--- Log opened Sun Sep 16 00:00:27 2012
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04:46 < kirka> Hi guys
04:47 < chris_99> hello
04:48 < kirka> I'm interested in molecular manufacturing, and I'm doing some web searching about companies that do it
04:48 < kirka> By quite some time now
04:49 < kirka> It's interesting that there are few such companies, and most of them have became inactive some years ago
04:49 < kirka> For example Nanorex
04:51 < kirka> It just became inactive in 2008, and if you serach a lot you just find that some employees just don't work there anymore
04:53 < kirka> But I couldn't find a financial reason of Nanorex diying
04:53 < chris_99> interesting,  their webpage is still up
04:53 < kirka> Yes it is.
04:54 < kirka> And their software NE1 is quite usable (though written in bad programming style), but it doesn't work with modern OSes
04:55 < kirka> It's ridiculous that such a program just lies abandoned for 4 years
04:55 < chris_99> is it OSS?
04:55 < kirka> Yex
04:55 < kirka> *yes
04:55 < kirka> https://github.com/kanzure/nanoengineer
04:56 < kirka> kanzure could know more about this
04:57 < kirka> Inside is spaghetti code, no wonder that it's so unportable
04:58 < chris_99> heh
04:58 < kirka> And Nanorex isn't the only company that ceased activity: Institute for Molecular Manufacturing is like this too
04:59 < chris_99> hmm, is there examples of the kind of things they made?
04:59 < kirka> Both of these organisations research theoretical aspects of MNT
05:00 < chris_99> MNT?
05:00 < kirka> Molecular NanoTechnology
05:00 < chris_99> oh i assumed they actually manufactured stuff
05:00 < chris_99> based on their designs
05:01 < kirka> Zyvex does that, but it;s in early stage
05:01 < chris_99> maybe that's why they folded, if noone bought their designs?
05:01 < kirka> by the way Zyvex seems to me the only active firm doing real MNT
05:03 < kirka> Well, designs by themeselves are just curiosities, but the software is good. Maybe it's the financial crisis that dried them out of funding
05:03 < kirka> But they just suddenly stopped
05:04 < kirka> The whole situation around nanotechnology is strange today
05:05 < kirka> Adepts of nanoparticle & nanocoatings receive 100% of gov funding
05:06 < kirka> While real MNT is pushed to the site
05:06 < kirka> *side
05:07 < kirka> It's strange because Drexler, who established the field had molecular assebler as final goal
05:08 < kirka> So, the term "nanotechnology" has been redefined by synthetic chemists and material sciencists to include their work
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05:10 < chris_99> i love the idea of a molecular assembler, that'd be amazing
05:11 < kirka> As a result we have now very few people who research molecular nanotechnology.
05:11 < kirka> Yes, I love the idea too
05:14 < kirka> So, I don't understand, why there is so little funding given to projects that lead to moecular assebler
05:15 < kirka> There seems to be a lot of politics in this question
05:17 < chris_99> are they any proposed ideas for how a molecular assembler would work
05:17 < chris_99> *there
05:18 < kirka> Yes, here is bibliography http://www.molecularassembler.com/Nanofactory/AnnBibDMS.htm
05:19 < kirka> This paper for example http://www.molecularassembler.com/Papers/MinToolset.pdf
05:19 < chris_99> cheers :)
05:20 < kirka> Actually, Drexler published a solid book on the subkect 20 years ago: "Nanosystems:    Molecular Machinery,    Manufacturing,and Computation"
05:23 < kirka> Hmm, my timing isn't right - it's early morning in US
05:24 < kirka> That's why not so many active users
05:24 < kirka> I'm from Russia
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05:30 < kirka1> reconnected
05:31 < chris_99> yeah it's a weekend too
05:33 < kirka1> Well, I'm not in a hurry, heh
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06:27 < nmz787> kirka1: i am holding a ruusian toy terrier (dog)
06:27 < kirka1> heh
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06:51 < kirka1> Logs of your channel are interesting
06:51 < kirka1> >< kanzure> just got off the phone with the nanoengineer-1 funder
06:52 < kirka1> >< kanzure> he stopped funding it
06:52 < kirka1> As expected.
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07:10 < kirka1> btw is kanzure often here?
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07:13 < nmz787> kirka1: yes
07:13 < kirka1> That's good
07:13 < kirka1> He worked on NE-1
07:19 < nmz787> well he saved it from being completely abandoned
07:20 < nmz787> I was trying to get it to run without all the chroot stuff, but haven't been successful at getting it to work
07:20 < kirka1> Good pice of aoftware, but inside it's pretty messy
07:20 < kirka1> *piece
07:21 < kirka1> Such programs shouldn't be written in python.
07:21 < chris_99> nmz787, why's it need chroot?
07:21 < kirka1> Old libraries
07:21 < chris_99> ah
07:21 < chris_99> theres nothing inherently wrong with python
07:21 < kirka1> And it doesn't use multithreading
07:22 < kirka1> Speed, portability, threading, standartisation - python doesn't have it
07:22 < kirka1> I have used it years ago
07:22 < chris_99> hmm, i'm not sure i'd agree with all of those
07:23 < chris_99> it can do multiprocessing
07:23 < kirka1> Yes, you are right
07:23 < chris_99> but the lack of decent threading is annoying
07:24 < kirka1> I agree that it's not bad language
07:24 < kirka1> But if a had to write something like NE1 it would be clojure@jvm, or C.
07:25 < kirka1> Of course simuation modules should be written in C
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07:27 < nmz787> python is the get-shit-done language though
07:27 < eudoxia> I'd write the whole thing in some relatively high-performance language
07:27 < nmz787> and there are JIT compilers/interpreters
07:27 < eudoxia> NE1 goes slow as balls with anything over 10,000 atoms
07:27 < nmz787> eudoxia: C?
07:28 < eudoxia> nmz787: or C++, maybe Java
07:28 < eudoxia> I thought that Python JIT thing had failed?
07:28 < kirka1> Yes
07:28 < kirka1> C++/Java could be used
07:29 < kirka1> Python isn't suited for compilation
07:29 < kirka1> There is PyPy, but it has even more compatibility problems
07:30 < nmz787> Java is not high-performance IMO, at least not compared to python
07:30 < kirka1> Personally, I like lisp for speed and expressivnes, but for a project with team of developers it's too alien technology
07:30 < kirka1> So C++/Java
07:30 < eudoxia> which lisp?
07:30 < kirka1> nmz787 JVM is very fast today.
07:30 < kirka1> Scheme and Common Lisp
07:31  * eudoxia high-fives kirka1
07:31 < chris_99> Java has proper threading nmz787
07:31 < kirka1> heh
07:31 < nmz787> hmm
07:31 < chris_99> unlike python
07:31 < nmz787> ever since I learned java applets like 15 years ago, I never liked it much
07:31 < nmz787> hmm
07:31 < eudoxia> you are into MNT and use Common Lisp? I thought I had split personality for a while there
07:31 < nmz787> i know a lot of big companies use java
07:32 < chris_99> Java is very different to Java applets
07:32 < kirka1> Why? NOte that Merkle and Drexler have ties with AI and AI was strongly connected to common lisp
07:32 < kirka1> eudoxia I'm also into robotics http://rghost.ru/40311893.view
07:33 < eudoxia> kirka1: what does it do?
07:33 < chris_99> wow nice :) have you built that?
07:34 < kirka1> It;s a second version of my prototype, I'm learning the first one to walk (though servos are quite weak)
07:34 < kirka1> First one is pretty DIYsh: http://rghost.ru/40398113.view
07:35 < chris_99> did you make the plastic with a 3d printer?
07:35 < kirka1> You guys are probably older than me, I'm student in cybernetics faculty of my city's university
07:35 < kirka1> No, it's polycaprolactone, handmade
07:36 < kirka1> Thermo-polymer
07:36 < kirka1> Second prototype will be 3d-printed
07:36 < nmz787> kirka1: http://www.youtube.com/watch?v=gDsKEexQtwI
07:36 < nmz787> my old roommate built that
07:36 < kirka1> Cool
07:36 < nmz787> http://www.youtube.com/watch?v=83LnRTKE1qw
07:37 < nmz787> "Hexapod Robot Movement and Walking Demo"
07:38 < kirka1> Robotics is cool, some 20-30 years ago people thought that in future robots will do hard work for them
07:39 < kirka1> But it didn't happen exactly that way
07:40 < kirka1> Though today service robotics market begins to emerge
07:40 < kirka1> Heartland, Redwood robotics
07:41 < kirka1> It's good that investment moves from internet to ral world again
07:41 < kirka1> *real
07:43 < eudoxia> kirka1: have you heard of http://www.zyvexlabs.com/Research.html
07:43 < eudoxia> http://nextbigfuture.com/2010/05/jim-von-ehr-founder-and-owner-of-zyvex.html
07:44 < eudoxia> "We are confident that we will be able to create simple, blocklike objects within the next five years. From that point, capabilities should grow fairly rapidly. Once simple block objects are created, we can programmably assemble them to make more complex objects. Zyvex has already identified a number of market opportunities for these. Once we get the basic capability of creating these simple objects, we can expand thei
07:44 < eudoxia> r complexity and sophistication rapidly."
