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| JayDugger | .botsnack | 05:58 |
|---|---|---|
| yoleaux | :D | 05:58 |
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| justanotheruser | What are a journals expenses? Do they pay the institutions for peer review? | 07:01 |
| Betawolf | They pay distribution costs. | 07:03 |
| Betawolf | Peer review is voluntary, though organised by the editors. | 07:03 |
| kanzure | vast majority of them do not pay for peer review | 07:03 |
| justanotheruser | peer review is voluntary? Don't most journals have a required standard? | 07:03 |
| justanotheruser | e.g. you must have this peer reviewed by some institution we trust | 07:04 |
| Betawolf | They contact professionals and request their services as reviewers. The systems vary from journal to journal. | 07:04 |
| Betawolf | institutions don't review things, individual academics do | 07:04 |
| kanzure | their editors arrange the peer review | 07:04 |
| justanotheruser | so part of the cost is paying editors to know who appropriate reviewers are | 07:05 |
| Betawolf | somewhat, though editors can also be non-paid academics | 07:05 |
| kanzure | and editors are also often not paid | 07:07 |
| Betawolf | The majority of journal expenses _used to be_ the costs of physically printing and distributing journals to institutions and individuals with subscriptions. The internet has broken down the theoretical cost of that considerably. | 07:07 |
| kanzure | .title https://www.youtube.com/watch?v=L8kjdObjZpY | 07:10 |
| yoleaux | DynaFlash: High-speed 8-bit image projector at 1,000fps with 3ms delay - YouTube | 07:10 |
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| kanzure | bleh hacker news proposes storing blood samples from athletes so as to test the blood in the future for whatever things sports agencies should have been testing for in the past :-/ https://news.ycombinator.com/item?id=9973179 | 08:30 |
| AmbulatoryCortex | maybe we should have an enhancement league :P | 08:32 |
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| FourFire | kanzure, seen http://www.rifters.com/crawl/?p=6116 | 08:40 |
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| kanzure | .title | 09:01 |
| yoleaux | No Moods, Ads or Cutesy Fucking Icons (Re-reloaded) » No Brainer. | 09:01 |
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| nmz787_i | http://hackaday.com/2015/07/30/the-biohacking-movement-and-open-source-insulin/ | 09:12 |
| nmz787_i | .title | 09:12 |
| yoleaux | The Biohacking Movement and Open Source Insulin | Hackaday | 09:12 |
| nmz787_i | 'by Dan Maloney' | 09:12 |
| nmz787_i | it seems to be more of a historical article, not talking about any progress | 09:12 |
| nmz787_i | mentioning some biohackerspaces, ryan bethencourt, and some opensource insulin project | 09:13 |
| nmz787_i | 'Dan Maloney' doesn't seem to have actually talked about any of his contributions other than I guess writing that article | 09:13 |
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| cluckj | nmz787, there's not really any progress afaik, I think it's still in the "how are we going to make this work" phase | 09:18 |
| cluckj | ugh | 09:19 |
| cluckj | "To be honest, the biohacking movement seems a bit moribund right now." fuck youuuuuuuuuuuuuuuuuuu | 09:19 |
| chris_99 | heh | 09:19 |
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| cluckj | to be honest, spending 20 minutes doing some internet searches isn't a good way to determine if things are happening in meatspace | 09:22 |
| chris_99 | so insulin is normally produced using yeast? | 09:23 |
| nmz787_i | i thought ecoli | 09:23 |
| chris_99 | wiki mentions both of those | 09:23 |
| nmz787_i | ecoli could have been the old way | 09:23 |
| chris_99 | ah | 09:24 |
| nmz787_i | .tell yashgaroth insulin is mostly via e.coli or yeast these days? | 09:24 |
| yoleaux | nmz787_i: I'll pass your message to yashgaroth. | 09:24 |
| chris_99 | the hard part would be getting the plasmids then? | 09:24 |
| cluckj | I thought the A/B chains were made separately, then enzymed together | 09:24 |
| nmz787_i | it seems like it would be a few thousand to just make a new plasmid | 09:25 |
| nmz787_i | but you might be able to grab them from some cell line storage place | 09:25 |
| cluckj | there are a bunch of different synthetic insulins, so it could be both yeast and e coli | 09:25 |
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| cluckj | genentech's insulin was e. coli | 09:27 |
| cluckj | one of the others is yeast | 09:27 |
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| nmz787_i | https://hackaday.io/project/6592-dipsy | 10:05 |
