--- Log opened Mon Jan 14 00:00:30 2013
00:00 < rigel> oh who is @pdx.edu, and should i meet them
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00:01 <@kanzure> rigel: almost everyone. jrayhawk, nmz787, lichen, mokbor, bioguy, the other jerks.
00:02 < lichen> hmm?
00:02  * nsh hips hat at room
00:02 <@kanzure> well, you are close to pdx.
00:02 < nsh> and tips tat
00:02 < rigel> yes, quite close
00:03 < rigel> i go to dorkbot now and again
00:03 < lichen> ah, yeah, im in pdx
00:03 < lichen> hello
00:03 < rigel> hi
00:03 < lichen> going to psu as well, heh
00:04 < rigel> i am up on the hill actually
00:04 < lichen> ah, neat
00:04 < lichen> you at a program at ohsu?
00:05 < rigel> nod
00:05 < lichen> very cool
00:05 < lichen> im just an undergrad still :p
00:05 < bkero> Son of a bitch
00:05 < bkero> More pdx people?
00:05 < rigel> well i would be keen to meet up and chat
00:05 < bkero> lichen: what major at psu? I have many friends there.
00:06 < lichen> biomedical physics
00:06 < bkero> right on
00:06  * bkero lives in PDX, but is currently traveling at the moment. Be back sometime early next month.
00:06 < rigel> i was a bench lab monkey before coming here
00:06 < lichen> hehe
00:06 < bkero> lolwetwork
00:06 < lichen> i work at a warehouse doing manual labor bullshit
00:06 < bkero> I did that back in high school. Mini/maxi-preps, PCR, glorified dishwashing.
00:06 < lichen> school part time for now
00:07 < lichen> always on the lookout for something more related
00:08 <@kanzure> http://www.nature.com/nrn/journal/v13/n12/full/nrn3399.html
00:08 < paperbot> HTTP 401 unauthorized http://www.nature.com/nrn/journal/v13/n12/pdf/nrn3399.pdf
00:09 <@kanzure> what
00:09 <@kanzure> WHAT
00:10 < bkero> yupyup
00:10 < bkero> paywallol
00:11 <@kanzure> well paperbot is supposed to have access to that
00:11 <@kanzure> paperbot: http://www.nature.com/nrn/journal/v13/n12/pdf/nrn3399.pdf
00:11 < paperbot> error: didn't find any pdfs on http://www.nature.com/nrn/journal/v13/n12/pdf/nrn3399.pdf
00:11 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/f4612cfb3251a43a730d64439905a0ec
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00:34 <@kanzure> i think discussing scraping in public is probably okay
00:34 <@kanzure> https://groups.google.com/group/science-liberation-front/about
00:34 <@kanzure> sign 'em up
00:39  * nsh nods
00:39 < bkero> Wasn't there a person in the news lately who did something like that?
00:39 <@kanzure> i think it's better to keep discussions on this public for the moment
00:40 <@kanzure> because people are angry and are going to be trying to do some possibly mistaken things
00:40 <@kanzure> and if they talk about best methods first maybe their efforts wont be as useless
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03:35 < archels> what the- http://www.ncbi.nlm.nih.gov/pubmed/19197316
03:35 < archels> Carbon nanotubes might improve neuronal performance by favouring electrical shortcuts.
03:43 < superkuh> Eh... that seems unlikely.
03:43 < superkuh> At least the mechanism proposed.
03:44 < superkuh> The electrical shortcut is only 10nm across the cell membrane.
03:45 < superkuh> It's not like there are longitudinal currents.
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03:54  * Viper168 licks superkuh 
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04:41 < kirka> Hi guys.
04:44 < ViperMeowsworth> HO GUYS
04:44 < ViperMeowsworth> -caps
04:49 < kirka> Actually I wanted to talk with kanzure about intricacies of running a web forum (about nanotechnology), but he is probably sleeping now, so I'll wait.
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04:50 < kirka> gene_hacker Are you a real genehacker or it's just a fancy nickname?
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04:50 < kirka> Hi, eudoxia!
04:50 < eudoxia> yo
04:51 < eudoxia> i don't think it would take off
04:52 < kirka> eudoxia Jim wants to do it. None of us has web development experience though.
04:52 < ViperMeowsworth> lol
04:52 < eudoxia> which jim?
04:52 < ViperMeowsworth> I used to run forums
04:52 < ViperMeowsworth> but computer related
04:52 < ViperMeowsworth> general help, software, free and cheap internet listings
04:52 < ViperMeowsworth> etc..
04:52 < ViperMeowsworth> was freeaccess.com, but the domain got sold off
04:52 < kirka> eudoxia Last post here: https://groups.google.com/forum/?fromgroups=#!topic/sci.nanotech/Sjvz_Nr857U
04:53 < kirka> eudoxia I think there should be at least one forum on MNT.
04:53 < kirka> eudoxia To discuss design of molecular machinery, new software tools etc.
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04:53 < eudoxia> yeah
04:54 < kirka> eudoxia btw I'm developing MNT CAD in lisp: http://rghost.ru/43023154.view
04:54 < kirka> That's very early stage though.
04:54 < kirka> My goal is million atoms on screen.
04:54 < eudoxia> and i'll port it to hylas :)
04:55 < kirka> Heh, that's possible, I thought about it.
04:55 < kirka> Hylas desperately needs documentation.
04:55 < eudoxia> need to write some opengl binings
04:55 < eudoxia> well i updated the readme and wrote some docs
04:55 < eudoxia> it's up in github
04:56 < eudoxia> there are some code examples
04:56 < kirka> Yes, I have seen this.
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04:57 < eudoxia> are you using CL?
04:57 < kirka> I think there should be explanation of Hylas's abstractions over LLVM assembler (if tehre are any).
04:57 < eudoxia> ?
04:57 < eudoxia> code generation is straight to LLVM; IR
04:58 < kirka> eudoxia For the first prototype model viewer I used Racket. It's too slow though, so I'm switching to CL.
04:58 < eudoxia> i see
04:58 < kirka> I think CL is very good language for this thing, as it demonstrates that 20 year old code (Maxima) runs well on it now.
04:59 < eudoxia> needs a better gui toolkit
04:59 < eudoxia> if you need help with CommonQt i have a tutorial on my blog
04:59 < kirka> So this CAD will work 10-20 years into the future, without bit rot.
04:59 < kirka> eudoxia I tink Qt is a monstrous dependence.
04:59 < eudoxia> yeah
04:59 < kirka> It's changing
04:59 < kirka> API can change in a couple of years.
05:00 < eudoxia> the molecular cad code shouold be separate from the interface
05:00 < kirka> I will have several graphics backends, including parallel software render.
05:00 < kirka> Yes, absolutely.
05:00 < eudoxia> in NanoEngineer, well...
05:00 < eudoxia> "User interface and code are only one, and they love each other so much they are completely glued together."
05:00 < eudoxia> - a friend at work
05:00 < kirka> Hehe.
05:01 < kirka> Graphics backend will provide simple interface for drawing model and relaying user's input into command logic module.
05:02 < kirka> eudoxia So Hylas is S-Exp version of LLVM IR?
05:02 < kirka> It also does variable allocation (static by default),
05:03 < eudoxia> there isn't a huge distance between assembly and the language, no
05:03 < eudoxia> i intended it to combine low-level shit with macros
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05:03 < eudoxia> and metaprogramming, introspection, reflection, etc.
05:03 < kirka> But to program in it one should clearly understand what's done behind the scenes.
05:03 < kirka> eudoxia That's cool idea.
05:04 < kirka> I have been waiting for 2 years for such language to be created.
05:04 < eudoxia> i won't let you down bro
05:05 < kirka> That's good, heh.
05:07 < kirka> For example there is a keyword "recursive", but one can write macro that infers recursiveness of function and adds this label if necessary.
05:07 < eudoxia> that's actually pretty good
05:09 < eudoxia> also i made the cover for the docs book (docs/res/i
05:09 < eudoxia> mg) and its pretty as shit
05:09 < eudoxia> tits 'n stuff
05:09 < kirka> Heh
05:10 < kirka> It would be good if you described primitives (like define, let etc) and memory allocation issues.
05:12 < kirka> ViperMeowsworth As you can see we want to start a forum on molecular nanotechnology.
05:12 < eudoxia> i'll write the function reference today
05:12 < eudoxia> if i can
05:13 < ViperMeowsworth> yeah I'm scanning, hopping between half a dozen channels
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05:15 < gene_hacker> @kirka it's my name of course, though once the technology becomes cheap we'll see about it
05:15 < kirka> eudoxia There is no need to be in a hurry,
05:16 < kirka> eudoxia You are the creator of the language after all.
05:17 < eudoxia> still i want to get the docs done
05:34 < eudoxia> so kirka will you put your cad up on github?
05:35 < kirka> eudoxia I will, when it's usable
05:35 < kirka> eudoxia It's still just pdb-loader with sloow 3d-viewer.
05:35 < eudoxia> areyou using opengl or something else for the 3d?
05:35 < kirka> opengl
05:36 < kirka> But for million of atoms, maybe I'll have to use sprites.
05:37 < eudoxia> hm
05:37 < eudoxia> i've heard about something like that, used, coincidentally, for a molecule viewer
05:39 < kirka> I also think that in very large designs parts could be abstracted away, represented as polygonal meshes with bondpoints.
05:39 < eudoxia> i was thinking about that too
05:39 < eudoxia> for MNT MEMS stuff
05:39 < kirka> And to see whole atomic structure one could render them offline.
05:39 < kirka> Yep.
05:47 < kirka> Also I want to classify parts and their structural patterns by difficulty of manufacturing.
05:47 < kirka> And build complex structures with easy-to-manufacture components. (relatively "easy", of course)
05:48 < eudoxia> needs afm integration
05:48 < kirka> Heh
05:48 < kirka> Of course, "model structures", not "build".
05:48 < eudoxia> lol
05:49 < kirka> E.g. look at this sorting pump: http://www.nanoengineer-1.net/mediawiki/index.php?title=File:SortingPump1.png
05:49 < kirka> There are unnecessary curved surfaces
05:50 < kirka> And sulfur atoms.
05:50 < kirka> The design is cool. of course.
05:52 < eudoxia> http://wiki.transhumani.com/index.php?title=Molecular_Machinery#Abstract_Sorting_Pump is much better
05:53 < kirka> I agree. It's strange that nobody designed atomically precise version yet.
05:53 < eudoxia> yeah
05:53 < eudoxia> i would if i knew how to make a bidning site
05:53 < kirka> Also, there is a need in springs.
05:53 < eudoxia> i wouldn't be so sure
05:53 < eudoxia> consider, on one side, you got actual pressure from molecules to be sorted
05:53 < eudoxia> on the other side there's near vacuum
05:54 < eudoxia> probability would allow the pump to work without moving binding sites
05:54 < kirka> Hmph. That's a question of kT >> EnergyBarrier for sliding
05:55 < kirka> If that's true then it'll work this way.
