--- Day changed Thu Nov 20 2008
02:39 < kanzure> Heh.
02:39 < kanzure> opencyc, whee I have those guys local
02:39 < kanzure> so I just got back from the nextgen biofuel/algae conference
02:42 < drazak> nice
02:42 < drazak> kanzure: have you ever watched ReGenesis?
02:43 < kanzure> No, but bkero has.
02:44 < kanzure> So for some reason these people expect to scale up to 30 million barrells of biofuel from algae per day in 20 years.
02:48 < drazak> well, if we can make fuel that way, why not
02:49 < kanzure> because it's not as easy as just saying "ok, 30 million barrels please" - the scaling factor there is something close to ridiculous
02:49 < kanzure> but 
02:49 < kanzure> for what it's worth, I went back to an 'old' idea that I had been turning around while listening to these CEOs of Exxon talk about random stuff
02:49 < kanzure> it would be interesting to scale the system with the growth of algae itself.
02:50 < fenn> it would be interesting
02:50 < kanzure> oh
02:50 < kanzure> excuse me, got distracted
02:50 < kanzure> uh, so if you can grow the apparatuses to scale with the bloom cycles
02:50 < kanzure> so that you organically scale
02:51 < kanzure> such as plastics
02:51 < fenn> or vanadium
02:51 < kanzure> anyway, I think I'm going to get to use the cnc machine from the machine shop.
02:51 < kanzure> fenn, suggestions on 3D models to gcode?
02:51 < fenn> what format
02:52 < kanzure> haha
02:52 < kanzure> no
02:52 < fenn> hmm
02:52 < kanzure> I have no idea, haven't looked into it much yet
02:52 < fenn> well if it's just 2.5d, uh, image-to-gcode i guess
02:52 < fenn> blender has a mesh to heightmap script
02:52 < fenn> probably not what you wanted to hear
02:52 < kanzure> technically I haven't even ran some optimizers on shape for gene's membraneless filter but supposedly on Friday I'm meeting with some CFD "expert" to talk about that
02:53 < kanzure> image-to-gcode? 
02:53 < fenn> it's a script that comes with emc
02:53 < kanzure> isn't there certain cutting directions that have to be made or something
02:53 < kanzure> um
02:53 < fenn> raster scan
02:53 < kanzure> the blender thing?
02:53 < fenn> yeah, there's lots of "shoulds" and "coulds" but we dont have any cool software worth mentioning
02:53 < kanzure> raster scan of what data (file type in particular)?
02:53 < fenn> any image readably by imlib
02:53 < kanzure> hrm. that's unfortunate.
02:53 < kanzure> I wonder what the Austin Robot Group ended up using for that
02:54 < fenn> or python-imaging or whatever it's called
02:54 < kanzure> they eventually had an ubuntu setup with an interface to their Fireball 'cnc' 
02:54 < kanzure> oh
02:54 < fenn> fireball.. isnt that a hard disk?
02:54 < kanzure> maybe they were just doing 2D images too
02:54 < kanzure> technically they were cutting chunks out of old CDs
02:54 < fenn> fascinating
02:54 < kanzure> yes, but fireball apparently is also a desktop milling machine
02:55 < kanzure> a $2k machine thingy that I've mentioned before
02:55 < fenn> mdf router
02:55 < fenn> oh it's probotix
02:55 < kanzure> mdf?
02:55  * kanzure is not at his search engine at the moment
02:55 < fenn> medium density fiberboard
02:56 < kanzure> yes, probotix sounds familiar.
02:56 < fenn> its that frozen gorilla snot mixed with sawdust you see in cabinets
02:56 < fenn> they paint it black so you dont notice
02:57 < fenn> hah "PLEASE NOTE: The shopping cart is currently not able to handle a package this large. 
02:57 < fenn> the internet never ceases to amaze me
03:02 < gene> kanzure you got any arguments against dualism?
03:06 < kanzure> the brain is the brain.
03:12 < kanzure> Neat, google.org has been updated.
03:16 < kanzure_> http://groups.google.com/group/openmanufacturing/msg/4a37dc2d82c8d46d?dmode=source
03:16 < kanzure_> Oh god.
03:17 < kanzure_> Please killfile?
03:17 < kanzure_> fenn: what do I do
03:18 < kanzure> I feel a rant coming on.
03:27 < fenn> "But is there actually a consistent way" -> "yes"
03:28 < kanzure> for ridiculously specialized, one-time things, I'm sure you can argue that there's no format that you can use, but then you're just being an ass for choosing the one possibility that breaks it, the one very rare possibility I might add ..
03:29 < kanzure> Fuck it, if you have to get down to it and record exact movements of humans via grid tracking and wearing funny suits, then so be it, but I'll be damned if you can't capture information about how somebody makes this supposedly highly arbitrary thingy.
03:31 < gene> So kanzure could you disprove dualism, in argument with room mate
03:32 < gene> you aren't taking that despicable philosophy class are you Kanzure?
03:32 < kanzure> At the very least does he agree that the brain is then the conduit by which the mind and physical reality communicate?
03:32 < kanzure> I'm taking Building Brains, which has a philosophical component to it.