| nmz787_i | $5 ice40 board in DIP config | 10:06 |
| kanzure | "1280 logic cells" heh | 10:15 |
| nmz787_i | apparently enough to emulate an AVR | 10:15 |
| nmz787_i | "If going back in history then this FPGA is 16 times large than the first Xilinx FPGA's (XC2064), plus there are 14 small dual port RAM blocks, and two internal oscillators (10KHz and 48MHz)." | 10:16 |
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| kanzure | fenn: apparently the cool kids are calling it "cargotecture" :-/ https://news.ycombinator.com/item?id=9974944 | 10:43 |
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| kanzure | fluffypony: logs, http://gnusha.org/logs/2015-07-30.log | 10:45 |
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| fluffypony | awesome tks | 10:46 |
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| kanzure | apparently 1 ms latency is magical https://www.youtube.com/watch?v=vOvQCPLkPt4&feature=youtu.be&t=52s | 11:08 |
| CaptHindsight | ehhh they will just get everyone used to 100mS the same as they did to blue screens :) | 11:19 |
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| delinquentme | MPI-1 and MPI-2 used 32-bit integers for all counts. This means that programs using MPI – the lingua franca of supercomputing, in an era when already outputing terabytes of data being routine – could not (for instance) write out more than 2e9 objects at once without taking some meaningless additional steps. | 11:25 |
| delinquentme | can someone explain why the 2e9 relation exists here ? | 11:25 |
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| delinquentme | erm. Sorry . how the 2e9 relates to the memory | 11:32 |
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| kanzure | .title http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14862.html | 11:35 |
| yoleaux | Protein synthesis by ribosomes with tethered subunits : Nature : Nature Publishing Group | 11:35 |
| kanzure | "Here we show that ribosomes with tethered and thus inseparable subunits (termed Ribo-T) are capable of successfully carrying out protein synthesis. By engineering a hybrid rRNA composed of both small and large subunit rRNA sequences, we produced a functional ribosome in which the subunits are covalently linked into a single entity by short RNA linkers. Notably, Ribo-T was not only functional in vitro, but was also able to support the ... | 11:35 |
| kanzure | ... growth of Escherichia coli cells even in the absence of wild-type ribosomes." | 11:35 |
| kanzure | "Ribo-T can be used for exploring poorly understood functions of the ribosome, enabling orthogonal genetic systems, and engineering ribosomes with new functions." | 11:36 |
| kanzure | someone should combine that with https://www.google.com/patents/US5358862 | 11:38 |
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| CaptHindsight | http://hackaday.com/2015/07/30/the-biohacking-movement-and-open-source-insulin/ | 12:29 |
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| kanzure | CaptHindsight: scroll up for commentary | 12:38 |
| CaptHindsight | ah missed it, sorry for the redundant redundant post | 12:39 |
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| nmz787_i1 | heh, they think i'm trolling them | 12:45 |
| nmz787_i1 | by they i mean one person | 12:45 |
| CaptHindsight | if there is a way to take a comment wrong on forums, IRC etc it will happen | 12:47 |
| juri_ | nmz787_i1: do you have the .escad that you were having resolution problems with? | 12:48 |
| juri_ | nmz787_i1: I just upgraded the internals of ImplicitCad to use Doubles instead of Floats. | 12:48 |
| CaptHindsight | most often it's from non-native English speakers | 12:48 |
| CaptHindsight | nmz787: how dare you ask a question and apologize for any misunderstandings in advance! | 12:49 |
| juri_ | nmz787_i1: I don't see much of a difference, but, I'm not really exercising it on this P4. | 12:50 |
| AmbulatoryCortex | wasn't there some group a while back that figured out how to fix the pancreas? | 12:52 |
| nmz787_i1 | juri_: umm, it might be on the microfluidics github i have | 12:55 |
| nmz787_i1 | from what I was reading, it results from inexact calculations and rounding errors... requiring to use some tolerance specification when checking for intersections and such.... i think | 12:56 |
| nmz787_i1 | juri_: it was this one... I had to bump the quality up a lot though, as I recall https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/tobacco_mesophyll_protoplast_fusion_device.escad | 12:57 |
| juri_ | thank you. | 12:59 |