07:44 < eudoxia> "[...] by 2020 we should have rudimentary molecular manufacturing systems in operation"
07:44 < kirka1> Yes, I researched about their activity
07:44 < kirka1> There was one presentation
07:45 < eudoxia> yeah, you mean the transcript on the Accelerating Future people blog?
07:45 < kirka1> No, it's hard to find
07:45 < kirka1> www.nnin.org/doc/snmr10/zyvex-cornell-2010.pdf
07:45 < kirka1> That's it
07:46 < kirka1> And also seems that this corp works with Zyvex: http://www.icspicorp.com/
07:46 < kirka1> I have high hopes about that
07:46 < kirka1> Finally, integrated parallel MEMS-AFM
07:47 < eudoxia> oh I remember this one
07:47 < kirka1> Tey still keep their products in secret
07:47 < kirka1> *they
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07:47 < kirka1> NOtice that both Zyvex and icspi are working with DARPA
07:49 < eudoxia> their APM page has nothing but a logo
07:49 < eudoxia> Since DARPA seems to make everything out of sci-fi, I should just ship them a copy of The Diamond Age to see if it will speed up their program :)
07:49 < kirka1> Yes, but they say "2011 icspi reports the first images taken with a CMOS-MEMS scanning probe microscope"
07:49 < kirka1> Heh, you are right
07:50 < kirka1> I love that book, Stephenson does a lot of technical research before writing a book
07:51 < eudoxia> It's really refreshing when fiction is factually accurate, and I thought the idea of the feed line was a very creative and plausible addition
07:51 < eudoxia> It's a plausible midpoint between completely offloading manufacturing capabilities to the end user: Complex atomic structures are manufactured at Source Victoria, and the assemblers don't have to do any molecular manufacturing, they just grab the prefab pieces and put them together
07:51 < kirka1> Yes, that's a way for big nanotech corps to protect their IP
07:52 < kirka1> And a good way to prevent disasters
07:53 < eudoxia> So, big complex SPMs and vacuum chambers are not needed for the personal assemblers, they are only used at the source. The personal nanofactories are just a micropositioning system with a billion end-effectors
07:53 < eudoxia> Disasters? Like gray goo or people printing MOABs?
07:53 < kirka1> Yes.
07:54 < eudoxia> If nanotech is limited to silicon or diamond I doubt people will be able to print bombs
07:54 < eudoxia> Although, you could print a machine to make ammonia and build fertilizer explosives
07:54 < eudoxia> You know, probably
07:55 < kirka1> It's complex to label object being manufactured as "dangerous", yes.
07:55 < kirka1> There should be a lot of heuristics.
07:55 < kirka1> It's also interesting that there is only one time the word "spaceship" is mentioned in book.
07:56 < eudoxia> I think it's pretty useless to try and scan pdb files for potential weapons
07:56 < kirka1> Probably Stepehenson understood that, but it ruined stabe settings
07:56 < eudoxia> The entire periodic table is a fucking bomb
07:57 < kirka1> And probably everybody who wanted to fly to space did it, and stable conservative part of society remained on Earth.
07:57 < kirka1> Yes, the question of safety worries me
07:57 < kirka1> Active defence systems should be developed first
07:58 < kirka1> But anyway transient time is most dangerous
07:58 < eudoxia> Active shields like what Drexler talked about in Engines?
07:58 < eudoxia> the ones for gray goo?
07:58 < kirka1> Yes, something like that
07:59 < kirka1> Gray goo is an old concept, but I think that precise weapon systems targeted at humans (and even specific persons) are possible
08:00 < kirka1> Viruses are such systems, and they are even atomically precise, heh
08:00 < eudoxia> I don't think gray goo will ever happen, all the plausible MNT systems I've seen are too big to fit inside, say the volume of a Respirocyte, and simply not fast enough
08:01 < eudoxia> But viruses are made of protein, which is made with ribosomes but can't be made with MNT
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08:02 < kirka1> I too don't think that gray goo is possible, but less devastating weapons seem possible.
08:02 < kirka1> Yeah, virus is just an analogy
08:03 < eudoxia> Maybe a cookie cutter may be possible
08:03 < eudoxia> I mean, it doesn't take any tooltips, any logic, it's just two counter-rotating rods in a vacuum bag
08:03 < eudoxia> i mean, disks
08:03 < kirka1> I just imagine respirocyte filled with good poison.
08:03 < kirka1> They had control system inside
08:03 < eudoxia> Pure diamond or silicon crystals may be enough
08:04 < kirka1> Maybe.
08:04 < eudoxia> I wonder what happens when one swallows diamond powder...
08:04 < eudoxia> They did?
08:04 < kirka1> Yes, to destroy prisoners
08:05 < kirka1> Actually I've read that fullerenes make mouses live two times longer
08:05 < eudoxia> Oh right the seven-minute timer
08:06 < kirka1> btw, before possibility of nano-weapons there will be some time (it begins now, actually) when bioweapons will become dangeous
08:06 < kirka1> Molecular biology develops at fast pace
08:06 < kirka1> We already design simple proteins
08:06 < eudoxia> definitely a faster pace than MNT
08:06 < kirka1> Yes, sadly
08:06 < eudoxia> I mean, it's basically just Merkle and Freitas who last published anything in 2008, and Moriarty is, well
08:07 < kirka1> BUt self-assembly is also viable route
08:07 < eudoxia> I suppose
08:07 < kirka1> MOriarty did already published results?
08:07 < eudoxia> He wrote a paper about flipping bonds on Silicon surfaces
08:08 < kirka1> I'll search for it, thanks
08:08 < eudoxia> last I checked they had just achieved atomic resolution on C(110) diamond with a qPlus AFM
08:09 < eudoxia> The grant runs out in 2013
08:09 < kirka1> I don't like tha fact that Drexler, Merkle and Freitas ere marginalized in their own field by bunch of synthetic chemistry and material science guys.
08:09 < eudoxia> So unless they had some major breakthroughs, I doubt anything will come out of it. Definitely not a full-implementation of the Minimal Toolset.
08:09 < eudoxia> Oh yeah I was pretty pissed off when I first found out about that.
08:10 < kirka1> The question is, what could I do about that.
08:10 < kirka1> Well, I'm studying physics.
08:11 < eudoxia> The quickest path to MNT is probably patterned epitaxy
08:11 < kirka1> Yes, Zyvex does that.
08:11 < kirka1> I hope they'll succeed.
08:12 < eudoxia> I doubt I can just call DARPA and ask "Yo how is your APM program doing?"
08:12 < kirka1> Heh
08:13 < kirka1> Actually I suspect that military has some APM program.
08:13 < eudoxia> Well they better
08:13 < kirka1> But it doesn't change situation for us, civilians (yet).
08:14 < eudoxia> Even if it ends up like in the Diamond Age, at least I'll be able to laugh and angrily shake my fist at people and say "Drexler was right, he was right ALL ALONG"
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08:15 < kirka1> Seems that he'll become a major historical figure in future history textbooks.
08:15 < eudoxia> I'll be very disappointed if he doesn't
08:19 < eudoxia> DARPA's living foundries program might be worth looking into
08:19 < kirka1> But again - I don't like passivity and technical incompetence (no offence meant) of h+ movement - it consists mostly of philosophers and non-sciencists, that wait for Future to solve their problems. Moore's law isn't a "law", it's a consequence of tens of thousands of physicists and engineers working hard to create even more complex ICs.
08:19 < kirka1> So, the main question is "How can I influence future according to my wishes".
08:20 < eudoxia> It's okay dude everyone here feels the same
08:20 < kirka1> Yes, thanks, I'll check.
08:20 < kirka1> That's good.
08:21 < eudoxia> we're always bitching about humanity+ and SIAI
08:23 < kirka1> Heh
08:23 < kirka1> btw J.C.Venter right now is probably debugging his synthetic minimal genome
08:25 < kirka1> afk for ~1 hour (inline skates)
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08:39 < Mokbortolan_1> kirka1: so, are you saying "the h+ movement" should endeavor to be more technically competent, or that more technically competent people should join, or what?
08:47 < eudoxia> I bet it's the first
09:06 < kanzure> kirka1: nanorex closed down because mark sims didn't want to keep funding it
09:06 < kanzure> kirka1: Institute for Molecular Manufacturing is just a thing for freitas and merkle to publish stuff
09:06 < kanzure> kirka1: zyvex doesn't really do anything mnt related.. just some materials stuff, maybe positioning stuff.