03:32 < gene> lol dunno
03:33 < kanzure> dualism v. physicalism v. computationalisms, connectionist approaches, control theorists, all sorts of wacky things, plus neurophysiology, Hodgkin-Huxley models, etc.
03:33 < gene> and this: http://www.physorg.com/news146319784.html
03:33 < kanzure> gene: If he at least agrees that the brain is the conduit then you might be able to catch him on a sort of "infection theory of reality" -- if it must interface with reality, reality takes over and there must exist *something*
03:33 < kanzure> otherwise he's just bullshitting.
03:34 < kanzure> the news article on connectionism?
03:34 < gene> yeah
03:34 < gene> this guy proposes a new one that says the brain might be a top down system
03:36 < kanzure> How is that new? Top-down, bottom-up, feedback and connectional approaches have been explored often.
03:36 < gene> lol dunno
03:36 < kanzure> Bleh. The eurodance channel on di.fm is depressing tonight. /me switches
03:37 < gene> eurodance?
03:37 < gene> btw got anymore scimusic on hb?
03:37 < gene> i mean scifi music
03:37 < gene> do you want more?
03:38 < gene> I got me some IP free stuff
03:38 < kanzure> yes, I have some scifi stuff, like Ayreon and Space One (some space metal), and filk
03:38 < kanzure> Creative commons?
03:39 < gene> lol maybe
03:39 < gene> http://www.tettix.net/archive.html
03:39 < gene> got some of this
03:39 < gene> and videogame music
03:40 < kanzure> yeah I have a large archive of 8 bit music if you want a link
03:40  * kanzure looks
03:40 < gene> woo chiptunes
03:40 < gene> the stuff I have isn't really 8 bit
03:40 < gene> but it did have an interesting compression algorithm
03:41 < kanzure_> http://heybryan.org/books/music/2008-06-01/
03:41 < kanzure> http://heybryan.org/books/music/2008-06-01/
03:42 < gene> lol /books/
03:42 < gene> oh yeah
03:42 < gene> that's right
03:42 < gene> I can't download shit
03:43 < gene> odd
03:43 < gene> I can open gifs
03:43 < gene> but not mp3s
03:43 < gene> OH SHIT!
03:44 < gene> is that 8 bit stuff CC?
03:44 < gene> I might be being watched
03:45 < gene> by the RIAA!
03:45 < gene> or firefox has an error
03:47 < gene> firefox has an error
03:49 < gene> I have to use IE
03:51 < fenn> haruhi suzumiya is pretty awesome so far
03:53 < kanzure> hulu?
03:53 < kanzure> on hulu?
03:55 < gene> heh
03:55 < fenn> hooloolooloolooloooo
03:55 < gene> Did I get you addicted fenn?
03:55 < gene> Sub or dub?
03:55 < fenn> both :\
03:55 < fenn> no japanese audio tho
03:55 < gene> hehehe
03:56 < fenn> and i cant turn off the subtitles
03:56 < gene> subs are better
03:56 < gene> like for instance explaining japanese similes
03:56 < gene> heh
03:56 < gene> Haruhi
03:56 < gene> how far have you gotten?
03:57 < gene> to the point that you figure out that 
03:57 < fenn> just after the first computer battle-whatsit
03:57 < gene> computer battle or information battle?
03:58 < fenn> uh. program battle i spose
03:58 < gene> oh yeah that one
03:58 < fenn> nice effects
03:58 < gene> are you watching them in chronological order
03:59 < fenn> i watched 00 first
03:59 < fenn> hmm sorry for temporarily anime-izing the channel
03:59 < gene> it's fine
03:59 < gene> well there are several different sequences 
04:00 < gene> there's the dvd sequence, broadcast sequence, and chronological sequence
04:00 < fenn> literal translation = "spring day disenheartened palace"
04:00 < gene> only chronological sequence makes sense
04:00 < gene> hmm...
04:00 < fenn> well i'm afraid i dont know the difference at this point
04:01 < gene> so you know that Yuki is an alien right?
04:01 < fenn> i knew that before i downloaded it
04:01 < gene> bah
04:01 < gene> you read the plot summary on wikipedia didn't you?
04:01 < fenn> i had to see what you were ranting about
04:02 < gene> you might call yuki post- whatever so to say
04:02 < fenn> erm, at least that's how i remember it.. the logs disagree with my memories however
04:03 < gene> oh wait kanzure is probably hearing the spoilers too
04:03 < kanzure> I also read the wikipedia article, fwiw.
04:03 < gene> heh
04:04 < gene> I think I did too
04:04 < gene> before I saw it too
04:04 < gene> but not the whole plot summary
04:04 < ybit> what movie do you all speak of?
04:04 < gene> not movie
04:04 < ybit> book?
04:04 < gene> animu
04:04 < ybit> play?
04:04 < ybit> animu, wtf
04:04 < gene> anime
04:04 < ybit> aha :)
04:05 < gene> The Melancholy of Haruhi Suzumiya
04:05 < ybit> arigatou
04:05 < gene> huh?
