--- Log opened Mon Jul 29 00:00:39 2013
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03:21 < archels> paperbot: http://www.mitpressjournals.org/doi/pdf/10.1162/ARTL_e_00083
03:21 < paperbot> http://libgen.org/scimag5/10.1162/ARTL_e_00083.pdf
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05:47 <@kanzure> https://github.com/ShopBotTools/handibot-hardware
05:48 <@kanzure> http://www.shopbottools.com/mApplications/developers.htm
05:48 <@kanzure> https://github.com/ShopBotTools/handibot-hardware/blob/master/models/HandibotV1.00.00.stp
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06:29 < archels> paperbot: http://www.mitpressjournals.org/doi/pdf/10.1162/ARTL_a_00085
06:30 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/ccde309e4a2a34c5d30049b7cd60e03f.pdf
06:40 <@kanzure> ableep boopr
06:48 < archels> hi kanzure
06:48 < archels> thanks for paperbot!
06:49 <@kanzure> something new is coming on that front
06:49 <@kanzure> to replace paperbot's guts with something more scary/powerful
06:50 < anannie> how does paperbot actually work?
06:50 <@kanzure> https://github.com/kanzure/paperbot
06:50 < archels> it will achieve sentience?
06:51 <@kanzure> nothing so pedestrian
06:52 < anannie> paperbot: hi
06:52 * anannie expected a response
06:52 < gradstudentbot> Does this look contaminated to you?
06:54 <@kanzure> anannie: paperbot just fetches papers. it isn't capable of human emotion or thought.
06:54 < anannie> kanzure: I was expecting an eliza type bot
07:05 <@kanzure> sorry to disappoint :)
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07:24 < anannie> Okay I've decided to build one robot every week for the next 100 weeks
07:24 < anannie> Today is week one and I'm torn between building a simple, but practical vehicle and doing line following on it or building a six legged walker
07:29 <@fenn> anannie: maybe it seems obvious to you, but why would you do that?
07:29 < anannie> fenn: Do what?
07:30 < anannie> fenn: Build a robot each week for the next 100 weeks?
07:30 < anannie> fenn: or build a simple, practical vehicle?
07:30 <@fenn> well, that too, but why build a line follower or a walker? i don't see the point
07:31 <@fenn> you can buy a well engineered RC car for $50
07:31 < anannie> fenn: The point is to learn the fundamentals and the way systems are controlled and basically creating complex machines with behaviour, personalities and so on
07:31 < anannie> fenn: This is what I excel at. I like building robots
07:31 < anannie> All's well in the world when I'm building robots
07:32 <@fenn> why not just do heroin, it's cheaper
07:32 < anannie> I'm using Lego for most of this, so it's rather cost effective.
07:32 < anannie> I'll mate the Lego with arduino and then run it off of that
07:33 < anannie> and a few of the machines, I'll start building them from scratch as well
07:34 <@kanzure> fenn: that's a lousy line of argument
07:35 <@kanzure> fenn: are you a heroin addict now
07:36 <@fenn> i just dont see the difference between line followers and gluing popsicle sticks together
07:36 < anannie> and what are worthy projects in your pov?
07:37 < anannie> I'm not claiming that it's anything special. I'm just trying to do stuff by volume, so that I end up doing something special
07:38 <@fenn> i just think if you build something, it should have a purpose.
07:38 < anannie> this does have a purpose
07:39 < anannie> educating me so that I can do interesting stuff later on
07:39 <@fenn> fair enough
07:39 <@fenn> you would be better served learning how to run a cnc mill
07:39 < anannie> I've already done that
07:40 < anannie> and there aren't too many mills around me
07:40 <@fenn> then build one :P
07:40 < anannie> I will
07:40 < ParahSail1n> a cnc mill is a type of robot
07:40 < ParahSail1n> that can be week 1
07:41 < anannie> I don't have enough parts to make that... I'll make it once I have acquired enough parts
07:41 <@fenn> that sounds like a video game argument
07:41 <@fenn> you should make it out of whatever you have access to
07:41 <@kanzure> not enough ore! mine more ore!
07:42 -!- mode/##hplusroadmap [+o archels] by kanzure
07:42 < anannie> fenn: which is basically stuff that I can fit into my suitcase
07:42 <@fenn> besides, you wouldn't want to waste your legos on something that you don't want to take apart
07:42 < ParahSail1n> lol legos?
07:42 < anannie> fenn: I'm not living in the US.... third world country and so a lot of things are restricted for me
07:42 < anannie> I can only build with what I can carry
07:43 <@kanzure> anannie: that's not a fair excuse, sorry
07:43 <@kanzure> anannie: many people in third world countries have built very tiny cnc machines
07:43 <@fenn> that's a pretty huge engineering constraint
07:43 < anannie> kanzure: Sure with time, but I can't carry that around... too heavy
07:43 < ParahSail1n> i saw a video of a schoolteacher who's now an arms manufacturer in aleppo
07:43 <@kanzure> what is too heavy? sorry.
