--- Log opened Sun Jun 10 00:00:36 2012
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00:48 < klafka1> http://www.seanbonner.com/blog/archives/piratesarecool.jpg
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03:51 < augur> klafka1: i think that shows that pirates are hot
03:51 < augur> oh no it doesnt
03:52 < augur> it uses very confusion layout
03:52 < augur> horrible
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08:10 <@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/
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08:17  * Urchin wants submarine
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10:00 < archels> random http://24.media.tumblr.com/tumblr_m0m5vaGQqp1r46py4o1_1280.jpg
10:02  * chris_99 wants a nuclear submarine
10:02 < chris_99> is that supposed to be a fancy exoskeleton archels
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13:24 <@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
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13:58 < delinquentme> I think there was another sleep LED blinker already
13:58 < delinquentme> and that one kicked ass and brought in tons of cash
13:59 < chris_99> do they actually do much?
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14:07 < delinquentme> chris_99, IDk but i'd be interested to try em out
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14:08 < chris_99> i don't think it'd be hard to make one yourself
14:10 < chris_99> http://en.wikipedia.org/wiki/Ganzfeld_effect
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15:33 <@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."
15:34 < Urchin> and, given the interface it bears little to no resemblence to reality
15:35 < Urchin> at least where I'm from
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16:18 < dixiebassline> humanity is a bunch of apes
16:18 <@kanzure> humaniwhat?
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16:24 < dixiebassline> apes, really more like dogs
16:24 < dixiebassline> there are the alphas
16:24 < dixiebassline> the h+
16:24 < dixiebassline> and everyonelese
16:25 < yashgaroth> ...
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16:27 <@kanzure> yashgaroth: i don't know how to get rid of these people
16:27 <@kanzure> yashgaroth: ideas welcomed.
16:28 < yashgaroth> well, +b I guess
16:28 <@kanzure> yes but it's also a general trend
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16:30 < 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
16:31 < yashgaroth> falmot seems to have disappeared, or was perhaps committed...either way it's been a while
16:36 < yashgaroth> is this channel still listed in #reddit-nootropics' topic? that might be a factor :/
16:38 < delinquentme> http://www.economist.com/node/21556098?fsrc=scn/tw_ec/when_code_can_kill_or_cure
16:38 < delinquentme> open source medical devices
16:44 < _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.
16:45 < _Sketch_> Sorry, not FSF. Gnome Foundation executive directory, and formerly Software Freedom Law Center general counsel.
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17:18 < 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
17:19 < 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
17:20 < 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
17:21 < 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
17:22 < 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?
17:23 < 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
17:24 < 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
17:25 < yashgaroth> electroporation, digestion, ligation etc is all generic by now
17:29 < delinquentme> sure sure but where am i using these enzymes?
17:29 < delinquentme> as like end steps for final purification of the molecules?
17:30 < 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...
17:31 < 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
17:32 < 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
17:33 < 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*
17:34 < 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
17:35 < delinquentme> which would essentially build up some additional structure to the p1_yield
17:35 < delinquentme> and the p2 would also have a modification
17:36 < 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
17:37 < 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
17:39 < 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
17:40 < yashgaroth> the insertions are going to be the coding sequence for an enzyme, in this case from a cow
17:41 < 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 ?
17:42 < 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
17:43 < 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
17:44 < 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
17:45 < 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
17:46 < 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
17:49 < 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?
17:50 < 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
17:51 < 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"
17:53 < 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
17:54 < delinquentme> what does a spectrophotometer do?
17:54 < delinquentme> measuring the air content?
17:56 < 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
17:58 < yashgaroth> nmz was trying to fund an open source one a while ago, that would always be nice
18:01 < 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
18:02 < 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
18:03 < 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
18:04 < 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
18:05 < 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
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18:10 < delinquentme> ^
18:10 < delinquentme> yeah i saw that
18:10 < delinquentme> cool idea but what we want is the motion controller
18:11 < 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
18:12 < 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
18:15 < delinquentme> so protein quantification... why?
18:15 < yashgaroth> so you know how much protein you have
18:17 < 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
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18:21 < yashgaroth> and of course you can use it to quantify DNA as well, see how much contaminating RNA/protein there is, all that
18:27 < delinquentme> yashgaroth,  you know about the life science speed challenge right?
18:27 < yashgaroth> nope
18:32 < delinquentme> 1 million to cut the DNA prep time for a life sciences machine from 8 hours to 4?
18:33 < 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'
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18:35 < yashgaroth> is this just for doing minipreps from bacterial cultures?
18:43 <@kanzure> maybe he means lifetech
18:47 < yashgaroth> 8 hours seems like a really long time
18:47 <@kanzure> ParahSailin: that kickstarter is mostly excited reddit people, sadly
18:48 < 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
18:49 <@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
18:50 < yashgaroth> they all kind of do...ah for sequencing that time scale sounds more reasonable
19:13 <@kanzure> hrmm
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20:05 <@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
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20:06 <@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.
20:07 <@kanzure> are you definitely going if i don't?
20:27 < _Sketch_> I don't suppose there are any open-source dog-brain projects?
20:28 < _Sketch_> Odd question, but I figure the best pet could be the one I build myself. ;)
20:36 <@kanzure> there are some open source cnidarian brain projects
20:36 <@kanzure> i guess that's not quite a dog.
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20:43 < _Sketch_> Although still interesting.
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23:17 <@kanzure> beep boop
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23:25 -!- srangewarp is now known as strangewarp
--- Log closed Mon Jun 11 00:00:37 2012