04:05 < ybit> thank you
04:06 < gene> Now hopefully Spielberg won't make a live action movie out of Haruhi
04:06  * fenn scowls at logs
04:07 < gene> as he is trying to do with Ghost In The Shell
04:07 < gene> logs are quite useful to burn fenn
04:08 < gene> Anyway sorry for becoming meme typhoid mary, all of you are probably going to get infected and becoming Haruhi fans
04:08 < fenn> bah, how could the phrase "artificial human" have never been uttered in this channel
04:09 < gene> why are you asking fenn?
04:09 < gene> battle angel alita?
04:09 < fenn> i'm drawing a lot of blank queries that's all
04:09 < gene> trying to do what paracelsus tried to do?
04:09 < fenn> uh, no?
04:10 < gene> make replicants?
04:10 < gene> start a clone farm?
04:10 < gene> I hear clone meat is tasty
04:10 < fenn> dead clones :(
04:10 < fenn> i for one only suck the blood of vegetables
04:11 < fenn> it's necessary, for now
04:11 < gene> why?
04:11 < fenn> sigh.. definitions of 'selfhood' and all that
04:12 < gene> just kidding about clone meat
04:12 < gene> but c'mon real meat is good
04:12 < fenn> meh.. meat on a stick is probably not going to happen any time soon (whereas clones are real)
04:12 < gene> like from cows and all
04:13 < fenn> not that i want to eat tissue culture either
04:13 < kanzure> meat on a stick is already happening though
04:13 < kanzure> it's not quite the same type of meat that people who eat meat come to expect
04:14 < gene> yeah no kidding kanzure
04:14 < fenn> well, cloned cows are out running around in the dirt
04:14 < fenn> but tissue culture requires buttloads of antibiotics and special little plastic flasks that need to be decanted and babied constantly
04:14 < gene> I don't like to eat necrotic tissue
04:15 < fenn> necrotic tissue?
04:15 < gene> necrotic core = gross!
04:15 < gene> in tissue culture
04:15 < gene> you don't have blood vessels 
04:15 < gene> most of the time
04:15 < fenn> either keep the thickness under the diffusion limit  or figure out how to grow vessels
04:15 < fenn> cancer figures it out all the time
04:16 < gene> so what happens when the tissue grows past diffusion limit, is a necrotic core develops
04:16 < fenn> you dissolve it before that happens
04:16 < fenn> then split into two or more containers
04:16 < fenn> i suppose you could do some kind of continuous moebius strip process if you were clever
04:17 < gene> well you still have a problem
04:17 < gene> much of the meat experience involves having fibrous meat
04:17 < gene> meat that's been used
04:17 < fenn> ok well i'm not going to get into that
04:18 < gene> yeah
04:18 < fenn> ADM already solved it with TVP if you ask me
04:18 < fenn> google for enlightenment
04:18 < gene> that's what makes cultured meat not so succesful
04:18 < kanzure> 'textured vegitable protein'
04:18 < kanzure> vegetable
04:19 < gene> hey would you eat algae fenn?
04:19 < gene> it's very nutrional
04:21 < fenn> i have it for breakfast sometimes, but the good japanese stuff is rather expensive 
04:22 < fenn> oh, and i always wanted to make spirulina chocolate
04:23 < gene> no different species
04:23 < gene> not spirulina
04:23 < gene> Kanzure we really need to try cooking the algae
04:23 < fenn> well i'm not going to do a champion worldwide algae tasting survey to find out which ones are good and which will kill you
04:24  * fenn mumbles about kainic acid
04:25 < kanzure> gene: Do you mean "just add an open flame" ?
04:26 < gene> don't worry fenn I'm sure you have a great toxin resistance and would make a good test subject
04:26 < gene> No I mean cook
04:26 < kanzure> There's a few different variations that still have to be tested: set the algae pellets on fire, flame a test tube from underneath, etc. but we would need a mechanism for measuring smoke volume or whatever.
04:26 < gene> as in prepare in a meal
04:26 < gene> maybe we could try making it into little green strips
04:26 < fenn> i hear you can squeeze it out of a pasta press into noodles
04:26 < fenn> but they probably just dissolve into water if you try to cook them
04:27 < gene> http://en.wikipedia.org/wiki/Image:SolyentGreen28d.png
04:27 < fenn> ice-cream-like-substance might be worth pursuing
04:27 < gene> add some artificial flavoring and it'll taste like just about anything
04:31 < gene> even chicken
04:42 < gene> or saunteed onions
07:24  * ybit server may be up this weekend ^.^
07:24 < ybit> the freecycle guy's processor worked just fine
07:24 < ybit> but i'm too tired to mess w/ it tonight
07:24 < ybit> anyone used nginx?
07:24 < ybit> thinking about using it
07:25 < ybit> i will atleast try it out
08:11 < kanzure> So if I was going to fail all of my classes anyway, is this good excuse for not showing up?
08:29 < kanzure_> http://heybryan.org/books/Biology/Ultrasound-mediated%20DNA%20transfer%20for%20bacteria.pdf  40 kHz ultrasonoporation for bacterial transformation. or just go look at the old acinetobacter links that I was throwing around in here. I've lost the page on my server, of course.
08:30 < kanzure_> while looking for that lost page - http://heybryan.org/Lain's-Room-001.jpg
08:36 < fenn> is that a hemi?
08:40 < kanzure> hemi?