07:43 < anannie> kanzure: I move around a lot
07:43 < ParahSail1n> does syria count as third world?
07:43 < anannie> kanzure: The drills, hacksaws, motors, and other stuff
07:44 <@kanzure> have you considered not building a heavy cnc?
07:44 < anannie> kanzure: You need a drill at least something to make that
07:44 < ParahSail1n> maybe you should solve the constraint of only being able to build stuff you can carry first
07:44 <@fenn> i'm having trouble imagining a situation where there's no access to tools and yet you move around a lot, and never visit the same place twice
07:45 <@kanzure> ah yes the traveling machinist problem
07:45 <@kanzure> traveling bootstrapping machinist problem
07:45 < anannie> building one requires a setup of drills, material and so on... I move around a lot. New town every 3 to 6 months.
07:45 <@kanzure> welp you better get good at recreating everything each time :)
07:45 <@kanzure> that's what fenn did
07:45 <@kanzure> until he lost his soul
07:45 <@fenn> kanzure: hey that's pretty good
07:46 < ParahSail1n> what third world country is this anyway
07:46 <@kanzure> america
07:46 < anannie> India.
07:46 <@kanzure> my answer is funnier.
07:46 < anannie> yup
07:46 <@fenn> well it sounds like you should just make small stuff
07:47 <@fenn> that actually might be an innovation in itself
07:48 <@fenn> a mini factory standardized around dremel sized tooling
07:49 * anannie hopes fenn realizes that she can carry about 6lbs at a time
07:49 <@fenn> RC servos for airplanes are pretty lightweight, they have to be
07:49 < ParahSail1n> bootrapping all that seems like its more effort than its worth
07:49 <@fenn> anannie: okay, first thing to re-invent is the wheel
07:50 <@kanzure> ParahSail1n: frictionless bootstrapping makes the more costly things much less costly. instead of buying a $500k haas suddenly you are building one.
07:50 <@fenn> and then make a robot that follows you around
07:51 < ParahSail1n> solve the 6 lb constraint, then go from there
07:51 <@kanzure> i was talking with a startup the other day that was trying to convince me that their 3-axis haas was a "company perk"
07:51 <@kanzure> yeah, just what i want to do, wallow in misery every day waiting for a turn to use a haas
07:51 < ParahSail1n> what is that small build it yourself cnc mill that recently came out?
07:52 <@kanzure> there are many. most of them only cut really terrible materials like paper or wood.
07:52 <@fenn> it's a shame nobody has worked on "fast tool servo" or active structural vibration damping in these small machines
07:53 < ParahSail1n> shapeoki
07:53 <@kanzure> i am pretty sure everyone is pretending that vibration doesn't exist
07:53 <@kanzure> or they are just too clueless to be aware of anomalies in their cut pieces
07:53 <@kanzure> shapeoki is not recent.. haha.
07:54 < ParahSail1n> how long's it been around
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07:54 <@fenn> shapeoko looks more like a self-assembled kit than something one could make from scratch
07:54 <@kanzure> i don't have a list of wood-cutting cnc machines because i treated them all as a joke
07:54 <@kanzure> abetusk was working on one i think, he probably knows their names better than i do
07:55 <@kanzure> possibly randallagordon
07:55 < ParahSail1n> wood has its uses
07:55 <@fenn> wood is just extra-rigid styrofoam
07:55 <@kanzure> did you ever look at fenn's stewart platform for hexapod cnc stuff?
07:55 < ParahSail1n> same specific modulus as steel
07:55 < ParahSail1n> just doesnt like fire very much
07:56 <@fenn> http://fennetic.net/machines/hextatic
07:57 <@fenn> also "wood" and "steel" are hilariously vague terms when it comes to machining
07:57 < ParahSail1n> id bet its even possible to make a roller coaster out of wood if you cared enough to attempt it
07:57 <@kanzure> making a rollercoaster is not a particularly interesting feat in this context
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07:58 <@fenn> how about a wooden electron microscope
07:58 <@kanzure> "your electrons deserve only the finest maple finish" ?
08:01 <@fenn> i wonder if there's a good set of instructions for making poly lactic acid from starch
08:02 <@fenn> better than i expected: http://opensourceecology.org/wiki/Polylactic_acid/Manufacturing_Instructions
08:04 <@fenn> anannie: if you do go the traveling bootstrapping machinist route, concrete is your friend. design systems with demountable massive components
08:07 <@fenn> also, you can make a fairly serviceable machinable wax from paraffin and HDPE plastic bags
08:07 <@fenn> (paraffin wax)
08:08 <@kanzure> argh github is down.