| nmz787_i1 | juri_: you can also see some defects in this output image... I can't remember what quality setting I had this on... but if it was too low the small features would be all melded together, and at the higher quality it would get all freaky and more stuff would be resolved, but still there were really strange things (like the posts being missing) | 13:05 |
| nmz787_i1 | https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device__3D.png | 13:05 |
| nmz787_i1 | this is the svg rendering https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.svg | 13:05 |
| nmz787_i1 | and a jpg of that svg (svg clear areas appear thatched on chrome, so its harder to see in-browser) https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.jpg | 13:06 |
| nmz787_i1 | huh, in that JPG you can actually see some defects too | 13:07 |
| nmz787_i1 | in the posts | 13:07 |
| nmz787_i1 | you can see the same defects in the JPG in the SVG too | 13:10 |
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| nmz787_i1 | (which makes sense) | 13:11 |
| juri_ | oh neat. you exposed a bug in my engine. | 13:12 |
| juri_ | thanks. ;) | 13:12 |
| juri_ | you've got four undefined variables... | 13:14 |
| juri_ | you turned the resolution up. you should have turned it down. | 13:15 |
| nmz787_i1 | http://digitalscan3d.com/services/reverse-engineering/ | 13:19 |
| nmz787_i1 | yeah there was no syntax checking when I used it... I just had to debug until it didn't crash when i went to export | 13:20 |
| nmz787_i1 | turn the quality down? when I did that the small features went away | 13:20 |
| nmz787_i1 | juri_: which vars were undefined? | 13:22 |
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| kanzure | marcin is still up to his old tricks ("we are building a 12 ton bulldozer") http://opensourceecology.org/bulldozer-workshop/ | 13:30 |
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| kanzure | weird, the supermemo-style spaced repetition memorization system is being sold to dish tv as a training supplement for their customer support staff (hikory (some ycombinator company)). i guess keeping track of their retention is cheaper than always propagating requests upstream. | 13:35 |
| juri_ | At 209: Variable output_connection_width not in scope | 13:35 |
| juri_ | At 210: Variable output_connection_width not in scope | 13:35 |
| delinquentme_ | Guys I think i just had a small realization w regards to making optimized organisms | 13:35 |
| delinquentme_ | blah. | 13:36 |
| delinquentme_ | phrasing needs work though | 13:36 |
| kanzure | "optimized organisms" almost like selection might be useful or something | 13:36 |
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| FourFire | delinquentme_, please, do rephrase and tell it again, bro | 13:40 |
| delinquentme_ | kanzure, sure but prior to selection we need to ensure optimized search spaces | 13:41 |
| kanzure | not following. do you mean the landscape? you can only change the landscapes by picking different problems. | 13:41 |
| FourFire | delinquentme_, sorry that was a bit to snarky, define optimized search spaces ? | 13:42 |
| kanzure | FourFire: he means things like "make mutants more likely, make irrelevant mutants less likely". | 13:43 |
| FourFire | I know someone who's got an algorithm which lossily compresses images into fewer pixels and with very few colours | 13:43 |
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| FourFire | cool stuff, you can have what seems like a recognizable face at a distance, but up close, it's pixel art | 13:44 |
| FourFire | he told me that obvious tricks for minimizing the search space like | 13:44 |
| delinquentme_ | i keep going back and forth w a friend on wether we have the collective knowledge to make useful mutants more intelligently than pure randomization | 13:44 |
| FourFire | making the corners all dark don't work | 13:44 |
| kanzure | delinquentme_: for many problems, yes we can make guesses better than randomization | 13:44 |
| FourFire | like you might need lighter colours a couple of places where it doesn't make sense | 13:44 |
| kanzure | delinquentme_: but there's no way to guarantee that we can always do better than chance | 13:44 |
| delinquentme_ | I dont think i've packaged the thought properly but here it is anyways | 13:45 |
| FourFire | delinquentme_, genetic algorithm | 13:45 |
| FourFire | ? | 13:45 |
| FourFire | or are you batch producing physical bacteria or something? | 13:45 |
| kanzure | he's sacrificing 10 million rabbits for some anti-cancer drugs | 13:45 |
| FourFire | 10 million, that's a lot | 13:46 |
| delinquentme_ | its cheaper to synthesize specific insertions into a genome ( multiplexed landing spots for CRISPR ) than it is to sequence that same number of organisms. | 13:47 |