08:43 < fenn> looks like a diesel generator the more i look at it
08:43 < fenn> with a water muffler.. that can't be healthy indoors
08:44 < fenn> see it's mounted on vibration isolating springs
08:47 < kanzure> yes, I see now
08:48 < fenn> god bless the usa: http://www.uberreview.com/wp-content/uploads/2006/09/hemi trike.jpg
08:48 < fenn> http://www.uberreview.com/wp-content/uploads/2006/09/hemi%20trike.jpg for you clickers
08:49 < kanzure> you type?
08:49 < fenn> well i drag the cursor instead of clicking
08:49 < fenn> so it gets spaces too
08:55 < kanzure> heard a number yesterday: "algae is 3% efficient as just using a pv cell off the shelf today"
08:55 < kanzure> which is weird because I always hear photovoltaics compared to photosynthesis productiity.
09:09 < kanzure_> Harmful Phytoplankton Section, Harmful Algal Bloom Division, National Research Institute of Fisheries and Environment of Inland Sea 
09:09 < kanzure_> Keizo Nagasaki
09:09 < kanzure_> heh, cool department title
09:12 < fenn> silly number.. they neglect the fact that you're carpeting vast swaths of land with essentially free 3% efficient "solar panels"
09:13 < fenn> based on electrical conversion efficiency alone, a stirling engine or OTEC would be way better than PV panels
09:15 < fenn> ending to haruhi suzumiya makes me want to go kill myself
09:17 < kanzure> any quick ideas on directed viral evolution?
09:18 < kanzure> directed as in, targetted
09:18 < kanzure> molecular recognition sites I guess
09:18 < kanzure> I think this is what the recombinant shotgun studies do, right?
09:18  * fenn shrugs helplessly
09:18 < kanzure> Generate a random pool of mutations of types of proteins for the viruses to try out as their recognizer complexes, and then 
09:19 < kanzure> bah..
09:19 < fenn> off to cry myself to sleep...
14:34 < kanzure_> http://www.picturetrail.com/sfx/album/view/21008688 convergence08 photos
14:37 < UtopiahGHML> anybody good with history of science? Im looking for a study over time of the evolution of tools used ( notebook and all the cognitive supports, notation systems, etc... )
14:37 < UtopiahGHML> (its the the history of the computer museum that made me think again about this)
14:56 < kanzure> yes
14:56 < kanzure> go find robothistory or robotstory
14:56 < kanzure> uh
14:56 < kanzure> I suspect it's robothistory. The guy claims to have had the first blog ever.
15:01 < kanzure> robotknowledge ?
15:02 < kanzure> Huh. Well this isn't bologna! "Asim Roy", Mr. Control Theory himself, famous for that physorg article that gene_ linked to yesterday, has posted an advertisement of his work on the comp-neuro mailing list. Big fucking surprise.
21:24 < gene> http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRT-4TYRF97-6-3&_cdi=6243&_user=108429&_coverDate=11%2F20%2F2008&_sk=%23TOC%236243%239999%23999999999%2399999%23FLA%23display%23Articles_in_Press%23tagged%23Volume%23first%3D0%23date%23(20_November_2008)%23&view=c&_gw=y&wchp=dGLbVtb-zSkWb&md5=863cc203cf5795bafac37f656ad150d7&ie=/sdarticle.pdf
21:24 < gene> AN HUEG PROTIST
21:25 < gene> it rolls
21:33 < kanzure> gene: Did you see my email about viral lysis of algae?
21:33 < kanzure> http://heybryan.org/books/bioreactor/lysis/
21:33 < gene> damn
21:33 < gene> no
21:33 < kanzure> There's a few papers in there that are ok.
21:33 < gene> I was about to suggest viral lysis to sata last night
21:33 < gene> genetically modded viruses?
21:33 < kanzure> Chlorella has the best studied lytic virus.
21:34 < kanzure> yeah, I emailed him about it at 4 am so he knows.
21:34 < kanzure> well
21:34 < kanzure> that's the thing,
21:34 < kanzure> there's two ways to do this if we wanted to stick with neochloris
21:34 < kanzure> 1) modify the organism to express the recognition molecules
21:34 < kanzure> 2) modify the virus via 'directed evolution', a way of doing bio experiments.
21:35 < kanzure> #2 is more likely if the virus works within the family of algae
21:35 < kanzure> *more likely to work
21:35 < kanzure> I went through the full list of algae that we have from the packet
21:35 < kanzure> and there's PBCV-1, CsNIV, PCMV.
21:36 < kanzure> gene: That's not how it works.
21:36 < kanzure> gene: You get a sample of the viral population that is 'doing well' or something. Uh. Hm.
21:36 < gene> yeah
21:36 < gene> guess we might get to do some genuine biohacking
21:36 < kanzure> there's a way of doing this with crossover
21:37 < kanzure> mutagenesis+crossover in the search query
21:37 < kanzure> yeah, I don't know why sata tends to be opposed to that
21:37 < kanzure> he's already doing algae+insulin, so why not this? etc.
21:37 < kanzure> (the "let the lipid leak out of the membrane" method would be neat, but I don't know of any organism already doing this)
21:38 < gene> well how about we make the virus magnetic
21:38 < gene> oh lysis
21:38 < gene> that's right
21:38 < gene> ok
21:39 < gene> I didn't get your email
21:39 < kanzure> and then to filter them out, if the membraneless filter works, it would be basically the same physics.