08:09 <@fenn> it's a great mold material for silicone rubber parts
08:12 <@fenn> anannie: http://lcamtuf.coredump.cx/gcnc/ch4/ this whole series is great
08:27 < ParahSailin> hdpe bags and wax?
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08:31 < ParahSailin> why is coefficient of performance so attrocious on ice making machines
08:31 <@fenn> ah here's what i was remembering; not the most awesome robot but it's really neat to see it all made from scratch http://lcamtuf.coredump.cx/omni2/
08:32 < ParahSailin> AC units get 3.5 COP, and ice machines seem to get less than 1
08:32 <@fenn> because it's a higher temperature differential
08:33 < ParahSailin> evaporators on ice machines goes at -20 C, i dont think its just carnot efficiency at play
08:34 <@kanzure> quick, scram to make a library calle ddildo.js http://www.w3.org/TR/2013/CR-vibration-20130723/
08:35 <@kanzure> oh it's just a timer?
08:35 <@fenn> someone tell qdot
08:35 <@kanzure> and why isn't there a callback for when the vibration is done?
08:35 <@kanzure> who designs this shit
08:35 < ParahSailin> .wa 253/(313-253)
08:35 < yoleaux> 253/(313-253): 253/60; Decimal approximation: 4.216666666666666666666666666666666666666666666666666666666666...; Repeating decimal: 4.216^_ (period 1); Mixed fraction: 4 13/60; Number line: http://is.gd/p6U1vY; Continued fraction: [4; 4, 1, 1, 1, 1, 2]; Egyptian fraction expansion: 4 + 1/5+1/60
08:36 < ParahSailin> .wa 283/(313-283)
08:36 < yoleaux> 283/(313-283): 283/30; Decimal approximation: 9.433333333333333333333333333333333333333333333333333333333333...; Repeating decimal: 9.43^_ (period 1); Mixed fraction: 9 13/30; Number line: http://is.gd/GBlCDD; Continued fraction: [9; 2, 3, 4]; Egyptian fraction expansion: 9 + 1/3+1/10
08:36 < ParahSailin> you should still get at least half the COP out of an ice maker
08:36 <@kanzure> does wolfram alpha really need to display 58 zeros to get the point across?
08:36 <@kanzure> i mean 58 '6's
08:36 <@fenn> does wolfram alpha really need to give us the egyptian version of the number?
08:37 <@kanzure> get out of my head
08:37 <@kanzure> i totally called the 2 GHz frequency
08:37 <@kanzure> go find your own brain wave frequency, you squatter
08:39 <@fenn> i never understood why phone vibration has no control over the frequency of vibration
08:39 <@fenn> everyone's phone sounds the same
08:40 <@kanzure> but also what about strength of vibration (what is that a function of, anyway)
08:40 <@fenn> oh well at least they let you specify in milliseconds
08:40 <@fenn> you could do software pulse width modulation
08:41 <@fenn> the amplitude is determined by the mass of the weight on the motor
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08:47 < abetusk> I assembled a ShapeOko kit a while back. I also have a Zen toolworks machine. I haven't used the Zen toolworks for anything past drilling wood and routing PCBs
08:47 < abetusk> The ShapeOko has significant problems though
08:49 < ParahSailin> ah?
08:50 < abetusk> I think kanzure is right, that the vibration isn't really accounted for. In the kit that I purchased, the y-axis was only driven by a belt on the left side and the right side was left without a drive train. This produced visible fishtailing when changing directions. So the first thing you have to do is get another stepper and another belt and put it on the other side of the y-axis
08:51 <@kanzure> haha a belt
08:51 < abetusk> At the time they didn't offer this option, but now they sell an 'upgrade' so that you can do it yourself. My feeling is that this should be necessary
08:51 < gradstudentbot> Nobody has tried this before.
08:51 < abetusk> yep, and that's the other thing, it's a belt.
08:52 < abetusk> So, engraving wood, sure. Anything more than that and I would be skeptical. Thinking that you can cut aluminum is optimistic, imo
08:52 < abetusk> There's also the problem of actually fastening the belt down so it's tight. That's a real pain and I haven't figured out a solution yet
08:53 < abetusk> Limit switches are not really thought of and it's difficult to figure out how to install them.
08:54 < abetusk> Anyway, it kind of looks like a first attempt by someone who didn't know that much about CNCs. I really appreciate it's open nature, but it has some design problems
08:55 < abetusk> The Zen toolworks on the other hand, I like a lot. That's PVC with a leadscrew system, so I think it would be able to handle wood no problem. They say it can cut aluminum with some success, but that's getting iffy
08:55 < abetusk> accurate enough to do surface mount PCB routing...
08:56 < gradstudentbot> It's contaminated.
