--- Day changed Thu Oct 02 2008
00:16 < ybit> http://www.unicornscan.org/
02:28 < ybit> pk, nooooo!
02:28 < ybit> ...
02:28 < ybit> oi faceface
02:29 < ybit> why are we not subjected to three faces currently?
02:53 < ybit> procto: what exactly is logarchy doing?
02:53 < ybit> sounds like they have a good idea for a future civ
02:53 < UtopiahGHML> ybit: want to apply to Blinkenshell?
02:53 < ybit> UtopiahGHML: sure
02:54 < ybit> if it takes awhile, i will have to do it tomorrow night or this weekend
02:54 < UtopiahGHML> nope the test=10min
02:54 < UtopiahGHML> the rest is getting vouched by 2 persons and that just hanging around in the channel helping
02:54 < UtopiahGHML> if you are social it's like 2 days max
02:54 < UtopiahGHML> then the following day the admin opens you account
02:55 < UtopiahGHML> so in the end if you are "dedicated" you could have it opened tomorrow :P
02:55 < UtopiahGHML> (they "work" on .se time)
02:55 < ybit> i might wait until this weekend when i am most active
02:58 < kanzure> Hi all.
02:58 < kanzure> ybit: skype please
02:59 < procto> ybit: it's just a general framework that can be applied
02:59 < procto> ybit: I'm involved with seasteading, and hoping to have a logarchy up on a seastead at some point during my life
02:59 < procto> thing about logarchy is that it's compatible with different electoral, political, and economic systems
03:04 < kanzure> fenn: nathan and michel on skype if you want to be bothered to have yet another chat protocol
04:05 < ybit> http://www.magcloud.com
04:07 < UtopiahGHML> I need a graph database library in PHP...
04:09 < ybit> UtopiahGHML: http://datamob.org/resources maybe?
04:10 < ybit> http://www.infochimps.org -- i think this belongs on the hplusroadmap wiki somewhere...
04:11 < ybit> or maybe it should just be bookmarked
04:15 < kanzure_> what is it? 
04:16 < UtopiahGHML> ybit: graph as in mathematical graph, networks, not visually displaying data
04:17 < ybit> kanzure: infochimps -- "Free Redistributable Rich Data Sets"
04:17 < kanzure_> cool :)
04:17 < kanzure_> http://theinfo.org/
04:18 < ybit> ah, i visited theinfo.org recently. me likey
04:19 < ybit> UtopiahGHML: http://www.hotscripts.com/Detailed/16749.html PHP+Graphviz tool
04:20 < ybit> a lot of php tools for graphiz: http://www.graphviz.org/Resources.php
05:24 < kanzure> ybit: soon you will have a fancy data set from me
05:24 < kanzure> and throwing it into graphviz will be simple
07:47 < willPow3r> kanzure, one login isn't enough?
07:50 < faceface> UtopiahGHML, graph database? What doing?
07:50 < faceface> ybit, I have enough face
08:18 < UtopiahGHML> faceface: relational database, no, object database, no, graph database specialized in network oriented datastructure, yes.
08:24 < faceface> yes
08:24 < faceface> what doing?
08:24 < faceface> I wanted to write a MySQL 'graph plugin', but I didn'y get round to it
08:25 < UtopiahGHML> I guess the best thing to do is too look at a real life example :
08:25 < faceface> I had a big 'graph database' hand out at one point... 
08:25 < UtopiahGHML> http://neo4j.org/
08:25 < faceface> kanzure___, are you still interested in this http://www.nature.com/nprot/journal/v2/n3/abs/nprot.2007.96.html?
08:25 < faceface> or was that last week?
08:26 < faceface> or should I say kanzure
08:26 < faceface> they do good stuff in Gronigen
08:27 < faceface> UtopiahGHML, OK, I know what a GraphDB is, my question is, what do you want one for? I am curious
08:28 < UtopiahGHML> oh
08:28 < faceface> I am interested in graph queries
08:28 < faceface> specifically traversing ontologies 
08:29 < UtopiahGHML> to evolve from a wiki with a classical filesystem or classical DB to a way to handle data it holds in a consistent fashion
08:29 < UtopiahGHML> and be able to have a fully "querable" wiki
08:29 < UtopiahGHML> (mixing user modification and API modification basically)
08:29 < faceface> UtopiahGHML, its the future
08:29 < UtopiahGHML> thus facilitating automated agent suports
08:29 < faceface> UtopiahGHML, have you groked SMW yet?
