2016-02-01.log

--- Log opened Mon Feb 01 00:00:20 2016
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nmz787ugh, I just spent like 6 hours or more trying to upgrade grbl on an arduino clone... key takeaway point, doing this (https://www.arduino.cc/en/Tutorial/ArduinoISP)  does not allow you to burn a 'sketch', only the bootloader, after that, you have to switch over to using the rx and tx pins to program the sketch03:33
gnusha_https://secure.diyhpl.us/cgit/laser_etcher/commit/?id=e9f5221c nmz787: attachment upload >> http://diyhpl.us/laser_etcher/NEJE_Laser_Etcher/IMAG1624.jpg03:47
gnusha_https://secure.diyhpl.us/cgit/laser_etcher/commit/?id=5e340268 nmz787: attachment upload >> http://diyhpl.us/laser_etcher/NEJE_Laser_Etcher/03:51
gnusha_https://secure.diyhpl.us/cgit/laser_etcher/commit/?id=8c71a58a Nathan McCorkle: added images of back of circuit board >> http://diyhpl.us/laser_etcher/NEJE_Laser_Etcher/IMAG1625.jpg04:22
chris_99nmz787, you ever played with PMTs out of interest?04:23
nmz787nah04:30
nmz787jrayhawk: idk but it doesn't seem like the git push I pushed made it fully to ikiwiki... cgit sees it though04:31
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abetusknmz787, you can reflash the bootloader if you like05:32
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delinquentmehmmmm10:04
delinquentmekanzure: anyone in here right now10:04
delinquentmewhos the dude i hate?10:04
delinquentmeummmmm10:04
delinquentmeParahSailn10:04
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delinquentmenot in here10:04
delinquentmebolz10:04
FourFirehello delinquentme10:05
delinquentmehio four10:05
delinquentmeFourFire are you a chemist by any chance :D10:05
FourFireyou seem...drunk or something10:05
FourFiredelinquentme, less of a chemist than a biologist and less of either of those than a computer technician, atm10:06
delinquentmegot it10:07
FourFirebut more of a chemist than most people10:07
delinquentmecool10:07
FourFireI also have close contact with a synthesis company who do stuff "up to 1000 dalton"10:08
delinquentmeahhh cool10:09
FourFireAdittionally I know a student, post Chem masters Degree who is interested in transhumanisty ideas10:09
delinquentmebasically i need to know if all bong types can be simplified to " positions and attractions created with electrons "10:09
delinquentmeafter some reading im pretty sure this is a thing10:09
FourFireah, yeah I'm not adequate a chemist enough to answer that question, sorry.10:10
xentrac_bond types10:11
xentrac_apparently I've been hanging out to much with pot smokers, because it took me a long time to realize that was a misspelling10:11
xentrac_and although I'm not a chemist either, I'm pretty sure the answer is "yes"10:12
delinquentmeFourFire: is the masters chemist kid in here?10:13
delinquentmexentrac_: appreciated10:13
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FourFirenope, not sure if they irc, I'll have to spend some time chatting with them, I only met them last week or so10:13
xentrac_too much10:13
FourFirealso, they are older than me...10:13
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TMAdelinquentme: from what I remember from high school chemistry classes regular bonds are pairs of electrons shared between atoms. double bonds are quartets shared, triple bonds sextets shared; covalent bonds are way too tricky to explain to high school students; the bonds in the benzene ring (aromatic ring) is somewhat special as there are three electrons per bond totalling 18 for the six bonds; polycyclic aromatic stuff is too dificult to explain to high scho10:51
TMAdelinquentme: then there is a hydrogen "bond" between water molecules, where the hydrogen of one is attracted to the electron cloud of oxygen of the other -- this explains why water is liquid while H2S is not liquid, though the latter is heavier -- these bonds are not bonds at all10:53
TMAdelinquentme: the underlying quantum physics is way more complex. ;; in summary (tl;dr): most chemical bonds are of the kind you described. the others are way too complex for a layperson to grasp10:56
xentrac_well, but all of those are positions and attractions created with electrons11:01
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delinquentmebingo11:04