09:11 < kanzure> http://diyhpl.us/~bryan/papers2/nanotech/ might be helpful
09:11 < kanzure> freitas is always looking for new papers to publish, but most of his simulations aren't entirely practical yet(?)
09:20 < kanzure> "In particular, presumably as a result of this case, JSTOR now requires strong authentication from the individual MIT account holder, instead of permitting access from MIT's IP address space as they used to"
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09:32 < kanzure> well so much for kirka
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09:33 < kanzure> kirka: welcome back.
09:33 < Mokbortolan_1> I think I'm pretty technically competent... within my sphere.
09:33 < kanzure> Mokbortolan_1: that's the first sign that you're not
09:33 < Mokbortolan_1> d'oh!
09:34 < Mokbortolan_1> though, my sphere is in corporate IT
09:34 < Mokbortolan_1> I'm competent at taking things out of the box and turning them on!
09:37 < Mokbortolan_1> and regurgitating things I read on the internet: http://i.imgur.com/P8eig.jpg
09:38 < kirka> kanzure Hi
09:39 < kanzure> kirka: hello.
09:39 < kirka> kanzure I wanted to discuss Nanorex and NE1
09:39 < kanzure> i left you some messages http://gnusha.org/logs/2012-09-16.log
09:40 < kirka> Jh, thanks
09:41 < kirka> Well Mark Sims didn't look like MNT guy
09:41 < kirka> It was business for him
09:41 < kirka> If IMM is active, it's good
09:42 < kirka> And what about NE1? Would it be useful for anybody?
09:43 < kanzure> nanorex started working with paul rothemund to integrate some dna origami stuff into nanoengineer
09:43 < kanzure> they were thinking that dna origami would be more practical than molecular nanotechnology stuff
09:43 < kirka> And it didn't work? Seems that only Seeman continues developing DNA origami
09:44 < kanzure> dna origami works fine. paul rothemund and erik winfree's labs still do dna origami. ned seeman is doing crystallography stuff i think.
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09:47 < kanzure> mark just didn't know how to make money off of nanoengineer, and he was afraid there was no practical utility in it
09:48 < brownies> how does one make money off it?
09:48 < kirka> Mokbortolan_1: I think that h+ movement should have active, not passive attitude toward science/technology. It would be logical for such movement to actually move science/technology forward. From PR point of view it makes movement serious.
09:49 < nmz787> kirka: we are active
09:49 < kirka> You are oldschool guys. heh
09:50 < nmz787> huh?
09:50 < skorket> ???
09:50 < nmz787> we're all pretty 'young'
09:50 < kanzure> brownies: off of nanoengineer? well, i still want it to continue existing even without funding.
09:50 < nmz787> 20-30
09:50 < kirka> Then, oldschool by spirit
09:51 < skorket> what are you talking about?
09:51 < kirka> In media h+ looks like pop-scientific religion
09:52 < kanzure> ignore the media
09:52 < kirka> I do
09:52 < kirka> But there are people who don't
09:52 < kanzure> ignore those people
09:52 < kirka> And with this image theu discard the whole ide of technoprogressivism
09:52 < kirka> *idea
09:52 < kanzure> technowhat?
09:52 < kirka> You name it
09:52 < nmz787> normal people are not scientific or progressive
09:53 < nmz787> they follow the media and that's it, and the media is controlled by old white dudes who just want slavery to come back
09:53 < skorket> kirka, instead of talking about it, do it.  If you want something changed, help change it
09:54 < kirka> Yes, you are right, that's my attitude
09:55 < kirka> But in the end PR influences funding, without money it's ahrd to do anything
09:55 < kanzure> we have money available for projects
09:55 < kanzure> more funding is always nice, but not necessary
09:56 < kirka> Ok [by the way, my english is rather dry becaouse I read mostly technical texts]
09:56 < kirka> So, about NE1
09:56 < kirka> I ran it recently, the interface is quite convenient
09:57 < nmz787> kirka: dry is good, as long as you can spell OK
09:57 < kanzure> kirka: linux?
09:57 < nmz787> we're all pretty much scientists or computer nerds
09:57 < nmz787> or engineers
09:57 < kirka> No, winXP@VM
09:57 < kirka> That's good
09:58 < kanzure> i suggest learning linux :)
09:58 < kirka> I know it
09:59 < kirka> Actually, I think that monolithic OSes and X86 are things from second millenium
10:00 < kirka> But we have this technology and have to use it
10:01 < kirka> So, NE1 source is complex
10:01 < kirka> And it's slow
10:01 < kanzure> it runs pretty fast for me
10:02 < kirka> btw do you still have to use old libraries to run it on Linux?
10:02 < kirka> Would you write it in another way, if you were to do it?
10:02 < kanzure> yes you must use older libraries for now https://github.com/kanzure/nanoengineer#installing
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10:02 < brownies> kanzure: well, sure. i would like lots of things to continue without funding.
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10:03 < kanzure> kirka: once i finish upgrading the old libraries, i will split off different sections into smaller libraries.
10:03 < kirka> Is it python or architecture fault that it's so unportable?
10:03 < kanzure> it's very portable
10:04 < nmz787> i have it on my laptop
10:04 < nmz787> i take my laptop all over the place!
10:04 < nmz787> :P
10:04 < kirka> On WinXP?
10:04 < kanzure> yes it runs on windows xp :(
10:04 < kirka> Does Win7 have very diffrent API?
10:04 < kanzure> i have not tried windows 7
10:05 < kirka> As far as i know sciencists often use windows.
10:05 < kanzure> nope
10:05 < nmz787> nah
10:05 < kanzure> fuck windows
10:05 < nmz787> it depends
10:06 < brownies> haha
10:06 < kirka> Well, there was time when I used only linux, but then I began working in some heavy CADs, and had to move to windows.
10:06 < nmz787> i had an english teacher (b.s. in electrical engi, phd in history) that totally surprised me when he was talking about linux
10:06 < kanzure> yes, CAD is a good reason to use windows. true.
10:06 < kanzure> if you do not need solidworks/catia/pro-engineer/autocad, you can use brlcad.org
10:06 < nmz787> i hate that video drivers generally suck in linux
10:07 < nmz787> unless you're super cautious about choosing hardware
10:07 < kirka> Yes, that thing too.
10:07 < nmz787> which in laptops is a bit of a pain
10:07 < kirka> Two screens were very complex to set up
10:07 < nmz787> also i have a tablet PC that I love (2nd tablet in last 5 years) and it kinda sucks on linux
10:07 < kanzure> kirka: ask jrayhawk about setting up 20 screens.
10:07 < ThomasEgi> kanzure, well for a while now, there's medusa for linux.
10:07 < kanzure> http://www.omgwallhack.org/home/jrayhawk/img/hovel/20120512_008.jpg
10:07 < nmz787> multi monitors are a breeze in ubuntu
10:07 < kirka> Heh
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10:08 < kirka> kanzure If NE1 is just a GUI (simulattion is done by another programs/libraries) Wouldn't it be better to write it about some JVM language?
10:08 < brownies> why do you need 20 monitors? o.O
10:08 < ThomasEgi> brownies, because of moar?
10:09 < kanzure> kirka: nanoengineer has lots of other things going on underneath like modeling and heuristics, rules, CAD, etc.
10:09 < brownies> ThomasEgi: oh, well, alright then.
10:09 < kanzure> the GUI is just one small part of nanoengineer
10:09 < kirka> Yes, nanodynamics is written in C
10:09 < brownies> but he's not even using half of the monitors in his picture!
10:09 < kanzure> iirc python can run on the jvm. i don't think that's a problem.
10:09 < kanzure> no not just nanodynamics, there are other things
10:10 < kanzure> like the file format python stuff
10:10 < kanzure> and the pdb support
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10:12 < ThomasEgi> kanzure, is that jrayhawk guy autistic/asperger or so? he ordered the gpu's by the position of their vga connector...
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10:12 < nmz787> ThomasEgi: i don't think so
10:12 < kanzure> jrayhawk is a hero
10:13 < kirka> kanzure Don't python's different versions make it more difficult to maintain? 2.6 2.7 3.1 and so on
10:13 < kanzure> not really
10:13 < kanzure> 2.7 has some minor differences to 2.6, but it's not important for nanoengineer really
10:13 < kanzure> i fixed the incompatibilities for python 2.x
10:13 < kanzure> support for python 3.x is not necessary
10:13 < kanzure> (at least, not now)
10:13 < kirka> Ok
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10:14 < ThomasEgi> yo
10:14 < kirka> So the only problem is old libraries?
10:14 < kanzure> yes
10:14 < kanzure> these are instructions for getting it to work with the old library versions:
10:14 < kanzure> https://github.com/kanzure/nanoengineer#installing
10:14 < kirka> Yes, thanks, I have read this repo
10:15 < nmz787> kirka: are you good with python?
