2008-11-20.log

--- Day changed Thu Nov 20 2008
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	02:39
drazak	nice	02:42
drazak	kanzure: have you ever watched ReGenesis?	02:42
kanzure	No, but bkero has.	02:43
kanzure	So for some reason these people expect to scale up to 30 million barrells of biofuel from algae per day in 20 years.	02:44
drazak	well, if we can make fuel that way, why not	02:48
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.	02:49
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	02:50
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	02:51
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	02:52
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	02:53
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	02:54
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	02:55
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	02:56
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	02:57
gene	kanzure you got any arguments against dualism?	03:02
kanzure	the brain is the brain.	03:06
kanzure	Neat, google.org has been updated.	03:12
kanzure_	http://groups.google.com/group/openmanufacturing/msg/4a37dc2d82c8d46d?dmode=source	03:16
kanzure_	Oh god.	03:16
kanzure_	Please killfile?	03:17
kanzure_	fenn: what do I do	03:17
kanzure	I feel a rant coming on.	03:18
fenn	"But is there actually a consistent way" -> "yes"	03:27
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 ..	03:28
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.	03:29
gene	So kanzure could you disprove dualism, in argument with room mate	03:31
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	03:32
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.	03:33
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	03:34
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	03:36
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?	03:37
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?	03:38
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	03:39
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	03:40
kanzure_	http://heybryan.org/books/music/2008-06-01/	03:41
kanzure	http://heybryan.org/books/music/2008-06-01/	03:41
gene	lol /books/	03:42
gene	oh yeah	03:42
gene	that's right	03:42
gene	I can't download shit	03:42
gene	odd	03:43
gene	I can open gifs	03:43
gene	but not mp3s	03:43
gene	OH SHIT!	03:43
gene	is that 8 bit stuff CC?	03:44
gene	I might be being watched	03:44
gene	by the RIAA!	03:45
gene	or firefox has an error	03:45
gene	firefox has an error	03:47
gene	I have to use IE	03:49
fenn	haruhi suzumiya is pretty awesome so far	03:51
kanzure	hulu?	03:53
kanzure	on hulu?	03:53
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	03:55
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?	03:56
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?	03:57
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	03:58
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	03:59
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	04:00
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	04:01
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	04:02
gene	oh wait kanzure is probably hearing the spoilers too	04:03
kanzure	I also read the wikipedia article, fwiw.	04:03
gene	heh	04:03
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 :)	04:04
gene	The Melancholy of Haruhi Suzumiya	04:05
ybit	arigatou	04:05
gene	huh?	04:05
ybit	thank you	04:05
gene	Now hopefully Spielberg won't make a live action movie out of Haruhi	04:06
* fenn scowls at logs		04:06
gene	as he is trying to do with Ghost In The Shell	04:07
gene	logs are quite useful to burn fenn	04:07
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	04:08
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?	04:09
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	04:10
fenn	it's necessary, for now	04:11
gene	why?	04:11
fenn	sigh.. definitions of 'selfhood' and all that	04:11
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	04:12
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	04:13
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	04:14
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	04:15
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	04:16
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	04:17
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	04:18
gene	hey would you eat algae fenn?	04:19
gene	it's very nutrional	04:19
fenn	i have it for breakfast sometimes, but the good japanese stuff is rather expensive	04:21
fenn	oh, and i always wanted to make spirulina chocolate	04:22
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	04:23
* fenn mumbles about kainic acid		04:24
kanzure	gene: Do you mean "just add an open flame" ?	04:25
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	04:26
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	04:27
gene	even chicken	04:31
gene	or saunteed onions	04:42
* 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	07:24
ybit	i will atleast try it out	07:25
kanzure	So if I was going to fail all of my classes anyway, is this good excuse for not showing up?	08:11
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.	08:29
kanzure_	while looking for that lost page - http://heybryan.org/Lain's-Room-001.jpg	08:30
fenn	is that a hemi?	08:36
kanzure	hemi?	08:40
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	08:43
fenn	see it's mounted on vibration isolating springs	08:44
kanzure	yes, I see now	08:47
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	08:48
kanzure	you type?	08:49
fenn	well i drag the cursor instead of clicking	08:49
fenn	so it gets spaces too	08:49
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.	08:55
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	09:09
fenn	silly number.. they neglect the fact that you're carpeting vast swaths of land with essentially free 3% efficient "solar panels"	09:12
fenn	based on electrical conversion efficiency alone, a stirling engine or OTEC would be way better than PV panels	09:13
fenn	ending to haruhi suzumiya makes me want to go kill myself	09:15
kanzure	any quick ideas on directed viral evolution?	09:17
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	09:18
kanzure	bah..	09:19
fenn	off to cry myself to sleep...	09:19
kanzure_	http://www.picturetrail.com/sfx/album/view/21008688 convergence08 photos	14:34
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)	14:37
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.	14:56
kanzure	robotknowledge ?	15:01
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.	15:02
