanzure_> gene_: Give me a few moments.
06:17 < gene_> did you write the differential equation your self?
06:21 < kanzure_> http://heybryan.org/school/buildingbrains/superneuron.html
06:21 < kanzure_> gene_: There you go.
06:21 < gene_> heh
06:21 < kanzure_> Hrm. That looks like an older version. Oh well.
06:21 < gene_> why even have dendrites
06:22 < kanzure_> It was group work in class, but I had to give them a nudge to understand psuedocode.
06:22 < gene_> when you can have lots of dendrites
06:22 < kanzure_> It was restricted to two dendrites.
06:22 < gene_> or a function that describes dendrite branching
06:22 < kanzure_> Right, that's the Proper Thing to do.
06:23 < gene_> anyway
06:23 < gene_> how do you figure in noise?
06:24 < gene_> real neurons are noisy am I not correct?
06:24 < kanzure_> This is not precise.
06:24 < gene_> due to a whole bunch of things
06:24 < kanzure_> There's some distortion and degradation in amplitude in the axon that is included in the pseudocode there.
06:25 < gene_> would your simulated version of a brain diverge with time with the real version of the brain being simulated
06:25 < gene_> given that both brains are being given equal stimulation
06:26 < kanzure_> Yep, because this is a simplistic neuron, and it can't be configured to become the types of neurons found in a real brain without some serious modification.
06:26 < gene_> I know
06:27 < kanzure_> The mauk.zip stuff doesn't diverge though.
06:27 < gene_> over the course of how long?
06:27 < kanzure_> http://heybryan.org/~bbishop/docs/mauksimzip.zip
06:27 < kanzure_> He sits around in his lab for hours with rabbits strapped up to an oscilloscope.
06:28 < gene_> what about years?
06:28 < kanzure_> His software remains consistent.
06:28 < kanzure_> The rabbit would die by then. ;-)
06:28 < gene_> I know
06:28 < kanzure_> It's open-skull for reading the variables.
06:28 < kanzure_> uh, it might not be open skull. I'm pretty sure it is.
06:28 < gene_> I bet it is
06:29 < gene_> would a simulated version of someone actually be them so to say?
06:29 < kanzure_> What the hell is identity?
06:29 < kanzure_> ;-)
06:30 < gene_> as in would divergence ever occur?
06:30 < kanzure_> Don't you diverge each moment?
06:30 < gene_> ok
06:30 < gene_> now your freaking me out
06:31 < gene_> I mean given the same stimulation would they diverge
06:31 < kanzure_> ?
06:31 < kanzure_> Do you mean any general simulation of a neuron, and then comparing it to a real neuron?
06:31 < kanzure_> Or do you mean a specific neuron simulation that you want to compare to?
06:32 < gene_> I mean specific neuron simulation
06:32 < kanzure_> Which one, then?
06:32 < gene_> no
06:33 < gene_> as in approximates neuron exactly
06:33 < kanzure_> If by definition it's exact, then you've already claimed it's exact
06:33 < kanzure_> If by definition it's only an approximation, then it's by definition just an approximation
06:33 < kanzure_> I am confused, what do you ask?
06:34 < gene_> so if I get my brain scanned in, then have it simulated would it be me?
06:34 < kanzure_> What is "me" though?
06:34 < gene_> that is what I'd like to define
06:34 < Nofaris> It's too vague a conceptual wrapper to define
06:35 < gene_> now this is really freaking me out
06:35 < kanzure_> "Identity" is a folk psych concept. I rank it up (down?) there along with 'money' and 'intelligence'.
06:36 < gene_> I know
06:36 < Nofaris> Money is a folk psych concept?
06:36 < gene_> so then Kanzure, can I have your money?
06:36 < gene_> damn
06:37 < gene_>  I shouldn't think about existentialism stuff
06:37 < kanzure_> Nofaris: The hypothetical list that I was talking about there is not made up of only folkpsych.
06:37 < kanzure_> This isn't existentialism.
06:37 < gene_> I know
06:38  * Nofaris is confused
06:38 < gene_> so the question is am I am who I am from moment to moment?
06:38 < gene_> man
06:38 < Nofaris> You are constantly changing
06:38 < kanzure_> gene_: Try http://heybryan.org/quotes.html for some help.
06:38 < gene_> I really wish they had whole brain maps
06:38 < gene_> I don't what damn quotes
06:39 < kanzure_> The map is not the territory.