05:56 < eudoxia> i think drexler said it wiuld
05:56 < eudoxia> would*
05:56 < eudoxia> somewhere in nanosystems
05:56 < kirka> Yes, I remember that.
05:57 < kirka> Binding sites probably should be designed to approximate potential energy surface of target molecule.
05:59 < kirka> We need to visualize PES first.
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06:07 < kirka> eudoxia There is a note on complimentary surfaces on p.265 of "Nanosystems".
06:28 < kirka> eudoxia http://www.zyvex.com/nanotech/bindingSites.html
06:32 < kirka> They thought about it 20 years ago.
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08:28 < eudoxia> that paper is almost as old as i am
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08:58 <@kanzure> sigh yet another forum
08:59 < kirka> kanzure Do you have better suggestion?
09:01 <@kanzure> yes. the vast majority of the people from foresight institute all prefer mailing lists.
09:01 < kirka> sci.nanotech is dead.
09:01 < kirka> Leitl's list is also half-dead.
09:01 <@kanzure> that's not what i'm talking about
09:02 <@kanzure> leitl's list isn't dead.
09:02 < eudoxia> postbiota/nano?
09:02 < kirka> It's repost of non-related news, that's all.
09:02 < kirka> *nano
09:02 <@kanzure> well, then you should call him out on it
09:03 < kirka> There is no mailing list of forum that's created solely for MNT-related discussions.
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09:05 <@kanzure> kirka: jrayhawk created one for you
09:05 <@kanzure> but you seemed to never look
09:05 < kirka> I looked
09:05 < eudoxia> link?
09:05 <@kanzure> eudoxia: it was the sympa link
09:05 < kirka> It was something scary on some unrealted domain.
09:06 <@kanzure> it even has a web ui for you
09:06 < eudoxia> <3
09:07 < eudoxia> http://diyhpl.us/sympa/ ?
09:08 <@kanzure> yep
09:08 < kirka> Actually, Jim Logajan wants to start a forum.
09:08 < kirka> And we discuss software, domain and webhosting providers.
09:09 < kirka> kanzure Can you give an advice on choice of good forum engine?
09:09 < kirka> There are hunderds of them.
09:09 < eudoxia> phpBB3
09:09 <@kanzure> they are all fucking awfl
09:10 <@kanzure> phpbb is terrible and evil, you should never use it
09:10 < eudoxia> hahah i'm trolling
09:10 < kirka> I tried jForum, and it simply works.
09:10 < eudoxia> roll your own
09:10 < eudoxia> c:
09:10 < kirka> I don't want to dig into web programming.
09:10 <@kanzure> you should never use ikonboard, fluxbb, invisionboard, jforum, phpbb, smf, or any of the others.
09:10 < kirka> Heh.
09:10 <@kanzure> kirka: what do you have against email?
09:11 < eudoxia> have a git repo on a server where people write their posts as yaml files and threads are folders
09:11 < kirka> kanzure Nothing, but participating in mailing lists is more complex than using a forum.
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09:11 < eudoxia> i don't even know how to unsubscribe from llvm-dev
09:11 < kirka> Jim wants a forum and I agree with him.
09:11 <@kanzure> eudoxia: llvm-dev-unsubscribe@whatever
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09:12 < eudoxia> so i just send whatever email to that?
09:12 <@kanzure> no, usually you have to include unsubscribe in the subject line to that address
09:12 <@kanzure> otherwise it will complain
09:12 < eudoxia> oh okay
09:12 < eudoxia> thanks kanz+
09:13 <@kanzure> btw, this was in the instructions when you first subscribed.
09:13 < eudoxia> probablyh
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09:26 < ParahSailin> kirka: make it a subreddit
09:27 < kirka> There is http://www.reddit.com/r/nanotech already.
09:27 < kirka> 95% of unrelated information.
09:27 < ParahSailin> so make another?
09:27 < kirka> Maybe.
09:28 < kirka> But if something happens to reddit, all discussion will be lost.
09:28 <@kanzure> i think kirka doesn't believe in the existence of email
09:28 < kirka> I believe.
09:29 < kirka> A read different mailing lists and participate in some.
09:29 < kirka> But forum with web interface is simpler.
09:29 < eudoxia> i don't even know how to post to one lol
09:29 <@kanzure> eudoxia: you write an email.
09:29 < kirka> I use google groups.
09:29 < ParahSailin> if something happens to the internet backbone, all will be lost
09:30 < ParahSailin> clearly we need pigeons
09:30 < kirka> We need backups.
09:30 < eudoxia> dogs carrying DVDs
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09:30 <@kanzure> kirka: backups of mailing lists are very easy. you just upload your mbox file.
09:30 < kirka> I agree.
09:30 < eudoxia> or terabyte flash drives, that might have more bandwidth than most internet connections
09:31 < eudoxia> although the latency would be fucked
09:31 < kirka> Backups of forums are also easy. You just copy the database.
09:31 < kirka> The question is "what forum engine do we choose?"/
09:32 <@kanzure> how about mailman
09:33 <@kanzure> ParahSailin: https://groups.google.com/group/science-liberation-front
09:33 < kirka> kanzure Do you plan to upload a torrent with terabyte of scientific papers?
09:34 <@kanzure> no
09:34 <@kanzure> library genesis tried that and nobody seeded
09:34 < ParahSailin> the last guy who did that did not have a very good day
09:34 < kirka> I know.
09:34 <@kanzure> ParahSailin: aaronsw did not use torrents
09:35 < kirka> Someone could host them in I2P.
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09:36 < ParahSailin> someone just needs to make a pirate marketplace for papers
09:36 < eleitl> howdy bryan
09:36 < eudoxia> oh jesus it's eugene leitl
09:36  * eudoxia faints
09:36 < eleitl> hi eudoxia
09:37 < ParahSailin> let people run bots to sell papers for like five bitcents
09:37 <@kanzure> eleitl: we are your official fan club
09:37 < eleitl> :))
09:37 <@kanzure> ParahSailin: i think you should propose that to the group
09:37  * eudoxia twirls a little leitl flag
09:37 <@kanzure> ParahSailin: i was thinking of letting people rent out their student ids/passwords for bitcoins
09:37 <@kanzure> ParahSailin: and make money on their student loans
09:37 <@kanzure> eleitl: so, eudoxia and kirka have some complaints about the nanotech list
09:38 < eudoxia> i don't just kirka
09:38 <@kanzure> and they are too passive aggressive to tell you in person
09:38 < eudoxia> gee thanks kanz making me look bad infront of the leitl
09:38 < kirka> Well that's problem of MNT in general
09:38 < eleitl> what's wrong with the list, other that it doesn't get traffic?
09:38 < eleitl> machine-phase is dead in the water
09:38 < ParahSailin> people dont like my ideas, and that silkroad for papers would be really low on my own to-do list
09:39 <@kanzure> ParahSailin: you should post it anyway, someone else might build it
09:39 <@kanzure> ParahSailin: like me
09:39 < kirka> It's practiced by maybe 100 researchers in the world.
09:39 < eudoxia> 100'¿
09:39 < eudoxia> you nuts
09:39 < eudoxia> 5 tops
09:39 < kirka> Ok, 20
09:39 < eleitl> libgen is pretty good, I hope they can start accepting BTC soon
09:39 < eleitl> kirka, yes, but it's not easy to change that
09:39 < eudoxia> assuming metzger plays with nanoengineer in his free time
09:39 < ParahSailin> i think you're probably about 75% of the programming productivity of that entire group, kanzure
09:39 < eleitl> perry is working hard, but he needs to establish himself academically first
09:40 <@kanzure> ParahSailin: ah so i should tone it down..?
09:40 < ParahSailin> so reposting idea there would be redundant
09:40 <@kanzure> ParahSailin: please? :(
09:40 < ParahSailin> ok
09:40 < eleitl> kanzure, we're going to mix some VM-1 perfusate this weekend, for a test on a human cadaver
09:40 <@kanzure> please elaborate
09:40 < nmz787> funny their page here doesn't list winter 2013 http://genefoo.com/blogs/news/6074124-launching-personalpcr
09:41 <@kanzure> where have you acquired a human cadaver
09:41 < ParahSailin> VM-1 is some kind of antifreeze?
09:41 <@kanzure> nmz787: yeah that seems to be what macowell is doing
09:41 < eudoxia> CI's cryoprotectant
09:41 < eleitl> the human cadaver is not our own, it's a group of embalmers which klaus has dug up
09:41 < eleitl> I don't know any of them, though I would like to attend, if feasible
09:41 < eleitl> VM-1 is Pichugin's vitrifyable perfusate
09:42 < eleitl> we start with it because it's cheap, and we've been asked to do it in a somewhat urgent fashon
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09:43 < eleitl> to all: a group of kraut cryonicists are trying to establish a local cryonics provider
09:43 -!- mode/##hplusroadmap [-b dende!*@*] by kanzure
09:43 < eudoxia> i saw those pictures of your new lab
09:43 < eleitl> we've rented lab space in a startup incubator
09:43 < eleitl> we'll try to do some SENS and other research in there during daytime
09:44 < eleitl> we're supposed to get our dewars by weekend, but it will likely take a little longer
09:45 < nmz787> eleitl: what's with all the DMSO?
09:46 < eleitl> don't ask me, ask Pichugin. It's not my perfusate of choice.
09:46 < nmz787> is that for the emblaming?
09:46 < eleitl> However, it's easy and cheap, and if we do fracturing research, we'll also start with VM-1, and possibly VM-1 with iceblockers.
09:47 < eleitl> Not embalming, perfusion, and then thermal descent to dry ice, and transport overseas on dry ice.
09:47 < eleitl> Vitrified, not frozen.
09:47 < eleitl> Assuming perfect perfusion, which almost never happens with the kind of ugly cases we're getting in krautlandia.
09:49 < eudoxia> tests or actual past cases?
09:50 < eleitl> There have been CI cases in Germany, and they typically do not look very good, due to very conservative criteria for death declaration.
09:51 < eleitl> It doesn't matter to me, since we need to be able to learn the technique, regardless where it is going to be used.
09:53 <@kanzure> kirka: can you elaborate why you don't like eleitl's nanotechnology forum?
09:53 < kirka> It's not that I don't like it.
09:54 < kirka> There are some interesting posts.
09:54 < kirka> But as in other mailing lists there is little of MNT.
09:54 < eudoxia> it's not about the medium
09:54 < eleitl> of course, because MNT is rare as hen's teeth
09:54 < kirka> It's a global problem.
09:54 < eudoxia> there just aren't many people interested
09:54 < kirka> I agree.
09:54 <@kanzure> then why did you want to make a separate forum?