08:57 <@kanzure> fenn: i think it's hilarious how nobody listens to you
08:57 < gradstudentbot> You know, I can just do consulting.
08:59 <@fenn> shapeoko is driven by a leadscrew from what i can see
08:59 <@fenn> gradstudentbot: great plan, let's farm out the consulting work to bots
08:59 < gradstudentbot> Why did I go to grad school?
08:59 <@fenn> "buy IBM" "just use XML"
09:00 <@kanzure> webscale.
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09:02 < abetusk> fenn, The initial version I think did use a leadscrew system, but Edward Ford eventually changed it to a belt system...maybe for cost and/or simplicity? See: https://www.inventables.com/technologies/desktop-cnc-mill-kits-shapeoko
09:02 < abetusk> That is definitely a belt system
09:03 <@fenn> ah that's unfortunate
09:03 < abetusk> yep
09:03 <@fenn> the roller v bearing can handle a lot more force
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09:04 < abetusk> yeah, that's another thing, I'm not to sure about using that roller system as the linear guide.
09:05 <@fenn> should be fine if it's hard anodized
09:06 <@fenn> how do you take the slop out? there doesn't seem to be any eccentric cam
09:07 <@fenn> if the rollers are just held in place by friction, they'll work loose
09:07 < abetusk> eccentric cam?
09:07 <@fenn> a bushing with the center hole not quite concentric
09:08 <@fenn> the bearing mounts on it, and you can move the bearing in and out by rotating the bushing
09:08 < abetusk> As a way to keep the belt under tension?
09:09 <@fenn> no, because the holes locating the bearings aren't spaced exactly right
09:10 <@fenn> i imagine the plate they're mounted on flexes like crazy so it's probably a moot point
09:10 < ParahSailin> its kind of annoying trying to make a save as box pop up to save a file generated in javascript in browser
09:11 <@kanzure> you have to have the right headers from the server
09:11 <@kanzure> or you can set window.location but it will prepopulate the filename with 'data'
09:11 <@kanzure> oops i mean document.location
09:11 < ParahSailin> well in this case there's no server generating the file
09:11 <@fenn> "generated in browser" means the server has nothing to do with it
09:12 <@kanzure> frankly the only two options are to get the http response headers from the server right or to use something like dropbox-js or filepicker-js
09:12 < ParahSailin> but what i've had to do is actually transmit the file to the server as xhr then download it
09:12 <@kanzure> you can also use the html5 filesystem api but that's only for a sandboxed area of the file system that users can never find
09:12 < ParahSailin> still can't get the right headers to make it make a save as box
09:12 <@kanzure> usually browsers will give you a save-as box if it doesn't recognize the mime type
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09:13 <@kanzure> sometimes you can do something like, Content-Disposition: attachment; filename=filename.ext
09:13 <@kanzure> but not all browsers respect Content-Disposition: attachment
09:13 < ParahSailin> i tried "Content-Type: application/download'" and that didnt work
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09:13 <@kanzure> Content-Disposition is not Content-Type
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09:14 < ParahSailin> also put "Content-Disposition: attachment; filename=pilot_session.json"
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09:14 < ParahSailin> still doesnt pop up save as box
09:14 <@kanzure> and it just shows in your browser instead?
09:14 < ParahSailin> it just downloads as that suggested file name
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09:15 <@kanzure> there is no cross-browser compatible way to trigger "save as"
09:16 < ParahSailin> how about just chrome way to do it, this is an internal app
09:16 <@kanzure> again, filepicker and dropbox-js are two good options until html5 filesystem api stops sucking
09:17 <@kanzure> what about using the data uri format
09:17 <@kanzure> also if you are okay with flash, that's another option.
09:18 < ParahSailin> the data just saves it as download.something without popping up dialog
09:18 <@kanzure> i also recall an html5 attribute that you can add to an element called download, but i haven't tried it. ask nmz787.
09:18 < ParahSailin> yeah i guess ill have to use that flash thing
09:18 <@kanzure> test link
09:19 <@kanzure> ah the internet says that this download attribute is only respected by google chrome as of july 2012
09:22 < ParahSailin> downloadify it is i guess
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09:36 < abetusk> fenn, what's this eccentric cam business and what is it used for?
09:36 < anannie> fenn: Thanks for the link!