10:15 < nmz787> i started trying to port it to newer libs
10:15 < kirka> I have used it years ago
10:15 < nmz787> so far i can get the GUI to come up, but a few buttons are missing and demo files dont load/show up
10:15 < kanzure> nmz787: you started in the wrong direction
10:15 < nmz787> ?
10:15 < kanzure> you took a non-working version and tried to make it work, which meant everything was broken
10:16 < kirka> It would be of great help if someone draw diagram of NE1 architecture
10:16 < nmz787> huh
10:16 < nmz787> it world
10:16 < nmz787> worked
10:16 < kanzure> i suggest taking a working version of nanoengineer, and breaking it one piece at a time
10:16 < kirka> There is a hundred of files, it's quite complex
10:16 < nmz787> that's what massive find-replace is for!
10:17 < kanzure> it starts here:
10:17 < nmz787> but the main complaint was actually numeric -> numpy/scipy
10:17 < kanzure> https://github.com/kanzure/nanoengineer/blob/master/cad/src/main.py
10:17 < nmz787> and scipy has a converter script
10:17 < kirka> afk 50 min
10:17 < nmz787> which helped with most of that
10:17 < kanzure> and these things:
10:17 < kanzure> https://github.com/kanzure/nanoengineer/tree/master/cad/src
10:17 < nmz787> now it seems i've got qt bugs
10:17 < nmz787> but i havent pushed recently to github
10:18 < kanzure> btw you should fix your commits :P it said "--NathanMcCorkle" instead of "Nathan McCorkle <nmz787@gmail.com>"
10:18 < kanzure> if you use the second format then github will know to link to your account
10:18 < kanzure> and git/email tools will know how to contact you
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10:19 < kanzure> oh also another thing i've neglected to mention is that there is a lack of unit tests
10:19 < kanzure> if unit tests are written, then it becomes much much easier to tell when things are broken
10:19 < kanzure> so few :( https://github.com/kanzure/nanoengineer/tree/master/cad/src/tests
10:20 < Mokbortolan_1> I just use what's in front of me or what's best for the job
10:20 < Mokbortolan_1> OS wars are stupid
10:21 < Mokbortolan_1> it's like saying "I prefer to use a rounded shovel."
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10:21 < strangewarp> Fool! Pointed shovels are superior!
10:21 < kanzure> Mokbortolan_1: it's not an OS war, it's a simple fact: i will not be able to help you if you continue to use windows
10:22 < kanzure> and since all you windows users have so far been completely unhelpful, i don't see much value in switching to windows
10:22 < Mokbortolan_1> that's fine
10:22 < kanzure> s/switching to/using
10:22 < Mokbortolan_1> what is this "switch"
10:22 < kanzure> i corrected myself already, you can't call me on that.
10:22 < Mokbortolan_1> like, dual-booting?
10:22 < Mokbortolan_1> :p
10:23 < Mokbortolan_1> I use Windows when I don't want to fiddle with stuff, and I use Linux when I do
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10:26 < Mokbortolan_1> so really, what you're saying is, "my mental toolkit doesn't contain that tool"
10:26 < nmz787> i have a VM of ubuntu running often
10:26 < nmz787> its OK fast
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10:27 < nmz787> but not native fast
10:27 < nmz787> but from what i've read there are too many issues with linux on this laptop
10:27 < Mokbortolan_1> I have a VM of OSX I use to help me write documentation :)
10:27 < nmz787> and i'm not a good enough coder (or not devoted enough with enough concentration/attention span)
10:27 < nmz787> kinda like Mokbortolan_1 said, it works in windows
10:28 < nmz787> and the VM works flawlessly because it doesn't need any of the real drivers
10:28 < nmz787> last summer I used a mac book pro and developed in a ubuntu VM
10:28 < Mokbortolan_1> I like to think that as a user, I've transcended OS choice
10:28 < nmz787> that worked surprisingly well
10:29 < kanzure> why a vm? why not just ssh into something?
10:30 < nmz787> you need tubes for that
10:30 < nmz787> and i had no reliable tubes at home that summer
10:32 < nmz787> kanzure: if you were a bear, i think this is what you'd look like http://upload.wikimedia.org/wikipedia/commons/6/63/Lippenbaer-24.jpg
10:35 < Mokbortolan_1> http://i.imgur.com/H0poN.jpg <-- chemistry joke
10:47 < kanzure> nmz787: if that's a link to winnie the pooh, i will be amused
10:48 < kanzure> jrayhawk: there is a surprising lack of content in http://diyhpl.us/~bryan/papers2/nutrition/ and i blame you. will you fix this?
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10:51 < kirka> kanzure Does there exist desigm document, or feature list for NE1? It would be helpful to know how the complete CAD should work.
10:54 < skorket> finally!  got a V-USB example to work
10:55 < kanzure> kirka: no. there are some documents on the wiki, but i don't think they are complete. mostly they are tutorials.
10:58 < chris_99> nice skorket, i've just been trying to get USB to work on the PIC
10:59 < skorket> I imagine it might be easier depending on what you're doing.  (some) PICs are way faster, might even have some USB built in and probably have a lot more supporting software for it
10:59 < kanzure> hm i should recover the nanoengineer wiki before it goes poof. it's been spam-attacked a few times in the past few years.
10:59 < chris_99> skorket, the lib is a bit crap tbh
11:00 < kirka> kanzure Wiki went offline some days ago.
11:00 < skorket> V-USB?
11:00 < chris_99> no, the one for the PIC
11:00 < kanzure> http://www.nanoengineer-1.net/mediawiki/index.php
11:00 < kanzure> fuck.
11:00 < kirka> kanzure It would be godd if you made archived version of wiki articles
11:00 < kirka> *good
11:02 < kanzure> ok i will call mark in a few hours and ask him wtf
11:02 < skorket> ah, interesting.  Not that V-USB is probably much better.  There's the ATMega32u which has some USB built in but I'm not in the position to switch over to that yet.  Plus it's slightly more expensive
11:03 < kirka> skorket I program MCUs too
11:03 < kirka> skorket For USB I use PL2303 converter. Cheap and easy.
11:05 < chris_99> what interface does that use kirka
11:06 < kirka> chris_99 It's UART to USB converter
11:06 < skorket> $6 single quantity from mouser.  FTDI chips are about $5 single quantity.  ATMega328 are about $3 single quantity.  FTDI seems to be the standard go-to chip (it's what Arduino uses).  I've been recommended PL2303 before but I don't understand why that's desirable over the FTDI chip or why I shouldn't just use V-USB on an ATMega for low speed applications
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11:06 < chris_99> hmm, doesn't that mean you can only do serial comms kirka
11:06 < kirka> Yes I do, heh
11:07 < kirka> I'm more intrested in applying MCUs in robotics
11:07 < kirka> There interfaces are irrelevant
11:08 < kirka> I seriously learned programming with AVR assembly
11:09 < chris_99> yeah it's a nice way to learn asm, with MCUs
11:09 < skorket> interfaces are the ways you communicate with the widgets you build.  They're important
11:10 < kanzure> kirka: do you know Медведев Данила?
11:10 < kirka> chris_99 Yes, x86 is full of legacy hacks, it's pain to programm it in assembly
11:10 < kirka> kanzure He is leader of russian transhumanists society, I am coutious about him.
11:10 < kirka> *cautious
11:11 < kanzure> do you talk with him regularly?
11:11 < kirka> kanzure It's about nanoinventor CAD?
11:11 < kirka> No, not at all
11:11 < kirka> I'm on my own
11:11 < kanzure> ah okay.
11:11 < kirka> Rusnano is a fraud mostly
11:11 < kanzure> oh? i know very little about rusnano
11:11 < kanzure> i know they have about $10 billion USD
11:11 < kirka> Don't take them seriously, it'll save your time
11:12 < kirka> That's some scheme of some officials to use gov's money according to their interests
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11:13 < kanzure> i thought maybe rusnano companies would use nanoengineer
11:14 < kirka> It's possible, but rusnano is just another fund that invests in nanoparticles, nanocoatings, LEDs, and so on.
11:15 < kirka> It is a part of PR company, executed bu government circles to make Russia a better place for investnment in investor's eyes
11:16 < skorket> woot!  I made an LED turn on!
11:16 < kirka> I wouldn't invest in Russia if I were an investor, heh.
11:17 < kirka> kanzure: Do you plan to continue sime work on NE1?
11:17 < kanzure> yes
11:18 < kirka> Do you search for investors?
11:18 < kanzure> no
11:18 < kirka> That's good
11:18 < kanzure> but! if you have piles of money, i will take these piles from you.
11:19 < kirka> Heh, I'm just young university student
11:21 < kirka> Matvey Ezhov looks naive with his proposal
11:21 < kirka> I'm rereading NE-dev mailing list
11:22 < kirka> NE1 uses Nanodynamics becaouse there are motors and anchors available?