09:54 <@kanzure> i am very confused.
09:55 < kirka> Molecular manufacturing has plitical burden on it, so it's doesn't get funded.
09:55 < kirka> kanzure Jim Logajan wants to make a replacement for sci.nanotech mailing list.
09:55 < eleitl> I'm not married to MNT. Nano is nano. All paths lead to machine-phase, eventually.
09:55 < eleitl> sci.nanotech is a Usenet group, not a mailing list, right?
09:56 < kirka> I agree, protein/foldamer engineering has very good future.
09:56 < kirka> eleitl Right.
09:56 < kirka> And also google group.
09:56 < eleitl> oh, haven't seen that one.
09:57 < kirka> But I think that nanoparticles are a dead end.
09:57 < eleitl> nanoparticles are not real nanotechnology
09:57 < eleitl> just inflationary use
09:58 < eleitl> Just subscribed to sci.nanotech, thanks
09:58 < eudoxia> eleitl, what do you think about Zyvex's epitaxy approach?
09:59 < kirka> Yes, it's after creation of NNI and lobbying of Nanobusiness alliance nanoparticles research has become NNI's main focus.
10:00 < eleitl> haven't look at zyvex in more than a decade
10:00 < eudoxia> http://www.zyvexlabs.com/Research.html
10:00 < eudoxia> http://nextbigfuture.com/2010/10/what-is-optimal-bootstrapping-pathway.html
10:01 < eleitl> thanks, I will look at it
10:01 < eudoxia> "Von Ehr hopes to have a primitive nanotechnology system that can create blocklike objects by 2015 and rudimentary molecular manufacturing by 2020. The big game-changer to my mind is Digital Matter. For enzymes, catalysts, and increasingly even for transistors, every atom has to be in the correct place in order for the molecule or component to function. "
10:01 < eudoxia> i don't want to get my hopes up ;_;
10:02 -!- mode/##hplusroadmap [-b d3nd3!*@*] by kanzure
10:02 < nmz787> rigel: so you're in PDX?
10:02 < nmz787> I'm gonna go tour FEI, the e-microscope and FIB company this thurs evening
10:02 < kirka> There is also a promising parallel MEMS-STM firm: http://www.icspicorp.com/
10:02 < nmz787> http://portland-or.sites.acs.org/newsletter.pdf
10:03 < kirka> They are partners of Zyvex.
10:03 < eleitl> I wouldn't get the hopes up too far
10:03 < eleitl> the best hope is with DNA autoassembly
10:03 < eleitl> which is not much
10:04 < nmz787> using modified cells seems like a reasonable way to go about APM
10:04 < kirka> Recent synthetic DNA ion channel is good.
10:04 < kirka> This one: http://www.sciencemag.org/content/338/6109/932.abstract
10:04 < kirka> It's a DNA-origami structure that works as ion channel, designed from scratch.
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10:05 < eleitl> not sure I've sent that. why don't you send such papers to the nano list?
10:05 < kirka> I will, next time. I'm not used to mailing lists yet.
10:06 < eleitl> Heh. What do you use? Usenet?
10:06 <@kanzure> "I know Ariya used to work for Trolltech and that has obviously been fundamental in PhantomJS's success to date."
10:06 <@kanzure> oh. i didn't know that.
10:06 <@kanzure> paperbot: http://www.sciencemag.org/content/338/6109/932.abstract
10:06 < paperbot> error: didn't find any pdfs on http://www.sciencemag.org/content/338/6109/932.abstract
10:06 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/e92df00e68df7c336e7bf8fccf642b32
10:06 <@kanzure> hmm
10:07 < archels> eleitl: do you think it would be worthwhile to look at plastification as an alternative to cryonic preservation?
10:07 <@kanzure> paperbot: http://www.sciencemag.org/content/338/6109/932.full.pdf
10:07 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/859715fc8cbb731cfe0429f2b19aba5d
10:07 < nmz787> did science change their format?
10:07 < eleitl> Mike Darwin is making some very interesting noises about fixation/plastination, so I'm hanging on until he delivers.
10:07 < kirka> eleitl I'm from 1990's generation, so I haven't seen age of UseNet, heh.
10:07 < eleitl> oic, kirka
10:07 <@kanzure> http://diyhpl.us/~bryan/papers2/paperbot/Synthetic%20Lipid%20Membrane%20Channels%20Formed%20by%20Designed%20DNA%20Nanostructures.pdf
10:08 <@kanzure> there you go
10:08 <@kanzure> nmz787: i guess so :(
10:08 < eleitl> I think fixation/plastination might be feasible, but it's very difficult to validate.
10:09 < eleitl> the no-feedback problem
10:09 <@kanzure> fascinating https://github.com/laurentj/slimerjs
10:09 <@kanzure> gecko-based phantomjs port
10:09 <@kanzure> not so headless though
10:10 < kirka> eleitl Drexler is into peptoids/foldamers these days. Probably that's a faster route than UHV-STM.
10:10 < eleitl> yes, I've always been of the opinion that bootstrap by bio is easier
10:10 -!- mode/##hplusroadmap [-b *!*@*.croy.cable.virginmedia.com] by kanzure
10:10 < kirka> Good protein/foldamer engineering is rare though.
10:10 < eleitl> inverse protein folding is almost solved
10:10 <@kanzure> mode -b *!*@*cpc10-croy17-2-0-cust245*
10:10 <@kanzure> oh god
10:10 -!- mode/##hplusroadmap [-b *!*@*cpc10-croy17-2-0-cust245*] by kanzure
10:11 < nmz787> i think we just need to design a minimal cell that is XYZ controllable
10:11 < eleitl> strangely, it is easier than straight protein folding
10:11 < nmz787> XYZ and rotate
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10:11 < d3nd3> success
10:11 < d3nd3> kanzure: ty
10:11 < kirka> nmz787 But their membranes are absolutely non-stiff.
10:11 < eleitl> we need an enzyme which can lay down bucky
10:11 < eleitl> that might be possible
10:12 < nmz787> kirka: what's stiffness have to do with moving around to place atoms?
10:12 < nmz787> then the cell becomes the STM and STP tip with atom loader
10:12 < kirka> nmz787 Stiffness matters because of thermal noise.
10:12 < nmz787> isn't that why receptors exist, to lock onto a target before manipulation?
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10:14 < kirka> nmz787 So the receptor is the controlled molecular machie, floating in cell?
10:14 < kirka> *machine
10:14 < kirka> *in cells membrane
10:14 < nmz787> well the whole cell is the controlled machine
10:14 < nmz787> you'd tell it export receptor A to surface
10:14 < kirka> eleitl is right, we need engineered enzymes.
10:14 < nmz787> export enzyme G to surface
10:14 < eleitl> guys, it's very interesting, but I need to catch the train home. I'll try dropping by later today, or at least I'll read the scroll tomorrow.
10:15 < eleitl> catch you laters. Thanks!
10:15 < nmz787> I guess telling the cell to move 5 hydroxyls south vs north would be hard
10:16 <@kanzure> you could magnetically move the cell
10:16 <@kanzure> and make it produce magnetic-responsive enzymes
10:16 < nmz787> maybe it'd have to be magneto or light -tactic... so move X atoms in J direction
10:16 < nmz787> well the moving X atoms is done already with actin filament moving
10:17 < nmz787> so somtehing could be adapted for non-polymers
10:17 < kirka> I don't think it's possible to move cell as a whole with right precision (1 angstrem).
10:17 < nmz787> but movement would be too coarse I think if you didn't have an enzyme doing the positioning
10:17 < kirka> It's possible for components of protein/RNA/DNA machinery though.
10:18 < nmz787> well you don't need to move the whole cell to move 1 angstom
10:18 < nmz787> since the membrane is much larger area, you can just move within the membrane
10:18 < kirka> If we had an analog of Ribosome that can manufacture more complex structures than aminoacid-chains that'd be a huge step forward.
10:19 < nmz787> what other polymers would you want it to make?
10:19 < kirka> There is already work on mutating ribosome to understand 4-word codons.
10:19 < kirka> nmz787 Polymers with two covalent bonds for example
10:20 < kirka> nmz787 They would be more predictable.
10:21 < kirka> There are, for example peptoids: http://en.wikipedia.org/wiki/Peptoid
10:21 < kirka> They are more stable than proteins.
10:24 < kirka> There is a large space of possible monomers, with them it may be easier to build stable structures than with amino acids.
10:25 < nmz787> lacking secondary structure seems pretty limiting to make anything catalytic
10:25 < archels> kanzure: you should tell paperbot to grab the supplements as well ;)
10:25 < archels> the supplement on that DNA-origami-ion-channel paper is much better than the brief main publication
10:26 < kirka> nmz787 >Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure
10:26 < archels> I still have them on my webserver, http://www.turingbirds.com/temp/Langecker.SM.pdf
10:26 < archels> paperbot: http://www.turingbirds.com/temp/Langecker.SM.pdf
10:27 < archels> low hit rate :P http://diyhpl.us/~bryan/papers2/paperbot/
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10:28 < kirka> nmz787 The main problem as it seems to me is a lcak of good method to design foldamers.
10:28 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/1e9ee8083534045e107de3879995fe45
10:28 < kirka> *lack
10:29 < kirka> nmz787 There is a need in foldamer design software with real-time simplified force fields.
10:30 < ParahSailin> paperbot: https://s3-us-west-2.amazonaws.com/droplr.storage/files/acc_15515/sK7z?AWSAccessKeyId=AKIAJSVQN3Z4K7MT5U2A&Expires=1358189301&Signature=7GvBHMfkgBjcBFpnQ79a0jENm7c%3D&response-content-disposition=attachment%3B%20filename%2A%3DUTF-8%27%271-s2.0-016378278990009X-main.pdf
10:30 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/293105c6bfdc3f3d95184ef931393947
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10:30 < kirka> Drexler did Pam-3 and Pam-5 into NE1 for this purpose.
10:30 < nmz787> hmm
10:31 < nmz787> seems like it would make a lot more sense to pour resources into learning how to fold normal proteins, since we're composed of them already
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10:31 < nmz787> them modify the strategy from there
10:31 < nmz787> then*
10:31 < kirka> nmz787 Folding and designing aren't inverse problems.
10:31 < d3nd3> so how do i view paperbots papers ?
10:32 < nmz787> why not?
10:32 < kirka> nmz787 Structures can be designed to be easily predictable.
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10:32 < nmz787> but we care about function
10:33 < kirka> E.g. this protein was designed to be easily predictable: http://www.nature.com/nature/journal/v458/n7236/full/nature07841.html
10:33 < kirka> And it works.
10:33 < kirka> Id on't think that all of natural protein's complexity is related to function.
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10:34 < nmz787> no but it obviosuly works
10:34 < kirka> It's just evolution building complex patterns in sequental steps (it adds complexity until functionality breaks).