TMAbeware, the memories are more than 15 years old; I have never encountered chemistry since11:05
xentrac_you left out ionic bonds, which are simlilar to hydrogen bonds, and van der Waals bonds11:06
xentrac_which are also positions and attractions created with electrons11:06
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@kanzuremost of chemistry can be described by a giant database of graph transformations11:11
@kanzurenaturally, this database is completely proprietary and you don't have access11:11
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delinquentmehttps://www.collaborativedrug.com/11:16
delinquentmekanzure: ^ they've got a bunch im sure11:16
delinquentmealso.  libgen is down11:16
delinquentmesomeone needs to commercialize that shit11:16
xentrac_or decentralize it11:21
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FourFiredelinquentme, ok yeah I thought you mean Bong11:31
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delinquentmeBong?11:32
FourFireyeah bond types are generalizable, but the energy required to break them has variation for pretty much every permutation of different molecules11:32
delinquentme^11:32
delinquentmealso I found another mechanical synthesis paper11:33
FourFireso like, Carbon Oxygen in CO² is different to Carbon Oxygen in Gluclose11:33
FourFireeven when both are a double bond11:33
FourFiredelinquentme, I can try and see if I have some sources on specific energies if that's relevant11:34
delinquentmeI think i just need additional substantiation that mechanical forces can distort electron clouds so that atoms can be pushed into conformation11:35
delinquentmei have 2 papers currently11:35
delinquentme( reading the second one )11:35
FourFiredelinquentme, https://web.archive.org/web/20100625121758/http://www.jhu.edu/chem/lectka/Extras.html11:35
FourFireonly IA now sadly, but I think everything is there11:35
delinquentmehttp://foundry.lbl.gov/11:36
delinquentmethinking ill be submitting a proposal to these guys11:36
fennhttp://foundry.lbl.gov/events/seminar-20151124.html The Rosetta Disk, developed at The Long Now Foundation, is a microscopic archive designed to last for thousands of years. The 7 cm diameter disk is made of nickel, created by electroplating a silicon master etched with a FIB.11:55
chris_99cool!11:56
fenntoo bad they chose a religious text instead of something aliens might possibly be able to interpret11:57
fennor you know, something useful11:57
chris_99wheres it say religious text?11:58
chris_99oh yeah, got it - https://archive.org/details/rosettaproject11:59
xentrac_fenn: they only started with the religious text, because that's what they have the most translations of.  the bulk of the Rosetta texts are not genesis12:00
fennyeah there is a bunch of linguistic commentary in english12:00
xentrac_mostly in English, yes12:00
chris_99http://www.mdisc.com/ is interesting too12:01
fennthere's a lot of whitespace12:01
fenn640GB ought to be enough for anybody12:07
fenn"A disc with data layer composed of rock-like materials."12:08
xentrac_sounds like a minimal but not sufficient standard12:09
xentrac_I mean you don't want it to be olivine!12:09
xentrac_or obviously halite12:09
fenn25GB * 15 qty for $67 is not bad12:10
fenn179/TB12:10
chris_99i like the idea of the rosetta one, as you can read with a microscope, that seems really cool12:11
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fennsupposedly the data layer is "glassy carbon" whatever that means12:37
fenn.title http://www.google.com/patents/US838909512:38
yoleauxPatent US8389095 - Optical data storage media containing substantially inert low melting ... - Google Patents12:38
chris_99maybe it's diamond heh12:38
@kanzurecould someone help this person out https://github.com/kanzure/pdfparanoia/issues/4812:39
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chris_99https://en.wikipedia.org/wiki/Glassy_carbon12:40
fennhttps://en.wikipedia.org/wiki/Q-carbon  discovered in 2015, ferromagnetic and harder than diamond12:47
fenni'll wait for reproducibility confirmation before getting excited12:48
chris_99sounds very interesting12:53
delinquentmefenn: is this the stuff where its carbon but with no discernable crystaline structure?12:53