08:29 < faceface> cool
08:30 < UtopiahGHML> nop, doesn't ring a bell, what is it?
08:30 < faceface> I really want to get my head into SMW, semantic media wiki
08:30 < faceface> but I haven't had time
08:30 < faceface> its semantic web for mediawiki
08:30 < faceface> they have a query interface that seems to mirror XSLT
08:30 < faceface> or XPah
08:31 < faceface> it was so strange thinking about hierarchical queries after so many years of thinking about relations
08:31 < faceface> UtopiahGHML, about 'api modifications', the guy behind DPL is going in that direction with his DPL + graph vis wiki
08:32 < UtopiahGHML> hmmm yep I checked SMW a while ago (>1 year) but it wasn't what I was looking for at the time (too complex for the end-user and too little applications ready, basically very low ROI)
08:32 < faceface> ROI?
08:32 < UtopiahGHML> return on investment
08:32 < faceface> UtopiahGHML, there is a SMW extension called Semantic Query or something
08:32 < UtopiahGHML> technical cost vs concrete features benefits
08:32 < faceface> OK
08:32 < faceface> this is friendly http://semeb.com/dpldemo/index.php?title=Dynamic_Page_List
08:32 < faceface> ROI ROI
08:33 < UtopiahGHML> having just 23h57 per day you have to think ROI :)
08:34 < faceface> It allows you to combine Wgraph with DPL to generate 'software' in the wiki
08:34 < faceface> http://semeb.com/dpldemo/index.php?title=Main_Page
08:34 < UtopiahGHML> hmmm problem is my current wiki is using pmWiki, do those solutions prodive way to "import" existing data?
08:34 < faceface> pmWiki?
08:34 < UtopiahGHML> very flexible wiki
08:35 < faceface> UtopiahGHML, there are libraries for wiki to wiki conversion, then you need to run MW to enable the DPL / Wgraph stuff
08:35 < UtopiahGHML> but that unfortunately doesn't provide a clear API and can't handle massive amount of data
08:35 < faceface> he is forging ahead
08:35 < faceface> UtopiahGHML, not in a 'live' system... I'm thinking of a one off migration
08:35 < faceface> http://semeb.com/dpldemo/index.php?title=Scatter_Demo_2
08:35 < faceface> its so cool
08:35 < UtopiahGHML> the good think with MW is... that I guess it has the largest active community
08:36 < faceface> yup, and WP proves its scaleable
08:37 < Utopiah> sorry, irssi crash...
08:38 < Utopiah> faceface: ideally Id use a structure like #OpenCog will use since Im into AI, the thing is (by luck?) my targeted architecture (hypergraph) is also what OpenCog decided to use
08:38 < faceface> what is the open cog?
08:38 < Utopiah> what I consider the more prosiming unifying AI project today
08:39 < Utopiah> (what some like to call "AGI")
08:39 < faceface> Utopiah, ... you want ... your wiki to be intelligent?
08:40 < Utopiah> not really :)
08:40 < Utopiah> what is the structure of a wiki?
08:41 < faceface> what is the way of tao?
08:41 < Utopiah> what is the structure of a brain?
08:41 < Utopiah> the hypergraph seem to be the most ready to use model for a convergence let's say
08:42 < Utopiah> so let's imagine one who would to enjoy what the Net can offer since it's (probably) the fastest evolvy ecosystem today
08:42 < Utopiah> one would want its data organized in a fashion that agent (including remote agents like API from other websites) to "play" with the data
08:43 < Utopiah> eventually seing his system itself as a potential useful other agents
08:43 < faceface> yes, thats the idea of SMW
08:43 < faceface> have you read the 'cyber infrastructure for Biology' paper?
08:44 < faceface> also my friend Vincent has worked on some neat stuff like this
08:44 < faceface> you can find his publications here: http://www.vincent-wolowski.net/
08:44 < faceface> Building a Semantic Search Engine. Presentation, Department of Chemical System Engineering, Komiyama Laboratory, Tokyo University, Tokyo, Japan, February 3, 2004. [.pdf]
08:45 < Utopiah>  'cyber infrastructure for Biology' ? based on mimetic?