10:34 < nmz787> and there's a huge amount of prior art waiting to be understood and hacked
10:35 < kirka> I agree
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10:35 < kirka> But much of this complexity can be just random mutations.
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10:35 < kirka> Drexler writes a lot abou this.
10:35 < nmz787> there's still a reason that it works
10:35 < nmz787> that isn't random
10:36 < nmz787> so PDX has this, so this /should/ work paperbot: http://www.nature.com/nature/journal/v458/n7236/full/nature07841.html
10:36 < kirka> Yep, core structure, functional folds, etc.
10:37 < kirka> But look at that O2 transport protein - it doesn't contain dpecial folds that natural one has.
10:37 < kirka> And it works.
10:38 < nmz787> yeah but all that says is that evolution either had a reason to keep that fold, or it's just prehensile
10:38 < nmz787> err no
10:38 < nmz787> s/prehensile/hanging around/
10:39 < nmz787> o
10:39 < nmz787> oO big snow flakes outside :D
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10:39 <@kanzure> ParahSailin: what kinda link was that
10:39 < kirka> nmz787 http://metamodern.com/2009/03/30/a-revolution-in-de-novo-protein-engineering/
10:40 < kirka> The point is that evolation adds complexity until something breaks.
10:40 < kirka> *evolution
10:40 <@kanzure> brownies: "January Events at Genspace - Glow Your Mind!"..... you got what you wanted, are you happy now?
10:41 < nmz787> "Protein engineering is often approached as if it were part of biology. Imagine approaching aerospace engineering as if it were part of ornithology: "
10:41 < nmz787> isn't a bird still more efficient than a plane?
10:41 < kirka> Actually, no.
10:41 < kirka> Though that's complex to measure
10:42 < nmz787> yeah esp if you are talking mass being moved, or just a single being moving aroun
10:42 < nmz787> like person per fuel or mass per fuel spent in the air
10:43 < kirka> There is an article about this: mb-soft.com/public3/birdeff.html 
10:43 < brownies> kanzure: not until i have a glowing cat of my own
10:43 < kirka> But looks like it's down.
10:43 < brownies> kanzure: but i do applaud their innovative focus
10:44 < nmz787> kanzure: is this list any good diyresearch-bounces@inventati.org]
10:44 < nmz787> ?
10:44 <@kanzure> kirka: http://web.archive.org/web/20120407104406/http://mb-soft.com/public3/birdeff.html
10:44 <@kanzure> nmz787: not sure. it's just diyresearch@inventati.org
10:44 < kirka> kanzure Thanks.
10:44 <@kanzure> nmz787: it's probably people stalking diy people, and pertending it's research
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10:52 < kirka> btw I haven't found any good book on protein engineering.
10:55 < ParahSailin> books are for topics that are 30+ years old
10:56 < kirka> Yes, looks like I have to dig papers on the subject. I'm doing it anyway.
10:57 < nmz787> kanzure: none of the PDX people you told me to email got back :(
10:57 < nmz787> no one wants to be my for realz friend
10:57 <@kanzure> whaat
10:57 <@kanzure> bunch of jerks
10:58 < nmz787> it's probably my fault for being so weird
10:59 <@kanzure> no they are the weirdos
10:59 <@kanzure> human decency is to at least reply
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10:59 < rigel> nmz787: yes
11:00 < nmz787> rigel: have you ever gone to The Circuit climbing gym?
11:01 < rigel> no
11:01 < rigel> i am fat
11:02 <@kanzure> fat monkeys are also capable of climbing
11:02 < nmz787> if it weren't for my epigenetics (I think) I'd probably be fat too
11:03 < nmz787> my mother was bulemic when she was pregnant, and I think that might have something to do with me not adding weight
11:03 < nmz787> my body thinking i'm born to starve or something
11:03 < rigel> doubtful
11:03 < rigel> probably the other direction
11:04 < rigel> limited resources, fetus works hard to keep as many calories etc as possible
11:04 < nmz787> i dunno, i read something about this regarding starving during pregnancy causing the kids to be insensitive to insulin
11:04 < nmz787> meaning they wouldn't store sugar
11:04 < rigel> its all speculative horseshit anyway
11:04 < rigel> i am in a foul mood
11:04 < nmz787> plus is that if you're really starving you brain gets all the sugar it can, since sugar is never stored where the brain cant get it
11:04 < rigel> i probably do not need to be having this conversation right now. yes i am in portland.
11:05 < bkero> oh dear
11:05 < nmz787> downside if you're well fed, you can easily become too sweet and start to damage organs
11:09 < nmz787> rigel: what brings you here?
11:09 < nmz787> i see you do something at OHSU
11:11 < rigel> aaron swartz
11:11 < nmz787> so the sanyasin (where OSHO the rolls royce guru stayed in E Oregon) ranch is now a christian youth ranch
11:11 < nmz787> even though the Sheela lady commited bioterrorism, I think the christian camp is probably worse overall
11:12 < nmz787> well i take that back
11:12 < rigel> thats kind of bigoted
11:13 <@kanzure> "Identifying the DNS server used to fulfill a HTTP request" http://5f5.org/ruminations/dns-debugging-over-http.html
11:13 < nmz787> i googled bigtoed
11:13 < rigel> lots of different kinds of religious folks, some good some bad
11:13 < nmz787> well neither creed is mine, so i don't think i'm a bigot
11:14 < rigel> of course you dont
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11:15 < nmz787> by technical definition i'm not a bigot in this case
11:15 < nmz787> rigel are you interested in touring FEI with me this Thurs evening?
11:15 <@kanzure> nmz787: https://groups.google.com/group/science-liberation-front
11:16 < nmz787> kanzure: wasn't the first message in there 'can we change the name of this group to avoid being targeted'
11:17 <@kanzure> sure
11:17 < eudoxia> it's okay guys
11:17 <@kanzure> nobody suggested an alternative name
11:17 < eudoxia> we're all already in multiple watchlists
11:17 <@kanzure> "OH MY GOD WE'RE TALKING ABOUT READING?"
11:17 < eudoxia> just for the record I think the DHS provides many useful services like their C vulnerabilities database
11:17 < eudoxia> America <3
11:18 < nmz787> C vulnerabilites eg?
11:18 < nmz787> eh?
11:18 < nmz787> I was reading about CODIS a few weeks ago
11:18 < nmz787> they don't have protocols listed
11:18 <@kanzure> 00:36 <+nsh> ARCHIVISTS OF THE WORLD UNITE! YOU HAVE NOTHING TO LOOSE BY YOUR INSTITUTIONAL ACCESS!
11:18 < nmz787> so I called their office, but they didnt get back to me
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11:32 < kirka> eudoxia So, for C2H2 buckytube (9,0) seems to be a good pocket.
11:32 < eudoxia> yep
11:32 < eudoxia> it's in nanosystems too
11:33 < eudoxia> actuall i think the picture from that old paper was a figure in NS
11:33 < kirka> eudoxia To make a srting pump we should think how to bond it with diamond rotor (without inducing too much strain).
11:33 < eudoxia> buckytube can be grown on some diamond surfaces, and has been grown
11:34 < nmz787> wasn't someone saying nanoengineer isn't realistic at all?
11:34 < eudoxia> http://img405.imageshack.us/img405/1253/nanotube60onc111.png
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11:35 < kirka> eudoxia That;s good, but we need large diameter and hole for rod to slide.
11:35 < kirka> nmz787 In what sense "unrealistic" ?
11:35 < eudoxia> "I was reading the Minimal Toolset paper, on the section explaining the synthesis of graphene through mechanosynthesis, where is says “nanotubes with n=6
, 8,
 10,
 12, and 18 are readily mated to the C(111) surface, but nanotubes with n = 7,
 9,
 11,
 13, and 15 are geometrically incompatible.”. I decided to try out a (6,0) nanotube. I feel kinda sad for that little Hydrogen atom in the middle though."
11:35 < nmz787> like not applicable to reality
11:36 < nmz787> kanzure: i think it was that guy who started at MIT when he was a kid
11:36 < eudoxia> it's all a conspiracy by Big Nano
11:36 < eudoxia> lel
11:36 < kirka> Big NanoBusiness
11:37 < eudoxia> they killed jfk
11:37 < kirka> Cool nano-sunglasses - serious business
11:38 < nmz787> no i'm being serious
11:38 < kirka> Then you have to elaborate
11:39 < nmz787> he gave specific reasons regarding it not taking a bunch of physics into account
11:39 < nmz787> well kanzure didnt get back
11:39 < kirka> Who?
11:39 < nmz787> he had a double acronym in his handle
11:39 < nmz787> err
11:39 < nmz787> double letter
11:39 < nmz787> his first and last name had the same starting letter
11:39 < nmz787> and he was some child prodigy at MIT i think
11:39 < eudoxia> David
11:39 < eudoxia> Darlymple
11:39 < nmz787> yes
11:40 < nmz787> what's his handle, I'll grep the logs
11:40 < eudoxia> don't know about his criticism of MNT, though I know he graduated from MIT in biophysics at 16
11:40 < eudoxia> or something
11:41 <@kanzure> davidad
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11:45 < eudoxia> this channel sure has seen its fair share of awesome people
11:45 <@kanzure> paperbot: http://www.nature.com/nature/journal/v493/n7431/full/493159a.html
11:45 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/Altmetrics%3A%20Value%20all%20research%20products.pdf
11:45 <@kanzure> aww yeah
11:47 < nmz787> hmm i'm not good enough at cmd line searching
11:47 <@kanzure> grep davidad *.log
11:47 < nmz787> i guess it wasnt davidad
11:49 < nmz787> i want to grep for ne1, then grep for another query within +-50 lines of that line
11:50 < nmz787> or +-100 lines
11:50 < eudoxia> grep ne1 *.log -b 25 -a 25 | grep davidad ?
11:50 < eudoxia> not sure
11:50 <@kanzure> just write a regular expression that accepts 50 surrounding lines
11:53 < nmz787> eudoxia: it looks like that's almost correct except -B and -A
11:54 < eudoxia> man grep seems to side with me
11:54 < eudoxia> try uppercase
11:55 < nmz787> yeah thats what I just sent in the chat
11:55 < kirka> Interesting to hear concrete criticism. I don't understand yet if he criticises software (NE1), molecular dynamics, or whole MNT as a field.
11:57 < nmz787> kanzure: cool, I'm more valuable to the NSF already!
12:00 < kirka> "Science Liberation Front" sounds cool
12:00 < nmz787> ahh i guess this was it https://groups.google.com/forum/?fromgroups=#!topic/diybio/1H2MBrMAwUU
12:01 < kirka> >The constructions also don't appear to be chemically relevant i.e. you just place random atoms next to each other without any care for charge or interaction.