delinquentmeits just lik a smoosh12:53
fennglassy carbon is different from amorphous carbon; it only has sp2 orbitals12:54
@kanzuredelinquentme: you should tell fenn about your fleet of microscopes13:05
@kanzurehe does not know13:05
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delinquentmefenn: me has STMs which aer taking scans13:10
delinquentmepics or GTFO you say?13:10
delinquentmegladly13:10
delinquentmewhat emaulz13:10
cpopell6delinquentme : are you in touch with azonenberg?13:22
delinquentmecpopell6:I ma13:24
delinquentmehes SUPER helpful13:24
cpopell6delinquentme : I got to hang out in his lab a couple times13:25
delinquentmehe was the one who confirmed the newstons cradle behavior of electron energy conveyance13:25
delinquentmehes just like endlessly helpful . great dude.13:25
delinquentmeand hes got a solid lab setup at his place too13:25
cpopell6yep13:26
@kanzurecpopell6: did you know that i met his roommate (john) back in 2007? it was before he met azonenberg.13:27
delinquentmeOK so13:27
@kanzureapparently he was the one that convinced azonenberg to do all the decapping work.13:27
cpopell6kanzure : nope. I think in 07 zonenberg and I didn't know each other, that didn't come til later13:27
delinquentmequestion on the index above. Those are the facilities at the molecular foundry13:27
cpopell6Marc Chevrette I met via college political club stuff :P13:27
delinquentmewhich would be best suited to the work of mechanoligation that im after?13:27
@kanzureprobably you need to do femtoliter water bubbles with single molecules inside of the bubbles13:28
@kanzureand then move the bubbles into position for chemical reactions13:28
@kanzuredunno if femtoliter water bubbles are possible13:29
@kanzureplus, water causes side reactions here13:29
delinquentme"Organic and Macromolecular Synthesis Facility" or "Biological Nanostructures Facility" ... and possible the "Nanofabrication Facility" .. which works on "biological nanosystems"13:29
@kanzureso... not water.13:29
delinquentmekanzure:all of the experiments i've seen arent in solution13:29
delinquentmehence they'd not be using STM ... unless its like oil immersion STM13:30
delinquentmealso i read 3 research papers over the last 24 hours13:31
delinquentmeyay13:31
delinquentmeIDK if this is what I want to be doing w my life though13:31
delinquentmemore engineering13:31
delinquentmeless sitting and reading13:31
cpopell6Hmmmm13:35
cpopell6I can't remember13:35
cpopell6I think we were doing femtoliter bubbles in my research13:35
cpopell6well, I guess it wasn't a bubble, it was a droplet13:35
delinquentmekanzure: cpopell6 thats the scale that you  have to like mechanically FLING the droplet out of its well no?13:47
delinquentmehow do that separation?13:47
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delinquentmealso. FUCKING capillary action13:47
delinquentmekanzure: cpopell6 fenn nmz787 did i mention how much i fucking HATED capillary action when we were doing demonpore shit?13:48
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delinquentmei feel like thats some method for getting TINY fucking volumes of liquid though13:48
cpopell6delinquentme : electrohydrodynamic ink-jet printing13:49
cpopell6with low-wick titanium nozzles13:50
cpopell6delinquentme : I can dig up my thesis if you want13:51
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delinquentmecpopell6: nah thats sufficient of a method for me :D13:56
cpopell6delinquentme : I did shape modeling. normal electrohydrodynamic printing will give you bubbles on rebound in certain fluid regimes, but you won't get it in the femtoliter regime--13:56
cpopell6delinquentme : surface energy is something like a hard times larger than kinetic energy13:56
delinquentmeat that scale absolutely13:57
cpopell6my profs made me prove it to them13:57
cpopell6because they were dicks13:57
cpopell6>_>13:57
delinquentmesomething about #dominantForcesAtGivenScales13:57
cpopell6'Are you really going to make me model vortex forces here?'13:57
delinquentmebecause they could13:57
delinquentmelol13:57
cpopell6*3 months later*13:57
cpopell6'Why did you waste time on this?'13:57
delinquentmeKEK13:57
cpopell6'You told me to.'13:57
cpopell6'Why didn't you tell us <DOMINANT FORCES>'13:58
* delinquentme comforts cpopell613:58