06:39 < Nofaris> I like quotes
06:39 < gene_> I want me some fucking data
06:39 < Nofaris> Good quote
06:39 < kanzure_> "Truly, I cannot know what you are. Conscious or not, aware of your existence or not, I cannot know what you are. But you are only you, you are what you are. Isn't this enough?"
06:40 < gene_> SYSTEM ERROR
06:40 < Nofaris> not so good a quote
06:40 < kanzure_> Wrong system.
06:40 < kanzure_> Nofaris: I'm citing it wrong. It's on the page though. Search for "Truly,".
06:41 < Nofaris> Don't worry about it
06:41 < Nofaris> I think I understand what it amounts to
06:41 < kanzure_> And what's that?
06:41 < Nofaris> "If mathematical thinking is defective, where are we to find truth and certitude?"
06:42 < Nofaris> I like this a lot
06:42 < Nofaris> Thank you for the quotes.
06:42 < gene_> now the real question is what is feeling?
06:42 < kanzure_> What is what?
06:42 < Nofaris> chemicals
06:42 < gene_> feeling
06:42 < Nofaris> moving in your brain
06:42 < gene_> yeah
06:42 < gene_> I know that
06:42 < kanzure_> No, answer me this: what is what?
06:43 < kanzure_> (in response to your question)
06:43 < gene_> feeling
06:43 < kanzure_> Yes, but what is that?
06:43 < gene_> you know very well what I am referring to Kanzure
06:43 < gene_> even if it is a folk psychological concept
06:44 < Nofaris> Gene_
06:44 < kanzure_> Heh.
06:44 < Nofaris> What are you referring to?
06:44 < gene_> it's results can be observed
06:44 < kanzure_> The map is not the territory.
06:44 < kanzure_> Results?
06:44 < gene_> yeah
06:45 < gene_> I sense the temperature of an object and can act in response to the temperature
06:45 < kanzure_> "Siren Call of Metaphor: Subverting the proper task of systems neuroscience"
06:46 < gene_> so how am I able to process information from my hands into what I would call a feeling
06:46 < gene_> is said information stored in something like a variable?
06:47 < kanzure_> Not really.
06:47 < gene_> like a variable
06:47 < kanzure_> The mapping between experiences, genotypes and phenotypes is not obvious.
06:47 < gene_> genotypes?
06:47 < kanzure_> Source code.
06:48 < gene_> http://en.wikipedia.org/wiki/Surface_structure
06:48 < gene_> do you mean that?
06:49 < kanzure_> Not really.
06:50 < gene_> so then
06:50 < gene_> how does mri work?
06:50 < gene_> it just images blood right?
06:51 < kanzure_> Magnetic resonance is a nuclear physics phenomena that you really should look into. It's because of the alignment of subatomic particles etc.
06:51 < gene_> ok
06:51 < gene_> so you are looking for rotating magnetic fields
06:51 < kanzure_> SciAm had an article this month about a portable MRI unit.
06:51 < gene_> hmmmm....
06:52 < kanzure_> gene_: Assume identity is wrong. Do you know the alternative?
06:52 < kanzure_> Think of it as a brain teaser.
06:52 < gene_> what is the alt?
06:52 < gene_> ok
06:52 < gene_> so if you introduced small magnetic particles into the brain
06:52 < gene_> you could see where they are?
06:53 < kanzure_> What are you trying to do?
06:53 < gene_> sweet
06:53 < gene_> they use paramagnetic materials as contrast agents
06:54 < gene_> make a super contrast agent
06:54 < gene_> for imaging where neurons are
06:54 < gene_> and when they are firing
06:54 < kanzure_> httP;//heybryan.org/mediawiki/index.php/Neuroimaging
06:54 < kanzure_> Look at EROS.
06:54 < gene_> I have an idea
06:54 < gene_> I don't know if it will work
06:55 < kanzure_> http://heybryan.org/books/mousebrain/ <- "Brain Conqueror" and "Brain Builder", some old stuff I was working on.
06:55 < gene_> especially because it invloves introducing compounds into neurons
06:56 < gene_> there are proteins that are paramagnetic
06:56 < kanzure_> Why do you want to image neurons?
06:56 < gene_> So I can know how I work
06:56 < gene_> that's why
06:57 < kanzure_> Only by writing programs do you learn to program.
06:57 < gene_> indeed
06:57 < kanzure_> "I am program, programmer and that which is programmed." 
06:57 < kanzure_> (quotes.html again)
06:57 < gene_> plus it would be really cool
06:57 < kanzure_> So, imaging isn't enough.
06:57 < gene_> and useful for making back ups
06:57 < kanzure_> Oh, that's certainly true.