| FourFire | delinquentme_, what mechanism does the drug work on, or are there lots of different mechanisms? | 13:47 |
| delinquentme_ | but in looking back over the statement Im not sure why thats novel inside my understanding | 13:47 |
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| kanzure | delinquentme_: sequencing is very very cheap. you throw everything together, then you assemble the different variants out of the single pot. | 13:47 |
| kanzure | but yes, you would synthesize specific plasmids or nucleatable strands | 13:47 |
| kanzure | site-directed mutagenesis is definitely a thing that is useful | 13:48 |
| delinquentme_ | maybe its just that in this case synthesis acts as a smart prior to sequencing ... and that the few modifications to the base pairs to get to specific landing sites within the genome ... can be relatively cheap ... thus enabling that additional intelligent placement, along side the easily performed pure random insertions , to be run side by side | 13:48 |
| delinquentme_ | again, 'opening up that search space ' | 13:48 |
| kanzure | however, there's often no guarantees that isolating mutation to a specific amino acid residue is going to produce the desired effect in your target organism- indeed it might be that the genetic landscape requires you to pass over an incomprehensibly huge chasm to get to your desired behavior (or not)- it's very hard to tell from the outside, unless you know the solution already. | 13:48 |
| delinquentme_ | ^ | 13:49 |
| delinquentme_ | that chasm is something that keeps poking around in my brain | 13:49 |
| kanzure | but yea, building a million variants of a plasmid is basically the right strategy | 13:49 |
| kanzure | and then inject each one into a separately tracked cell (inside a separate droplet) then you can judge their individual performance | 13:50 |
| delinquentme_ | like quantifying how much change is needed ... quantifying how large of a population you'd need to get ... or even decomposing intelligent intermediary steps which would have good chances of creating meaningful precursors | 13:50 |
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| FourFire | > it might be that the genetic landscape requires you to pass over an incomprehensibly huge chasm to get to your desired behavior (or not)- it's very hard to tell from the outside, unless you know the solution already. | 13:51 |
| kanzure | also, it's common to use "unnatural nucleotides" and "unnatural amino acids" to try to open up additional search space either as an intermediate or for the final form (as an intermediate it just means you eventually try to mutate the mutant in such a way where it no longer needs the unnatural amino acids, but keeping the other related mutations that wouldn't have been possible without the unnatural amino acid in the mean time) | 13:51 |
| delinquentme_ | this very quickly beings to resemble a tree structure when it comes to the history and modifications we might want to make to an orgnaism | 13:51 |
| FourFire | That's what I hope to optimize against with my simulations of specific proteins | 13:51 |
| kanzure | delinquentme_: intelligent intermediate steps is slightly easier, but again this is sometimes only easy when you are allowed to change the problem... | 13:52 |
| kanzure | delinquentme_: for example, a protein that mechanically computes arithmetic is technically possible, but there's no easy way to select for it | 13:52 |
| FourFire | the continuation of the gene(s) (and thus protein(s) which are synthesized from it) doesn't depend on a whole organism surviving, just the fitness function of the protein going up | 13:52 |
| kanzure | delinquentme_: (although for a mechanically-computing protein, i would first select proteins that undergo multiple interesting types of physical conformational changes to only part of the protein or only inside the protein, rather than whole protein conformational changes- it's a good start to maintaining state i guess, other than chemical reactions and keeping magnesium as a precursor to partial addition) | 13:54 |
| kanzure | ((context: lots of proteins grab some random atoms from the environment, such as magnesium, to incorporate into its structure to maintain a sense of state)) | 13:55 |
| delinquentme_ | 'state' seems like a methylation analogue no? | 13:56 |
| delinquentme_ | idk thats just one of the first things that come to mind | 13:57 |
| kanzure | sure, there's many ways proteins get into different states | 13:57 |
| kanzure | where their behavior changes slightly | 13:57 |
| kanzure | as for how large of a population you need, i think you need a larger population if you want to accomplish things in fewer generations, although i don't know the exact quantification | 13:58 |