08:45 < faceface> what what?
08:45 < faceface> no
08:45 < faceface> not mimetic
08:46 < faceface> http://nrgwiki.nature.com/cyberinfrastructureforbiology/show/HomePage
08:47 < Utopiah> hmmm the more I look at those WM extensions the more Im considering a switch... what do you think is the core of the MW community? (to check what is available now, what is the spirit, etc... and betting on how it will evolve)
08:47 < faceface> Utopiah, uncertain
08:47 < faceface> see #mediawiki
08:48 < faceface> they are active... there are a few good devs...
08:48 < faceface> Byron is a controll freak...
08:48 < faceface> all revisions go through byron, and thats final
08:48 < faceface> (ime)
08:48 < fenn> control freak? wikipedia? you must be kidding!
08:48 < Utopiah> do you know if there is anything related to the use of GraphDB as the underlying strcture?
08:48 < faceface> heheh
08:48 < faceface> they are not too close to the wp community
08:48 < faceface> they are like... uh... users?
08:49 < wrldpc> wiki is all controlhawks.
08:49 < Utopiah> strange way to see an open community but maybe it's efficient...
08:49 < faceface> Utopiah, no
08:49 < faceface> just a pairs list or something
08:49 < faceface> Utopiah, I wanted to get svn commit access to one extension in the MW svn server - it was a no go
08:49 < faceface> just one extension!
08:50 < faceface> that is why many extensions are developed off site, and also just directly on mediawiki.org
08:50 < Utopiah> I see
08:50 < faceface> There are so many extensions because of an unwillingness to integrate into the core
08:50 < faceface> however... that said... there is a lot of exciting stuff going on in the extension community
08:50 < faceface> esp. bio.
08:51 < faceface> wrldpc, turns out that way for some reson often
08:51 < Utopiah> the last thing that amazed you there?
08:51 < faceface> wikipathways
08:51 < faceface> its a pahtway editor in the wiki
08:51 < wrldpc> does anyone here actually sub to nature?
08:51 < faceface> also (a bit boring) I am excited by the 'data integraton' efforts in MW
08:52 < faceface> wrldpc, http://network.nature.com/people/dan/profile
08:52 < wrldpc> I sent off a rather pointed message encouraging them to go "free."
08:52 < wrldpc> interesting
08:53 < faceface> Utopiah, my MW / bio projects are pretty amazing too ;-)
08:53 < faceface> http://pdbwiki.org/index.php/Main_Page
08:53 < faceface> http://biodatabase.org/index.php/Main_Page
08:54 < faceface> also you should see http://bio.cc/index.html/index.php/Main_Page
08:54 < faceface> wrldpc, write a 'letter to nature', get people to sign it
08:54 < wrldpc> good idea
08:55 < faceface> You just got to cram it all in to 200 words :-)
08:55 < faceface> well... I need to go do my day job... any tips on how to get by on less sleep?
08:57 < Utopiah> more sport, better nutrition but overall the trick is...
08:57 < Utopiah> PASSION! :D
08:58 < wrldpc> hey faceface have you heard of the project John Cumbers from Brown wants to do where people would swab their toilets and mouthes and so on and ...
08:58 < Utopiah> but ... A candle that burns twice as bright and twice as long
08:58 < wrldpc> Does anyone know about this?
08:58 < Utopiah> not sure it exsits, your choice though :)
08:58 < faceface> Utopiah, yeah... I get bored though ... I am a dysfunctional 
08:58 < faceface> wrldpc, no
08:59 < faceface> wrldpc, what is it?
08:59 < faceface> 'eco-genomics'?
08:59 < wrldpc> bioinformatics project
08:59 < wrldpc> sorta
08:59 < faceface> like environmental sampling?
08:59 < wrldpc> they want to track where stuff is ... open source, yes envirosamp
08:59 < faceface> its the future :-)
08:59 < wrldpc> bingo
08:59 < wrldpc> have a good day!
08:59 < faceface> you too
08:59 < Utopiah> faceface: how can you be bored in such a time and place... :)
08:59 < wrldpc> thanks
08:59 < faceface> Utopiah, I am 'purpose disoriented'
09:00 < faceface> I don't really know what I want or why... I am conflicted.