06:58 < kanzure_> Not entirely.
06:58 < kanzure_> You can't reconstruct from that information.
06:58 < kanzure_> Anyway, what's important in backups?
06:58 < kanzure_> What information, what characteristics and what functionality?
06:58 < gene_> so what do you need?
06:58 < kanzure_> Many minduploading skinheads think that they want everything, every single detail,
06:59 < kanzure_> they want "exact identity transferance", whatever the hell that means
06:59 < kanzure_> I'm not going for that.
06:59 < kanzure_> I'd rather do what works.
06:59 < gene_> well if you don't capture everything
06:59 < xp_prg4> kanzure__ your going to be so proud of me!
07:00 < gene_> you end up diverging from yourself
07:00 < kanzure_> YOu end up diverging anyway.
07:00 < kanzure_> *You end up diverging anyway.
07:00 < kanzure_> "How do you capture a beautiful bird without killing its spirit?" (also quotes.html)
07:00 < kanzure_> (an answer is found in the Neverness books, btw.)
07:01 < gene_> ok so you have real and simulated system
07:01 < gene_> denoted r and s
07:02 < gene_> initially system r and s start out in the same state
07:02 < kanzure_> How do you know?
07:02 < gene_> given the exact same stimulating
07:02 < gene_> this is a hypothetical case
07:03 < gene_> system s might go down a decision path that results in it receiving different stimulation than system r
07:04 < kanzure_> What's a decision?
07:04 < gene_> ie whether a system looks left or right
07:05 < kanzure_> How do you define left and right in a brain?
07:05 < kanzure_> That makes no sense.
07:05 < gene_> this is a hypothetical situation
07:06 < gene_> if you look right you receive different stimulation than if you looked left resulting a path of changes that leads to more changes
07:07 < gene_> so the question is, are systems r and s the same?
07:07 < kanzure_> What is sameness?
07:07 < gene_> if they diverge no?
07:08 < gene_> going down the same decision path
07:08 < kanzure_>  Didn't you just answer your own question then?
07:08 < gene_> performing all the same actions in the same order
07:08 < gene_> as the other system
07:12 < gene_> if the systems perform different actions they receive different stimulus which results in different actions
07:13 < gene_> ERROR: STUCK IN INFINITE LOOP
07:13 < kanzure_> xp_prg4: are you ever going to tell me or not?
07:14 < xp_prg4> I have roughly 50% duplication of generates sbmlfile of that created with designer
07:14 < xp_prg4> I clearly understand what they are doing
07:14 < kanzure_> What's the other 50%?
07:14 < xp_prg4> just still coding it, wat me to send you the comparison files?
07:14 < kanzure_> Sure.
07:15 < xp_prg4> ok
07:17 < xp_prg4> sent
07:18 < xp_prg4> look at lacl in particular
07:32 < xp_prg4> added reactants!
07:32 < xp_prg4> want to see it now kazure__ ?
07:33 < kanzure_> Sure.
07:34 < xp_prg4> sent
07:38 < xp_prg4> added products
07:38 < kanzure_> Are you allowing for a variable number of these elements per the HTML forms did? (The dynamically generated forms with the help of the PHP scripting.)
07:43 < xp_prg4> yes they are stored as variables
07:44 < kanzure_> No, a variable number of them.
07:44 < xp_prg4> yes
07:44 < xp_prg4> that is not difficult
07:44 < xp_prg4> this is actually exremely easy
07:44 < kanzure_> I know.
07:44 < kanzure_> I wasn't sure if you were doing it though.
07:45 < kanzure_> If you're doing the parameter version, then it's simply a pre-specified number in one instance, or if the STDIN version then that's the simple ask-if-the-user-wants-to-do-blah version.
07:45 < xp_prg4> just added Reactions
07:45 < xp_prg4> well it is a little late, I must go to bed
07:46 -!- xp_prg4 is now known as xp_bed
10:14 < fenn> "if you patent something you have to sell it" <- wrong
10:15 < UtopiahGHML> lots of patents are defensive
13:59 < UtopiahGHML> 01:03:00 -=>  http://quicksilverscreen.com/watch?video=52571
14:00 < UtopiahGHML> (little part on Citizen/P2P R&D as "Politics" from  Zeitgeist Addendum)
15:10 < willPow3r> http://sandiego.craigslist.org/csd/sci/900879701.html
15:12 < willPow3r> too bad i dont have any of those quals
15:15 < willPow3r> or even a Ph.D. that would be nice.
16:06 < kanzure_> UtopiahGHML: I read "CItizen/P2P R&D" as "Citizen-P2P Radio"
16:06 < kanzure_> Technically there's enough content to do a radio show.