11:22 < kirka> *because
11:26 < kanzure> i think so, yes. i have focused more on the "under the hood code" and less the simulation stuff.
11:26 < kanzure> so cad/src/* not sim/src/*
11:27 < kirka> I looked in sim/src, it would be a pain to multithread this.
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11:35 < kirka> kanzure btw were does Drexler work now? It's hard to find.
11:36 < kanzure> dunno
11:36 < kanzure> he just blogs once a year or something
11:36 < kirka> Also, he is writing a book
11:36 < kanzure> meh
11:36 < kanzure> http://metamodern.com/
11:37 < kirka> Yes, I'm reading him
11:37 < kirka> He couldn't have given up on his vision
11:38 < kanzure> vision is worthless, everyone has that.
11:38 < kirka> Well, he is Phd
11:38 < kanzure> so?
11:38 < kirka> He has the knowledge to realize his vision
11:39 < kirka> Maybe he doesn't have enough money, yes
11:39 < kanzure> iirc he didn't write any of the nanoengineer software while working at nanorex
11:39 < kirka> He isn't a programmer
11:39 < kanzure> programming is not difficult
11:39 < kanzure> and is a necessary task to make mnt a reality
11:39 < kanzure> mnt is difficult
11:40 < kirka> Personally, I program math intensive software, there math id more important than code (for example - computer vision).
11:41 < kirka> He has written Nanosystems, good physical book on subject.
11:41 < kanzure> http://gnusha.org/stuff_to_deal_with/nanosystems.tar.gz
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11:41 < kirka> Oh, cool
11:41 < kirka> Full version
11:41 < kirka> Thanks
11:41 < eudoxia> Drexler is at Oxford now I think
11:42 < eudoxia> I think Drexler only gave up on direct-to-diamondoid, he now prefers proteins and peptides and stuff
11:42 < eudoxia> which is rather sad
11:42 < kirka> Well, biotech rises
11:43 < eudoxia> Oh definitely, it's just that, after 25 years of spearheading the idea of dry UHV MNT
11:43 < kirka> And we'll have to deal with proteins anyway
11:43 < eudoxia> he sort of gave up
11:43 < eudoxia> breaks my heart
11:44 < kirka> kanzure Why do you think that Zyvex doesn't do APM? www.nnin.org/doc/snmr10/zyvex-cornell-2010.pdf says that they are making progress with atomic layer epitaxy
11:44 < kirka> eudoxia It is sad, if it's true
11:45 < eudoxia> epitaxy might scale better than the min toolset
11:45 < eudoxia> although, germanium can be expensive
11:45 < kanzure> kirka: i am underinformed on zyvex :) their website is pretty bad.
11:46 < kanzure> kirka: are you familiar with diybio? http://diyhpl.us/wiki/diybio/faq
11:46 < kirka> Yes, and they seem to be quiet about their work
11:46 < eudoxia> If Germanium can be recovered from the post-etching fluid then it could be made a little cheaper
11:46 < kirka> kanzure I'm intrested in molecular biology
11:47 < kirka> eudoxia DCB6Ge contains just one Ge atom, whole nanofactory shouldn't include more than ~ten grams of Ge
11:47 < eudoxia> that's the minimal toolset
11:47 < eudoxia> epitaxy just uses an SPM on a Hydrogenated Si surface
11:48 < eudoxia> the whole assembler can be a UHV chamber and a scanning tunneling microscope with a few thousand tips
11:48 < kirka> btw IBM/Zurich pushes state-of-the-art in AFM
11:48 < kirka> *few billion tips
11:49 < eudoxia> I bet the first application of Zyvex's work will be the synthesis of atomically-precise AFM tips
11:49 < eudoxia> not that they would last anything, but, you know, it's useful
11:50 < kirka> kanzure If I will have a good idea, I have a whole cytology university nearby, they could get intrested
11:50 < kirka> eudoxia Yes, and I don't ubderstand why we don't still have ALE patterned tips
11:51 < kirka> kanzure eudoxia: http://www.icspicorp.com/ does next generation AFM.
11:51 < kirka> MEMS parallel tips
11:52 < kirka> They are affilated with Zyvex
11:52 < eudoxia> I know you told me this morning
11:52 < eudoxia> or, whatever time it was in Russia
11:52 < kirka> kanzure could be interested
11:52 < kirka> Heh
11:52 < kirka> It's already ~23:00
11:53 < kirka> Tomorrow's Control Theory
11:53 < kirka> Cool subject
11:53 < kanzure> time has no meaning in this place
11:54 < eudoxia> the APMC's website is depressingly vacuous
11:54 < eudoxia> https://apmc.zyvex.com/
11:55 < kirka> Yes, it's either they are unsuccessful, or they are so successful that they don't talk about it.
11:55 < eudoxia> exactly
11:55 < kirka> DARPA is there
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12:00 < eudoxia> which is great
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12:00 < eudoxia> but I want results, not reassurances
12:01 < kirka> I agree
12:01 < kirka> Well, precise ALE patterning of rectangle is good sign
12:02 < eudoxia> wake me up when they get to 3D :P
12:03 < kirka> Heh
12:03 < kirka> From the other front, reprogramming ribosome is promising.
12:04 < kirka> Making it read 4-codons vs 3-codons
12:05 < kirka> Actually, if we could predict folding of long proteins, we could also design new ones.
12:06 < kirka> But neither current supercomputers, nor algorhitms are not sufficient for this task.
12:12 < kanzure> kirka: http://diyhpl.us/laser_etcher/laser_etcher/
12:12 < kanzure> kirka: http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf
12:13 < kanzure> brownies: i'm having a brain fart. i wrote a unit test to test something that sometimes make an http request to get something unrelated to the actual unit test.
12:13 < kanzure> brownies: instead of passing in a boolean to disable that http request on the target function i'm testing, what should i do?
12:16 < kirka> kanzure cool
12:18 < kirka> kanzure But sequence design is musch bigger problem
12:19 < kirka> kanzure: If I knew innovative new gene or gene combination which does useful stuff, I would go straight to some big biotech company
12:20 < kirka> kanzure: Low price is good for iterationg design
12:20 < kirka> *iterating
12:21 < brownies> kanzure: write a getter function for that thing; the function will make the real http request in production, and simply return a cached/locally-stored value in test
12:21 < kirka> kanzure I do DIY, but I understand that it rarely pushes state-fo-the-art
12:21 < brownies> kanzure: although, hm, that's not quite right. you want to still test the asynchronous nature of it.
12:21 < brownies> kanzure: with ruby you'd use something like the VCR gem. with non-ruby you basically need to implement that sort of functionality.
12:22 < brownies> kanzure: i guess it depends how the bigger thing (that you're testing) uses the http request functionality; if it fires a request asynchronously, then there should already be an existing hook for the response anyway.
12:23 < brownies> so, yeah, do that.
12:24 < kanzure> brownies: it does not require the http request, or rather, i'm not testing that aspect
12:25 < kanzure> kirka: you aren't going to make up a "new sequence" like that. you will either find it in nature or do directed evolution or maaybe some rational protein design, but not much.
12:26 < kirka> kanzure Yes, so I think that the main problem is rational, computational design of proteins
12:26 < kanzure> brownies: maybe i will just make a mock object for the http request thing. http://www.voidspace.org.uk/python/mock/
12:27 < kanzure> kirka: "main problem" with what?
12:27 < kirka> kanzure Synthetic biology
12:27 < kanzure> synthetic biology does not focus on protein design
12:28 < kirka> Yes, there are metabolic networks and bunch of other stuff
12:28 < kirka> DIY DNA synthesizer is cool,of course
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12:29 < kirka> Oh, of course molecular biology
12:29 < kirka> Synthetic biology deals also with whole cells and organisms
12:29 < kirka> btw, have you seen Cyber Elegans ?
12:30 < kirka> http://code.google.com/p/openworm/
12:30 < kanzure> yes.
12:30 < kanzure> have you seen the nematode upload project?
12:30 < kirka> Yes
12:30 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/nematodeuploadproject/
12:30 < kirka> They still cannot determine synaptic weights
12:31 < kanzure> todd huffman thinks that vesicle placement is more important
12:31 < kanzure> http://3scan.com/
12:31 < kirka> I have digged cyber elegans code, it's quite simple, just point masses, springs and integrate-and fire neurons. And Euler integrator.
12:31 < kanzure> also you might be interested in http://github.com/kanzure/netmorph
12:32 < kirka> Cool
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12:32 < kirka> >Simulated Development of Neuron Morphology
12:33 < kirka> But personally, I don't like the idea of "mind uploading", it does lead to death of the subject and creation of the copy.
12:34 < kanzure> people should just say "neuron scanning"
12:34 < kanzure> "mind uploading" carries too much baggage. i want neuron data regardless of whether or not there is a "mind".
12:34 < kirka> Do you think that non-invasive mechanism is possible?