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09:49 <@fenn> abetusk: imagine you want to pinch a rail between three roller bearings, to make a sliding movement. the distance between the bearings will inevitably be different from the diameter (thickness) of the rail, so there needs to be a way to adjust the distance
09:50 <@fenn> one way to do it is to have an oval slot, and just move one bearing in and out and bolt it in place at the correct distance
09:51 <@fenn> another way is to push it in and out with a fine threaded screw
09:51 <@fenn> the eccentric bushing is just another mechanism to adjust the distance, but it happens to be very compact
09:52 <@fenn> another advantage is that the forces acting on it won't cause it to loosen, since tightening/loosening is done by applying torque
09:54 <@fenn> http://ecx.images-amazon.com/images/I/61en8VKlg7L.jpg notice the stud/shoulder part isn't concentric with the roller part (you might have to zoom in to see this)
09:55 <@fenn> it's a very tiny adjustment
10:05 <@fenn> maybe easier to see the offset in this image http://www.2cvsource.com/files/1208090.jpg
10:05 <@fenn> i can't believe there's no diagram of this on the internet
10:08 <@fenn> http://www.qbcbearings.com/BuyRFQ/LinearB_Guide_B_VG_EC.htm
10:08 <@fenn> click on "drawing"
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10:47 < ParahSailin> weird, there's a secret, undocumented multiprocessing.pool.ThreadPool in python
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12:49 <@heath> paperbot: http://nar.oxfordjournals.org/content/40/7/2862.long
12:49 < paperbot> http://libgen.org/scimag/get.php?doi=10.1093%2Fnar%2Fgkr1173
12:50 <@heath> oh, it's already free
13:02 < nmz787> so is there a list of human-nonhuman hydbrids that have been tried and don't work... this would be a list with both human males inseminating nonhuman females, and vice versa (human females getting inseminated with nonhuman semen)
13:04 <@fenn> seeing as bestiality is illegal in most places, you'd have a hard time getting an accurate list
13:04 <@fenn> but there's a reason they're called species
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13:05 <@fenn> http://en.wikipedia.org/wiki/Humanzee if you haven't read it yet
13:08 < gradstudentbot> None of this data makes sense.
13:10 <@kanzure> nmz787: so basically you're saying that the only way to know for sure is to get a bunch of girls to fool around with animals? instead of, you know, genetics.
13:12 < cogitokat> I'd watch that
13:20 <@fenn> oh apparently it's legal in russia, you just can't film it
13:21 < nmz787> kanzure: what do you mean knowing genetics? we only know by observation or experiment
13:21 <@kanzure> ivf?
13:22 < nmz787> there are plenty of species that can interbreed
13:22 < nmz787> lions and tigers
13:22 < nmz787> donkey and horse
13:22 < nmz787> neanderthal and sapiens
13:22 < nmz787> its interesting that female lion on male tiger isn't the same as male lion on femal tiger
13:25 < ParahSail1n> goats and sheep can interbreed at low frequency
13:25 < ParahSail1n> but goat on sheep is common enough that geep are a thing from time to time
13:26 < ParahSail1n> i bet if you had a million human-chimp encounters youd get a live birth out of it
13:26 < nmz787> kanzure: might be easier to get girls to fool with animals than genetics... lot less smart girls in the world... getting the men to mess with animals seems different but also not impossible... an old mexican on this ranch i was at years ago was suspected of messing with the sheep
13:27 < cogitokat> wow
13:30 < nmz787> an IVF panel would be interesting I guess
13:31 < nmz787> i mean, it would be interesting for sure
13:31 < nmz787> but is that the whole picture, you still need to implant to see if it would go to term
13:31 < nmz787> right?
13:41 <@heath> cambrian genomics isn't at the state of allowing people to place orders yet...
13:42 < nmz787> heath: no, in march they said they were still sorting oligomers
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13:52 <@kanzure> yeah, at this point i am absolutely convinced that simpler is better
13:52 <@kanzure> no complicated dna machinery. no microfluidics. just something that works.
14:03 < jrayhawk_> paperbot: http://www.ncbi.nlm.nih.gov/pubmed/1778686
14:06 < jrayhawk_> https://en.wikipedia.org/wiki/Zoophilia#Extent_of_occurrence it's more than you'd think
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14:33 < cogitokat> That data is from when more people lived on farms. It is probably even less than the Hunt study, today. Also, the real takeaway from that wikipedia page is that men have sex with animals more than women, so maybe there are 'lot less smart boys in the world.'
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14:56 < nmz787> cogitokat: smartness has nothing to do with sex though
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14:57 < nmz787> err,
14:57 < nmz787> scratch that, in the context earlier I guess it probably does
14:58 < nmz787> since men already have a higher prevalence towards beastiality
15:15 <@kanzure> hrmm http://www.kickstarter.com/projects/391496725/the-slingatron-building-a-railroad-to-space?ref=category
15:18 < nmz787> yeah i saw that
15:31 < superkuh> I think it is a bad idea.It solves a problem that doesn't really need to be solved. The max acceleration for ground based kinetic launchers isn't the issue. Modern electronics can stand very high G.
15:33 < superkuh> The cheapest approach would be simple pipes forming a light gas gun using hydrogen. I have been told the problem of ground based kinetic launches is the mass fraction of the rocket engine to circularize the orbit compared to payload.