| kanzure | probably something related to gene/trait saturation in a population over a number of generations | 13:59 |
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| kanzure | nottimschmidt (who was in here a few days ago) recently started working at http://beacon-center.org/ which does work on these types of problems apparently | 14:00 |
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| kanzure | interestingly, mike darwin claims that a lot of this is unnecessary and that rational engineering can accomplish most things without the assistance of brute force mutation search strategies... but he hasn't completely convinced me. | 14:01 |
| delinquentme_ | I have a similar feeling. One example is the methylated or coiled state of the DNA | 14:02 |
| delinquentme_ | techniques like the gene gun or chemical transformation will favor spots in the genome which are currently open / easily accessible | 14:02 |
| kanzure | at the moment, there is no way that rational engineering would have been able to construct the "type iv secretion system" protein nanoneedle, or polymerase for that matter. | 14:02 |
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| delinquentme_ | if we look at 'random' insertions ... but fail to realize that a prior probability is governed by that state .. were not *actually* doing random insertion | 14:03 |
| kanzure | theoretically you can use synthesis for random inserts | 14:03 |
| delinquentme_ | erm . governing* that state | 14:03 |
| kanzure | just permutate the hell out of all possibilities, etc. | 14:03 |
| kanzure | absolutely no different from any other brute force activity | 14:04 |
| delinquentme_ | yeah thats one advantage of what we're working on | 14:04 |
| delinquentme_ | that selection for what we're considering is incredibly simple | 14:04 |
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| nmz787_i | juri_: do you mean this line and the next? https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/tobacco_mesophyll_protoplast_fusion_device.escad#L211 | 14:30 |
| nmz787_i | juri_: seems that var is one of the parameters of the function call | 14:30 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b8e21bf0 Bryan Bishop: fix typo about a sighash type >> http://diyhpl.us/diyhpluswiki/transcripts/sf-bitcoin-meetup/2015-02-23-scaling-bitcoin-to-billions-of-transactions-per-day/ | 14:58 |
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| nmz787_i | is edwin katz in here kanzure? | 15:26 |
| kanzure | not to my knowledge | 15:27 |
| kanzure | at one point we had an edwin rosero maybe | 15:27 |
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| nmz787_i | kanzure: he keeps contacting me on linkedin, and I thought it said you were already his friend... or maybe you only know someone he knows (common connection or whatever they call it) | 15:46 |
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| kanzure | hello xtalmath | 16:43 |
| xtalmath | hi | 16:43 |
| kanzure | sup? | 16:43 |
| xtalmath | I read a comment on HAD and wanted to check this channel out | 16:44 |
| xtalmath | did we meet before, or are you just very welcoming? (i'm bad at remembering nicks) | 16:44 |
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| kanzure | xtalmath: if we met, it was before 2009. but not after. | 16:51 |
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| xtalmath | who's page is at http://diyhpl.us/wiki/homecmos/si2dlithoprocess/ ? | 16:53 |
| xtalmath | this person has a home cmos lab? | 16:53 |
| kanzure | nah, i don't have a home cmos lab at the moment | 16:55 |
| kanzure | the details were copied from azonenberg's homecmos wiki | 16:55 |
| kanzure | which is smart considering that code.google.com is vanishing soon | 16:55 |
| xtalmath | ah yeah, everyone gets his home cmos stuff from azonenberg :) | 16:56 |
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| nmz787_i | xtalmath: did you see something from that biohacking post? | 17:10 |
| xtalmath | nmz787_i: yes, the reference here | 17:11 |
| nmz787_i | that might have been me that posted the channel name then :) | 17:12 |
| xtalmath | what is the POSAM arrayer thing? | 17:13 |
| xtalmath | what was it used for? | 17:13 |
| xtalmath | ok reading wikipedia DNA_microarray | 17:14 |
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| kanzure | xtalmath: http://diyhpl.us/wiki/dna/synthesis/notes/ it makes oligonucleotides | 17:31 |
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| yashgaroth | nmz787, pretty sure most insulin these days is still made in e.coli | 19:20 |