12:35 < kanzure> non-invasive imaging is already possible
12:35 < kirka> But not on single neuron, dendrit, or synapse level.
12:36 < kanzure> well.. if you are allowed to be invasive :)
12:36 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/In%20vivo%20imaging%20of%20single%20axons%20in%20the%20mouse%20spinal%20cord.pdf
12:36 < kirka> Heh
12:37 < kirka> There is a group of people that believes that if they will be frozen, then scanned layer by layer and then this data simulated, they won't die.
12:37 < kirka> That's ridiculous.
12:38 < kanzure> okay
12:38 < docl> why?
12:38 < docl> isn't life a series of copies from moment to moment anyway?
12:38 < kirka> That depends on your philisophical position.
12:38 < kanzure> docl: he has philosophical tie-ups with death apparently
12:38 < kanzure> kirka: we have an almost-strict no philosophy rule in here
12:38 < kirka> Okay.
12:39 < docl> you go to sleep, you wake up. who's to say it's not a copy that really wakes up?
12:39 < chris_99> an uploaded mind couldn't be an exact copy anyhow
12:39 < kanzure> "almost strict" means it is allowed if you are careful, or have something new to say, but otherwise i get grumpy :)
12:39  * docl shuts up
12:39 < chris_99> regardless of how invasive you are
12:39 < kanzure> docl: hasn't that argument been argued a thousand ways by now?
12:39 < kirka> Yes.
12:40 < docl> pretty much. the most convincing form involves breaking out quantum mechanics stuff I barely (if that) understand.
12:40 < kirka> So, I think cell repair machines is a right way to go.
12:40 < kanzure> kirka: you might enjoy reading these.. http://diyhpl.us/~bryan/papers2/longevity/
12:40 < kirka> It does not (almost) involve complex philosophy.
12:41 < chris_99> an uploaded mind is only going to be a rough estimate right?
12:41 < kirka> kanzure That's some big library heh
12:41 < docl> like, qm describes particles as just wave amplitudes, so it doesn't make sense to talk about specific atoms. that's like talking about specific calories or specific degrees of temperature
12:42 < chris_99> was that to me docl
12:42 < kirka> But why cell reapir machines aren'y enough for you?
12:43 < kanzure> kirka: cell repair machines don't exist yet
12:43 < docl> chris_99: it was to kirka
12:43 < chris_99> ah
12:43 < kirka> They could be easier to build then theory, algorithms and machines for brain scanning
12:43 < kanzure> kirka: 3scan.com already has a scanning microscope..
12:44 < docl> kirka: the concern I have is we maybe can't do one and can only do the other. could be a problem if you put all your eggs in one basket.
12:44 < chris_99> until we get infinite resolution ADCs mind uploading doesn't work imo
12:44 < chris_99> and even then...
12:44 < kanzure> i think regardless of what your philosophical views are, scanning brains is a useful thing to do
12:44 < kanzure> it's better than letting them rot in a grave
12:44 < docl> chris_99: depends on variables we don't really know yet. could be that all that matters from day to day is the rough connectome.
12:45 < chris_99> i dunno, what about chaos theory
12:45 < kanzure> ....
12:45 < kirka> Yes, in noninvasive way. And as a person who learned some amount of physics I cannot imagine how this much data could be transferred through electromagnetic field.
12:46 < chris_99> and how much a single change can effect something like a magnet on a pendulum
12:46 < docl> I agree with kanzure on that. even a rough copy is a historical document of sorts. worth keeping in its own right.
12:46 < chris_99> maybe, but i don't think it'll ever be an exact 'copy'
12:47 < docl> chris_99: you aren't an exact copy from one moment to another though. heat, brownian motion, chemical reactions... why should this be different?
12:47 < kirka> Trying to infer brain structure by EM radiation around it becomes ill inverse problem, it has multiple solutions.
12:47 < kirka> Yes, it's worth keeping, I agree.
12:47 < docl> there has to be some level at which we are self-repairing and stable otherwise we'd fall apart at the slightest shock. evolution has built us tougher than that.
12:48 < kanzure> docl: or maybe we are good at avoiding shocks
12:48 < kanzure> for instance, have you fallen off a cliff today?
12:48 < chris_99> docl, we're a transisition of internal states, which imo you can't just copy
12:49 < docl> kanzure: sure on a relative scale. I couldn't handle falling off a cliff. but I've undergone scads of solar radiation without even noticing it.
12:49 < chris_99> until you can do it on a molecular/quantum level
12:49 < kirka> Well, I'm glad that I have 50+ years to think about it.
12:50 < docl> chris_99: where do you think the empirical line is drawn? if you had a person with exactly the same connections between all of its neurons and very similar biochemistry, do you expect it to have no similar thoughts or many similar thoughts?
12:51 < kirka> Yes, MNT is something necessary for me to live longer than that. That partly explains my interest in it.
12:51 < chris_99> i think if you could 'copy' using some magic process that replicates the same atoms and quantum states, then yeah, it'd be an exact copy
12:53 < chris_99> however i think it wouldn't be a true copy in the sense of the word, when you turn it 'on' as its senses would cause an immediate divergance
12:53 < kanzure> so?
12:53 < docl> chris_99: I think you're falling into a quantum woo trap... It seems highly unlikely to me that anything subtler than say a covalent or ionic bond is relevant to the person having the same thoughts. there's too much noise for subtler stuff to survive in a human.
12:54 < kirka> I'm not sure about it. I do not know how brain works.
12:54 < kanzure> brownies: http://garybernhardt.github.com/python-mock-comparison/
12:54 < chris_99> even if there are no quantum effects, i still think you'd have to copy down to the atomic level
12:55 < kanzure> chris_99: why? the atomic configuration is constantly discarded
12:55 < docl> chris_99: most of the body is highly repeated biochemical components that are damaged and replaced routinely.
12:55 < kanzure> a nick in a certain protein isn't going to be propogated to the next protein that is built, unless it was of genetic or epigenetic origin
12:55 < chris_99> subtle variation in voltages etc. in the brain
12:56 < chris_99> basically i think the synapse weights etc. are highly analogue
12:56 < kirka> Probably chris_99 says that in highly nonlinear system arbitrary small change of input can produce arbitrary large change in output.
12:56 < chris_99> and the only way to make a true copy is to go to the atomic level
12:57 < chris_99> yeah exactly kirka
12:57 < kirka> I'm not sure about it.
12:57 < kanzure> chris_99: how do you explain neural networks that operate the same in a petri dish and in a simulation?
12:57 < chris_99> what about that kanzure?
12:57 < kanzure> do you think it's just magic??
12:57 < chris_99> no
12:57 < chris_99> resolution.
12:57 < chris_99> the brain is highly analogue
12:57 < kirka> I just think that if cell repair machines will constantly repair molecular machinery of the brain, it will continue to work good.
12:58 < docl> I don't think we're dealing with that kind of system chris_99. people wake up from hypothermia with the same memories. huge change in brain activity there.
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12:58 < chris_99> it appears to give the same output, but is it giving it the same to the nth decimal place kanzure
12:58 < kanzure> chris_99: i think you should read more neurophysiology papers.
12:58 < kanzure> or do more neurophysiology projects.
12:58 < kanzure> preferably both.
12:58 < docl> sure if you have thought A instead of thought B on a particular day it changes the course of your life. but we don't question the identity of the person because of it.
12:58 < chris_99> i've simulated neurons before
12:58 < kirka> kanzure btw >neural networks that operate the same in a petri dish and in a simulation looks interesting
12:58 < chris_99> and done ANNs
12:59 < kanzure> ANNs of course are not what we're talking about - too primitive, etc.
12:59 < chris_99> i'm not saying they are
12:59 < chris_99> i've simulated neurons themselves
12:59 < kanzure> you were talking about the atomic composition of neurons
12:59 < kanzure> ANNs do not model that
12:59 < chris_99> no shit
12:59 < kirka> Heh, russian h+ guys have exactly same arguments.
12:59 < kanzure> oh sorry i read you saying "i'm not sure they are", not "i'm not saying they are". big difference.
13:00 < kanzure> kirka: this is why i ban philosophy
13:00 < kirka> Heh.
13:00 < chris_99> see what i'm saying is the output of systems in a petri dish may appear the same
13:00 < chris_99> but they're _far_ too simplistic
13:00 < kanzure> but if chris_99 has a neurophysiology paper that proves or demonstrates his point, then i will look at it
13:01 < kirka> kanzure >neural networks that operate the same in a petri dish and in a simulation
13:01 < chris_99> i'd like to see a paper that says you can replicate complex organism's brains
13:01 < kirka> I would read about it.
13:02 < kirka> Do you know authors?
13:02 < kanzure> kirka: oh i dunno. lots. berge?
13:02 < kanzure> berger
13:02 < kirka> That's a very cool result, if true.