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	21:24
gene	it rolls	21:25
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.	21:33
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.	21:34
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.	21:35
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	21:36
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)	21:37
gene	well how about we make the virus magnetic	21:38
gene	oh lysis	21:38
gene	that's right	21:38
gene	ok	21:38
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	21:39
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 ?	21:40
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	21:41
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?	21:42
kanzure	utex# LB 2905	21:43
gene	algae?	21:43
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	21:44
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	21:45
kanzure	oh	21:46
kanzure	stupid me	21:46
kanzure	http://heybryan.org/bioreactor/lysis/	21:46
gene	augh	21:47
gene	aureococcus isn't very related	21:47
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.	21:48
gene	chlorella is more closely related	21:50
kanzure	than volvox?	21:50
gene	i believe so	21:52
gene	http://en.wikipedia.org/wiki/Chlorococcaceae	21:52
kanzure	Flora -> Chlorophyta -> Trebouxiophyceae -> Chlorellales -> Chlorellaceae -> Chlorella	21:53
kanzure	Plantae -> Chlorophyta -> Chlorophyceae -> Volvocales -> Volvocaceae -> Volvox	21:53
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.	21:54
gene	I know	21:55
kanzure	http://algaebase.org/	21:55
gene	ok	21:57
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.	21:59
kanzure	Maybe John has something cooking on that..	22:00
gene	ugh	22:00
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.	22:01
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	22:02
gene	no membrane proteins	22:03
gene	sequenced at least	22:03
gene	so we need us a sequencer....	22:05
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.	22:06
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	22:07
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	22:08
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	22:09
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	22:10
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	22:11
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	22:12
* 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	22:13
gene	locality, sides of a small aquarium	22:14
kanzure	Indiana?	22:14
kanzure	we have an agent there	22:14
gene	huh?	22:14
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	22:15
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	22:16
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	22:17
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	22:18
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	22:19
kanzure	hm	22:20
kanzure	so in animals, viruses have glycoprotein spikes	22:20
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	22:21
* 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	22:22
gene	well I got to go	22:23
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	22:25
gene	btw who is John Grigg?	22:31
kanzure	Transhumanist.	22:31
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 :-)	22:32
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?	22:35
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	22:36
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	22:37
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?	22:38
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	22:39
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	22:40
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	22:41
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	22:42
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	22:43
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	22:44
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	22:45
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	22:46
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	22:47
xp_prg	what does the tree crawler -> db interfae do?	22:48
kanzure	why do you make me repeat everything?	22:48
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?	22:49
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	22:51
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	22:52
kanzure	that's why I say go download graphsynth	22:53
xp_prg	ya traversal algorithms etc... that is prolog's domain	22:56
xp_prg	just food for thought	22:56
kanzure	http://heybryan.org/graph/2008-11-20.zip	22:58
kanzure	drazak: http://heybryan.org/graph/2008-11-20.zip	23:02
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.	23:03
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		23:04
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.	23:05
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	23:06
kanzure	blargh, um	23:07
kanzure	ooh, one sec	23:07
kanzure	http://heybryan.org/books/	23:07
kanzure	check the flv file	23:07
drazak	where?	23:09
drazak	oh	23:10
kanzure	huh? it's not listed?	23:10
drazak	I got it	23:10
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?	23:11
ybit	aside from make money at an auction site...	23:12
drazak	ybit: 10GiGE>fibre	23:12
kanzure	drazak: What's my current upload?	23:12
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	23:13
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	23:20
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	23:23
kanzure	Billions!	23:24
kanzure	I2?	23:24
kanzure	Internet2 ?	23:24
fenn	over 9000	23:28
drazak	ew, I2	23:28
fenn	isnt that like "python 3000" i.e. always on the horizon	23:28
* fenn wonders what one does with a 100Gbit connection		23:30
kanzure	campbell and I were using one earlier this week	23:31
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	23:32
bkero	I2 is good for interuniversity speeds	23:34
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?	23:42
kanzure_	I mean, I can be a pirate. Right?	23:43
kanzure_	they seized it in 16 minutes	23:43
kanzure_	hah	23:43
kanzure_	two speed boats	23:44
kanzure_	Two speedboats with pirates armed with Kalashnikov rifles and rocket-launchers	23:44
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.	23:45
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	23:50
kanzure	Al Mukallah or mukalla	23:51
kanzure_	http://www.panoramio.com/photo/4520507	23:52
kanzure_	AL-HAMATI SWEETS BAKERIES	23:53
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	23:54

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