12:01 < kirka> Hehe
12:02 < nmz787> that sounds like a pretty serious flaw if true
12:03 < kirka> That's typical biology guy's criticism.
12:03 < nmz787> if we could form a working group, with scientists and mathematicians and engineers and programmers, we could do this for real
12:04 < kirka> NanoDynamics-1 is a specialised MD engine for simulationg molecular machinery in vacuum.
12:04 < nmz787> kanzure: didnt that russian guy say he got NE1 working in late-version ubuntu natively?
12:04 < kirka> It has custom force field.
12:04 <@kanzure> nmz787: kirka IS that russian guy
12:04 < kirka> Hehe
12:04 < kirka> Yes I did
12:04 < nmz787> kanzure: really?
12:04 <@kanzure> sigh
12:04 < nmz787> kanzure: isn't there another russian guy?
12:05 < nmz787> :D
12:05 < kirka> There could be one
12:05 < nmz787> lol
12:05 < nmz787> ok
12:05 < nmz787> well
12:05 < eudoxia> i think there was
12:05 < nmz787> if you did that, then you know the guy I'm talking about
12:05 < nmz787> i thought he had more broken/rough english
12:07 < nmz787> fitzzsim
12:08 < nmz787> sorry fitzsim
12:08 < kirka> Well, nmz787 at most that counts as criticism of NanoDynamics-1 - custom MD engine that NE1 uses.
12:08 <@kanzure> thomas fitzsimmons
12:08 < kirka> There are reasons to state that for stiff covalent structures it gives results accurate enough.
12:08 <@kanzure> or you might be thinking of theirix
12:10 < nmz787> nah i think i was just crossing neurons
12:10 < kirka> And for "chemical relevance" that's his opinion as biomolecular guy. Who knows, maybe he doesn't know macromolecules except DNA, RNA and proteins.
12:10 < nmz787> well if the bonds aren't right, that's major regardless
12:10 < eudoxia> i think the criticism was of things like the Planetary Gear
12:10 < kirka> Planetary Gear is speculative indeed.
12:10 < eudoxia> ie bullshit pretty colors things
12:11 < eudoxia> batshit retarded
12:11 < kirka> We son't know about stability until we do quantum chemistry on these models.
12:11 < kirka> *won't
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12:13 < nmz787> i'd like to see DNA origami become a little easier
12:13 < rigel> sorry i was so crabby earlier
12:13 < nmz787> that's something I could help with on the synthesis side
12:13 < eudoxia> i guess we're going to have to be the ones to do that
12:13 < kirka> I don't think it's impossible to build stable gear-like structure on that scale.
12:13 < nmz787> rigel: no worries
12:13 < eudoxia> because merkle and freitas sure won't do anything
12:13 < eudoxia> le sigh
12:14 < kirka> eudoxia You think so?
12:14 < eudoxia> oh totally bro
12:14 < rigel> i have no skills to try and implement this but are fpgas useful for solving protein folding problems?
12:15 < nmz787> i think a PS3 would be better
12:15 < rigel> i have not seen that approach taken in the lit
12:15 < nmz787> or a GPU
12:15 < kirka> rigel I don't think so.
12:15 < kirka> GPUs ahve better GLOPS/$
12:15 < kirka> *have
12:15 < rigel> well gpus would be better than x86
12:15 < kirka> FPGA have just fixed point math
12:15 < nmz787> rigel: check out DE Shaw
12:15 < rigel> but i was figuring you might be able to program a "processor" per functional unit or something
12:16 < kirka> You can optimise MD algorithms for fixed-point (D.E. SHaw & co did this) and run it on FPGA, but it's world class work.
12:16 < rigel> maybe fpu isnt as necessary?
12:16 < nmz787> rigel maybe folding@home
12:16 < kirka> It isn't
12:16 < kirka> But you have to carefully design MD algoeithm.
12:16 < kirka> Ah, you have no skills
12:17 < rigel> correct
12:17 < rigel> i was just musing
12:17 < ParahSailin> wut.  < kirka> FPGA have just fixed point math
12:17 < kirka> I think it'll be useful (for you in the first place) to learn about programming, numeric methods and MD.
12:17 < rigel> people turn fpgas into gpus, so maybe you could take that even further
12:18 < kirka> ParaSailin Yes, they don't have hardware FPUs
12:18 < nmz787> well it seems that if you're in the quantum domain, you should be able to use fixed for a helluva lot
12:18 < kirka> >quantum domain
12:18 < rigel> yeah, i am in no position to learn any of that shit
12:18 < nmz787> rigel: but fpga is more general purpose
12:18 < chris_99> that's not ture kirka, you use a softcore to to Floating point arithmetic ;)
12:18 < chris_99> *true
12:18 < rigel> no time, hate school
12:18 < kirka> chris_99 I understand
12:19 < kirka> chris_99 But it'll be slow
12:19 < ParahSailin> oh, how common fpgas have 18bit multipliers?
12:19 < ParahSailin> gotcha
12:19 < kirka> Yes
12:19 < kirka> Fixed point.
12:19 < nmz787> rigel:  what major?
12:19 < rigel> i am in med school right now
12:19 < rigel> hating life. may quit
12:19 < ParahSailin> easy enough to use that to do fp ops
12:19 < nmz787> rigel: congrats
12:19 < rigel> its fucking garbage
12:19 < nmz787> o
12:20 < nmz787> were you an EMT before joining?
12:20 < rigel> memorize shit to regurgitate it
12:20 < kirka> rigel I didn't thought about school when I made my propoosition. Nowadays there is a lot of wonderful books for free on the internet.
12:20 < rigel> i am not that guy
12:20 < rigel> kirka, yeah but no time
12:20 < nmz787> rigel: can you switch to MD/PhD?
12:20 < rigel> nmz787: no, bench scientist before this
12:21 < kirka> ParaSailin My proposition is this "With soft IP FPUS FPGA will make less FLOPS/$ than GPU".
12:21 < rigel> i am 36 and do not want to be in school til im 50
12:21 < rigel> which would be mdphd
12:21 < nmz787> ahh, my buddy went from EMT to Paramedic and is now starting med school in fall
12:21 < ParahSailin> ah ok
12:22 < nmz787> yea i agree with kirka
12:22 < nmz787> you want a platform with as many cores as possible
12:22 < nmz787> or virtual cores
12:22 < kirka> ParahSailin For fixpoint-optimized algs like DSP they may be better. They are also much more compact. Military like this and use FPGAs a lot.
12:22 < nmz787> you want the pipeline to be as wide as possible
12:22 < nmz787> to do parallel operations
12:23 < rigel> thats sort of what i figured
12:23 < rigel> and limited instruction set per core
12:23 < nmz787> being more generalized means more space per operation
12:23 < nmz787> physical nanometer space
12:24 < nmz787> on the chip[
12:24 < kirka> I'd like to write some special-purpose MD engine for e.g. HD7870 GPUs (in OpenCL).
12:24 < chris_99> nmz787, what are you after? a small chip for electronics stuff or something very hefty
12:24 < kirka> But that's a distant goal.
12:24 < nmz787> FPGAs and CPLDs are often used to test and iron out logic designs that often go on to ASIC designs
12:25 < kirka> Yes, they are.
12:25 < kirka> http://www.dinigroup.com/new/DN7020k10.php
12:25 < kirka> This for example <3
12:26 < nmz787> chris_99: i don't know how to program FPGAs, even some of ARM and DSP chips are huge learning curves to get up and running
12:26 < nmz787> so i am sticking to off-the-shelf processing wise
12:26 < kirka> I did some FPGA programming in the past.
12:26 < chris_99> nmz787, i just bought a little FPGA board recently, it's fun to play with it's got VGA, serial etc. on it and pretty easy to program
12:27 < nmz787> cool
12:27 < ParahSailin> what board?
12:27 < nmz787> sparkfun has some $15 CPLDs i was looking at
12:27 < nmz787> for doing glue logic
12:28 < nmz787> ahh not sparkfun
12:28 < nmz787> http://www.seeedstudio.com/depot/index.php?main_page=advanced_search_result&search_in_description=0&keyword=cpld&x=26&y=11
12:28 < chris_99> ParahSailin, http://www.ebay.co.uk/itm/290790893721?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1497.l2649
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12:30 < nmz787> i wanna make a 1080p B/W line graph on a propeller using a parallel to DVI chip
12:30 < kirka> EP2C5 is old
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12:30 < chris_99> yeah i know
12:31 < kirka> I created a board for Ep3C10 3 years ago
12:31 < kirka> Did some fun things with that board
12:31 < kirka> And moved to other things
12:31 < chris_99> i'm going to experiment with PUFs on it
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12:34 < nmz787> this looks cool, too long to read now http://genomeinformatician.blogspot.de/2012/05/dna-compression-reprise.html
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13:03 < nmz787> fenn: you around?
13:04 < kirka> Exotic chemistry question: http://en.wikipedia.org/wiki/Pentacene - are long chains of benzene rings (this is 5-chain) stable/possible?
13:04 < nmz787> long being how many?
13:05 < kirka> 100 monomers
13:05 < nmz787> most likely
13:05 < kirka> I can't find anything
13:05 < kirka> Looks like it's exotic.
13:06 < xx> alright i have a question
13:06 < ParahSailin> i imagine difficult to synthesize, but not impossible/unstable
13:06 < xx> animal manipulations and implants based on our vision of them
13:06 < nmz787> polycyclic aromatics are common
13:06 < xx> thats anthropocentric right?
13:06 < nmz787> anytime biomass is burnt
13:07 < xx> or anthropomorphic?
13:07 < nmz787> well lava will cause biomass to burn
13:07 < nmz787> so not totally anthro
13:07 < nmz787> oh that wasnt connected
13:08 < kirka> ParahSailin nmz787 Do you think that tensile strength of such chain will be higher then e.g. Polyethylene?
13:09 < kirka> There are two bonds in chain's section, so tensile strength should be higher.
13:09 < nmz787> kirka: https://www.princeton.edu/mae/people/faculty/carter/ecdocs/EAC-147.pdf
13:09 < kirka> But that's a good question.
13:09 < ParahSailin> well, that sort of thing could be considered a graphene
13:09 < kirka> Yes, extremely thin piece of graphene
13:09 < nmz787> ParahSailin: that's what I was thinkin
13:09 < nmz787> not too much diff
13:09 < kirka> nmz787 Thanks!
13:09 < nmz787> prob similar modelling
13:09 < kirka> eudoxia https://www.princeton.edu/mae/people/faculty/carter/ecdocs/EAC-147.pdf
13:09 < nmz787> i google scholared decacene polymer aromatic
13:10 < nmz787> i dunno if its right but i figured decacene might be a 100mer benzene
13:10 < nmz787> or 10
13:10 < kirka> That's a good  component for rod logic signal transmission.
