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| klafka1 | http://www.seanbonner.com/blog/archives/piratesarecool.jpg | 00:48 |
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| augur | klafka1: i think that shows that pirates are hot | 03:51 |
| augur | oh no it doesnt | 03:51 |
| augur | it uses very confusion layout | 03:52 |
| augur | horrible | 03:52 |
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| @kanzure | "owning and operating a luxury submarine" http://www.ussubmarines.com/submarines/luxury.php3 | 08:10 |
| @kanzure | and, finally, a social network where i can feel like i belong http://stalltalk.info/ | 08:10 |
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| * Urchin wants submarine | 08:17 | |
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| archels | random http://24.media.tumblr.com/tumblr_m0m5vaGQqp1r46py4o1_1280.jpg | 10:00 |
| * chris_99 wants a nuclear submarine | 10:02 | |
| chris_99 | is that supposed to be a fancy exoskeleton archels | 10:02 |
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| @kanzure | mitch altman threw up a kickstarter for his lucid-dreaming-inducer blinking thing. | 13:24 |
| @kanzure | http://www.neurodreamer.com/ | 13:24 |
| @kanzure | http://www.kickstarter.com/projects/maltman23/neurodreamer-sleep-mask-0 | 13:24 |
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| delinquentme | I think there was another sleep LED blinker already | 13:58 |
| delinquentme | and that one kicked ass and brought in tons of cash | 13:58 |
| chris_99 | do they actually do much? | 13:59 |
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| delinquentme | chris_99, IDk but i'd be interested to try em out | 14:07 |
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| chris_99 | i don't think it'd be hard to make one yourself | 14:08 |
| chris_99 | http://en.wikipedia.org/wiki/Ganzfeld_effect | 14:10 |
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| @kanzure | "don't be too quick to discard remarks about the security of hospitals and your medical data: right now, a complete medical record is worth more on the black market than a credit card number. Keep that in mind next time you see Windows NT machines while getting your annual check-up." | 15:33 |
| Urchin | and, given the interface it bears little to no resemblence to reality | 15:34 |
| Urchin | at least where I'm from | 15:35 |
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| dixiebassline | humanity is a bunch of apes | 16:18 |
| @kanzure | humaniwhat? | 16:18 |
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| dixiebassline | apes, really more like dogs | 16:24 |
| dixiebassline | there are the alphas | 16:24 |
| dixiebassline | the h+ | 16:24 |
| dixiebassline | and everyonelese | 16:24 |
| yashgaroth | ... | 16:25 |
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| @kanzure | yashgaroth: i don't know how to get rid of these people | 16:27 |
| @kanzure | yashgaroth: ideas welcomed. | 16:27 |
| yashgaroth | well, +b I guess | 16:28 |
| @kanzure | yes but it's also a general trend | 16:28 |
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| yashgaroth | true, but it's only once a month or so...perfectly manageable with the right tools | 16:30 |
| yashgaroth | I'm surprised there aren't more tbh | 16:30 |
| yashgaroth | falmot seems to have disappeared, or was perhaps committed...either way it's been a while | 16:31 |
| yashgaroth | is this channel still listed in #reddit-nootropics' topic? that might be a factor :/ | 16:36 |
| delinquentme | http://www.economist.com/node/21556098?fsrc=scn/tw_ec/when_code_can_kill_or_cure | 16:38 |
| delinquentme | open source medical devices | 16:38 |
| _Sketch_ | Karen Sandler of the Free Software Foundation gave an excellent talk on open-source pacemakers. She has a closed-source one, but it doesn't have wireless capabilities in it, I believe. Safer. | 16:44 |
| _Sketch_ | Sorry, not FSF. Gnome Foundation executive directory, and formerly Software Freedom Law Center general counsel. | 16:45 |
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| delinquentme | Ok so biology is no help atm | 17:18 |
| delinquentme | so when talking about taking about connecting up pathways in an organism | 17:18 |
| delinquentme | to yield a novel compound | 17:18 |
| delinquentme | what is required for the yield of p1 | 17:19 |