| yoleaux | 30 Jul 2015 16:26Z <nmz787_i> yashgaroth: insulin is mostly via e.coli or yeast these days? | 19:20 |
| kanzure | obv. what we need is batch synthesis of insulin | 19:21 |
| kanzure | giant centrifuges and massive 12 meter diameter oil pipes i mean insulin pipes | 19:21 |
| yashgaroth | million-liter refolding tanks, as far as the eye can see | 19:22 |
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| fenn | is it bad to inject random yeast stuff? like wouldn't it be easier to purify insulin from yeast because you don't have to worry so much about LPS? | 19:39 |
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| yashgaroth | LPS is pretty easy to remove, it's more of a hassle to digest and refold the e.coli insulin than to separate endotoxin | 19:50 |
| nmz787_i | /me remembers homer simpson choking out a carboxy group | 19:51 |
| nmz787_i | carboxyl* | 19:51 |
| nmz787_i | "The mechanism of electrophilic aromatic substitution and the effect of electron withdrawing/donating substituents. What better way to elucidate substituent effects on the doughnut cloud of pi electrons than by comparison to actual doughnuts! Featuring Homer Simpson as an electrophile (doughnut-phile)." heh heh | 19:53 |
| nmz787_i | .title https://www.youtube.com/watch?v=OOeEmbOJWpI | 19:53 |
| yoleaux | Electrophilic Aromatic Substitution - YouTube | 19:53 |
| nmz787_i | 'when homer takes a bite out of a donut, he generates a sigma complex' | 19:55 |
| nmz787_i | toluene donuts have more icing than benzene donuts | 19:56 |
| nmz787_i | today-i-learned | 19:56 |
| nmz787_i | oOo, heteroatoms (non carbon/hydrogen) are like sprinkles | 19:57 |
| nmz787_i | haha, nitro groups are the bran-muffin of the donutophilic analogy | 20:01 |
| nmz787_i | and this guy probably doesn't even know about the antinutrient content making them even worse than they would be compared to donuts from homer's position | 20:01 |
| nmz787_i | saw mission impossible last night... they featured what looked like punch cards | 20:05 |
| nmz787_i | http://babysimpson.co.uk/info/stranglings/small/aabf22_2.jpg | 20:13 |
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| nmz787_i | this article makes me want to go protest in front of chipotle http://www.slate.com/articles/health_and_science/science/2015/07/are_gmos_safe_yes_the_case_against_them_is_full_of_fraud_lies_and_errors.html | 20:17 |
| kanzure | the case against them is mostly from well-placed shitanger about monsanto | 20:54 |
| kanzure | although not well-articulated, for the most part | 20:57 |
| kanzure | i wonder if monsanto could be convinced to campaign against themselves in an attempt to get wider understanding that the hatred of monsanto is not a hatred of gmo (so that they can get back to selling more gmo stuff) | 21:01 |
| fenn | .ud shitlord | 21:02 |
| yoleaux | Amongst other things, an expression used by feminists to mock anyone who doesn't agree with their opinions. 1. A derogatory word used by fat activists on Tumblr to insult people who disagreed with th | 21:02 |
| fenn | .ud shitanger | 21:02 |
| yoleaux | ENOTFOUND | 21:03 |
| kanzure | yeah i'm just making stuff up | 21:03 |
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| kanzure | really it's because i wanted to use "shitposting" today but i didn't have a good opportunity :-( | 21:03 |
| fenn | you could just make your own shitpost | 21:03 |
| kanzure | i think the rule is that you can't claim your own shitpost is a shitpost | 21:04 |
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| kanzure | .ud shitpost | 21:06 |
| yoleaux | To make utterly worthless and inane posts on an internet messageboard. | 21:06 |
| kanzure | biology is even worse than "read a million pages of specifications and data sheets to make stuff", it's "read a million pages and then spend months in a lab trying to get anything at lal to work" | 21:15 |
| kanzure | it's an even more perverted version of the same problem | 21:15 |
| fenn | yeah but we can't just buy an off the shelf engineered replicator | 21:15 |
| fenn | nalso atomically precise assemblers for near zero cost | 21:17 |
| kanzure | is idt really just running 100s of single-column synthesizers? | 21:17 |
| kanzure | apparently geneart takes so long that they have some website where you can track where your molecules are in their assembly pipeline https://www.lifetechnologies.com/us/en/home/life-science/cloning/gene-synthesis/geneart-gene-synthesis.html | 21:19 |
| kanzure | "and delivery of 5 µg of lyophilized DNA plus a compact disc of the in silico analysis and quality control information." | 21:20 |
| kanzure | hm and they do site-directed mutagenesis. not bad. | 21:21 |