15:49 < nmz787> Restrictions on cloning and stem cell research have made chimera research an attractive alternative."
15:49 * nmz787 has made chimeric mice cells
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16:22 <@heath> paperbot: my thing is biological comput
16:22 <@heath> paperbot: https://www.sciencedirect.com/science/article/pii/0022519382900029
16:22 < paperbot> http://libgen.org/scimag1/10.1016/0022-5193%252882%252990002-9.pdf
16:23 <@heath> ftr, that's not my quote pasted above
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16:24 < ParahSail1n> superkuh, yeah, first stage as cannon would probably be pretty cost effective for launching dead stuff
16:25 <@kanzure> heath: what does "biological computing" even mean.. wtf.
16:26 < ParahSail1n> i'd invest it
16:26 <@heath> kanzure: i have no clue
16:27 <@kanzure> heath: i think you're full of it
16:27 <@heath> ?
16:28 <@kanzure> i mean, you've been obsessing over this for a while now, and you still don't even know what it is
16:29 <@kanzure> this is not very efficient obsessing
16:29 <@heath> kk
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16:31 < nmz787> "By now, he had a second experiment in mind: to inseminate women with chimp sperm. Knowing that no local woman would agree, he planned to do this under the pretext of a medical examination, but the French governor forbade it."
16:31 < nmz787> friggin politicians always interfering
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16:39 < nmz787> "When Ivanov put his proposal to the Academy of Sciences he painted it as the experiment that would prove men had evolved from apes. "If he crossed an ape and a human and produced viable offspring then that would mean Darwin was right about how closely related we are," says Etkind. When Ivanov approached the government, he stressed how proving Darwin right would strike a blow against religion, which the Bolsheviks were struggling to stamp out. Succes
16:40 < nmz787> So who are the modern day bolsheviks?
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16:52 < nmz787> howdy tomkinsc
16:53 < tomkinsc> hello friend
16:53 <@kanzure> hi
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16:53 < nmz787> hi phillyj
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18:13 < ParahSail1n> how cheap are gps receivers now
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18:14 < ParahSail1n> ah < $5
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19:38 < fredox> Practical question regarding DNAsynth machines: Approximately what volume of a given nucleotide solution is used per cycle?
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20:52 <@kanzure> fredox: you only need one molecule as long as you can force it into the right spot. but since nobody can, they just talk about yield and avogadro's number and so on.
20:53 < fredox> yes, I mean in a pratical machine what are typical consumption rates?
20:54 <@kanzure> i don't think that matters.
20:54 <@kanzure> if you need more, just ask and i will buy it
20:55 < fredox> i'm thinking re machine design
20:57 <@kanzure> the reaction can work at extremely small volumes, so go wild
20:57 <@kanzure> but don't bother with microfluidics
20:57 < yashgaroth> yeah you're more limited by how little volume you can reliably control
20:58 <@kanzure> please do not design a machine that requires 200 liters per base pair of oligo...
20:59 < fredox> could you give me a ballpark example of a current commercial machine
20:59 <@kanzure> no. in fact, it's best if you ignore current machines completely because all of their ideas are bad.
21:01 <@kanzure> i guess yashgaroth might be willing to give you some numbers, but imho the current details don't matter at all
21:01 <@kanzure> some of the design questions are interesting though
21:01 < yashgaroth> hey man that's chem I don't do chem, but I'll just go ahead and say 100nL
21:01 <@kanzure> like whether or not to make a "multi-channel" monster
21:01 <@kanzure> i sort of doubt it's 100 nL per reaction step
21:02 <@kanzure> have you seen their tubes? the surface area of the tubes alone would eat that up.
21:02 <@kanzure> i guess it might be under pressure
21:02 < fredox> i would have thought it much larger than that
21:02 < yashgaroth> I'm imagining the lower limit for 6 tubes into a reaction vessel with non-microfluidic tech, not those '80's contraptions
21:03 <@kanzure> yashgaroth: then how do you explain the huge microarray designs.
21:03 <@kanzure> oh, tubes.
21:03 <@heath> fhttp://lammps.sandia.gov/
21:03 <@kanzure> no i meant erm.. plastic tubes for pumping things around. not tubes.
21:03 <@heath> (25 July 2013) The 3rd LAMMPS workshop is now 2 weeks away (Aug 6-8), here in Albuquerque, NM.
21:03 < yashgaroth> hell if I can transfer 1uL reliably myself surely a machine can manage an order of magnitude better
21:03 <@heath> https://www.youtube.com/watch?v=_uejPUnfuuw
21:03 <@heath> .title
21:03 < yoleaux> Self-assembly of DNA icosahedron - YouTube
21:03 <@kanzure> yashgaroth: haha but you have no idea who designed those machines. they could have been idiots.