| delinquentme | to physically locate itself to where it can be processed on by p2 | 17:19 |
| delinquentme | p1 = pathway 1 | 17:19 |
| delinquentme | p2 = pathway 2 | 17:19 |
| delinquentme | is it just a process of stick genes in there and the different yield will float around until they get to something that can process on them | 17:20 |
| delinquentme | and eventually youll get output of your new compound? | 17:20 |
| yashgaroth | depends, but usually, yes | 17:20 |
| yashgaroth | in bacteria all the enzymes will sit around in the cytoplasm...they may form complexes with each other which will speed up the reaction time by localizing all the enzymes together | 17:21 |
| delinquentme | I mean I'm totally unqualified to say this | 17:22 |
| delinquentme | but it sound easy | 17:22 |
| delinquentme | whats the hard part? | 17:22 |
| delinquentme | keeping the novel genes in a transcription state? | 17:22 |
| yashgaroth | no that's easy as well | 17:23 |
| delinquentme | the tools to do the insertion are available | 17:23 |
| yashgaroth | the hard part is finding a product that's free of patents, and is worthwhile...oh and I guess optimizing/tweaking the expression of all the relevant enzymes in the pathway | 17:23 |
| yashgaroth | depends on what you're trying to make, really | 17:24 |
| delinquentme | electroporation cant be patented | 17:24 |
| delinquentme | sure the machine might be | 17:24 |
| yashgaroth | no, but enzyme X that does Y useful synthesis will be | 17:24 |
| yashgaroth | electroporation, digestion, ligation etc is all generic by now | 17:25 |
| delinquentme | sure sure but where am i using these enzymes? | 17:29 |
| delinquentme | as like end steps for final purification of the molecules? | 17:29 |
| delinquentme | Ohh or enzymes to cut the DNA at spots where I want to insert it | 17:30 |
| yashgaroth | no, to synthesize the molecule you want out of the precursors | 17:30 |
| delinquentme | thats what the modification to the DNA of the model organism does... | 17:30 |
| yashgaroth | no what | 17:31 |
| yashgaroth | you need to modify it with the gene for the presumably patented enzyme | 17:31 |
| delinquentme | im completely lost on where the enzymes come into play here | 17:31 |
| yashgaroth | give me a sample project where you'd be modifying pathways in the organism | 17:32 |
| delinquentme | Like we're feeding ecoli some agar / sugar / what have you | 17:32 |
| delinquentme | and the example given was to connect up 2 existing metabolic pathways within that organism | 17:33 |
| yashgaroth | connect? | 17:33 |
| delinquentme | through insertion of 2 novel DNA sequences from a cow or something | 17:33 |
| delinquentme | erm I mean the molecular yields from these separate pathways would be complimented by the novel DNA insertions | 17:33 |
| delinquentme | in order to get a desireable yeidl | 17:33 |
| delinquentme | yield* | 17:33 |
| delinquentme | so in the example he had 2 existing pathways ( IDK the designations ) | 17:34 |
| delinquentme | and 2 genes from another organism which would perform additional modifications the the yield molecule of p1 | 17:34 |
| delinquentme | which would essentially build up some additional structure to the p1_yield | 17:35 |
| delinquentme | and the p2 would also have a modification | 17:35 |
| delinquentme | and then im guessing that p1_yield and p2_yield would react and create the end product | 17:36 |
| delinquentme | so the insertions of the novel DNA would create the additional modifications to the normal molecules which would predispose them to create the end product | 17:36 |
| delinquentme | ( i think that makes sense ) | 17:37 |
| yashgaroth | well typically you're adding the gene for an enzyme that modifies either p1 or p2 or their respective _yield to create something useful | 17:37 |
| yashgaroth | oh wait p1 and p2 are enzymes I'm guessing | 17:39 |
| yashgaroth | well it'll modify the yield molecule | 17:39 |
| delinquentme | I guess I was assuming that the insertions would be something like a biobrick standar part? | 17:39 |
| delinquentme | standard* .... | 17:39 |
| delinquentme | you're saying that useful insertions are patented? | 17:39 |
| delinquentme | I mean that doesn't make much sense to me | 17:39 |
| yashgaroth | the insertions are going to be the coding sequence for an enzyme, in this case from a cow | 17:40 |