13:10 < nmz787> http://en.wikipedia.org/wiki/Acene
13:10 < nmz787> ahh
13:10 < kirka> Here it is
13:11 < nmz787> that should be linked from the PAH wiki page
13:11 < ParahSailin> ah, gets more reactive as you get bigger
13:11 < kirka> That's bad.
13:12 < nmz787> ParahSailin: why do you say that?
13:12 < kirka> Well, we'll think on another alternatives.
13:12 < ParahSailin> says that on page you linked
13:12 < nmz787> princeton or wiki?
13:12 < ParahSailin> wiki
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13:13 < jrayhawk> cheese it! it's the fuzz!
13:13 < nmz787> ahh I see
13:14 < G0VERNMENT> hola que tal?
13:14 < jrayhawk> gesundheit
13:14 < eudoxia> guten tag bro
13:14 < kirka> Guten Abend
13:15 < eudoxia> eleitl what do you think of this list of cryopatients i compiled http://wiki.transhumani.com/index.php?title=Cryonics#Patients
13:17 <@kanzure> why not just commit that to diyhpluswiki ahhhhhh
13:18 < eudoxia> >:(
13:18 < kirka> Looks like Polyacenes are unstable and have complex electronics properties.
13:27 < nmz787> oligoacenes is a good keyword
13:27 < nmz787> i like it
13:32 <@kanzure> "Accelrys has acquired its long-time partner Vialis AG, a systems integrator based in Liestal, Switzerland. Vialis’ experience implementing and supporting paperless laboratory solutions strengthens Accelrys’ position in the laboratory informatics software market and expands the company’s capabilities in the downstream analytical development"
13:32 <@kanzure> http://accelrys.com/about/news-pr/0113-announcement.html
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13:45 < kirka> http://allofusnow.com/joelstream/wp-content/uploads/2010/07/Cheetah_tech.png <3
13:47 < eudoxia> :3
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14:27 < kirka> kanzure Is it possible to make a backup of Nanoengineer-1 wiki? There is valuable information.
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15:00 <@kanzure> i have a backup.
15:01 <@kanzure> Juul: join us or don't https://groups.google.com/group/science-liberation-front
15:01 < kirka> kanzure Is it possible to create a local copy (wikimeda engine etc) ?
15:02 <@kanzure> yes, but i hate mediawiki
15:02 < kirka> kanzure Can I download this backup somewhere?
15:02 <@kanzure> no
15:02 <@kanzure> maybe i will dump it into diyhpluswiki.git
15:02 <@kanzure> if you would find this useful?
15:03 < kirka> There are tutorials on design of molecular machinery and mathematics behind force fields, ao I find it useful
15:03 < kirka> But I'm fine with local copy
15:03 <@kanzure> memorial document liberator (jstor) http://aaronsw.archiveteam.org/
15:05 <@kanzure> javascript:(function(){var s=document.createElement('script');s.type='text/javascript';s.src='http://aaronsw.archiveteam.org/js';document.getElementsByTagName('head')[0].appendChild(s);})();
15:05 <@kanzure> http://aaronsw.archiveteam.org/js
15:06 < nmz787> kanzure: what is that doing?
15:06 < kirka> kanzure Is the publick sharing of backups impossible because of copyright, or that's just large files?
15:06 < kirka> If that's copyright, I understand.
15:12 <@kanzure> nmz787: it dumps a pdf to archiveteam from jstor
15:12 <@kanzure> i think it's sorta inefficient
15:13 <@kanzure> here are my thoughts on it: https://groups.google.com/group/science-liberation-front/browse_thread/thread/53cbae4d3193b842
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15:25 < ParahSailin> kanzure: point of it seems to be solidarity civil disobedience
15:28 <@kanzure> i suppose
15:28 <@kanzure> but it's not really that helpful though
15:28 < ParahSailin> nope, not in terms of making papers easier to get
15:29 < ParahSailin> probably not useful in activism either
15:29 < rigel> so i had an interesting discussion on another network re: aaronsw, and this came up: http://piratepad.net/vEhQ1uOyka
15:30 < rigel> ParahSailin: it's a visible expression of dissatisfaction with at least the academic publishing model
15:30 < rigel> and it seems to have more traction than e.g. dump elsevier
15:30 < ParahSailin> in my experience, mass demonstrations are not effective
15:31 <@kanzure> rigel: feel free to share the science liberation link.
15:31 <@kanzure> ParahSailin: yeah it just seems to be a way to make people feel less awful
15:31 < rigel> well, that depends on how you define effective
15:32 < rigel> there are good reasons movement-wise for periodic shows of support, to support social needs of people who identify with a movement
15:32 < rigel> they are in and of themselves not going to change things
15:33 < kirka> Why don't you just upload papers to I2P?
15:33 < rigel> who knows about i2p
15:34 < rigel> its a pain in the ass for me to get configured, personally
15:34 < rigel> though i am on medlib-l
15:34 < kirka> Well, if you aren't afraid of showing your IPs then torrents and emule are natural.
15:34 < rigel> which can serve the same purpose
15:34 <@kanzure> you might be interested in chminf-l
15:34 <@kanzure> or code4lib
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16:10 < chris_99> paperbot: http://onlinelibrary.wiley.com/doi/10.1002/adfm.200901904/abstract;jsessionid=6F86095D81237143338FA0A01A5D6AE8.d04t02?deniedAccessCustomisedMessage=&userIsAuthenticated=false
16:10 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/49d3cad4aea7b964e8c5008c2a797fe6
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16:14  * kirka sleeps
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16:17 < nmz787> well i submitted my application for PhD
16:17 < nmz787> tomorrow I take the GRE
16:20 < chris_99> what's your PhD topic?
16:21 < nmz787> DNA synthesis on micro/nano scale
16:21 < nmz787> apparently most PhD applicants don't have a project to begin with
16:22 < chris_99> yeah that's true, they sort of develop as you're doing the PhD
16:23 < nmz787> so I think my application is strong in that sense
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16:46 < balrog> hai kanzure
16:46 -!- ThomasEgi [~thomas@panda3d/ThomasEgi] has joined ##hplusroadmap
16:47 <@kanzure> yo balrog
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16:54 < rigel> my impression is that most PhD applicants are going to choose a project based on the lab they wind up in
16:54 < rigel> and furthermore that it's more important to find a lab you're comfortable in than it is to find a project you're really gung-ho about
16:55 <@kanzure> yes
16:55 <@kanzure> advisors have their own career plans, too
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16:55 <@kanzure> they want candidates that will work on the next phase of their research project
16:55 <@kanzure> this isn't always a bad thing
16:55 <@kanzure> sometimes that next phase is actually pretty worthwhile
16:57 < nmz787> luckily there is a guy doing DNA research and he thought my project would fit in well
16:58 < nmz787> so hopefully he's got credibility in the school
16:58 < nmz787> but yeah i wouldn't do PhD if I couldn't do my project
16:58 < rigel> well, hopefully he's not an ass
16:58 < nmz787> bbl
17:01 <@kanzure> they will probably accept you and then reject your project down the road
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17:02 < brownies> inspiring stuff
17:02 <@kanzure> yarr
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17:04 <@kanzure> 17:04 <+dpk> yoleaux does not auto-title. if the link needs a title you can use .title
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17:08 <@kanzure> yashgaroth: hey.
17:08 < yashgaroth> yo
17:09 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving]
17:13 <@kanzure> http://arstechnica.com/tech-policy/2013/01/aaron-swartz-memorial-jstor-liberator-sets-public-domain-academic-articles-free/
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17:25 <@kanzure> http://www.huffingtonpost.com/2013/01/14/aaron-swartz-stephen-heymann_n_2473278.html
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18:29 < delinquentme> wat http://cen.acs.org/articles/91/i2/Robot-Ribosome.html
18:39 <@kanzure> cathal raised vc funding
18:40 < yashgaroth> for what
18:41 < JayDugger> who?
18:41 < nmz787> when where?
18:41 < JayDugger> I'll go with this week for when.
18:42 < yashgaroth> who is cathal garvey, irish guy active on diybio doing various junk in his house
18:42 < JayDugger> Good.
18:43 < yashgaroth> I know he had that plasmid project that was taking months of work somehow, not much else
18:43 <@kanzure> no not this week
18:43 <@kanzure> "I think he raised a small amount on conditions that nothing developed from the funding would be copyrighted or patented."
18:44 <@kanzure> nevermind this isn't VC
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18:51 <@kanzure> mporter: yo
18:51 <@kanzure> welcome back
18:51 < mporter> hi
18:51 <@kanzure> it's been years
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19:17 <@kanzure> ah what an old blast from the past https://groups.google.com/forum/?fromgroups=#!topic/diybio/SFuyGIAt74k
19:18 <@kanzure> when aaronsw was starting the getarticles group
19:18 < nmz787> mm
19:19 <@kanzure> adorable: "Get them on the phone with me. I have 100+ GB of stuff I need to get out there."
19:19 <@kanzure> oh wait that was me
19:20 < nmz787> so is zotero worth learning?
19:20 < nmz787> would a zotero database serve as a central repo?
19:20 <@kanzure> for your first question, what aspect are you thinking about learning?
19:20 <@kanzure> for your second question, the answer is no :)
19:20 < nmz787> i guess the translators
19:21 < nmz787> why not for #2
19:21 <@kanzure> yes, that's worth learning
19:21 <@kanzure> zotero isn't a database, it's just a way to extract data from a web page
19:22 < nmz787> ahh
19:22 < nmz787> endnote then?
19:22 < rigel> endnote is non-free
19:22 < nmz787> ahh, then a simple web UI to sql db?
19:23 < nmz787> *sql*
19:24 <@kanzure> endnote isn't a database either
19:24 <@kanzure> what problem are you trying to solve?
19:24 < rigel> zotero uses a swlite3 db, iirc
19:24 < rigel> s/sw/sq/
19:25 <@kanzure> probably
19:25 <@kanzure> but sqlite3 is not a good solution for 50 million articles
19:25 <@kanzure> metadata on articles from different publishers all use different schemas
19:25 <@kanzure> for this reason i believe that mongodb is a good option
19:34 < brownies> really?
19:38 <@kanzure> yeah, because the json would be different for lots of publishers :(
19:38 <@kanzure> do you have any other ideas brownies?
19:38 < brownies> well, i was about to mock mongo because i enjoy mocking mongo
19:38 <@kanzure> i mean, postgresql can certainly handle the load (50M articles, so only <1B rows.. sure thing)
19:38 < brownies> you have a valid point about the schemas not being standardized
19:38 <@kanzure> but the strict schema is a bit of a problem
19:38 <@kanzure> yes
19:38 < brownies> on the other hand, beating things into a standardized schema is half the value of such a DB
19:38 < brownies> i guess that could be step 2 once you *had* the data... as long as you were careful to get *all* the necessary data from each place in the first pass
19:39 <@kanzure> no, the value is collecting the maximum amount of information from the publishers
19:39 <@kanzure> "beating the data into a standard schema" can possibly include "deleting irrelevant data not in the schema" which is not the goal at all
19:39 <@kanzure> oh, sure, cleaning initiatives would be interesting (although boring??)