09:00 < Utopiah> strange since you seem to have your own projects
09:00 < faceface> anyway... I 'feel' like I should go do my boring day job... Its like a pressure... 
09:00 < faceface> I do them in my spare time... hence the need for less sleep
09:00 < faceface> nice talking to you Utopiah 
09:01 < Utopiah> my pleasure
09:01 < Utopiah> have a nice day
09:03 < fenn> faceface: try doing your personal projects while at normal job
09:04 < Utopiah> fuck your normal job, move to what you really live for, find a way to monetize it.
09:04 < fenn> well, yeah, but that takes passion
09:06 < Utopiah> indeed
09:07 < Utopiah> but that's when your life really starts :)
09:16 < faceface> anyone married
09:16 < faceface> ?
09:21 < Utopiah> gosh no
09:22 < faceface> heheh
09:22 < faceface> I thought I was taking a job that supported my interests
09:22 < faceface> but it was also a compremize for me and my wife
09:23 < faceface> I think I'll have to become a 'group leader' just to get to work on what I want to!
09:23 < Utopiah> entrepreneur is the spirit
09:23 < Utopiah> and it's a long time investment
09:23 < faceface> OK, lets start a business
09:23 < Utopiah> the risk is not not to bet but not to know that you are betting anyway
09:24 < faceface> I really need someone to talk to about that....
09:24 < Utopiah> opportunity cost basically
09:24 < faceface> I have a killer idea if we can get to prototype within 6 months
09:24 < Utopiah> well, Im a idea management pro
09:25 < faceface> cool... the problem with 'nextGen' sequencing is that its too good - too much data too quickly. We don't have enough disks.
09:25 < Utopiah> yep
09:25 < faceface> turn the problem on its head - lets encode our DNA data as DNA, then we can store vast quantities of data in a cupboard
09:25 < faceface> we can get massive data transfer rates by shipping DNA using UPS
09:26 < Utopiah> hmmm I met a woman on Berkeley working on a similar problematic but she wasn't going the same way
09:26 < faceface> the idea is to design a 'DNA encoding' that maximizes ease of reading
09:26 < Utopiah> yep I see
09:26 < faceface> exactly, we have a slight edge
09:26 < faceface> the two novel things that we bring together are 
09:26 < Utopiah> problem is... cost of "DNA printing", isn't it very brittle and costly so far? (maybe not 2D structures thought, dunno)
09:27 < fenn> lol i have a direct DNA to DNA nano sequencer data storage machine - polII
09:27 < fenn> III
09:27 < faceface> 1) the DNA encoding - lots of check sums and handeling of repeat regions, 2) the 'DNA protectant' molecule that we use to store data at rtp
09:27 < faceface> fenn, its error prone ;-)
09:27 < faceface> Utopiah, exactly, we need to design a micro fluidic dna sequencing chamber
09:28 < faceface> microfluidics is getting very cheap, so its easy to design and print a 'chip' that will controll the flow of ATCG into a reaction chamber.
09:28 < fenn> cost of DNA printing is what all the "retarded polymerase" stuff is about
09:28 < faceface> really?
09:29 < fenn> sorta
09:29 < faceface> that stuff where I was like 'what are you guys going on about'?
09:29 < fenn> it's also for realtime in-vivo expression of arbitrary genes
09:29 < fenn> but whatever, it's vaporware
09:30 < faceface> sure
09:30 < fenn> <- bitter old man
09:30 < faceface> taq isn't expensive though
09:30 < fenn> is the patent up yet?
09:30 < faceface> I need a prototype no?
09:31 < fenn> oh i was just curious
09:31 < fenn> always wanted a vat of e-coli spewing out metric tons of taq polymerase
09:31 < faceface> but my feeling is that there is only a short window on this one
09:32 < fenn> i dont really see what sort of situation would require dna data storage?
09:32 < fenn> i mean what do you do with it
09:32 < faceface> fenn, when I sequence your genome for $10, then the genome of your gut, then the genome of your brain, then again at age 2 and again at age 6 and again and agin, 
09:32 < faceface> then stick it into DNA
09:33 < faceface> its a 'permanant record' for re-reading
09:33 < faceface> like a tape backup
09:33 < fenn> why not use tapes?