| delinquentme | yashgaroth, so the process needs more than a simple catalyst as we're needing to create new mols here | 17:41 |
| delinquentme | well we need the enzyme yes for the reaction but also the novel molecular payload | 17:41 |
| yashgaroth | new to the e.coli or new entirely, like synthesizing noots or something? | 17:41 |
| delinquentme | does the term "enzyme" cover the cleavage / insertion and payload ? | 17:41 |
| yashgaroth | no | 17:42 |
| delinquentme | ok good to know | 17:42 |
| yashgaroth | enzymes are proteins that change a substrate molecule into something else | 17:42 |
| delinquentme | they chop up molecules at a particular recognized site | 17:42 |
| delinquentme | enzymes are used on DNA to cut at a particular sequence | 17:42 |
| yashgaroth | some of them do | 17:43 |
| delinquentme | are others used to indescriminately chop? | 17:43 |
| yashgaroth | sure, some others | 17:43 |
| delinquentme | indiscriminately ** | 17:43 |
| yashgaroth | and others, like the ones you'd presumably be wanting to insert, will convert say phenylalanine into tyrosine | 17:43 |
| delinquentme | thats a whole other discussion which i've never understood on DNA sequence preps | 17:43 |
| delinquentme | so the novel insertions need to code for a functional enzyme which will create the necessary molecule modifications | 17:44 |
| delinquentme | ? | 17:44 |
| yashgaroth | ...yes | 17:44 |
| delinquentme | kk | 17:44 |
| yashgaroth | they also need certain regulatory elements to make sure they express, but that's standard | 17:45 |
| delinquentme | yeah | 17:45 |
| delinquentme | now with ecoli | 17:45 |
| delinquentme | this insertion process and be much cleaner bc plasmid replication | 17:45 |
| delinquentme | than say something in animal cells | 17:45 |
| delinquentme | you dont need to shoot the damn DNA into the genome and hope it doesnt crap something up | 17:45 |
| delinquentme | you can just electroporate them in and theyll replicate | 17:46 |
| yashgaroth | that's a concern for any transfection, animal is only marginally harder than e.coli if you have the right tools | 17:46 |
| yashgaroth | e.coli are a lot easier to grow and handle though | 17:46 |
| delinquentme | well that and i think its a safe assumption that its the most studied organism | 17:49 |
| delinquentme | im curious as to the animal cell transfection... | 17:49 |
| delinquentme | how is it only marginally harder? | 17:49 |
| yashgaroth | keeping the cells alive and free from infection is annoying, but easy with the correct techniques | 17:50 |
| yashgaroth | they're a lot slower growing as well | 17:50 |
| yashgaroth | media is more expensive, you need a good incubator | 17:51 |
| yashgaroth | but if you have all that, the process is still the same, just "add DNA mixture to cells" | 17:51 |
| yashgaroth | however the DIY movement will be stuck with bacteria/yeast for quite a while...if biocurious doesn't even have a spectrophotometer I seriously doubt they have a CO2 incubator | 17:53 |
| delinquentme | what does a spectrophotometer do? | 17:54 |
| delinquentme | measuring the air content? | 17:54 |
| yashgaroth | measures concentration of dna, rna or protein in a liquid sample | 17:56 |
| yashgaroth | it's not absolutely essential for molbio work, but they...they really need one | 17:56 |
| yashgaroth | nmz was trying to fund an open source one a while ago, that would always be nice | 17:58 |
| ParahSailin | for a long-ass time the SENS rc refused to buy a spec | 18:01 |
| ParahSailin | to quantify dna, they ran a gel | 18:01 |
| ParahSailin | every single time | 18:01 |
| yashgaroth | hahaha | 18:01 |
| ParahSailin | they seemed to take a perverse pride in that | 18:02 |
| yashgaroth | even quantifying protein on a pre-cast gel is worthless without a scanner, unless 50% error margins are good enough...I can't imagine with handmade agarose | 18:02 |
| yashgaroth | getting a nanodrop was the happiest day in my old lab, I don't even know if I can go back to cuvettes now | 18:03 |
| ParahSailin | who are these suckers who are giving away money to build someone's capital? http://www.kickstarter.com/projects/260688528/clang | 18:04 |
| delinquentme | yash a calorimeter? | 18:04 |
| delinquentme | yashgaroth, ^ | 18:04 |