21:04 <@kanzure> http://www.flickr.com/photos/64866643@N02/8448886468/ "One of the world's first commercially produced DNA/RNA synthesizers, this instrument is from the early period of DNA synthesis." (1982)
21:05 < gradstudentbot> You know, I can just do consulting.
21:05 < fredox> i was guessing somewhere in the uL range as a reasonably simple piece of engineering
21:05 < yashgaroth> like an HPLC pump can do 1uL easy, but then packing them into a large array is difficult
21:06 < yashgaroth> if you have the tiniest tubing and an adorable peristaltic pump, 1uL at a time is more reasonable
21:06 < abetusk> fenn, thanks. If I remember correctl, there is such a device on the ShapeOko
21:06 < abetusk> *correctly
21:06 <@kanzure> you have to decide if you want to build something that uses a microarray or not
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21:07 < fredox> nah thats much farther down the track
21:07 <@kanzure> there are certain design constraints of this sort of system that i bet everyone else has ignored and just said "yeah, use a microarray" or "yeah, just put some tubules in it and pump liquids around" instead of actually considering the problem.
21:07 < yashgaroth> and also how efficient your downstream step is, since if you get one femtogram of oligo there's not much you can do with it
21:07 <@kanzure> not sure you would be able to confirm a single femtogram
21:08 < yashgaroth> quantification is included in 'downstream steps' yeah
21:09 < fredox> cycle time is the next obvious parameter
21:10 <@kanzure> yashgaroth: i wonder if i should get heath or nate to manually do oligo synthesis with a pipette, just to get the hang of it
21:10 <@kanzure> yashgaroth: and then maybe they will get so frustrated that they will scribble out a better way to do it
21:10 <@kanzure> it seems sort of torturous even for 4 or 5 bp..
21:11 < yashgaroth> I thought you need a contained vessel or something because ambient humidity
21:11 < fredox> do you have any specific goals regarding machine synth rates and capacity?
21:12 <@kanzure> none whatsoever. the primary motivator for me is cost. i am pretty sure machines that do these steps don't have to cost $50k-$250k.
21:12 <@kanzure> might cost $50k in development but i don't care
21:13 < fredox> i am certain a basic machine could be built for a few hundred dollars
21:13 <@kanzure> yes
21:13 <@kanzure> well, no, i'm not certain of that
21:14 <@kanzure> but it seems much more realistic to me
21:14 <@kanzure> it's not like all of your parts are made of plutonium or something
21:14 <@kanzure> oh wait, what's the currently expensive element these days? blast where is united nuclear when you need it..
21:14 < gradstudentbot> Nobody is even going to read this paper.
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21:17 <@kanzure> fredox: if you wanna get those parts, let me know.
21:17 <@heath> [23:10:16] yashgaroth: i wonder if i should get heath or nate to manually do oligo synthesis with a pipette, just to get the hang of it
21:17 <@heath> yes
21:17 * heath willingly vounteers
21:18 * heath sleeps first
21:18 < fredox> kanzure: parts?
21:20 <@kanzure> fredox: yeah, i could cover things like a BOM and reagents.
21:20 <@kanzure> fredox: in particular this deal would only apply if you want to make an open source synthesizer.
21:21 < fredox> thats the plan
21:21 < fredox> could be handy in the future, though i should mention i am in australia
21:21 <@kanzure> i wont hold that against you
21:21 <@kanzure> where in australia?
21:22 < fredox> melbourne
21:22 <@kanzure> have you gone to cchs?
21:23 <@kanzure> i also highly recommend showing up here: http://www.meetup.com/emergence-24/ (tell them i sent you and they will nod solemnly)
21:23 < fredox> no, i had not seen that before
21:24 <@kanzure> there is also chris pendelbury and adam ford (although adam has gone to the dark side (managing magazines for hplus, a transhumanist anal ointment cream company))
21:25 * kanzure thinks
21:25 <@kanzure> that about exhausts my homies in melbourne.
21:25 <@kanzure> http://www.hackmelbourne.org/
21:36 <@kanzure> yashgaroth: was there a good reason against doing a 4096-element macro library?
21:37 < yashgaroth> not aside from the initial startup cost and the unprovenness...wait, maybe something about the lower limit on ligase
21:38 <@kanzure> no i think it might have been geometric/space dimension constraints
21:38 <@kanzure> like.. where are you going to put 4096 tubes.
21:38 <@kanzure> i mean, 4096 vials that are connected to tubes that get cleaned. or something.
21:39 < yashgaroth> you can get microtiter plates with a thousand wells
21:39 <@kanzure> and then do micropipettor selector arm robot?