13:03 < kirka> Our neuron models are still not ideal as i know.
13:03 < kanzure> berger did the petri dishes controlling microsoft flight simulator
13:03 < chris_99> oh haha
13:03 < kanzure> kirka: markram's neuron database is pretty accurate for the different types
13:03 < chris_99> so controlling some digital system
13:04 < kanzure> kirka: http://channelpedia.epfl.ch/ionchannels/190
13:04 < chris_99> that's the rat brain thing?
13:04 < kanzure> m_alpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) If v neq -27
13:05 < kanzure> "Neocortical L5PC"
13:05 < kirka> kanzure I have read abou Markram's work, do you know any papers about validation of their models?
13:05 < kanzure> which models :)
13:05 < kirka> Any
13:05 < kirka> Neuron models of course
13:06 < kanzure> dunno.
13:06 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/A%20neuron%20membrane%20mesh%20representation%20for%20visualization%20of%20electrophysiological%20simulations%20-%20Markram%20-%202012.pdf
13:06 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Intense%20world%20syndrome%20-%20an%20alternative%20hypothesis%20for%20autism%20-%20Markram.pdf
13:06 < kanzure> i don't seem to have his other papers on the server at the moment
13:06 < kirka> I will search by myself, thanks
13:07 < kanzure> sorry to disappoint
13:07 < kirka> I didn't even expect that I will find it fast, heh
13:08 < kirka> Your server is cool
13:08 < kanzure> thank you
13:08 < chris_99> kirka, google 'integrate and fire model' for one
13:09 < kirka> I have read about different (but not most complex) models
13:09 < chris_99> and look at the nathanshepard pdf
13:09 < chris_99> it's a slide show with some interesting stuff
13:09 < kirka> But I haven't seen even once about validation
13:10 < kirka> I think that we will have to make MD run of single neuron to validate these models
13:10 < kirka> It's long way into the future
13:11 < kanzure> molecular dynamics is a lot of simulation effort for something that we know to have thresholds already
13:11 < kirka> Yes, but we still don't know what spike encoding is right
13:12 < kirka> There are diffirent hyptheses
13:12 < kirka> *different
13:13 < kirka> Maybe monte carlo simulation is enough, in principle
13:13 < chris_99> i'm not sure we know exactly how spike encoding works, like you say
13:13 < chris_99> oh someone linked to to an interesting paper
13:13 < chris_99> on trying to decode the visual cortex
13:14 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Reconstruction%20of%20natural%20scenes%20from%20ensemble%20responses%20in%20cat%20visual%20cortex%20-%20Stanley%20-%201999.pdf
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13:17 < chris_99> http://openscholarship.wustl.edu/etd/559/
13:18 < kirka> Interesting, I have read Hubel's book about neural mechanisms of vision, and this is newer research.
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13:22 < kirka> Oh, it's 00:22 already, I'll go to sleep
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13:59 < kanzure> "As a (bloated, inefficient, high-salary) non-profit, you can read JSTOR's financial filings for yourself:"
13:59 < kanzure> http://www.generalist.org.uk/blog/2011/jstor-where-does-your-money-go/
13:59 < kanzure> http://lists.wikimedia.org/pipermail/wikien-l/2011-July/109234.html
13:59 < kanzure> "They spend ~$4m a year on all computer costs. (To put that in perspective, they spend $1.3m a year on 'travel' & 'conferences, conventions, and meetings'.)"
14:03 < kanzure> "The average academic journal has 25%-30% profit margin (higher than the rest of the publishing industry), but it can take upto 5-7 years for a new STM journal to build enough of a reputation to break even."
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14:25 < kanzure> are weather predictions tested at the weather stations?
14:26 < kanzure> i mean, why don't my weather predictions come with error bars..
14:27 < chris_99> i wondered about this kind of thing, they must surely test their predicitions mustn't they
14:27 < kanzure> i'm sure their models are battle-tested, but what about instrument errors?
14:28 < chris_99> heh nice - http://www.metoffice.gov.uk/research/areas/seasonal-to-decadal/gpc-outlooks/user-guide/interpret-roc
14:29 < chris_99> and http://www.metoffice.gov.uk/science/specialist/seasonal/probability/glob_seas_prob_skill.html
14:29 < kanzure> ideally a weather model with the right instruments would be able to predict things like e.g. individual cloud movement to determine when a sensor will be under direct sunlight
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14:31 < chris_99> yeah
14:35 < chris_99> i'd like to have a go at creating a really crappy weather predictor from the sat imagery
14:35 < chris_99> just to see what you can do
14:36 < brownies> i've been wanting to try that too
14:36 < brownies> i was looking at the NWS APIs the other day. they're hilariously bad.
14:37 < brownies> but, they do exist, which i suppose is already pretty impressive for a government agency.
14:37 < chris_99> heh yeah
14:37 < chris_99> the UK gov. provide some quite interesting datasets actually
14:37 < chris_99> and APIs
14:49 < brownies> ah, true, you'd need global data, which ... damn, i don't even know where to begin for that.
14:50 < brownies> would you really have to go to every governments' weather service and look for an API and integrate with it?
14:50 < kanzure> brownies: i don't know why i thought mocks would do what i needed
14:50 < brownies> kanzure: i told you the answer. at this point, i figure you'll eventually read what i wrote and do it -_-
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14:55 < kanzure> brownies: "switch to ruby and async requests"? :)
14:57 < brownies> no, i outlined how to do it regardless of whether the request is sync or async
14:57 < brownies> and the ruby gem was just an example implementation of the approach
15:01 < kanzure> "write a getter function" that's great and all.. but the original problem was i wanted to avoid passing a boolean into the function for "test mode"
15:05 < brownies> if Rails.env.production ... heh.
15:05 < brownies> kanzure: alternately you could write a getter for production and a getter for testing, and your test logic would know to call one instead of the other
15:05 < brownies> kanzure: but, yes, at some fucking level, you are going to have to check to see if you are in testing mode or not -_-
15:06 < kanzure> i'd rather just forcefully inject code from my test method (the one that calls the target code)
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15:50 < eudoxia> oh goodness uploading discussions
15:50 < kanzure> sorry :(
15:50  * eudoxia *bluarrghhh*s all over the floor
15:50 < kanzure> are you going to eat that vomit?
15:51 < eudoxia> our robot servants can do that for us
15:52 < eudoxia> I'd just like to answer this: < kirka> So, I think cell repair machines is a right way to go.
15:53 < eudoxia> but with cell repair machines you are still human. with an uploaded brain, you can analyze and modify everything at any arbitrary level of resolution with ultimate precision, something you can't do currently, or in the near future
15:54 < eudoxia> it is the ultimate form of human enhancement because computers allow for unlimited variations
15:54  * eudoxia shuts up
15:54 < kanzure> do you feel better?
15:54 < eudoxia> yes
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15:56 < kanzure> brownies: vcr is pretty neat actually. https://github.com/myronmarston/vcr#synopsis
15:56 < kanzure> where does it store the http response?
15:59 < kanzure> python version was updated "18 minutes ago".. hrm. https://github.com/kevin1024/vcrpy
16:18 < brownies> kanzure: yup. oh, didn't know they had a python version... that's cool.
16:19 < brownies> kanzure: hilariously, we have your own VCR-like system with FakeWeb. i didn't know VCR existed when we were building out our infrastructure.
16:19 < brownies> kanzure: i suppose that's another option btw, totally decoupled from the particulars of when/where you call the HTTP thing.
16:19 < brownies> kanzure: when you enter testing mode, you can just set up an app-wide block on all external HTTP requests, and then instead spoof a response based on the URL of any outgoing requests your app makes.
16:27 < kanzure> i store some sample html files in tests/samples/, it looks like vcr just uses a custom yaml format for storing that stuff
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17:15 < kanzure> guerrilla open access manifesto http://pastebin.com/cefxMVAy
17:15 < kanzure> "Information is power. But like all power, there are those who want to keep it for themselves. The world’s entire scientific and cultural heritage, published over centuries in books and journals, is increasingly being digitized and locked up by a handful of private corporations. Want to read the papers featuring the most famous results of the sciences? You’ll need to send enormous amounts to publishers like Reed Elsevier."
17:15 < kanzure> "There are those struggling to change this. The Open Access Movement has fought valiantly to ensure that scientists do not sign their copyrights away but instead ensure their work is published on the Internet, under terms that allow anyone to access it. But even under the best scenarios, their work will only apply to things published in the future. Everything up until now will have been lost."
17:15 < kanzure> "That is too high a price to pay. Forcing academics to pay money to read the work of their colleagues? Scanning entire libraries but only allowing the folks at Google to read them? Providing scientific articles to those at elite universities in the First World, but not to children in the Global South? It’s outrageous and unacceptable."
17:16 < kanzure> "“I agree,” many say, “but what can we do? The companies hold the copyrights, they make enormous amounts of money by charging for access, and it’s perfectly legal — there’s nothing we can do to stop them.” But there is something we can, something that’s already being done: we can fight back."