cpopell6'I did'13:58
cpopell6'Well, we can't be expected to listen to what you have to say'13:58
delinquentmeHAHAHAHAHHAHAHA13:58
cpopell6it's okay, I almost got them fired for being shitheads >_>13:58
delinquentmefucking lold13:58
cpopell6other story: they miss dozens of meetings over 2 years--minimal apology13:58
cpopell6I miss one, they make me be on campus 9-5 the rest of my research time there to be available at their leisure, never take advantage13:59
cpopell6(I start skipping out again after 2 months)13:59
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delinquentmecpopell6: fuck man I want to like buy you a cheesecake or something hahaha14:05
delinquentmethats such fucking bullshit14:05
delinquentmeit also makes me happy I didnt take that path14:05
cpopell6delinquentme : meh. I got out with a masters degree in a field I don't do :P14:05
delinquentmenot all  bad :D14:05
cpopell6but it's a prestige degree so now I can do whatever I want degree wise (shut up kanzure) and they don't care because they see 'MS from RPI' on it14:05
delinquentmestill though. cheesecake is delicious.14:05
cpopell6yes it is14:06
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cpopell6delinquentme : probably moving out to the west coast this late fall btw14:06
delinquentme^^14:06
delinquentmelol best !!!!14:06
delinquentmeNICEE14:06
delinquentmenorcal? socal?14:06
delinquentmei feel like fenn is still out here and hasnt fucking checkd out my stuff14:06
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cpopell6nah, Seattle14:06
delinquentmeOOOOO14:06
delinquentmewould love friends in the rainy haze14:06
cpopell6I grew up in SoCal and I don't want to deal with NorCal14:07
cpopell6Seattle has decent salaries and lower property prices14:07
cpopell6plus Sami (gf) wants to go work at Microsoft14:07
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delinquentmei love salamis14:10
delinquentmeand low property prices14:10
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delinquentmeJawmare: kanzure says you're a bad ass chemist14:23
delinquentmeWhat are your thoughts on the plausibility of ligating long chains of DNA mechanically ? IE without ligase .14:23
Jawmareyou mean with organometallic catalysts?14:25
JawmareIt is plausible, yes14:26
delinquentmeJawmare: there are no catalysts involved14:26
Jawmarebut sometimes nature does things better than us14:26
delinquentmeunless catalysts means some organic / inorganic molecule pair14:27
Jawmareoh I didn't saw mechanically14:27
delinquentmetrue.  Yeah Im about to submit the first round of research backing to someone at the Molecular Foundry to see what they think on the plausibiliyt14:28
delinquentmeya.14:28
delinquentmegrabbing DNA and shoving it into another piece of DNA14:28
delinquentmedistorting / reforming the electron clouds to create the covalent bonds on the sugar phosphate backbone14:28
delinquentmei've got 2 papers which demonstrate the viability of mechanical bond breaking / making in inorganics14:29
JawmareYes. it is plausible14:29
delinquentmecool14:29
Jawmarebut is it financially viable? I would say no14:29
Jawmareor I don't think you can do it better than how nature does it14:30
delinquentmeJawmare: the application is in sourcing ~2kbp chains from current denovo providers14:31
delinquentmeand pushing those into linear chains14:31
delinquentmeto be determined: if we can get useful molar weights of the DNA14:31
delinquentmehigh fi polymerase will probaby be a big part of the amplification14:31
delinquentmebut right now the market shows that ~2kbp is around what can easily be outsourced14:32
delinquentmeand then theres an upper limit on the market size of 1) whats the biggest commerical genome of interest and 2) replication fidelity invivo vrs in vitro ( ecoli or yeast )14:33
delinquentmethe commercial DNA denovo market is ~2billion right now14:33
JawmareI don't really know that much about the biotech side14:33
delinquentmeyeah im just kinda practicing my pitch14:33
delinquentmewe also have icecream sandwitches14:34
Jawmareonce you talk about money14:34
Jawmaretheir eyes light up14:34
delinquentme$$$$14:36
delinquentmeI mean we both want financially stable businesses :D14:36
xentrac_VCs don't14:40