21:39 < kanzure> uhm, well, I just told you everything. I gave him that list of 3 good algae viruses
21:39 < kanzure> and that link 
21:39 < kanzure> yay sleep deprivation
21:39 < kanzure> btw, the CryoFeast is December 7, not on thanksgiving
21:39 < kanzure> can you make it?
21:39 < gene> well we might goto saudia arabia and go virus hunting
21:40 < gene> lol maybe
21:40 < kanzure> you remember how you wanted me to do a student transhumanist group?
21:40 < kanzure> the CryoFeast people want me to do it too
21:40 < kanzure> so we're going to talk about that.
21:40 < gene> hey you got anything that infects volvox?
21:40 < UtopiahGHML> any progress regarding the origins of viruses ?
21:41 < kanzure> volvox? is that a pokemon?
21:41 < kanzure> volpix. Nevermind.
21:41 < gene> no
21:41 < gene> but it could be one
21:41 < kanzure> gene: yes
21:41 < gene> found one
21:41 < kanzure> gene: Volvox carteri osser virus, VcaOssV
21:42 < gene> yeah
21:42 < kanzure> VcaOssV :)
21:42 < gene> excellent
21:42 < kanzure> spherical colonies?
21:42 < gene> volvox is in the same family as Neochloris
21:42 < gene> yeah cool huh?
21:43 < kanzure> utex# LB 2905
21:43 < gene> algae?
21:44 < kanzure> yep
21:44 < gene> now if could get some sick algae
21:44 < kanzure> you think sick algae has a viral infection?
21:44 < gene> hey didn't venter sequence a whole bunch of ocean virus
21:45 < gene> es
21:45 < kanzure> yeah, Sorcerer 2
21:45 < kanzure_> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2186209
21:45 < gene> the heybryan lysis page doesn't work
21:45 < kanzure> uh
21:46 < kanzure> oh
21:46 < kanzure> stupid me
21:46 < kanzure> http://heybryan.org/bioreactor/lysis/
21:47 < gene> augh
21:47 < gene> aureococcus isn't very related
21:48 < kanzure> it's ok, VcaOssV infects volvox.
21:48 < gene> indeed
21:48 < kanzure> also, PBCV-1 does chlorella, CsNIV does cylindrotheca, PCMV does phaeodactylum tricornutum.
21:50 < gene> chlorella is more closely related
21:50 < kanzure> than volvox?
21:52 < gene> i believe so
21:52 < gene> http://en.wikipedia.org/wiki/Chlorococcaceae
21:53 < kanzure> Flora -> Chlorophyta -> Trebouxiophyceae -> Chlorellales -> Chlorellaceae -> Chlorella
21:53 < kanzure> Plantae -> Chlorophyta -> Chlorophyceae -> Volvocales -> Volvocaceae -> Volvox
21:54 < gene> odd
21:54 < gene> http://en.wikipedia.org/wiki/Chlorococcaceae
21:54 < kanzure> Plantae -> Chlorophyta -> Chlorophyceae -> Chlorococcales -> Chlorococcaceae -> Neochloris
21:54 < kanzure> I don't think this is a family purely classified due to lipid content.
21:55 < gene> I know
21:55 < kanzure> http://algaebase.org/
21:57 < gene> ok
21:59 < gene> So how much do we know about neochloris?
21:59 < kanzure> We know it's alive.
21:59 < gene> ok
21:59 < kanzure> Does that count?
21:59 < gene> yeah
21:59 < kanzure> I don't even think we have a life cycle phase plot thing.
22:00 < kanzure> Maybe John has something cooking on that..
22:00 < gene> ugh
22:01 < gene> has it been sequenced?
22:01 < kanzure> No.
22:01 < gene> yes it has
22:01 < gene> partially
22:01 < kanzure> But we can splice in a marker to express on the membrane, I think.
22:02 < kanzure> link?
22:02 < gene> http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&cmd=search&term=neochloris%20oleoabundans
22:02 < kanzure> Excellent.
22:02 < kanzure> Good way to be wwrong.
22:02 < kanzure> *wrong.
22:02 < gene> it's not much
22:03 < gene> no membrane proteins
22:03 < gene> sequenced at least
22:05 < gene> so we need us a sequencer....
22:06 < kanzure> Doesn't matter, we can still splice in alternative markers for the membrane.
22:06 < kanzure> Although an excuse to use a sequencer is always nice.
22:07 < gene> you need to know the source code before you can hack it
22:07 < kanzure> Heh. Not really.
22:07 < gene> ok
22:07 < kanzure> http://heybryan.org/genetic-circuits.html
22:07 < kanzure> Look at the bottom.
22:07 < gene> I am not a programmer I wouldn't know
22:07 < kanzure> That's the famous oxytocin circuit.
22:07 < kanzure> rawr
22:07 < kanzure> Do more programming.
22:07 < gene> guess that just leaves directed evolution
22:07 < kanzure> This isn't quite the same as programming though. 