17:16 < kanzure> "Those with access to these resources — students, librarians, scientists — you have been given a privilege. You get to feed at this banquet of knowledge while the rest of the world is locked out. But you need not — indeed, morally, you cannot — keep this privilege for yourselves. You have a duty to share it with the world. And you have: trading passwords with colleagues, filling download requests for friends"
17:16 < kanzure> "Meanwhile, those who have been locked out are not standing idly by. You have been sneaking through holes and climbing over fences, liberating the information locked up by the publishers and sharing them with your friends."
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17:16 < kanzure> "But all of this action goes on in the dark, hidden underground. It’s called stealing or piracy, as if sharing a wealth of knowledge were the moral equivalent of plundering a ship and murdering its crew. But sharing isn’t immoral — it’s a moral imperative. Only those blinded by greed would refuse to let a friend make a copy."
17:16 < kanzure> "Large corporations, of course, are blinded by greed. The laws under which they operate require it — their shareholders would revolt at anything less. And the politicians they have bought off back them, passing laws giving them the exclusive power to decide who can make copies."
17:16 < kanzure> "There is no justice in following unjust laws. It’s time to come into the light and, in the grand tradition of civil disobedience, declare our opposition to this private theft of public culture."
17:16 < kanzure> "We need to take information, wherever it is stored, make our copies and share them with the world. We need to take stuff that's out of copyright and add it to the archive. We need to buy secret databases and put them on the Web. We need to download scientific journals and upload them to file sharing networks. We need to fight for Guerilla Open Access."
17:16 < kanzure> "With enough of us, around the world, we’ll not just send a strong message opposing the privatization of knowledge — we’ll make it a thing of the past. Will you join us? Aaron Swartz July 2008, Eremo, Italy"
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17:42 < skorket> I'm in
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20:08 < roksprok> so guy assembling his ycombinator pitch next to me 'hey bro send me your bio and competitive analysis...remember we need a pic of a hot girl like...partying or something'
20:13 < brownies> o.O
20:13 < brownies> truly he is a marketing genius
20:13 < roksprok> i know i'm going to ask him if i can be employee #1
20:14 < roksprok> paid in equity
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20:41 < Mokbortolan_1> let me play you the song of my people
20:41  * Mokbortolan_1 stares at you in stony silence.
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20:48  * delinquentme jams out
20:49 < delinquentme> i lik Mokbortolan_1
20:54 < AdrienG> hi delinquentme
20:55 < AdrienG> whats the best way to synth peptides?
20:55 < delinquentme> AdrienG, Howdahhh
20:55 < AdrienG> pls suggest
20:55 < delinquentme> AdrienG, chemistry.
20:55 < delinquentme> lol
20:56 < delinquentme> IDK man :D
20:56 < delinquentme> you've got to have a particular peptide you're after no?
20:57 < yashgaroth> what size of peptide
20:58 < AdrienG> Тrр-Аlа-Gly-Gly-Asp-Ala-Ser-Gly-Glu.
20:59 < yashgaroth> Delta sleep-inducing peptide
21:00 < yashgaroth> you could go with either chemical synthesis, but I'd recommend e.coli production
21:00 < AdrienG> Yes.
21:00 < AdrienG> yashgaroth: how do i mod e.coli
21:00 < yashgaroth> genetic engineering
21:01 < AdrienG> sounds hard
21:01 < yashgaroth> mhm
21:02 < yashgaroth> to be fair though, it's not as hard as injecting it into your brain
21:05 < AdrienG> you just have to administer it sub-q.
21:05 < AdrienG> with an insulin pen.
21:05 < AdrienG> once a day.
21:05 < AdrienG> peanuts
21:06 < yashgaroth> k I'll leave that stuff to you then
21:09 < yashgaroth> man, with how obviously fake all these "peptide suppliers" are on the bodybuilding forums, there's a remarkable amount of placebo effect
21:11 < AdrienG> what makes yuo think they are fake
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21:11 < yashgaroth> http://www.cemproducts.com/peptides/dsip-5mg.html has 5 milligrams for $37 which is far below the cost of a legit product
21:13 < chevbird> if they have QC metrics on the site i wouldnt worry about it
21:13 < chevbird> but i doubt they do
21:13 < yashgaroth> they never do
21:14 < chevbird> kids today...
21:14 < yashgaroth> "all our products are totally legit" is about as QC as they get
21:14 < chevbird> totally
21:15 < yashgaroth> it probably works in the sense that they put in some cheap chinese sleep drug or something, because bodybuilders don't have mass spectrometers
21:15 < chevbird> just mass
21:16 < yashgaroth> ...heh
21:16 < yashgaroth> I'm stealing that one
21:29 < AdrienG> when we will finally have chemical printers:<
21:29 < AdrienG> just print whatever small molecule at home
21:29 < yashgaroth> the drexler model 1 should be out in about 50 years
21:30 < AdrienG> :<
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21:40 < AdrienG> yashgaroth: melanotan is clearly legit on many sites
21:40 < AdrienG> its effects are very noticable.
21:40 < AdrienG> and its a far more complex molecule.
21:43 < yashgaroth> ehhhh
21:45 < yashgaroth> hey I'm not stopping you from throwing your money at some site
21:48 < yashgaroth> oh hey peptide synthesis is cheaper than I thought
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21:50 < yashgaroth> ok back to your original question, it would be far easier to pay a service to make it for you unless you need grams of it
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22:05 < nmz787> grams of what?
22:05 < nmz787> I will check logs
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22:06 < yashgaroth> he wants a short peptide, I was surprised to learn how cheap they actually are
22:06 < nmz787> kanzure: "You’ll need to send enormous amounts to publishers like Reed Elsevier."
22:06 < nmz787> amounts of what though?
22:06 < nmz787> how much?
22:06 < nmz787> wait
22:06 < yashgaroth> oh, delta sleep-inducing peptide I think
22:06 < yashgaroth> logs consist of an hour of me being dumb if you wanna read 'em
22:06 < nmz787> err
22:06 < nmz787> not now
22:09 < nmz787> well you didnt ramble too long
22:09 < nmz787> yashgaroth: ^
22:09 < yashgaroth> heh
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22:10 < yashgaroth> I'd no idea peptide synth was like 1000x cheaper than dna synth
22:12 < nmz787> how much for a gram of protein?
22:12 < nmz787> link??
22:12 < nmz787> oh 5mg
22:12 < nmz787> 37
22:12 < nmz787> $
22:12 < nmz787> hmm
22:13 < yashgaroth> admittedly it's only good up to maybe 30 aa's, but that's most peptide hormones
22:13 < nmz787> oh wait
22:13 < nmz787> http://www.cemproducts.com/peptides/dsip-5mg.html
22:13 < nmz787> isnt it
22:14 < yashgaroth> http://www.genscript.com/peptide.html
22:14 < nmz787> oh
22:14 < nmz787> you cant do proteins?
22:15 < nmz787> what does a place like you work for charge?
22:15 < nmz787> where can i order a protein, rather than a gene?
22:15 < yashgaroth> it gets exponentially harder the longer the protein is
22:15 < nmz787> it says up to 200
22:16 < yashgaroth> not for that low low price though
22:17 < nmz787> yeah it doesnt list pricing for the higher ones
22:17 < yashgaroth> we're at maybe $ten thousand a gram for GMP grade with e.coli synthesis, though it varies and that's at multi-gram production batches
22:18 < nmz787>  hmm
22:19 < kanzure> i hate cable modems
22:19 < kanzure> i hate tethering apps. if the app is dead, i shouldn't have other devices on my network connected to the interwebs.
22:19 < yashgaroth> like we're growing one that's 70-80 aa's long because it becomes cheaper than synth at that length
22:22 < nmz787> ahh
22:22 < yashgaroth> at least for the required quality levels, since it's extremely hard to separate a peptide from one that's 1-2 aa's shorter and the FDA ain't having no mixed formulation
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22:23 < roksprok> how do you grow a peptide? add aa's one at a time and wash in between?
22:23 < yashgaroth> pretty much
22:24 < kanzure> long-term link for that pastebin link i dropped earlier.. http://p2pfoundation.net/Guerilla_Open_Access_Manifesto
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22:35 < kanzure> "Greg Maxwell just released 33GB of JSTOR scientific papers via The Pirate Bay because of the indictment against Aaron."
22:35 < kanzure> https://thepiratebay.se/torrent/6554331/Papers_from_Philosophical_Transactions_of_the_Royal_Society__fro
22:36 < kanzure> 31 seeders
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22:53 < skorket> adc conversion done, USB communication done, now onto the next phase
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23:00 < Mokbortolan_> ???
23:00 < Mokbortolan_> and then, profit
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--- Log closed Mon Sep 17 00:00:28 2012