| kanzure | https://www.lifetechnologies.com/us/en/home/life-science/cloning/gene-synthesis/geneart-gene-synthesis/geneart-gene-synthesis-frequently-asked-questions.html | 21:22 |
| kanzure | "assembly of constructs from 10 kb to several hundred kilobases, with timelines starting from 25 business days" | 21:24 |
| kanzure | hm. | 21:25 |
| kanzure | i sort of disagree with the "well we have never used primers before" argument. | 21:25 |
| kanzure | there's quite a lot of trivial projects that are otherwise expensive or ridiculous http://diyhpl.us/wiki/dna/projects/ | 21:29 |
| kanzure | "transformation of the bee gut bacteria with the NHase gene to degrade the neonicotinoid thiacloprid" http://2015.igem.org/Team:Austin_UTexas | 21:33 |
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| delinquentme_ | kanzure, | 21:56 |
| delinquentme_ | do we have a stock purchase agreement ? | 21:56 |
| delinquentme_ | im sure I can find some online | 21:56 |
| delinquentme_ | but " if X is developed with MNO features we agree to buy 4 in an evaluation agreement" | 21:57 |
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| nmz787 | xtalmath: so what brings you here, that the other readers of that hackaday article didn't have (and thus why they aren't here) | 22:59 |
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| xtalmath | I was curious I guess, I also wonder what kind of tools most urgently need an open hardware design? | 23:13 |
| xtalmath | curious which tools were necessary, and how many of them have open designs? | 23:14 |
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| xtalmath | I have a mini milling machine, and ordered a 3d printer a few days ago,... I think I will be trying to design micromanipulators not necessarily for bio-work though | 23:15 |
| xtalmath | I am thinking of full arm & hand micromanipulator | 23:16 |
| xtalmath | I am thinking of affordable microfabrication, and then perhaps affordable microdevices can follow? | 23:18 |
| * xtalmath imagines miniature drill press etc | 23:20 | |
| xtalmath | alumin(i)um "tin foil" could become a cheap source for metal plates | 23:21 |
| lsparrish | Thinking of trying to build a replicator? | 23:21 |
| xtalmath | lsparrish: in the far back of my mind yes. but we need "impedance matching" for the scales in between. just the boring stuff, like mini elevators and tracks to store projects/parts | 23:22 |
| xtalmath | even if we can make and machine small parts, we will need ways to pick them up and assemble them together | 23:23 |
| xtalmath | I am thinking more like feynman's hands. make smaller hands step by step, say decibel steps | 23:23 |
| lsparrish | I saw a video for a cool assembley robot, called YuMi | 23:23 |
| xtalmath | every time 10^1/10 smaller | 23:24 |
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| lsparrish | https://www.youtube.com/watch?v=2KfXY2SvlmQ | 23:25 |
| xtalmath | lol thats the second high tech commercial that uses pangea soundtrack | 23:26 |
| xtalmath | that i have seen this week | 23:26 |
| lsparrish | heh, sorry about that | 23:27 |
| nmz787 | ah, cool | 23:27 |
| nmz787 | electron microscopes and Focused Ion Beam mills would be awesome to have open plans for | 23:28 |
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| lsparrish | I've been focusing on the concept of replication in general. I'm not convinced it needs to be nano to be extremely useful. A one year doubling rate would be extremely fast by industry standards, and if you put it in space it does not need to be very energy efficient at all. | 23:28 |
| nmz787 | I've been studying whatever I can in my spare time lately on the deflection coil high-voltage controlling an electron beam | 23:28 |
| nmz787 | so I can try to get my SEM working | 23:29 |
| lsparrish | Freitas Atomic Separator Replicator is kinda cool. http://www.molecularassembler.com/KSRM/3.14.htm | 23:30 |
| nmz787 | yea, we've talked about that in here a bunch | 23:31 |
| xtalmath | lol, what would happen to all the uranium being sorted together? | 23:34 |
| lsparrish | Hmm. Maybe just sort that into very thin rods. | 23:35 |
| nmz787 | err, I guess we've talked more about Freitas atomic assembler | 23:35 |
| lsparrish | Yeah, the macroscale ideas don't get as much press. | 23:36 |
| nmz787 | isn't that basically just a solar-powered ion-implant machine? | 23:37 |
| nmz787 | seems just like a mass-spec with a deposition system | 23:37 |
| lsparrish | His numbers: weighs 120 tons, processes 1.25 grams per second, uses 11 MW of energy, and replicates once every 3 years | 23:37 |
| lsparrish | yes | 23:38 |
| lsparrish | it's a huge, inefficient monster of a system. | 23:38 |