xentrac_I don't know Molecular Foundry14:42
delinquentmehttp://foundry.lbl.gov/facilities/index.html14:42
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nmz787_ifenn: FWIW I work part-time at the company that fabricated that rosetta disc... I actually have a similar piece at home (except it is a buddhist knot, where the knot is actually some sanskrit text)16:15
nmz787_ithe ones I have were unsealed... so they will get scratched easily16:15
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xentrac_they won't oxidize, though, will they?16:19
nmz787_iit's gold, so shouldn't16:20
nmz787_ialso pretty much unreadable without differential interference contrast microscopy16:21
nmz787_i(you can see the knot feature)16:21
nmz787_iactually maybe the features are large enough to see without DIC16:21
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xentrac_why don't they etch the pits deep enough to get iridescent color contrast?16:29
xentrac_Like 300nm deep should give you deep blue, right?16:29
nmz787_inot sure, probably better to read the papers/press-releases that longnow has put out16:30
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xentrac_yeah, sorry16:31
xentrac_I guess 150nm16:31
nmz787_ikanzure: jrayhawk  any idea why this commit isn't reflected in ikiwiki? http://diyhpl.us/cgit/laser_etcher/commit/?id=8c71a58a3a54ee631bdb155fdf80f22ce7cd254e16:31
nmz787_ixentrac_: probably something with hardiness, sputter rate, something like that16:31
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jrayhawk[Mon Feb 01 03:47:34 2016] [error] [client 50.39.166.238] Aborting commit due to empty commit message., referer: https://secure.diyhpl.us/write/laser_etcher/ikiwiki.cgi?page=NEJE_Laser_Etcher&from=index&do=create16:52
jrayhawkhow odd16:52
jrayhawkwell, I can confirm this is at least totally Ikiwiki's fault.16:56
nmz787_iyay!16:58
nmz787_i(in that it isn't apparently MY fault)16:58
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Aurelius_HomeI have a friend looking for a job in the SF area. Background is a code school type thing. She's a fast learner.17:19
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gnusha_https://secure.diyhpl.us/cgit/laser_etcher/commit/?id=3cc209d3 laser_etcher: Commit failed ikiwiki.cgi changes >> http://diyhpl.us/laser_etcher/index/17:55
gnusha_https://secure.diyhpl.us/cgit/laser_etcher/commit/?id=4edf3c60 laser_etcher: Merge branch 'master' of /srv/git/laser_etcher >> http://diyhpl.us/laser_etcher/NEJE_Laser_Etcher/17:55
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@kanzurewha17:56
jrayhawknmz787_i: I just upgraded Ikiwiki. Let me know if the problem recurs.17:56
nmz787_i.title http://hackaday.com/2016/02/01/3d-printing-fumes-new-science/18:00
yoleauxNew Research Sheds Light on 3D Printing Fumes | Hackaday18:00
nmz787_ijrayhawk: Thanks! the wiki page looks like it got the message now!18:00
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nmz787_idiybio I guess: http://hackaday.com/2016/02/01/build-your-swarm-control-cockroaches-for-under-30/20:37
nmz787_i.title20:37
yoleauxBuild Your Swarm: Control Cockroaches for Under $30! | Hackaday20:37
Jawmarewowwww20:39
Jawmarewow20:39
Jawmarethats so cool20:39
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nmz787_iyou know it is not really new?20:41
nmz787_ias they mention, backyard brains did this (openly) and even sold a kit years ago20:41
Jawmareno i dont20:42
nmz787_ihttps://backyardbrains.com/products/roboroach20:42
nmz787_i.title20:42
yoleauxThe Roboroach20:42
nmz787_ihttps://www.kickstarter.com/projects/backyardbrains/the-roboroach-control-a-living-insect-from-your-sm20:42
nmz787_iI am even a contributor on their paper, thanks to a kickstarter (I think) donation: https://www.kickstarter.com/projects/backyardbrains/the-roboroach-control-a-living-insect-from-your-sm20:43
nmz787_i.title20:43
yoleauxThe RoboRoach: Control a living insect from your smartphone! by Backyard Brains —Kickstarter20:43
nmz787_i(well maybe not a contributor, but I was thanked or something)20:43
nmz787_i"acknowledged"20:43
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@kanzuresince when is a sarcasmiculum not a cellular organelle? what happened to it?22:02
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