09:33 < faceface> too expensive
09:33 < faceface> too many data
09:33 < faceface> too slow
09:33 < fenn> is there no compression algo?
09:34 < fenn> i mean you and me are 99% similar
09:34 < faceface> well...
09:34  * faceface sulks
09:34 < faceface> but its good to talk about 'alternatives' 
09:34 < faceface> I mean a patent needs that right?
09:35 < faceface> fenn, also tissue expression could vary a lot, next gen gives you expression levels, splice variants etc.
09:36 < fenn> dont get me wrong, DNA is a fantastic data storage device
09:36 < fenn> but it's a pain in the ass to work with
09:36 < faceface> it seems to work
09:36 < faceface> ah... you know about any microfluidic considerations when working with DNA?
09:37 < faceface> there is a formidible group in cambridge that develops microfluidics for biotech
09:37 < fenn> um, how do you get past the typo problem?
09:37 < faceface> fenn, checksums
09:37 < fenn> probability of a typo increases exponentially with sequence length
09:37 < faceface> and redundancy... like read correction on any modern disk
09:38 < faceface> I am sure we can think of some 'optimal encodings'
09:38 < fenn> i dont know much about how microfluidics actually works (beyond  a popular science level)
09:38 < faceface> also, we need read optimized ... i.e. taylored to certain hardware
09:38 < faceface> you trap a bubble of your aquious reagent in an oil flow. then you can manipulate the bubbles 
09:39 < fenn> but how does this actually build up a sequence?
09:39 < faceface> i.e. read off bubble colour, sort, merge, store etc
09:39 < fenn> is it just the conventional modified NTP + cap molecule?
09:40 < faceface> you have a chamber with some fixed primers and taq,  then you flow ATCG over the primer... actually I don't know!
09:40 < faceface> that is where my plan falls down... I'm an idiot!
09:40 < fenn> hrm
09:40 < fenn> "where the bits hit the road"
09:40 < faceface> somehow we need to keep taq in the 'reaction chamber' then we need to flow ntp at a time, then we need to get out the DNA and put in new primers.
09:41 < fenn> flow one ntp at a time won't work
09:41 < faceface> why?
09:41 < fenn> either too much diffusion or it's too slow
09:41 < faceface> I don't mean one molecule, just one type
09:41 < faceface> microfluidics is fast, you can process 100's of bubbles per second
09:42 < fenn> my idea was that you sensitize the taq with some frequency of laser and this only allows it to pick up a certain nucleotide
09:42 < faceface> each bubble needs to be one NTP.... and we need to only add one base per bubble...
09:42 < faceface> fenn, any ref?
09:42 < fenn> no
09:42 < faceface> any chem to spontainously 'prime' the end of the DNA for reaction?
09:43 < fenn> not needed, taq does that
09:44 < faceface> DNA-* + NTP -> DNA-NTP + * -> DNA-NTP-* +NTP -> DNA-NTP-NTP + * -> ...
09:44 < faceface> fenn, but I only want to add one base at a time
09:44 < faceface> taq is there ready to add as many NTP's as it can get its hands on right?
09:44 < faceface> or do you controll that with ATP?
09:44 < faceface> I'll need to read up to get more details
09:44 < fenn> well, the idea was to have another "clock" frequency
09:45 < fenn> so you have 3 lasers
09:45 < fenn> 2 spcify the nucleotide
09:45 < fenn> the third cements it in place
09:45 < faceface> I'll do some reading.
09:46 < faceface> I think there is scope for a 'strategic aliance' ;-)
09:46 < fenn> this was some idea i came up with years ago, i honestly have no idea if there's anything out there
09:49 < fenn> " An undefined problem has an infinite number of solutions.
09:49 < fenn> what a bunch of crap
09:50 < fenn> must have been a mathematician, not an engineer
09:51 < Utopiah> that's infinitely unuseful :)
11:00 < kanzure_> Utopiah: for what it's worth, I too want graphdb or graph-fs, and *not* in semantic mediawiki form.
11:01 < Utopiah> ideally I would find a Lisp wiki using GraphDB...