22:07 < kanzure> Basically we can splice in the new genes somewhere in the genome
22:08 < gene> lol yeah
22:08 < kanzure> now, I'm not actually sure how the virus recognition stuff works
22:08 < kanzure> http://heybryan.org/books/Biology/
22:08 < kanzure> the 700 MB Biology book in there is a good one on this topic
22:08 < kanzure> the Campbell book
22:08 < gene> what is virus recognition?
22:08 < kanzure> I think what they do is have endonucleases that the virus expresses
22:08 < gene> ok
22:08 < kanzure> and this splices up the DNA of the algae, and then the virus inserts its genes there or something
22:09 < kanzure> well
22:09 < kanzure> there are molecules on the surface of the cells
22:09 < gene> ok
22:09 < kanzure> and usually infecting agents recognize these based off of shape fitting
22:09 < gene> does it matter kanzure?
22:09 < kanzure> kind of like receptor sites on dendrites
22:09 < kanzure> huh? yeah, 
22:09 < kanzure> if the virus doesn't infect neochloris, we have to make sure it does
22:09 < gene> eventually you might get a mutation that from something similar 
22:09 < gene> get it to jump species
22:10 < kanzure> but you have to have the algae that it infects in the first place.
22:10 < gene> we could go on a vacation to saudia arabia find it's native habitat
22:11 < gene> and hunt viruses
22:11 < kanzure> let's start by trying out the volvox virus.
22:11 < gene> ok
22:11 < gene> damn if we could only find surface proteins
22:12 < kanzure> well
22:12 < kanzure> I should go read the book for a sec
22:12 < kanzure> I'm pretty sure that I'm completely wrong and viruses aren't recognizing surfaces
22:13  * kanzure checks
22:13 < kanzure> I guess some use ATP so they must have some energetic process
22:13 < gene> http://botany.natur.cuni.cz/algo/CAUP/H2701_Neochloris_aquatica.htm
22:13 < gene> heh
22:14 < gene> locality, sides of a small aquarium
22:14 < kanzure> Indiana?
22:14 < kanzure> we have an agent there
22:14 < gene> huh?
22:15 < kanzure> also, why don't our neochloris look that awesome? :(
22:15  * fenn lurks
22:15 < gene> because they're different
22:15 < kanzure> under the scope, ours don't really look like some on the foreground and some on the background
22:15 < kanzure> meh
22:16 < gene> damn where the heck does neochloris live?
22:16 < fenn> aquariums
22:16 < gene> besides the sides of an aquarium
22:16 < fenn> probably tropical rivers and ponds
22:17 < kanzure> want geocoords?
22:17 < gene> yeah
22:17 < gene> it's like in saudia arabia or something
22:17 < gene> sand
22:17 < kanzure> here's like
22:17 < kanzure> one pond
22:17 < fenn> you just want to go to saudi arabia
22:17 < kanzure> in saudia arabia
22:17 < kanzure> *there's like one pond in saudia arabia
22:17 < kanzure> can't be that hard to find, right?
22:17 < kanzure> hehe
22:17 < fenn> google maps
22:17 < fenn> "pond in saudia arabia"
22:17 < gene> they isolated it from sand
22:18 < fenn> that doesnt mean it grows in sand does it?
22:18 < kanzure> "google can't find 'pond in saudia arabia'. sorry."
22:18 < gene> sand
22:18 < gene> it's from sand
22:19 < kanzure> sand at the bottom of a pond
22:19 < gene> Chantanachat, S. & Bold, H.C. (1962). Phycological studies. II. Some algae from arid soils. University of Texas Publications 6218: 1-74.
22:19 < gene> some algae from arid soils
22:19 < gene> real enthusiastic name for a study
22:20 < kanzure> hm
22:20 < kanzure> so in animals, viruses have glycoprotein spikes
22:21 < kanzure> which bind to the molecules on the surface of the host target
22:21 < kanzure> guess this might be sort of specific.
22:21 < gene> wait a minute you seriously don't know how viruses work?
22:21 < gene> they imitate stuff going into the cell
22:21 < fenn> no they dont
22:22  * fenn challenges gene to a duel
22:22 < gene> not now fenn
22:22 < kanzure> I do know how viruses work, I didn't remember whether or not they are specific to a molecular surface recognition thingy :)
22:22 < gene> fairly specific
22:22 < gene> cell specific
22:22 < gene> in us at least
22:23 < gene> well I got to go
22:25 < gene> in the mean time contemplate this:
22:25 < gene> http://timpanogos.wordpress.com/2007/11/19/oceans-white-with-foam-mate/
22:25 < gene> and viruses
22:25 < gene> and why they might relate
22:25 < gene> heheheheh
22:31 < gene> btw who is John Grigg?
22:31 < kanzure> Transhumanist.
22:32 < kanzure> Participates on the extropy mailing list.
22:32 < gene> rTMS?
22:32 < gene> anything interesting?
22:32 < kanzure> Huh? I don't think Grigg does rTMS. 
22:32 < kanzure> I don't know much about him.
22:32 < gene> ok
22:32 < kanzure> He likes to talk about Jupiter brains :-)
22:35 < gene> well then
22:35 < gene> atmospheric intelligences?
22:35 < kanzure> Why, what brought this up?