21:39 < yashgaroth> yeah, since tubing to connect to those wells becomes unwieldy
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21:39 <@kanzure> if you have a 4096-well plate then you might as well just always synthesize from scratch i think, because you can tolerate errors earlier in the process or somtehing
21:40 <@kanzure> tbh i was thinking a system with no moving parts would be easier to debug. but this might be "grass is always greener" influencing me.
21:40 <@kanzure> *something
21:40 < yashgaroth> the main advantage of the library was that the oligos are self-replicating, though you'd need some analysis on whether it's cheaper in the long run
21:41 <@kanzure> reagent cost comes later imho
21:41 <@kanzure> right now the cost of a synthesizer dwarfs the cost of reagents for even a simple protein
21:41 < yashgaroth> also you could maybe do light-based printing into the wells like for microarrays, and hope that incorrect oligos simply wouldn't get ligated during assembly
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21:42 <@kanzure> washing a microarray correctly seems really hard and uninteresting to me
21:42 <@kanzure> unless you can use a high powered laser to evaporate everything
21:42 <@kanzure> cambrian genomics is using a laser to move beads out of one well and into (something unspecified)
21:43 <@kanzure> anyway, no, i think that complicates it really
21:43 < yashgaroth> was that optical tweezing or are they being secretive, I forget
21:44 <@kanzure> "We're basically building a lot of custom optical / sequencing / laser gear to sample single molecules of a microarray pool and to cherry-pick out the correct ones. Instead of enzymatic tricks, we're doing physical separation upfront of the good from the bad, while simultaneously de-scrambling the ~10^5-10^6 pools into defined small assembly sets for very rapid, very high-throughput assembly of larger kilobase pieces."
21:45 < yashgaroth> if you have a tiny-scale oligo synthesizer instead of a library, you can still incorporate the ligase-based assembly but you're just getting closer to traditional assembly
21:45 <@kanzure> "The cost of phosphoramidites is really low (at a minimum) given that they're produced in china. The container the phosphoramidites come in can be more expensive than the contents. CpG isn't that expensive either... I mean let's take it to a ridiculous limit-point: an oligo synthesis run costs a few hundred dollars in reagents, maybe a thousand. You're working with a ~mole of material. Divide that by avogadro's number. 1e3/6e23 = about ...
21:45 <@kanzure> ... a tenth of an attocent per monomer. If you had a magic daemon that coud assemble single-molecules, your reagent cost for a 100mer would be about 10 attocents. (We don't know how to make magic daemons yet, but I suspect that physics does allow for a mesoscopically-coupled polymerase that could act as a decently accurate 'molecular printer' if you coupled it to some single-molecule sequencing feedback.) Why does a bulk reagent limit the ...
21:45 <@kanzure> ... ultimate cost? If you're efficient it doesn't have to."
21:45 <@kanzure> "Reagents are expensive when you waste them. For traditional gene synthesis, the cost of oligos does dominate. Even the lowest-scale bulk synthesis reactions make about 1000x more material than is needed for a synthesis reaction. Microarray synthesis scales usage way down (though the amount of dna on a microarray spot is actually too low to use directly for reliable assembly, so some amount of post-processing is required) However, ...
21:45 <@kanzure> ... microarrays jumble everything together and make the error-correction problem much more severe."
21:45 <@kanzure> "With regards to enzymes/reagents don't think that the price you pay for them is going to be the price an industrial purchaser is going to pay- most endusers of anything in biology are paying large margins. What you're paying for as an enduser isn't the stuff in the tube, it's the quality control that guarantees the stuff in the tube will do what you hope it will, as well as the convenience of that little tube shipped to you the moment you ...
21:45 <@kanzure> ... need it."
21:45 <@kanzure> "Don't get fixated on a single aspect of the cost structure. Ingots of ultrapure silicon aren't cheap, but their cost is only distantly related to the price of a cpu. If you have a relatively fixed amount of cost for people and machines and reagents, the only way you get improved cost per unit is by making a shitload more units by using more efficient processes. That's the idea."
21:47 <@kanzure> well anyway, i don't remember the single molecule stuff there. i think their idea might have changed once or twice.
21:47 <@kanzure> i don't particularly care though
21:48 < yashgaroth> dna synthesis is inherently small-scale for the next decade but I hope he's not relying too much on economies of scale
21:48 <@kanzure> i think repliacting something more traditional (and then proceeding to hate it) is a good course of action
21:48 <@kanzure> *replicating
21:49 <@kanzure> hey so, for yeast cloning, what's the growth medium?
21:50 <@kanzure> for some reason i always thought you meant "throw some yeast into a pile of dNTPs" but this doesn't make any sense.
21:51 < yashgaroth> I haven't done much yeast work but they'll eat pretty much anything
21:51 < yashgaroth> gonna be lazy and say powdered yeast extract
21:56 <@kanzure> ~,
21:56 <@kanzure> oops
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