11:03 < Utopiah> (and super ideally be able to convert my existing wiki instance to it in 1 command ;)
11:05 < faceface> Similarly to concepts in electrical engineering, the objective in the Synthetic Biology is the development of standardized DNA building blocks, which can be easily combined and which allow the reconstruction of cells, e.g. bacteria into bioreactors. Scientists in the Synthetic Biology thereby aim at the development of bioreactors capable of producing far more complex compounds than currently possible using the conventional methods of classica
11:05 < faceface> l biotechnology
11:06 < faceface> http://sb4.biobricks.org/
11:07 < kanzure_> faceface: you might be interested in knowing of my synthetic biology circuit creator project
11:07 < faceface> kanzure_, I just pasted for your benefit
11:07 < kanzure_> http://heybryan.org/~bbishop/docs/biobricks/ contains my work in progress.
11:07 < faceface> but I'll have a look
11:07 < kanzure_> faceface: surely you knew about biobricks beforehand?
11:07 < faceface> not that they had a conference
11:07 < kanzure_> :)
11:08 < faceface> http://www.marketwatch.com/news/story/geneart-ag-presents-its-work/story.aspx?guid={3E3BE543-8D0C-4BC1-973C-DD3B37908D76}&dist=hppr
11:08 < kanzure_> yeah, I'm missing that this year
11:08 < faceface> (when I pasted I didn't realize it was BioBricks)
12:35 < kanzure> http://www.washingtonpost.com/wp-dyn/content/article/2008/10/01/AR2008100101149.html
12:35 < kanzure> http://globalnation.inquirer.net/mindfeeds/mindfeeds/view/20081002-164190/In-Crisis-A-View-from-the-Trenches
12:35 < kanzure> http://jama.ama-assn.org/cgi/content/full/300/13/1580
13:16 < faceface> jama?
13:17 < faceface> google won't let me look at the wahington post
13:30 < nsh> wgat?
13:30 < faceface> good idea
13:30 < faceface> ?
13:37 < fenn> what's with all the wall-street mumbo jumbo?
13:52 < Utopiah> fenn: just bankers requiring explicit forced donations from non-bankers in order to boost their ROI despite the market fluctuations, nothing new really
13:54 < Utopiah> (alias Robin Hood^-1 alias classical world resources redistribution)
13:55 < fenn> i meant why was kanzure posting links to these pointless newspaper articles
13:57 < nsh> the contain encoded messages, clearly
14:08 < faceface> complexity?
14:37  * nsh was just being glib
14:38 < bkero> glubglubglub
17:06 < kanzure___> fenn: received those links from somebody pointing out the commonality of 'complexity' between the recent articles
17:07 < kanzure___> not sure it has much relevance of course :)
17:08  * kanzure___ just saved and submitted http://heybryan.org/~bbishop/docs/me302/2008-10-02_terminal_support_final.jpg 
17:08 < kanzure___> 'part mating' is a joke.
17:08 < kanzure___> a bad joke.
17:10 < fenn> highly unenlightening, as any drafted diagram ought to be
17:15 < kanzure___> you already know I'm being prodded into following a workbook :)
20:36 < kanzure___> what's the longest you've gone writing code without testing it?
21:09 < kanzure___> bwaahahah. four hours of coding and only one syntax error.
22:39 < kanzure> http://heybryan.org/~bbishop/docs/repo/2008-10-02.pl
22:39 < kanzure> wtf
22:39 < kanzure> I don't remember writing the majority of that ..
23:13 < kanzure> "This goes to the heart of the infamous "Grounding Problem" in machine intelligence and to a pragmatic view of semantics.  Simply put, the "meaning" of any referent corresponds with its observed effect within a particular context.  No end-to-end grounding is ever ultimately needed nor ultimately possible."
23:13 < kanzure> "This strikes me as especially funny when it involves would-be AI creators imagining that a "relatively simple" computer program could encapsulate a process delivering "intelligence" while they remain blithely unaware and unconcerned about the essential contribution of the layers of software, microcode, electronic hardware, turtles all the way down... (within an environment of adaptation supporting such activity.)"
23:28 < kanzure> "Interesting that the first successful private commercial launch to orbit was achieved right at the peak of the end of capitalism."
23:57 < kanzure> 75359
23:57 < kanzure> :)