22:35 < fenn> jupiter brain != some floating cloud alien on jupiter
22:35 < gene> or brains the size of jupiter?
22:36 < fenn> that's the idea
22:36 < gene> heh
22:36 < fenn> realistically they're computers, but somehow the name "brain" stuck
22:36 < kanzure> sometimes it also refers to the idea of converting jupiter into a giant brain
22:36 < kanzure> not just the size of it.
22:36 < gene> turbulence is  a bitch Kanzure
22:36 < gene> it really is
22:37 < kanzure> what about jupiter brains do you bring up turbulence for?
22:37 < gene> do you know how they design waterslides kanzure?
22:37 < gene> I thought the whole concept of a jupiter brain was where vortices and fluids make up the intelligence
22:38 < gene> or whatnot
22:38 < kanzure> nope
22:38 < kanzure> but 
22:38 < kanzure> but there are some people who talk about things like that, i.e. "ocean intelligences"
22:38 < gene> so they don't design waterslides
22:38 < kanzure> but the idea of a Jupiter brain is this giant solid of computronium basically
22:38 < kanzure> with giant heat exhaust pipes going through for the overhead cost
22:38 < kanzure> huh? who doesn't design waterslides?
22:39 < gene> they don't design waterslides
22:39 < fenn> <- not convinced spherical geometry is best arrangement for megascale computers
22:39 < gene> they build then and hope for the best
22:39 < gene> then add sections on to them where the water comes out
22:39 < kanzure> who's they?
22:39 < gene> it's because there is a certain speed at which water becomes chaotic
22:39 < gene> waterslide companies
22:40 < gene> a single piece of dust can influence the flow
22:40 < kanzure> ugh
22:40 < kanzure> don't get all "chaos theory" on me
22:41 < kanzure> you just need a finer CFD
22:41 < kanzure> *finer CFD simulation
22:41 < gene> you can't
22:41 < kanzure> you can make finer systems, yes
22:41 < kanzure> finer simulations
22:42 < gene> you have to model each atom
22:42 < kanzure> according to who?
22:42 < gene> according to a book I read
22:42 < gene> about chaos theory
22:42 < gene> crap forgot author
22:43 < kanzure> that's kind of biased, gene.
22:43 < gene> kanzure
22:43 < gene> read about chaos theory
22:43 < gene> anyway you don't need finer CFD
22:43 < kanzure> Oh, I have.
22:43 < gene> you just have to approximate it
22:44 < xp_prg> kanzure did you ever use the script or does it just sit there staring at you?
22:44 < kanzure> xp_prg: It's in progress
22:44 < kanzure> Do you want to write it for me?
22:44 < kanzure> Go right ahead.
22:44 < xp_prg> yes I do
22:44 < xp_prg> tell me what you want and I will do it
22:44 < kanzure> what the fuck man
22:45 < kanzure> what about all of the times that I've described the system?
22:45 < kanzure> :(
22:45 < xp_prg> you told me to do this one part and I did it
22:45 < kanzure> yeah\[
22:45 < xp_prg> I am not aware of another part you want, you specifically told me don't do other parts etc...
22:45 < kanzure> and you asked me what it was all about
22:45 < kanzure> multiple times
22:45 < kanzure> during and after
22:45 < xp_prg> well I wanted to do more and you stopped me before
22:46 < xp_prg> can I do more now?
22:46 < kanzure> yeah, I did tell you specifically to not do other parts because the way you were going it didn't seem like you comprehended
22:46 < kanzure> go right ahead..
22:46 < kanzure> hm
22:46 < xp_prg> you are my project manager what is the next part you want me to work on?
22:46 < kanzure> wonder where I put the latest zip file of the system
22:46 < kanzure> at the moment I'm writing the tree crawler -> db interface
22:47 < kanzure> dhcp-84-92.me.utexas.edu is it?
22:47 < kanzure> I need to go zip up some stuff if you want to take a look
22:48 < xp_prg> what does the tree crawler -> db interfae do?
22:48 < kanzure> why do you make me repeat everything?
22:49 < kanzure> I get really annoyed about this
22:49 < xp_prg> well I don't remember that part :(
22:49 < kanzure> basically, if you were listening the other day, what I have is this tree search of the possibility space of constructed graphs, with db lookup calls at the top of the recursion function so that a preference modeling script can tell the traversal algorithm to go back upwards if the user starts to hate some of the results
22:49 < kanzure> xp_prg: why don't you read your backlogs?
22:51 < xp_prg> ok
22:51 < xp_prg> what you writing it in?
22:51 < kanzure> um, this is rather embarrasing, but there's a few aspects here
22:52 < kanzure> C#, JS, CSS, HTML, 
22:52 < kanzure> some perl too
22:52 < kanzure> you should go install graphsynth
22:52 < xp_prg> can I do it with prolog if I want?
22:52 < kanzure> what part
22:52 < xp_prg> graph searching
22:52 < kanzure> no, the graph searching is already done
22:53 < kanzure> that's why I say go download graphsynth
22:56 < xp_prg> ya traversal algorithms etc... that is prolog's domain
22:56 < xp_prg> just food for thought
22:58 < kanzure> http://heybryan.org/graph/2008-11-20.zip
23:02 < kanzure> drazak: http://heybryan.org/graph/2008-11-20.zip
23:03 < drazak> what's in that?