| nmz787 | anyone in here in phoenix, AZ? | 23:41 |
| nmz787 | and also an EE? | 23:41 |
| xtalmath | I think cheap diy microfabrication tools is the best bet for discovery/invention/innovation | 23:41 |
| nmz787 | I had some ideas for a laser lithography tool using a microscope and video feedback of a grid of dots moving offset from the lasering-area | 23:42 |
| xtalmath | nmz787 can you elucidate? about the grid of dots? | 23:43 |
| nmz787 | just so you can track where you're at... and the dots should have a high-resolution accuracy to begin... such that you can watch the dots in the video, know where in the XY plane you are, and also know if you need to speed up or slow down the motors because the screw position you're at is longer than it was a moment before | 23:45 |
| xtalmath | on a 2D galvano mirror with flex hinges, theres typically 2 mirrors, one on top for the power laser beam, and a square on other side, a led shines on the bottom mirror, and the square beam reflects on a quadrant photodiode, so that the signal is proportional to deviation | 23:48 |
| xtalmath | this way the system knows where the mirror is pointing at | 23:49 |
| xtalmath | I just read about this in a book called "practical opto-electronics" by protopopov ... | 23:50 |
| nmz787 | huh | 23:50 |
| nmz787 | I guess my thinking was that microscopes are pretty common | 23:51 |
| xtalmath | yes, microscopes are | 23:51 |
| nmz787 | so something that could ride on top of that might be nice | 23:51 |
| xtalmath | in theory, all you need is an inspection objective | 23:51 |
| xtalmath | they have a beamsplitter, so one can insert a beam, but not sure what powers we are speaking of, and if it would damage optics somewhere | 23:52 |
| xtalmath | oh and the 2d deflection mechanism of course | 23:52 |
| nmz787_i | ah, well i was thinking offset so you could just use a bluray drive writer head unmodified optically, just connected to a power controller for the beam diode | 23:53 |
| nmz787_i | they have near-TEM00 beams | 23:53 |
| nmz787_i | at close to the diffraction limit | 23:54 |
| nmz787_i | and also quite common | 23:54 |
| nmz787_i | moreso than microscopes I guess | 23:54 |
| xtalmath | that is a good idea, I wonder how far their focal point is from the lens? | 23:54 |
| nmz787_i | but at least they are the part that would wear out more | 23:54 |
| nmz787_i | pretty close | 23:54 |
| xtalmath | seems problematic | 23:54 |
| nmz787_i | like half a millimeter I think | 23:54 |
| nmz787_i | not for litho | 23:54 |
| nmz787_i | and that's only for the smallest spot size too | 23:55 |
| xtalmath | then how do you get feedback from the microscope? | 23:55 |
| nmz787_i | http://diyhpl.us/~bryan/papers2/optics/photolithography/High%20resolution,%20low%20cost%20laser%20lithography%20using%20a%20Blu-ray%20optical%20head%20assembly.pdf | 23:55 |
| nmz787_i | raspi with camera and 120FPS I guess | 23:55 |
| nmz787_i | idk, might be too slow, and you just have to calibrate once with the grid | 23:56 |
| nmz787_i | scanning with the camera in video record mode along the x and y axes, to correlate and setup a table of position corrections | 23:56 |
| xtalmath | thanks for the paper! | 23:56 |
| nmz787_i | but then in that case (the lookup table of corrections) you can't account for a motor skipping steps (if using a stepper) | 23:57 |
| nmz787_i | I don't think that would be a problem with a DC motor though | 23:57 |
| nmz787_i | though I'm not sure | 23:57 |
| xtalmath | I mean, how do you view with microscope, while the bluray module is in the way? | 23:57 |
| nmz787_i | (since you can be sure to reliably pulse a DC motor) | 23:57 |
| nmz787_i | oh, just slap it off to the side | 23:57 |
| nmz787_i | 'slap' -> mount | 23:57 |
| nmz787_i | it would be a constant offset from the video | 23:58 |
| nmz787_i | but the video would only be used for feedback or calibration... and otherwise used as a normal microscope | 23:58 |
| nmz787_i | maybe for inspecting what you just lasered | 23:58 |
| xtalmath | oh, so the video is for position feedback, not for monitoring the pattern as it is being burned? | 23:58 |
| nmz787_i | or if the colored fluid you are trying to pump through your lasered and developed and processed microfluidic is working | 23:59 |
| nmz787_i | yeah | 23:59 |
| xtalmath | ok I see, thats interesting | 23:59 |
| nmz787_i | you can monitor the beam current | 23:59 |
| nmz787_i | and a lot of laser diodes have built in photodiodes for brightness feedback | 23:59 |
| nmz787_i | since the laser photo output changes with temperature | 23:59 |
| --- Log closed Fri Jul 31 00:00:09 2015 | ||
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