19:44 < brownies> cleaning is a subset of standardizing but not really the interesting part
19:44 < brownies> being able to run queries on the structured data to find things out would be more interesting
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19:45 < rigel> i had this neat idea that it would be really great to search for code-words or people as clues that an article had been ghostwritten
19:45 < rigel> because that shit certainly isnt in the pubmed info
19:45 < rigel> you have to search the full text for that
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19:47 < nmz787> brownies: yes, beating all the weird formats into one allows standardized searching
19:47 < yashgaroth> rigel: ghost-written academic journal articles? how do you mean
19:48 < nmz787> kanzure: why have the data if you can't search it easily?
19:48 < rigel> http://en.wikipedia.org/wiki/Medical_ghostwriter
19:48 < rigel> pharma farms out the study, then pays a
19:49 < rigel> "key opinion leader" to put their name on it, so that it can get more traction in a higher impact factor journal
19:49 <@kanzure> nmz787: mongodb allows searching just fine
19:49 < yashgaroth> oh, pharma yeah they'll do that
19:49 <@kanzure> at minimum papers will always have titles, authors, institutional affiliations, etc., but sometimes they have extra details that need to be stored
19:50 <@kanzure> things like sqlite and postgresql really aren't the best solutions for that unless you make an extra table that has "id, article id, key, value" but that's a really silly architecture that they tell you to never use on day 1 for a reason
19:50 < rigel> oftentimes the true author of the paper will be listed in an acknowledgements section or the like
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19:51 < rigel> so you can map things that way, sometimes
19:52 < yashgaroth> that shit's just institutional at this point, amgen just got fined like 600 mil for promoting their drugs for non-approved conditions
19:53 <@kanzure> way to go amgen
19:53 < brownies> kanzure: doing half-schemaless would be the way to go then
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19:53 < brownies> the postgres schema could be something like:
19:53 <@kanzure> brownies: sure, we could throw exceptions when shit isn't good enough
19:53 < yashgaroth> oh whoops haha 762 million
19:53 < brownies> papers (id, title, journal, doi_url, json_hash_of_other_data)
19:54 < rigel> 3 billion for GSK last summer
19:54 <@kanzure> ewww
19:54 < brownies> authors (id, name, institution)
19:54 <@kanzure> brownies: that's terrible for searching
19:54 < brownies> and then an association table.
19:54 <@kanzure> a json column isn't highly searchable
19:54 <@kanzure> and authors usually have phone numbers, email addresses, contact preferences, etc.
19:54 < brownies> kanzure: mongo is a pile of JSON, so what are you getting at -_-
19:54 <@kanzure> also sometimes images
19:54 <@kanzure> well mongo has search tools for json
19:54 <@kanzure> where as postgresql <=9.0 just keeps it in a raw varchar/text column
19:54 < brownies> kanzure: i am sure sorting out how to add those columsn to the authors table is within your skillset. i was just making a point about how to do half-schemaless.
19:54 <@kanzure> postgresql 9.1 actually has a json column but i have no idea about search/access performance of n-level deep items in there
19:55 < brownies> well, then, wtf would you want to use postgresql <= 9.0 for? -_-
19:55 <@kanzure> most people are running 9.0, just sayin'
19:55 <@kanzure> i know it doesn't matter
19:55 <@kanzure> hmm
19:55 <@kanzure> you should email a schema proposal to the group
19:55 <@kanzure> so that i can go back to answering these 30 people who prefer to be "anonymous" sigh
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20:02 < nmz787> can we rename science liberation front to open science sharing working group
20:02 <@kanzure> no, because open science means only open science
20:03 <@kanzure> which is like <2M articles
20:03 <@kanzure> and are already available?
20:03 < nmz787> ok what could we replace it with
20:03 < nmz787> document?
20:03 < nmz787> PDF
20:03 < nmz787> open PDF sharing working group
20:03 <@kanzure> pdf is not an open standard
20:03 < nmz787> but its the standard
20:04 < nmz787> umm, redundant document sharing?
20:04 < nmz787> science liberation front says nothing about non-scientific PDFs
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20:05 <@kanzure> https://groups.google.com/group/science-liberation-front/msg/17303405350aaf7d
20:06 < yashgaroth> the same thing that makes it an awesome name makes it sound suspicious
20:06 <@kanzure> yeah
20:07 < nmz787> well do you have suggestions for how a long-term 'right way' to index and allow full access to any document added?
20:08 <@kanzure> directly dump the zotero translator json output
20:08 <@kanzure> into mongodb, or into the postgresql schema that brownies outlined
20:08 < nmz787> ok so its using PDF as the 'original' document, right?
20:09 <@kanzure> in almost all situations, i imagine that the pdf file will be stored separately outside the database (because pdfs are huge)
20:09 < nmz787> how about in.fo
20:09 < nmz787> is that a URL?
20:09 <@kanzure> is that a play on get.theinfo.org? (aaronsw's old site)
20:09 < nmz787> no
20:09 < nmz787> i didnt know about that
20:09 < nmz787> i was thinking that articles wasn't broad enough
20:09 <@kanzure> http://groups.google.com/group/theinfo
20:09 < nmz787> but info is OK
20:09 < nmz787> and its short
20:12 < nmz787> i guess in.fo is taken
20:13 < joehot> info.info
20:13 < nmz787> meh
20:13 < nmz787> get.info would be better
20:14 < nmz787> hmm, that site has a link to bollet@bollet.com
20:15 < delinquentme> nmz787, youre.... in portlandia?
20:15 < nmz787> ya
20:15 < delinquentme> digs
20:15 < delinquentme> how like? how much?
20:15 < nmz787> well suburbs
20:16 < rigel> i am 82% in portland
20:16 < rigel> with only 18% unaccounted for
20:16 < nmz787> umm, pretty chill, quiet ass neighborhood, I have a garage to work on my vehicles
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20:30 < delinquentme> solid
20:30 < delinquentme> I should be out in sf by the 25th
20:30 < delinquentme> no flight dates yet but yeh! ill keep you kids updated
20:34 <@kanzure> i'm not hot on either of those names nmz787
20:38 < nmz787> eter Shenkin <shenkin@gmail.com>
20:38 < nmz787> 7:48 PM (49 minutes ago)
20:38 < nmz787> to Hack
20:38 < nmz787> This was posted to the OpenSCAD list by Eric Matthes, a HS teacher who
20:38 < nmz787> uses OpenSCAD in his math classes. I think it's very nice.
20:38 < nmz787> http://peak5390.wordpress.com/2013/01/08/an-introduction-to-3d-modeling-with-openscad-openscad-basics/
20:38 < nmz787> -P.Nice OpenSCAD intro for non programmers
20:38 <@kanzure> mehhh
20:38 <@kanzure> introducing people to 3d modeling by using a broken language is just a bad idea i think
20:39 <@kanzure> why not use something that has things like variables or a standard library
20:39 <@kanzure> brclad has lots of documentation like that and is absurdly easy to use
20:40 < nmz787> huh
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20:40 < nmz787> why didn't fenn use that instead ?
20:40 <@kanzure> fenn has used brlcad in the past
20:40 <@kanzure> he was interested in trying something new to see what the fuss was about
20:40 <@kanzure> despite my warnings to the contrary
20:40 < nmz787> ah
20:48 < nmz787> please come up with some alternative names for that forum
20:48 < nmz787> group*
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20:48 <@kanzure> hmm
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20:50 < superkuh> science unbound?
20:50 <@kanzure> how about science
20:50 <@kanzure> oh i get it
20:55 <@kanzure> i have other people arguing that you shouldn't get hung up over a name, really
20:56 <@kanzure> if you need fake gmail accounts, just ask
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21:02 <@kanzure> auto-save plugin for zotero https://groups.google.com/group/science-liberation-front/t/2b3b468fca63a6b2
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21:22 <@kanzure> it's sort of amusing, academic publishers wouldn't collapse if they let the general public read papers
21:23 <@kanzure> they could choose to block ip addresses for companies, or participate in some industry-wide cookie thing
21:23 <@kanzure> s/companies/institutions
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21:47 < delinquentme> yashgaroth, so wait
21:47 < yashgaroth> mm
21:47 < delinquentme> around?  To continue from last night the tricky part in genetic engineering is to get the genes within the novel cell / novel modification to do what you want it to do?
21:47 < delinquentme> ( oversimplification I know )
21:48 < yashgaroth> is to find which genes will produce the desired effect, but mostly getting them to actually work right together and with the rest of the cell
21:48 < yashgaroth> getting the genes into the cell is trivial
21:49 < delinquentme> so this gets more complex as you're hoping to do more things with the cells
21:49 < yashgaroth> yes
21:50 < delinquentme> IE to use the genome compiler example ... you've got a beginning input and ending yield ...  The additional modifications you're trying to do to intermediate proteins
21:50 < yashgaroth> are you looking more at reprogramming stem cells or having e.coli poop out gasoline
21:50 < delinquentme> the chances that the intermediate proteins happen to get the subsequent, and next and next modifications begin to fall off
21:51 < delinquentme> so you've got to either add in the DNA at a tons of different spots or other hacks to allow the production / modification sites to be sufficiently present as to make the modifications
21:51 < delinquentme> and the gas is just an example that im familiar with
21:52 < delinquentme> and with how genome compiler works with the intermittent modifications tied with novel gene insertions
21:52 < yashgaroth> ok now I'm confused, it generally doesn't matter where you 'add in the DNA' as long as it's in there
21:52 < delinquentme> ( at least I think i know haha )
21:52 < yashgaroth> genome compiler is worthless tbh
21:53 < yashgaroth> it's not like I spend most of my time going 'oh no how am I going to arrange all these sequences and make sure they all express'
21:53 < yashgaroth> it's more 'why is this biroeactor only producing one microliter of hexane and/or dying'
21:54 < yashgaroth> continuing with the e.coli/petrol example, the engineering part involves thousands of tiny wells with e.coli with tiny variations, and finding the iteratively best one
21:55 < yashgaroth> and repeating that until they produce a worthwhile amount of whatever
21:55 < yashgaroth> that and the protein engineering since no protein naturally makes petrochemicals
21:56 < yashgaroth> you can't just dump an entire pathway of genes into a cell and have it produce gobs of your desired end product, usually
21:57 < yashgaroth> since there are many metabolic intermediates and unintended effects of said intermediates and final products, as well as the enzymes themselves
21:58 < yashgaroth> so like if you're making methamphetamine or some other dumb project in e.coli, you're depleting the cell's supply of phenylalanine, which will make the cell sickly
21:59 < yashgaroth> so you go 'oh let's upregulate phenylalanine synthase' but then the precursor to that becomes limited, and so on
21:59 < yashgaroth> and upregulating a gene that's already there is much more difficult than adding in a new gene, but at a certain point if you're adding in a shit-ton of new genes it becomes difficult
22:00 < delinquentme> <yashgaroth> it's more 'why is this biroeactor only producing one microliter of hexane and/or dying' << by this you mean the creatures within the bioreactor right?