23:03 < kanzure> synthetic biology + mechanical design automation stuffs.
23:03 < kanzure> http://dhcp-84-92.me.utexas.edu/graph/graph-easy/
23:03 < drazak> ooh
23:03 < kanzure> is one part.
23:04 < drazak> I was talking with someone about RNAi's in fighting cancer/hiv
23:04 < drazak> she doesn't like my idea of a viral vector with a defect to make it more suspectable to some sort of anti-viral
23:04  * kanzure roots for oncolytic viruses
23:05 < kanzure> Have you seen the Andrew Hessel SENS3 talk?
23:05 < drazak> well, a lot of the viruses they use are just to kill the cell
23:05 < drazak> er, cancer cells, rather
23:05 < drazak> but it's hard to target
23:05 < kanzure> right.
23:06 < kanzure> Andrew's approach is to synthesize a virus specific to *your* cancer
23:06 < drazak> and as long as you can target the right gene, you can get the cancer to stop growing like cancer, to shrink a tumor, then remove it with surgery and treat the area with antiviral so you don't accidentally block other genes
23:06 < drazak> hm, link me
23:07 < kanzure> blargh, um
23:07 < kanzure> ooh, one sec
23:07 < kanzure> http://heybryan.org/books/
23:07 < kanzure> check the flv file
23:09 < drazak> where?
23:10 < drazak> oh
23:10 < kanzure> huh? it's not listed?
23:10 < drazak> I got it
23:11 < kanzure> huh, 108 MB. not fun.
23:11 < drazak> yeah
23:11 < kanzure> well, it's made for streaming, no?
23:11 < kanzure> mplayer should have a streaming param.
23:11 < drazak> yeah, but can't rewind well with that
23:11 < ybit> so, all you fellow h-plusers... what to do with a fibre channel san switch?
23:12 < ybit> aside from make money at an auction site...
23:12 < drazak> ybit: 10GiGE>fibre
23:12 < kanzure> drazak: What's my current upload?
23:13 < drazak> flipping slow
23:13 < drazak> 40
23:13 < fenn> do not stare into fiber optic cable with remaining eye
23:13 < ybit> :)
23:13 < kanzure> bleh, 40
23:20 < kanzure> bkero: Can you host some of my content?
23:20 < kanzure> You surely have mad upload, right? _right_?
23:20 < drazak> I can host some when I get more disk space
23:20 < drazak> or if you can pay a little towards disk space
23:23 < kanzure> Money reserved for kickass transhumanisty projects.
23:23 < bkero> kanzure: I do.
23:23 < bkero> kanzure: How much content?
23:23 < bkero> Do you have I2 of commodity internet?
23:23 < bkero> *Want
23:24 < kanzure> Billions!
23:24 < kanzure> I2?
23:24 < kanzure> Internet2 ?
23:28 < fenn> over 9000
23:28 < drazak> ew, I2
23:28 < fenn> isnt that like "python 3000" i.e. always on the horizon
23:30  * fenn wonders what one does with a 100Gbit connection
23:31 < kanzure> campbell and I were using one earlier this week
23:32 < kanzure> to do a four or five stream two-way video conference with some other university
23:32 < kanzure> in a big giant conference room :)
23:32 < kanzure> I'm not sure but I could have sworn it felt like HD video
23:34 < bkero> I2 is good for interuniversity speeds
23:42 < kanzure> Hah
23:42 < kanzure> This is so stupid.
23:42 < kanzure_> http://www.google.com/hostednews/afp/article/ALeqM5gzZbPW51cXTcUW___nDFSonWXCNA
23:42 < kanzure_> Somali pirates demand 25 million dollars for Saudi oil tanker
23:42 < kanzure_> Can anybody explain why these are not heavily armed?
23:43 < kanzure_> I mean, I can be a pirate. Right?
23:43 < kanzure_> they seized it in 16 minutes
23:43 < kanzure_> hah
23:44 < kanzure_> two speed boats
23:44 < kanzure_> Two speedboats with pirates armed with Kalashnikov rifles and rocket-launchers 
23:45 < kanzure> 16 vessels, 350 crew members, off the coast of Somalia.
23:45 < kanzure> I think I'm going to visit these pirates.
23:45 < kanzure> the NASA bag of tools was "worth $100,000" .. okay. Enough news from me.
23:50 < kanzure_> oh how kind of them
23:50 < kanzure_> http://bbs.keyhole.com/ubb/showflat.php/Cat/0/Number/1242871/an/0/page/0
23:50 < kanzure_> http://maps.google.com/maps?q=http://bbs.keyhole.com/ubb/download.php?Number=1242871&t=k&om=1
23:51 < kanzure> Al Mukallah or mukalla
23:52 < kanzure_> http://www.panoramio.com/photo/4520507
23:53 < kanzure_> AL-HAMATI SWEETS BAKERIES
23:54 < kanzure_> "The New York Times quoted American officials as saying they have evidence that Osama bin Laden is using a network of shops that sell honey to generate income and secretly move weapons, drugs and agents throughout Al-Qa'ida. "
23:54 < kanzure_> hah