16:06 < kanzure_> webcast, I mean.
21:41 < UtopiahGHML> faceface: Is IT ready for the Dreaded DNA Data Deluge? by Andras Pellionisz http://www.youtube.com/watch?v=WJMFuc75V_w
23:13 < kanzure-_> http://heybryan.org/~bbishop/docs/neuro/Design_of_a_wearable_ultrasound_system.pdf <- See pg 44. 
23:13 < kanzure-_> fig 23
23:14 < kanzure-_> also pg 66 fig 44
23:23 < fenn> now there's a science fair winner
23:27 < fenn> haha 'make the embedded computer more "medical" in appearance"
23:29 < fenn> x86 processors generate so much heat that they're hard to waterproof
23:35 < fenn> one would think that embedded computers would take this into account, such that one could simply bolt the board to a suitable heatsink
23:42 < kanzure-_> http://heybryan.org/~bbishop/docs/neuro/Auditory responses in cats produced by pulsed ultrasound.pdf 
23:42 < kanzure-_> making cats hear things :)
23:43 < kanzure-_> if you can figure out the mapping between which ultrasound frequencies lead to which "phantom sounds" in the auditory nerve, you have another science faire winner.
23:43 < kanzure-_> *faire
23:43 < kanzure-_> **fair
23:47 < kanzure-_> Ok, so Ms. Majestic is recommending 600 to 700 kHz. 
23:47 < kanzure-_> This one does 12 to 50. http://web.archive.org/web/20060602085215/circuitos.cl.tripod.com/schem/r72.gif 
23:47 < kanzure-_> I'm not sure which variables would have to be modified.
23:47 < kanzure-_> Should I just go get a few variable-capacitors and variable resistors and plug them up to that 555 timer?
23:48 < kanzure-_> I wouldn't be doing any of the waveforms and sinewave generation that the Ultrasound_brain.pdf paper does, but I have seen schematics before showing sinewave generators and other functions.
23:49 < kanzure-_> http://www.reconnsworld.com/audio_tonegenerate.html <- suggests using an ultrasonic transducer for frequencies over 30 kHz. :-/
23:53 < fenn> 600-700kHz is doable with hardware PWM on an AVR
23:54 < fenn> uh i think :)
23:54 < kanzure-_> While technically a dog whistle is an ultrasonic transducer that converts mechanical energy in the form of air pressure into ultrasonic sound waves,
23:54 < kanzure-_> PWM?
23:54 < fenn> there are two pins which toggle based on the contents of a register and a clock w/divider
23:55 < fenn> so you can run a program and not be constantly worrying about i/o
23:55 < kanzure-_> http://www.explorecircuits.com/circuit/schematic/3.jpg and its explanation http://www.explorecircuits.com/circuit/cir_ultrasonic_transmitter_receiver.htm
23:55 < kanzure-_> hm
23:55 < fenn> 555 might not be fast enough.. dunno
23:56 < kanzure-_> hrm, these schematics say 40 kHz speakers.
23:56 < kanzure-_> blah
23:56 < fenn> yeah i think you need piezo transducers
23:56 < kanzure-_> There should be a simple formula for how the capacitors and resistors need to change with respect to the expected frequency.
23:56 < fenn> it's not that simple
23:57 < kanzure-_> I don't know anything about piezo transducers. Is there a circuit component I can pick up at Radioshack?
23:57 < fenn> the wires in the circuit act as inductors and capacitors (and radio antennae)
23:57 < fenn> forget radioshack
23:57 < fenn> pretend it doesn't exist
23:57 < kanzure-_> I don't have many other options :)
23:57 < kanzure-_> I suppose I can order a few things, but I was hoping to pick up a bag of goodies tonight.
23:58 < fenn> unless you have a real electronics company nearby, it's mail order
23:58 < fenn> jameco is probably easiest to figure out
23:58 < kanzure-_> mouser/digikey/jameco, right
23:58 < kanzure-_> digikey can burn in hell, yes yes, I know
23:58 < kanzure-_> anyway
23:58 < fenn> digikey is actually pretty good, but it's hard to sort through the 9 million options
23:59 < kanzure-_> I'm still not understanding. If I picked up a piezo transducer, let's call it part XYZ, then what? How do I know which capacitors and resistors to use?
23:59 < kanzure-_> I suppose I can go with variable resistors/capacitors and just keep it within the ranges I'm seeing on these schematics?
23:59 < fenn> ur... uh.. the 555 stuff?