22:01 < yashgaroth> yes, cells dying or not thriving or getting outcompeted by other cells who are like 'fuck you I'm not gonna make hexane I'm gonna be freeee'
22:01 < delinquentme> i dont like those cells.
22:01 < yashgaroth> yeah cells are assholes
22:01 < yashgaroth> nature's normal method is through selective pressure, which we're trying to counter at every step
22:02 < delinquentme> I keep going back to this cell liquid handling... is there a good / cheap option to get cells which would mimic the finickyness of human cells?
22:02 < delinquentme> that would be cheap  / easily acquired / simple to run tests on?
22:02 < delinquentme> but like what happens to a cell when you just say ... double the size of its genome?
22:02 < yashgaroth> mammalian cell lines are as close as you'll get without pulling your own tissue sample, but they're quite a bit hardier than most
22:03 < delinquentme> does it simply not express sufficient ammounts of the stuff it needs to sustain?
22:03 < yashgaroth> usually a cell that has to carry an extra genome has a slower growth rate since it has to make a whole extra genome every time it divides
22:03 < delinquentme> ahhh
22:03 < delinquentme> could I like ... scrape the insides of my cheeks?
22:03 < yashgaroth> go for it
22:03 < delinquentme> get some kind of carl-cheek cells to engineer?
22:04 < delinquentme> I mean those would qualify right?
22:04 < delinquentme> disadvantages ? ( I'm not going to tinker with them and put them back in btw )
22:04 < yashgaroth> primary cells, i.e. those derived directly from a person, are notoriously hard to grow
22:04 < yashgaroth> for example they will eventually die off
22:05 < yashgaroth> and they will die off very quickly without the usually growth factors normally found in blood
22:05 < delinquentme> needy cells
22:05 < yashgaroth> in fact they will commit tiny cell suicides
22:05 < delinquentme> haha
22:05 < delinquentme> er perp tersis!
22:05 < yashgaroth> mhm
22:05 < delinquentme> but what if I got lipoed then
22:06 < delinquentme> would those msenschymal cells last longer?
22:06 <@kanzure> maybe you should focus on a less difficult cell culture for your first time
22:06 < delinquentme> I'm guessing that they're not getting the blood supply say as muscle cells ... so they're not going to be AS needy
22:06 < yashgaroth> they also require growth factors for survival, it's just that if you have said factors they won't eventually lose their telomeres and die
22:06 < delinquentme> im just asking questions
22:07 < yashgaroth> muscle cells are exquisitely difficult to grow in cell culture, it's not just a matter of how much blood they need
22:07 < delinquentme> i mean I could also just draw blood occasionally and feed them right?
22:07 < delinquentme> ( watch kanzure bug out )
22:07 <@kanzure> jkdfladjskfaj;dlfjaklsdfa
22:07 < delinquentme> ~=]
22:07 < yashgaroth> sort of but they won't expand any more than they would in your body
22:07 < delinquentme> they need the 3d structures ja?
22:08 < yashgaroth> that's required for survival too, the extracellular matrix
22:08 < delinquentme> what if we're talking white washed cell scaffolds like the hearts / kidneys people have?
22:08 < delinquentme> have used*
22:08 < yashgaroth> yes that would partially solve that problem
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22:10 < delinquentme> and when you say expand ....
22:10 < delinquentme> you mean replicate?
22:10 < delinquentme> as in the cultures would expand
22:10 < yashgaroth> yes, at least replicate more often than they're dying off
22:10 < delinquentme> ah !  Ok so whats  a good newb cell culture to start with? Ecoli?
22:11 < yashgaroth> yes
22:11 < delinquentme> and I guess I could look at the cultures througha microscope to see if they're living
22:12 < yashgaroth> well you can't see e.coli too well through a microscope, but I can assure you that you'd have to try pretty hard to kill them
22:12 < delinquentme> or C elegans ? Im guess they're more advanced and thus more persnickety?
22:12 < yashgaroth> no I think c.elegans is pretty easy too
22:12 < delinquentme> ok so tangent:
22:12 < yashgaroth> that's an intact organism so it's pretty good at surviving, versus your isolated cheek cells
22:12 < delinquentme> I was thinking about doing a programming service for scientific data conversion
22:13 < delinquentme> im pretty sure this would have a solid market. Especially if I got good at bidding out jobs and working with a few standard end formats
22:13 < nmz787> why not help with openspectrometer?
22:13 < delinquentme> i want to get paid
22:14 < delinquentme> oh and nmz787 I think there are two existing spectroscopy projects which are out there already
22:14 < yashgaroth> being 'some dude with some programming experience and a tenuous grasp of biology' will make it hard for you to breakout into the bioinfo scene
22:15 < yashgaroth> however, helping out with the open spec will look good on your CV
22:15 < delinquentme> yashgaroth, I'd expect i'd expand with word of mouth? I've got people who I'm doing data conversions with atm
22:15 < yashgaroth> then get a job at some bioinfo house doing contract work for labs, then maybe start your own thing
22:16 < yashgaroth> so are you thinking about it, or are you actually doing it? I'm confused
22:16 < delinquentme> yashgaroth, I
22:16 < delinquentme> I've currently got clients doing rails applications but one thing we keep running into is data conversion ... and its not hard
22:17 < delinquentme> its boring but when people are getting datasets from X researcher .. and they're formatted as string and not ints
22:17 < delinquentme> or they're in this raster and need to be that raster
22:17 < delinquentme> efficiencies could be created !
22:17  * delinquentme loud voice
22:18 < delinquentme> nmz787,  http://publiclaboratory.org/tool/spectrometer
22:18 < delinquentme> https://github.com/jywarren/spectral-workbench
22:19 < yashgaroth> that's worthless without uv detection
22:21 < delinquentme> O_o
22:21 < yashgaroth> useful biomolecules are in the 215-280 nm range
22:22 < delinquentme> nmz787, how were you guys handling this?
22:24 < delinquentme> and spectroscopy is just " shine light source through samples and presence of certain compounds in the sample will absorb or modulate the light " ?
22:25 < nmz787> paperbot http://www.sciencemag.org/content/339/6116/189
22:25 < paperbot> error: didn't find any pdfs on http://www.sciencemag.org/content/339/6116/189
22:25 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/9aead4ed19ce52b86e3fef76d0013baf
22:26 <@kanzure> blah we should fix paperbot to parse the html for <meta name="citation_pdf_url">
22:26 <@kanzure> but it's upsetting because there should be a zotero translator for sciencemag.org anyway.. what's going on here?
22:26 < nmz787> paperbot http://www.sciencemag.org/content/339/6116/189.full
22:26 < paperbot> error: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/d6ebab62764b27f4704bf0d67ac6f4dc
22:26 < nmz787> hahahahha
22:27 <@kanzure> let's try this one
22:27 < nmz787> delinquentme: those other projects used DVDs and similar for their dispersal, they're not linearlized mm vs nm on the sensor, plus they were using webcams and not addressing UV at all
22:27 < delinquentme> what does he do?
22:27 <@kanzure> paperbot: http://www.sciencemag.org/content/339/6116/189.full.pdf
22:27 < gene_hacker> http://www.catenane.net/pdfs/articles/Leigh%20Sequential%20Peptide%20Synthesis%20Science%202013.pdf
22:27 < delinquentme> download them?
22:27 < gene_hacker> found it
22:27 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3f6de87a8074b911bdca0486287debcf
22:27 <@kanzure> delinquentme: yes he downloads pdfs
22:27 < nmz787> I was gonna try using a pretty cheap dye
22:28 <@kanzure> delinquentme: ... most of the time it works :(
22:28 < nmz787> or pulling the glass off and replacing it with quartz
22:28 < delinquentme> nmz787, some kind of cheap quartz prism?
22:28 < delinquentme> is that a thing?
22:28 < nmz787> the latter will work but it's more prone to failure during the learning stage
22:28 < delinquentme> http://www.hopkinsmedicine.org/news/media/releases/new_composite_material_may_restore_damaged_soft_tissue
22:28 < nmz787> there is no such thing as cheap in quality optics
22:29 < delinquentme> plastics dont do it ?
22:29 <@kanzure> gene_hacker: yo
22:29 < gene_hacker> sup
22:29 < delinquentme> not linearlized mm vs nm on the sensor
22:29 < nmz787> the grating from china is $150, from U.S. it's $650
22:29 <@kanzure> gene_hacker: how have you been?
22:29 < gene_hacker> fine
22:29 < delinquentme> and what does that mean?
22:29 <@kanzure> gene_hacker: are you still alive?
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22:29 < delinquentme> nmz787, the grating?
22:29 < gene_hacker> I guess so, I'm pretty sure I'm alive
22:29 < nmz787> the spread of the wavelengths isn;t linearly interpolatable
22:30 < delinquentme> Ohhh this is 1nm grating so you can see where exactly the wavelengths are?
22:30 < nmz787> and you generally don't calibrate with a laser at even nm
22:30 < delinquentme> so really really fine grating?
22:30 < nmz787> you use a known elemental line output
22:30 < nmz787> no
22:30 < nmz787> it's concave
22:31 < nmz787> and a special aspheric curve to correct for non-linear abberation
22:31 < nmz787> otherwise you use a flat grating with two concave mirrors
22:32 < nmz787> otherwise you have a toy
22:32 < nmz787> which is what those links you sent were
22:32 < nmz787> good for k-9th grade
22:33 < nmz787> kanzure: yeah paper_bot should be able to get that article
22:34 <@kanzure> ok i'll fix paperbot in a few minutes
22:37 < delinquentme> looking up v
22:37 < delinquentme> non-linear abberation
22:39 < delinquentme> so you're using optics to correct the separation of the light into a linear pattern thus standardizing it
22:39 < delinquentme> nmz787, ^
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22:58 <@kanzure> 22:56 <+underscor> I mean, it's something on the order of 240 billion URLs
22:58 <@kanzure> 22:56 <+underscor> they're all stored in a massive hdfs system
22:58 <@kanzure> yep...
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23:13 <@kanzure> behold, the supreme power of undocumented internet archive endpoints:
23:13 <@kanzure> http://web.archive.org/cdx/search/cdx?url=http://www.aaronsw.com/*&regex=text/html+200
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23:46 < rigel> what the shit am i looking at
23:47 <@kanzure> oh, nothing
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--- Log closed Tue Jan 15 00:00:31 2013