| yashgaroth | no it's not a calorimeter | 18:04 |
| yashgaroth | hey I like(d) neal stephenson, even if the kickstarter is dumb | 18:05 |
| yashgaroth | note that even the $10,000 pledge does not include a motion controller | 18:05 |
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| delinquentme | ^ | 18:10 |
| delinquentme | yeah i saw that | 18:10 |
| delinquentme | cool idea but what we want is the motion controller | 18:10 |
| delinquentme | yashgaroth, whats a nanodrop ? can I get a link to an example machine | 18:11 |
| yashgaroth | it's a spectrophotometer, but you pipette 1-2 micrliters onto a pedestal and it scans that | 18:11 |
| yashgaroth | versus traditional cuvette-style specs, which need like 200 microliters or something | 18:11 |
| yashgaroth | so if you have a valuable sample it's nice, even more nice if your sample is 200 microliters and you want to keep it sterile | 18:12 |
| yashgaroth | the intensity scanning range was also a lot higher on the nanodrop, at least versus our old cuvette spec | 18:12 |
| delinquentme | so protein quantification... why? | 18:15 |
| yashgaroth | so you know how much protein you have | 18:15 |
| yashgaroth | many assays require specific concentrations of protein, or perhaps you want to see yield/liter of culture, or testing recovery after purification, or or | 18:17 |
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| yashgaroth | and of course you can use it to quantify DNA as well, see how much contaminating RNA/protein there is, all that | 18:21 |
| delinquentme | yashgaroth, you know about the life science speed challenge right? | 18:27 |
| yashgaroth | nope | 18:27 |
| delinquentme | 1 million to cut the DNA prep time for a life sciences machine from 8 hours to 4? | 18:32 |
| delinquentme | protein quantification was a step ( which is what reminded me of it ) but it was one which could be skipped through careful pre-prep with the concentration | 18:33 |
| yashgaroth | define 'life sciences machine' | 18:33 |
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| yashgaroth | is this just for doing minipreps from bacterial cultures? | 18:35 |
| @kanzure | maybe he means lifetech | 18:43 |
| yashgaroth | 8 hours seems like a really long time | 18:47 |
| @kanzure | ParahSailin: that kickstarter is mostly excited reddit people, sadly | 18:47 |
| ParahSailin | i hope for their own sakes it doesnt reach 500k | 18:48 |
| @kanzure | ParahSailin: i think it would be very revealing if kickstarter revealed the incoming traffic sources | 18:48 |
| @kanzure | most of the contributors tend to be repeat contributors, but the other demographic is project-specific | 18:49 |
| ParahSailin | i feel bad when i see people voluntarily and needlessly concentrating wealth to the already wealthy | 18:49 |
| delinquentme | yashgaroth, one of the life sciences sequencing machines | 18:49 |
| delinquentme | the one that looks like a kids play toy | 18:49 |
| yashgaroth | they all kind of do...ah for sequencing that time scale sounds more reasonable | 18:50 |
| @kanzure | hrmm | 19:13 |
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| @kanzure | Juul: yo. i'll be in your area tomorrow. | 20:05 |
| Juul | kanzure, cool. I think there is a meetup planned at Noisebridge in the evening | 20:05 |
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| @kanzure | hmm i've never been very productive at noisebridge when i've visited | 20:06 |
| Juul | it can be good for meetings, but i guess mondays are actually crazy busy so it might be bad | 20:06 |
| Juul | we can always migrate to another location | 20:06 |
| @kanzure | might show up, sure. | 20:06 |
| @kanzure | are you definitely going if i don't? | 20:07 |
| _Sketch_ | I don't suppose there are any open-source dog-brain projects? | 20:27 |
| _Sketch_ | Odd question, but I figure the best pet could be the one I build myself. ;) | 20:28 |
| @kanzure | there are some open source cnidarian brain projects | 20:36 |
| @kanzure | i guess that's not quite a dog. | 20:36 |
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| _Sketch_ | Although still interesting. | 20:43 |
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| @kanzure | beep boop | 23:17 |
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| --- Log closed Mon Jun 11 00:00:37 2012 | ||
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